ViewVC Help

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

root/group/trunk/OOPSE_old/src/mdtools/libmdCode/TraPPE_ExFF.cpp

Comparing trunk/OOPSE_old/src/mdtools/libmdCode/TraPPE_ExFF.cpp (file contents):
Revision 270 by mmeineke, Fri Feb 14 17:08:46 2003 UTC vs.
Revision 293 by mmeineke, Thu Mar 6 16:07:57 2003 UTC

#	Line 9 | Line 9 | using namespace std;
9		#include "SRI.hpp"
10		#include "simError.h"
11
12	–
12		#ifdef IS_MPI
14	–
13		#include "mpiForceField.h"
14	+	#endif // is_mpi
15
16	+	namespace TPE {  // restrict the access of the folowing to this file only.
17
18	–	// Declare the structures that will be passed by MPI
18
19	<	typedef struct{
20	<	char name[15];
21	<	double mass;
22	<	double epslon;
23	<	double sigma;
24	<	double dipole;
25	<	int isDipole;
26	<	int last;      //  0  -> default
27	<	//  1  -> tells nodes to stop listening
28	<	} atomStruct;
29	<	MPI_Datatype mpiAtomStructType;
19	>	// Declare the structures that will be passed by MPI
20	>
21	>	typedef struct{
22	>	char name[15];
23	>	double mass;
24	>	double epslon;
25	>	double sigma;
26	>	double dipole;
27	>	double w0;
28	>	double v0;
29	>	int isSSD;
30	>	int isDipole;
31	>	int ident;
32	>	int last;      //  0  -> default
33	>	//  1  -> tells nodes to stop listening
34	>	} atomStruct;
35	>
36	>
37	>	typedef struct{
38	>	char nameA[15];
39	>	char nameB[15];
40	>	char type[30];
41	>	double d0;
42	>	int last;      //  0  -> default
43	>	//  1  -> tells nodes to stop listening
44	>	} bondStruct;
45	>
46	>
47	>	typedef struct{
48	>	char nameA[15];
49	>	char nameB[15];
50	>	char nameC[15];
51	>	char type[30];
52	>	double k1, k2, k3, t0;
53	>	int last;      //  0  -> default
54	>	//  1  -> tells nodes to stop listening
55	>	} bendStruct;
56	>
57
58	<	typedef struct{
59	<	char nameA[15];
60	<	char nameB[15];
61	<	char type[30];
62	<	double d0;
63	<	int last;      //  0  -> default
64	<	//  1  -> tells nodes to stop listening
65	<	} bondStruct;
66	<	MPI_Datatype mpiBondStructType;
67	<
68	<	typedef struct{
69	<	char nameA[15];
70	<	char nameB[15];
71	<	char nameC[15];
72	<	char type[30];
73	<	double k1, k2, k3, t0;
74	<	int last;      //  0  -> default
75	<	//  1  -> tells nodes to stop listening
76	<	} bendStruct;
51	<	MPI_Datatype mpiBendStructType;
58	>	typedef struct{
59	>	char nameA[15];
60	>	char nameB[15];
61	>	char nameC[15];
62	>	char nameD[15];
63	>	char type[30];
64	>	double k1, k2, k3, k4;
65	>	int last;      //  0  -> default
66	>	//  1  -> tells nodes to stop listening
67	>	} torsionStruct;
68	>
69	>
70	>	int parseAtom(    char *lineBuffer, int lineNum, atomStruct     &info );
71	>	int parseBond(    char *lineBuffer, int lineNum, bondStruct     &info );
72	>	int parseBend(    char *lineBuffer, int lineNum, bendStruct     &info );
73	>	int parseTorsion( char *lineBuffer, int lineNum, torsionStruct  &info );
74	>
75	>
76	>	#ifdef IS_MPI
77
78	<	typedef struct{
79	<	char nameA[15];
80	<	char nameB[15];
81	<	char nameC[15];
57	<	char nameD[15];
58	<	char type[30];
59	<	double k1, k2, k3, k4;
60	<	int last;      //  0  -> default
61	<	//  1  -> tells nodes to stop listening
62	<	} torsionStruct;
63	<	MPI_Datatype mpiTorsionStructType;
78	>	MPI_Datatype mpiAtomStructType;
79	>	MPI_Datatype mpiBondStructType;
80	>	MPI_Datatype mpiBendStructType;
81	>	MPI_Datatype mpiTorsionStructType;
82
83		#endif
84
85	+	} // namespace
86
87
88	+	// declaration of functions needed to wrap the fortran module
89	+
90	+
91	+
92	+	TraPPE_ExFF* currentTPEwrap;
93	+
94	+	using namespace TPE;
95	+
96	+
97	+	//****************************************************************
98	+	// begins the actual forcefield stuff.
