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 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 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 "UseTheForce/DarkSide/atype_interface.h"
54	<	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	<	namespace oopse {
53	>	#include "utils/Tuple.hpp"
54	>	namespace OpenMD {
55
56		ForceField::ForceField() {
57	+
58		char* tempPath;
59		tempPath = getenv("FORCE_PARAM_PATH");
60	<
60	>
61		if (tempPath == NULL) {
62		//convert a macro from compiler to a string in c++
63		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 66 | Line 66 | namespace oopse {
66		}
67		}
68
69	–
70	–	ForceField::~ForceField() {
71	–	deleteAtypes();
72	–	deleteSwitch();
73	–	}
74	–
69		AtomType* ForceField::getAtomType(const std::string &at) {
70		std::vector<std::string> keys;
71		keys.push_back(at);
#	Line 89 | Line 83 | namespace oopse {
83		if (bondType) {
84		return bondType;
85		} else {
86	<	//if no exact match found, try wild card match
87	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
86	>	AtomType* atype1;
87	>	AtomType* atype2;
88	>	std::vector<std::string> at1key;
89	>	at1key.push_back(at1);
90	>	atype1 = atomTypeCont_.find(at1key);
91	>
92	>	std::vector<std::string> at2key;
93	>	at2key.push_back(at2);
94	>	atype2 = atomTypeCont_.find(at2key);
95	>
96	>	// query atom types for their chains of responsibility
97	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
98	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
99	>
100	>	std::vector<AtomType*>::iterator i;
101	>	std::vector<AtomType*>::iterator j;
102	>
103	>	int ii = 0;
104	>	int jj = 0;
105	>	int bondTypeScore;
106	>
107	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
108	>
109	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
110	>	jj = 0;
111	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
112	>
113	>	bondTypeScore = ii + jj;
114	>
115	>	std::vector<std::string> myKeys;
116	>	myKeys.push_back((*i)->getName());
117	>	myKeys.push_back((*j)->getName());
118	>
119	>	BondType* bondType = bondTypeCont_.find(myKeys);
120	>	if (bondType) {
121	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
122	>	}
123	>	jj++;
124	>	}
125	>	ii++;
126	>	}
127	>
128	>
129	>	if (foundBonds.size() > 0) {
130	>	// sort the foundBonds by the score:
131	>	std::sort(foundBonds.begin(), foundBonds.end());
132	>
133	>	int bestScore = foundBonds[0].first;
134	>	std::vector<std::string> theKeys = foundBonds[0].second;
135	>
136	>	BondType* bestType = bondTypeCont_.find(theKeys);
137	>
138	>	return bestType;
139	>	} else {
140	>	//if no exact match found, try wild card match
141	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
142	>	}
143		}
144		}
145	<
145	>
146		BendType* ForceField::getBendType(const std::string &at1,
147		const std::string &at2,
148		const std::string &at3) {
#	Line 107 | Line 156 | namespace oopse {
156		if (bendType) {
157		return bendType;
158		} else {
159	<	//if no exact match found, try wild card match
160	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
159	>
160	>	AtomType* atype1;
161	>	AtomType* atype2;
162	>	AtomType* atype3;
163	>	std::vector<std::string> at1key;
164	>	at1key.push_back(at1);
165	>	atype1 = atomTypeCont_.find(at1key);
166	>
167	>	std::vector<std::string> at2key;
168	>	at2key.push_back(at2);
169	>	atype2 = atomTypeCont_.find(at2key);
170	>
171	>	std::vector<std::string> at3key;
172	>	at3key.push_back(at3);
173	>	atype3 = atomTypeCont_.find(at3key);
174	>
175	>	// query atom types for their chains of responsibility
176	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
177	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
178	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
179	>
180	>	std::vector<AtomType*>::iterator i;
181	>	std::vector<AtomType*>::iterator j;
182	>	std::vector<AtomType*>::iterator k;
183	>
184	>	int ii = 0;
185	>	int jj = 0;
186	>	int kk = 0;
187	>	int IKscore;
188	>
189	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
190	>
191	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
192	>	ii = 0;
193	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
194	>	kk = 0;
195	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
196	>
197	>	IKscore = ii + kk;
198	>
199	>	std::vector<std::string> myKeys;
200	>	myKeys.push_back((*i)->getName());
201	>	myKeys.push_back((*j)->getName());
202	>	myKeys.push_back((*k)->getName());
203	>
204	>	BendType* bendType = bendTypeCont_.find(myKeys);
205	>	if (bendType) {
206	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
207	>	}
208	>	kk++;
209	>	}
210	>	ii++;
211	>	}
212	>	jj++;
213	>	}
214	>
215	>	if (foundBends.size() > 0) {
216	>	std::sort(foundBends.begin(), foundBends.end());
217	>	int jscore = foundBends[0].first;
218	>	int ikscore = foundBends[0].second;
