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

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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	+	#include <algorithm>
52		#include "UseTheForce/ForceField.hpp"
53		#include "utils/simError.h"
54	<	#include "UseTheForce/DarkSide/atype_interface.h"
55	<	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	<	namespace oopse {
54	>	#include "utils/Tuple.hpp"
55	>	namespace OpenMD {
56
57		ForceField::ForceField() {
58	+
59		char* tempPath;
60		tempPath = getenv("FORCE_PARAM_PATH");
61	<
61	>
62		if (tempPath == NULL) {
63		//convert a macro from compiler to a string in c++
64		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 66 | Line 67 | namespace oopse {
67		}
68		}
69
70	<
71	<	ForceField::~ForceField() {
72	<	deleteAtypes();
73	<	deleteSwitch();
74	<	}
75	<
70	>	/**
71	>	* getAtomType by string
72	>	*
73	>	* finds the requested atom type in this force field using the string
74	>	* name of the atom type.
75	>	*/
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	+	/**
83	+	* getAtomType by ident
84	+	*
85	+	* finds the requested atom type in this force field using the
86	+	* integer ident instead of the string name of the atom type.
87	+	*/
88	+	AtomType* ForceField::getAtomType(int ident) {
89	+	std::string at = atypeIdentToName.find(ident)->second;
90	+	return getAtomType(at);
91	+	}
92	+
93		BondType* ForceField::getBondType(const std::string &at1,
94		const std::string &at2) {
95		std::vector<std::string> keys;
#	Line 89 | Line 101 | namespace oopse {
101		if (bondType) {
102		return bondType;
103		} else {
104	<	//if no exact match found, try wild card match
105	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
104	>	AtomType* atype1;
105	>	AtomType* atype2;
106	>	std::vector<std::string> at1key;
107	>	at1key.push_back(at1);
108	>	atype1 = atomTypeCont_.find(at1key);
109	>
110	>	std::vector<std::string> at2key;
111	>	at2key.push_back(at2);
112	>	atype2 = atomTypeCont_.find(at2key);
113	>
114	>	// query atom types for their chains of responsibility
115	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
116	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
117	>
118	>	std::vector<AtomType*>::iterator i;
119	>	std::vector<AtomType*>::iterator j;
120	>
121	>	int ii = 0;
122	>	int jj = 0;
123	>	int bondTypeScore;
124	>
125	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
126	>
127	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
128	>	jj = 0;
129	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
130	>
131	>	bondTypeScore = ii + jj;
132	>
133	>	std::vector<std::string> myKeys;
134	>	myKeys.push_back((*i)->getName());
135	>	myKeys.push_back((*j)->getName());
136	>
137	>	BondType* bondType = bondTypeCont_.find(myKeys);
138	>	if (bondType) {
139	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
140	>	}
141	>	jj++;
142	>	}
143	>	ii++;
144	>	}
145	>
146	>
147	>	if (foundBonds.size() > 0) {
148	>	// sort the foundBonds by the score:
149	>	std::sort(foundBonds.begin(), foundBonds.end());
150	>
151	>	int bestScore = foundBonds[0].first;
152	>	std::vector<std::string> theKeys = foundBonds[0].second;
153	>
154	>	BondType* bestType = bondTypeCont_.find(theKeys);
155	>
156	>	return bestType;
157	>	} else {
158	>	//if no exact match found, try wild card match
159	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
160	>	}
161		}
162		}
163	<
163	>
164		BendType* ForceField::getBendType(const std::string &at1,
165		const std::string &at2,
166		const std::string &at3) {
#	Line 107 | Line 174 | namespace oopse {
174		if (bendType) {
175		return bendType;
176		} else {
177	<	//if no exact match found, try wild card match
178	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
177	>
178	>	AtomType* atype1;
179	>	AtomType* atype2;
180	>	AtomType* atype3;
181	>	std::vector<std::string> at1key;
182	>	at1key.push_back(at1);
183	>	atype1 = atomTypeCont_.find(at1key);
184	>
185	>	std::vector<std::string> at2key;
186	>	at2key.push_back(at2);
187	>	atype2 = atomTypeCont_.find(at2key);
188	>
189	>	std::vector<std::string> at3key;
190	>	at3key.push_back(at3);
191	>	atype3 = atomTypeCont_.find(at3key);
192	>
193	>	// query atom types for their chains of responsibility