99	+	//****************************************************************
100	+
101	+
102		TraPPE_ExFF::TraPPE_ExFF(){
103
104		char fileName[200];
#	Line 74 | Line 107 | TraPPE_ExFF::TraPPE_ExFF(){
107		char temp[200];
108		char errMsg[1000];
109
110	+	// do the funtion wrapping
111	+	currentTPEwrap = this;
112	+	wrapMe();
113	+
114	+
115		#ifdef IS_MPI
116		int i;
117
118	<	// **********************************************************************
118	>	// **********************************************************************
119		// Init the atomStruct mpi type
120
121		atomStruct atomProto; // mpiPrototype
122	<	int atomBC[3] = {15,4,2};  // block counts
122	>	int atomBC[3] = {15,6,4};  // block counts
123		MPI_Aint atomDspls[3];           // displacements
124		MPI_Datatype atomMbrTypes[3];    // member mpi types
125
126		MPI_Address(&atomProto.name, &atomDspls[0]);
127		MPI_Address(&atomProto.mass, &atomDspls[1]);
128	<	MPI_Address(&atomProto.isDipole, &atomDspls[2]);
128	>	MPI_Address(&atomProto.isSSD, &atomDspls[2]);
129
130		atomMbrTypes[0] = MPI_CHAR;
131		atomMbrTypes[1] = MPI_DOUBLE;
#	Line 237 | Line 275 | void TraPPE_ExFF::initializeAtoms( void ){
275		#endif // is_mpi
276		}
277
278	+
279	+	void TraPPE_ExFF::wrapMe( void ){
280	+
281	+	char* currentFF = "TraPPE_Ex";
282	+	int isError = 0;
283	+
284	+	forcefactory_( currentFF, &isError, TPEfunctionWrapper, strlen(currentFF) );
285	+
286	+	if( isError ){
287	+
288	+	sprintf( painCave.errMsg,
289	+	"TraPPE_ExFF error: an error was returned from fortran when the "
290	+	"the functions were being wrapped.\n" );
291	+	painCave.isFatal = 1;
292	+	simError();
293	+	}
294	+
295	+	#ifdef IS_MPI
296	+	sprintf( checkPointMsg, "TraPPE_ExFF functions succesfully wrapped." );
297	+	MPIcheckPoint();
298	+	#endif // is_mpi
299	+	}
300	+
301	+
302	+	void TPEfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon,
303	+	double* sigma, int* isDipole,
304	+	int* isSSD, double* dipole, double* w0,
305	+	double* v0, int* isError ),
306	+	void (*p2)( int*, int*, int* ),
307	+	void (*p3)( double*,double*,double*,double*,
308	+	short int*, int* ) ){
309	+
310	+
311	+	newTPEtype = p1;
312	+	initTPEfortran = p2;
313	+	currentTPEwrap->setTPEfortran( p3 );
314	+	}
315	+
316	+
317	+
318		void TraPPE_ExFF::initializeAtoms( void ){
319
320		class LinkedType {
#	Line 253 | Line 331 | void TraPPE_ExFF::initializeAtoms( void ){
331		return NULL;
332		}
333
256	–	#ifdef IS_MPI
334		void add( atomStruct &info ){
335	+
336	+	// check for duplicates
337	+
338	+	if( !strcmp( info.name, name ) ){
339	+	sprintf( painCave.errMsg,
340	+	"Duplicate TraPPE_Ex atom type \"%s\" found in "
341	+	"the TraPPE_ExFF param file./n",
342	+	name );
343	+	painCave.isFatal = 1;
344	+	simError();
345	+	}
346	+
347		if( next != NULL ) next->add(info);
348		else{
349		next = new LinkedType();
350		strcpy(next->name, info.name);
351	<	next->isDipole = info.dipole;
351	>	next->isDipole = info.isDipole;
352	>	next->isSSD    = info.isSSD;
353		next->mass     = info.mass;
354		next->epslon   = info.epslon;
355		next->sigma    = info.sigma;
356		next->dipole   = info.dipole;
357	+	next->w0       = info.w0;
358	+	next->v0       = info.v0;
359	+	next->ident    = info.ident;
360		}
361		}
362	+
363	+	#ifdef IS_MPI
364
365		void duplicate( atomStruct &info ){
366		strcpy(info.name, name);
367	<	info.isDipole = dipole;
367	>	info.isDipole = isDipole;
368	>	info.isSSD    = isSSD;
369		info.mass     = mass;
370		info.epslon   = epslon;
371		info.sigma    = sigma;
372		info.dipole   = dipole;
373	+	info.w0       = w0;
374	+	info.v0       = v0;
375		info.last     = 0;
376		}
377
#	Line 282 | Line 380 | void TraPPE_ExFF::initializeAtoms( void ){
380
381		char name[15];
382		int isDipole;
383	+	int isSSD;
384		double mass;
385		double epslon;
386		double sigma;
387		double dipole;
388	+	double w0;
389	+	double v0;
390	+	int ident;
391		LinkedType* next;
392		};
393
394		LinkedType* headAtomType;
395		LinkedType* currentAtomType;
294	–	LinkedType* tempAtomType;
295	–
296	–	#ifdef IS_MPI
396		atomStruct info;
397		info.last = 1; // initialize last to have the last set.