219	>	std::vector<std::string> theKeys = foundBends[0].third;
220	>
221	>	BendType* bestType = bendTypeCont_.find(theKeys);
222	>	return bestType;
223	>	} else {
224	>	//if no exact match found, try wild card match
225	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
226	>	}
227		}
228		}
229
#	Line 122 | Line 237 | namespace oopse {
237		keys.push_back(at3);
238		keys.push_back(at4);
239
240	+
241	+	//try exact match first
242		TorsionType* torsionType = torsionTypeCont_.find(keys);
243		if (torsionType) {
244		return torsionType;
245		} else {
246	<	//if no exact match found, try wild card match
247	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
248	<	}
249	<
250	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
246	>
247	>	AtomType* atype1;
248	>	AtomType* atype2;
249	>	AtomType* atype3;
250	>	AtomType* atype4;
251	>	std::vector<std::string> at1key;
252	>	at1key.push_back(at1);
253	>	atype1 = atomTypeCont_.find(at1key);
254	>
255	>	std::vector<std::string> at2key;
256	>	at2key.push_back(at2);
257	>	atype2 = atomTypeCont_.find(at2key);
258	>
259	>	std::vector<std::string> at3key;
260	>	at3key.push_back(at3);
261	>	atype3 = atomTypeCont_.find(at3key);
262	>
263	>	std::vector<std::string> at4key;
264	>	at4key.push_back(at4);
265	>	atype4 = atomTypeCont_.find(at4key);
266	>
267	>	// query atom types for their chains of responsibility
268	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
269	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
270	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
271	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
272	>
273	>	std::vector<AtomType*>::iterator i;
274	>	std::vector<AtomType*>::iterator j;
275	>	std::vector<AtomType*>::iterator k;
276	>	std::vector<AtomType*>::iterator l;
277	>
278	>	int ii = 0;
279	>	int jj = 0;
280	>	int kk = 0;
281	>	int ll = 0;
282	>	int ILscore;
283	>	int JKscore;
284	>
285	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
286	>
287	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
288	>	kk = 0;
289	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
290	>	ii = 0;
291	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
292	>	ll = 0;
293	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
294	>
295	>	ILscore = ii + ll;
296	>	JKscore = jj + kk;
297	>
298	>	std::vector<std::string> myKeys;
299	>	myKeys.push_back((*i)->getName());
300	>	myKeys.push_back((*j)->getName());
301	>	myKeys.push_back((*k)->getName());
302	>	myKeys.push_back((*l)->getName());
303	>
304	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
305	>	if (torsionType) {
306	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
307	>	}
308	>	ll++;
309	>	}
310	>	ii++;
311	>	}
312	>	kk++;
313	>	}
314	>	jj++;
315	>	}
316	>
317	>	if (foundTorsions.size() > 0) {
318	>	std::sort(foundTorsions.begin(), foundTorsions.end());
319	>	int jkscore = foundTorsions[0].first;
320	>	int ilscore = foundTorsions[0].second;
321	>	std::vector<std::string> theKeys = foundTorsions[0].third;
322	>
323	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
324	>	return bestType;
325	>	} else {
326	>	//if no exact match found, try wild card match
327	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
328	>	}
329	>	}
330		}
331	+
332	+	InversionType* ForceField::getInversionType(const std::string &at1,
333	+	const std::string &at2,
334	+	const std::string &at3,
335	+	const std::string &at4) {
336	+	std::vector<std::string> keys;
337	+	keys.push_back(at1);
338	+	keys.push_back(at2);
339	+	keys.push_back(at3);
340	+	keys.push_back(at4);
341	+
342	+	//try exact match first
343	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
344	+	if (inversionType) {
345	+	return inversionType;
346	+	} else {
347	+
348	+	AtomType* atype1;
349	+	AtomType* atype2;
350	+	AtomType* atype3;
351	+	AtomType* atype4;
352	+	std::vector<std::string> at1key;
353	+	at1key.push_back(at1);
354	+	atype1 = atomTypeCont_.find(at1key);
355	+
356	+	std::vector<std::string> at2key;
357	+	at2key.push_back(at2);
358	+	atype2 = atomTypeCont_.find(at2key);
359	+
360	+	std::vector<std::string> at3key;
361	+	at3key.push_back(at3);
362	+	atype3 = atomTypeCont_.find(at3key);
363	+
364	+	std::vector<std::string> at4key;
365	+	at4key.push_back(at4);
366	+	atype4 = atomTypeCont_.find(at4key);
367	+
368	+	// query atom types for their chains of responsibility
369	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
370	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
371	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
372	+	std::vector<AtomType*> at4Chain = atype4->allYourBase();
373	+
374	+	std::vector<AtomType*>::iterator i;
375	+	std::vector<AtomType*>::iterator j;
376	+	std::vector<AtomType*>::iterator k;
377	+	std::vector<AtomType*>::iterator l;