194	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
195	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
196	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
197	>
198	>	std::vector<AtomType*>::iterator i;
199	>	std::vector<AtomType*>::iterator j;
200	>	std::vector<AtomType*>::iterator k;
201	>
202	>	int ii = 0;
203	>	int jj = 0;
204	>	int kk = 0;
205	>	int IKscore;
206	>
207	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
208	>
209	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
210	>	ii = 0;
211	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
212	>	kk = 0;
213	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
214	>
215	>	IKscore = ii + kk;
216	>
217	>	std::vector<std::string> myKeys;
218	>	myKeys.push_back((*i)->getName());
219	>	myKeys.push_back((*j)->getName());
220	>	myKeys.push_back((*k)->getName());
221	>
222	>	BendType* bendType = bendTypeCont_.find(myKeys);
223	>	if (bendType) {
224	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
225	>	}
226	>	kk++;
227	>	}
228	>	ii++;
229	>	}
230	>	jj++;
231	>	}
232	>
233	>	if (foundBends.size() > 0) {
234	>	std::sort(foundBends.begin(), foundBends.end());
235	>	int jscore = foundBends[0].first;
236	>	int ikscore = foundBends[0].second;
237	>	std::vector<std::string> theKeys = foundBends[0].third;
238	>
239	>	BendType* bestType = bendTypeCont_.find(theKeys);
240	>	return bestType;
241	>	} else {
242	>	//if no exact match found, try wild card match
243	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
244	>	}
245		}
246		}
247
#	Line 122 | Line 255 | namespace oopse {
255		keys.push_back(at3);
256		keys.push_back(at4);
257
258	+
259	+	//try exact match first
260		TorsionType* torsionType = torsionTypeCont_.find(keys);
261		if (torsionType) {
262		return torsionType;
263		} else {
264	<	//if no exact match found, try wild card match
265	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
266	<	}
267	<
268	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
264	>
265	>	AtomType* atype1;
266	>	AtomType* atype2;
267	>	AtomType* atype3;
268	>	AtomType* atype4;
269	>	std::vector<std::string> at1key;
270	>	at1key.push_back(at1);
271	>	atype1 = atomTypeCont_.find(at1key);
272	>
273	>	std::vector<std::string> at2key;
274	>	at2key.push_back(at2);
275	>	atype2 = atomTypeCont_.find(at2key);
276	>
277	>	std::vector<std::string> at3key;
278	>	at3key.push_back(at3);
279	>	atype3 = atomTypeCont_.find(at3key);
280	>
281	>	std::vector<std::string> at4key;
282	>	at4key.push_back(at4);
283	>	atype4 = atomTypeCont_.find(at4key);
284	>
285	>	// query atom types for their chains of responsibility
286	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
287	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
288	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
289	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
290	>
291	>	std::vector<AtomType*>::iterator i;
292	>	std::vector<AtomType*>::iterator j;
293	>	std::vector<AtomType*>::iterator k;
294	>	std::vector<AtomType*>::iterator l;
295	>
296	>	int ii = 0;
297	>	int jj = 0;
298	>	int kk = 0;
299	>	int ll = 0;
300	>	int ILscore;
301	>	int JKscore;
302	>
303	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
304	>
305	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
306	>	kk = 0;
307	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
308	>	ii = 0;
309	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
310	>	ll = 0;
311	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
312	>
313	>	ILscore = ii + ll;
314	>	JKscore = jj + kk;
315	>
316	>	std::vector<std::string> myKeys;
317	>	myKeys.push_back((*i)->getName());
318	>	myKeys.push_back((*j)->getName());
319	>	myKeys.push_back((*k)->getName());
320	>	myKeys.push_back((*l)->getName());
321	>
322	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
323	>	if (torsionType) {
324	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
325	>	}
326	>	ll++;
327	>	}
328	>	ii++;
329	>	}
330	>	kk++;
331	>	}
332	>	jj++;
333	>	}
334	>
335	>	if (foundTorsions.size() > 0) {
336	>	std::sort(foundTorsions.begin(), foundTorsions.end());
337	>	int jkscore = foundTorsions[0].first;
338	>	int ilscore = foundTorsions[0].second;
339	>	std::vector<std::string> theKeys = foundTorsions[0].third;
340	>
341	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
342	>	return bestType;
343	>	} else {
344	>	//if no exact match found, try wild card match
345	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
346	>	}
347	>	}
348		}
349
350	+	InversionType* ForceField::getInversionType(const std::string &at1,
351	+	const std::string &at2,
352	+	const std::string &at3,
353	+	const std::string &at4) {
354	+	std::vector<std::string> keys;
355	+	keys.push_back(at1);
356	+	keys.push_back(at2);
357	+	keys.push_back(at3);
358	+	keys.push_back(at4);
359	+
360	+	//try exact match first
361	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
362	+	if (inversionType) {
363	+	return inversionType;
364	+	} else {
365	+
366	+	AtomType* atype1;
367	+	AtomType* atype2;
368	+	AtomType* atype3;
369	+	AtomType* atype4;
370	+	std::vector<std::string> at1key;
371	+	at1key.push_back(at1);
372	+	atype1 = atomTypeCont_.find(at1key);
373	+
374	+	std::vector<std::string> at2key;
375	+	at2key.push_back(at2);
376	+	atype2 = atomTypeCont_.find(at2key);
377	+
378	+	std::vector<std::string> at3key;
379	+	at3key.push_back(at3);
380	+	atype3 = atomTypeCont_.find(at3key);
381	+
382	+	std::vector<std::string> at4key;
383	+	at4key.push_back(at4);
384	+	atype4 = atomTypeCont_.find(at4key);
385	+
386	+	// query atom types for their chains of responsibility
387	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
388	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
389	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
390	+	std::vector<AtomType*> at4Chain = atype4->allYourBase();
391	+
392	+	std::vector<AtomType*>::iterator i;
393	+	std::vector<AtomType*>::iterator j;
394	+	std::vector<AtomType*>::iterator k;
395	+	std::vector<AtomType*>::iterator l;
396	+
397	+	int ii = 0;
398	+	int jj = 0;
399	+	int kk = 0;
400	+	int ll = 0;
401	+	int Iscore;
402	+	int JKLscore;
403	+
404	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
405	+
406	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
407	+	kk = 0;
408	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
409	+	ii = 0;
410	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
411	+	ll = 0;
412	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
413	+
414	+	Iscore = ii;
415	+	JKLscore = jj + kk + ll;
416	+
417	+	std::vector<std::string> myKeys;
418	+	myKeys.push_back((*i)->getName());
419	+	myKeys.push_back((*j)->getName());
420	+	myKeys.push_back((*k)->getName());
421	+	myKeys.push_back((*l)->getName());
422	+
423	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
424	+	if (inversionType) {
425	+	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
426	+	}
427	+	ll++;
428	+	}
429	+	ii++;
430	+	}
431	+	kk++;
432	+	}
433	+	jj++;
434	+	}
435	+
436	+	if (foundInversions.size() > 0) {
437	+	std::sort(foundInversions.begin(), foundInversions.end());
438	+	int iscore = foundInversions[0].first;
439	+	int jklscore = foundInversions[0].second;
440	+	std::vector<std::string> theKeys = foundInversions[0].third;
441	+
442	+	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
443	+	return bestType;
444	+	} else {
445	+	//if no exact match found, try wild card match
446	+	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
447	+	}
448	+	}
449	+	}
450	+
451		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
452	+
453		std::vector<std::string> keys;
454		keys.push_back(at1);
455		keys.push_back(at2);
#	Line 143 | Line 459 | namespace oopse {
459		if (nbiType) {
460		return nbiType;
461		} else {
462	<	//if no exact match found, try wild card match
463	<	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
464	<	}
462	>	AtomType* atype1;
463	>	AtomType* atype2;
464	>	std::vector<std::string> at1key;
465	>	at1key.push_back(at1);
466	>	atype1 = atomTypeCont_.find(at1key);
467	>
468	>	std::vector<std::string> at2key;
469	>	at2key.push_back(at2);
470	>	atype2 = atomTypeCont_.find(at2key);
471	>
472	>	// query atom types for their chains of responsibility
473	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
474	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
475	>
476	>	std::vector<AtomType*>::iterator i;
477	>	std::vector<AtomType*>::iterator j;
478	>
479	>	int ii = 0;
480	>	int jj = 0;
481	>	int nbiTypeScore;
482	>