378
379	+	int ii = 0;
380	+	int jj = 0;
381	+	int kk = 0;
382	+	int ll = 0;
383	+	int Iscore;
384	+	int JKLscore;
385	+
386	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
387	+
388	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
389	+	kk = 0;
390	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
391	+	ii = 0;
392	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
393	+	ll = 0;
394	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
395	+
396	+	Iscore = ii;
397	+	JKLscore = jj + kk + ll;
398	+
399	+	std::vector<std::string> myKeys;
400	+	myKeys.push_back((*i)->getName());
401	+	myKeys.push_back((*j)->getName());
402	+	myKeys.push_back((*k)->getName());
403	+	myKeys.push_back((*l)->getName());
404	+
405	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
406	+	if (inversionType) {
407	+	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
408	+	}
409	+	ll++;
410	+	}
411	+	ii++;
412	+	}
413	+	kk++;
414	+	}
415	+	jj++;
416	+	}
417	+
418	+	if (foundInversions.size() > 0) {
419	+	std::sort(foundInversions.begin(), foundInversions.end());
420	+	int iscore = foundInversions[0].first;
421	+	int jklscore = foundInversions[0].second;
422	+	std::vector<std::string> theKeys = foundInversions[0].third;
423	+
424	+	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
425	+	return bestType;
426	+	} else {
427	+	//if no exact match found, try wild card match
428	+	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
429	+	}
430	+	}
431	+	}
432	+
433		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
434		std::vector<std::string> keys;
435		keys.push_back(at1);
#	Line 177 | Line 474 | namespace oopse {
474		keys.push_back(at4);
475		return torsionTypeCont_.find(keys);
476		}
477	<
477	>
478	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
479	>	const std::string &at2,
480	>	const std::string &at3,
481	>	const std::string &at4){
482	>	std::vector<std::string> keys;
483	>	keys.push_back(at1);
484	>	keys.push_back(at2);
485	>	keys.push_back(at3);
486	>	keys.push_back(at4);
487	>	return inversionTypeCont_.find(keys);
488	>	}
489	>
490		NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
491		std::vector<std::string> keys;
492		keys.push_back(at1);
493		keys.push_back(at2);
494		return nonBondedInteractionTypeCont_.find(keys);
495		}
496	+
497
188	–
498		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
499		std::vector<std::string> keys;
500		keys.push_back(at);
501		return atomTypeCont_.add(keys, atomType);
502		}
503
504	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
505	+	std::vector<std::string> keys;
506	+	keys.push_back(at);
507	+	return atomTypeCont_.replace(keys, atomType);
508	+	}
509	+
510		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
511		BondType* bondType) {
512		std::vector<std::string> keys;
#	Line 222 | Line 537 | namespace oopse {
537		return torsionTypeCont_.add(keys, torsionType);
538		}
539
540	+	bool ForceField::addInversionType(const std::string &at1,
541	+	const std::string &at2,
542	+	const std::string &at3,
543	+	const std::string &at4,
544	+	InversionType* inversionType) {
545	+	std::vector<std::string> keys;
546	+	keys.push_back(at1);
547	+	keys.push_back(at2);
548	+	keys.push_back(at3);
549	+	keys.push_back(at4);
550	+	return inversionTypeCont_.add(keys, inversionType);
551	+	}
552	+
553		bool ForceField::addNonBondedInteractionType(const std::string &at1,
554		const std::string &at2,
555		NonBondedInteractionType* nbiType) {
#	Line 250 | Line 578 | namespace oopse {
578		} else {
579		sprintf( painCave.errMsg,
580		"Can not cast GenericData to LJParam\n");
581	<	painCave.severity = OOPSE_ERROR;
581	>	painCave.severity = OPENMD_ERROR;
582		painCave.isFatal = 1;
583		simError();
584		}
585		} else {
586		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
587	<	painCave.severity = OOPSE_ERROR;
587	>	painCave.severity = OPENMD_ERROR;
588		painCave.isFatal = 1;
589		simError();
590		}
#	Line 286 | Line 614 | namespace oopse {
614		"\tHave you tried setting the FORCE_PARAM_PATH environment "
615		"variable?\n",
616		forceFieldFilename.c_str() );
617	<	painCave.severity = OOPSE_ERROR;
617	>	painCave.severity = OPENMD_ERROR;
618		painCave.isFatal = 1;
619		simError();
620		}
#	Line 294 | Line 622 | namespace oopse {
622		return ffStream;
623		}
624
625	<	void ForceField::setFortranForceOptions(){
298	<	ForceOptions theseFortranOptions;
299	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
300	<	setfForceOptions(&theseFortranOptions);
301	<	}
302	<	} //end namespace oopse
625	>	} //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 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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

Diff Legend

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