483	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
484	>
485	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
486	>	jj = 0;
487	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
488	>
489	>	nbiTypeScore = ii + jj;
490	>
491	>	std::vector<std::string> myKeys;
492	>	myKeys.push_back((*i)->getName());
493	>	myKeys.push_back((*j)->getName());
494	>
495	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
496	>	if (nbiType) {
497	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
498	>	}
499	>	jj++;
500	>	}
501	>	ii++;
502	>	}
503	>
504	>
505	>	if (foundNBI.size() > 0) {
506	>	// sort the foundNBI by the score:
507	>	std::sort(foundNBI.begin(), foundNBI.end());
508	>
509	>	int bestScore = foundNBI[0].first;
510	>	std::vector<std::string> theKeys = foundNBI[0].second;
511	>
512	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
513	>	return bestType;
514	>	} else {
515	>	//if no exact match found, try wild card match
516	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
517	>	}
518	>	}
519		}
520
521		BondType* ForceField::getExactBondType(const std::string &at1,
#	Line 177 | Line 547 | namespace oopse {
547		keys.push_back(at4);
548		return torsionTypeCont_.find(keys);
549		}
550	<
550	>
551	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
552	>	const std::string &at2,
553	>	const std::string &at3,
554	>	const std::string &at4){
555	>	std::vector<std::string> keys;
556	>	keys.push_back(at1);
557	>	keys.push_back(at2);
558	>	keys.push_back(at3);
559	>	keys.push_back(at4);
560	>	return inversionTypeCont_.find(keys);
561	>	}
562	>
563		NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
564		std::vector<std::string> keys;
565		keys.push_back(at1);
566		keys.push_back(at2);
567		return nonBondedInteractionTypeCont_.find(keys);
568		}
569	+
570
188	–
571		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
572		std::vector<std::string> keys;
573		keys.push_back(at);
574	+	atypeIdentToName[atomType->getIdent()] = at;
575		return atomTypeCont_.add(keys, atomType);
576		}
577
578	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
579	+	std::vector<std::string> keys;
580	+	keys.push_back(at);
581	+	atypeIdentToName[atomType->getIdent()] = at;
582	+	return atomTypeCont_.replace(keys, atomType);
583	+	}
584	+
585		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
586		BondType* bondType) {
587		std::vector<std::string> keys;
#	Line 222 | Line 612 | namespace oopse {
612		return torsionTypeCont_.add(keys, torsionType);
613		}
614
615	+	bool ForceField::addInversionType(const std::string &at1,
616	+	const std::string &at2,
617	+	const std::string &at3,
618	+	const std::string &at4,
619	+	InversionType* inversionType) {
620	+	std::vector<std::string> keys;
621	+	keys.push_back(at1);
622	+	keys.push_back(at2);
623	+	keys.push_back(at3);
624	+	keys.push_back(at4);
625	+	return inversionTypeCont_.add(keys, inversionType);
626	+	}
627	+
628		bool ForceField::addNonBondedInteractionType(const std::string &at1,
629		const std::string &at2,
630		NonBondedInteractionType* nbiType) {
#	Line 250 | Line 653 | namespace oopse {
653		} else {
654		sprintf( painCave.errMsg,
655		"Can not cast GenericData to LJParam\n");
656	<	painCave.severity = OOPSE_ERROR;
656	>	painCave.severity = OPENMD_ERROR;
657		painCave.isFatal = 1;
658		simError();
659		}
660		} else {
661		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662	<	painCave.severity = OOPSE_ERROR;
662	>	painCave.severity = OPENMD_ERROR;
663		painCave.isFatal = 1;
664		simError();
665		}
#	Line 286 | Line 689 | namespace oopse {
689		"\tHave you tried setting the FORCE_PARAM_PATH environment "
690		"variable?\n",
691		forceFieldFilename.c_str() );
692	<	painCave.severity = OOPSE_ERROR;
692	>	painCave.severity = OPENMD_ERROR;
693		painCave.isFatal = 1;
694		simError();
695		}
#	Line 294 | Line 697 | namespace oopse {
697		return ffStream;
698		}
699
700	<	void ForceField::setFortranForceOptions(){
298	<	ForceOptions theseFortranOptions;
299	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
300	<	setfForceOptions(&theseFortranOptions);
301	<	}
302	<	} //end namespace oopse
700	>	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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