398		// if things go well, last will be set to 0
399	<	#endif
399	>
400
401
303	–	char readLine[500];
304	–	char* the_token;
305	–	char* eof_test;
306	–	int foundAtom = 0;
307	–	int lineNum = 0;
402		int i;
403	<
403	>	int identNum;
404
405	+	Atom** the_atoms;
406	+	int nAtoms;
407	+	the_atoms = entry_plug->atoms;
408	+	nAtoms = entry_plug->n_atoms;
409	+
410	+
411		//////////////////////////////////////////////////
412		// a quick water fix
413
#	Line 342 | Line 442 | void TraPPE_ExFF::initializeAtoms( void ){
442
443		//////////////////////////////////////////////////
444
445	<	Atom** the_atoms;
346	<	int nAtoms;
347	<	the_atoms = entry_plug->atoms;
348	<	nAtoms = entry_plug->n_atoms;
349	<
350	<
445	>
446		#ifdef IS_MPI
447		if( worldRank == 0 ){
448		#endif
449
450		// read in the atom types.
451	<
357	<	rewind( frcFile );
451	>
452		headAtomType = new LinkedType;
359	–	currentAtomType = headAtomType;
453
454	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
455	<	lineNum++;
363	<	if( eof_test == NULL ){
364	<	sprintf( painCave.errMsg, "Error in reading Atoms from force file.\n" );
365	<	painCave.isFatal = 1;
366	<	simError();
367	<	}
368	<
369	<
370	<	while( !foundAtom ){
371	<	while( eof_test != NULL && readLine[0] != '#' ){
372	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
373	<	lineNum++;
374	<	}
375	<	if( eof_test == NULL ){
376	<	sprintf( painCave.errMsg,
377	<	"Error in reading Atoms from force file at line %d.\n",
378	<	lineNum );
379	<	painCave.isFatal = 1;
380	<	simError();
381	<	}
382	<
383	<	the_token = strtok( readLine, " ,;\t#\n" );
384	<	foundAtom = !strcmp( "AtomTypes", the_token );
385	<
386	<	if( !foundAtom ){
387	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
388	<	lineNum++;
389	<
390	<	if( eof_test == NULL ){
391	<	sprintf( painCave.errMsg,
392	<	"Error in reading Atoms from force file at line %d.\n",
393	<	lineNum );
394	<	painCave.isFatal = 1;
395	<	simError();
396	<	}
397	<	}
398	<	}
399	<
454	>	fastForward( "AtomTypes", "initializeAtoms" );
455	>
456		// we are now at the AtomTypes section.
457
458		eof_test = fgets( readLine, sizeof(readLine), frcFile );
459		lineNum++;
460
461	+
462	+	// read a line, and start parseing out the atom types
463	+
464		if( eof_test == NULL ){
465		sprintf( painCave.errMsg,
466		"Error in reading Atoms from force file at line %d.\n",
#	Line 410 | Line 469 | void TraPPE_ExFF::initializeAtoms( void ){
469		simError();
470		}
471
472	+	identNum = 1;
473	+	// stop reading at end of file, or at next section
474		while( readLine[0] != '#' && eof_test != NULL ){
475	<
475	>
476	>	// toss comment lines
477		if( readLine[0] != '!' ){
478
479	<	the_token = strtok( readLine, " \n\t,;" );
480	<	if( the_token != NULL ){
481	<
482	<	strcpy( currentAtomType->name, the_token );
483	<
422	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
423	<	sprintf( painCave.errMsg,
424	<	"Error parseing AtomTypes: line %d\n", lineNum );
425	<	painCave.isFatal = 1;
426	<	simError();
427	<	}
428	<
429	<	sscanf( the_token, "%d", &currentAtomType->isDipole );
430	<
431	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
432	<	sprintf( painCave.errMsg,
433	<	"Error parseing AtomTypes: line %d\n", lineNum );
434	<	painCave.isFatal = 1;
435	<	simError();
436	<	}
437	<
438	<	sscanf( the_token, "%lf", &currentAtomType->mass );
439	<
440	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
441	<	sprintf( painCave.errMsg,
442	<	"Error parseing AtomTypes: line %d\n", lineNum );
443	<	painCave.isFatal = 1;
444	<	simError();
445	<	}
446	<
447	<	sscanf( the_token, "%lf", &currentAtomType->epslon );
448	<
449	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
450	<	sprintf( painCave.errMsg,
451	<	"Error parseing AtomTypes: line %d\n", lineNum );
452	<	painCave.isFatal = 1;
453	<	simError();
454	<	}
455	<
456	<	sscanf( the_token, "%lf", &currentAtomType->sigma );
457	<
458	<	if( currentAtomType->isDipole ){
459	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
460	<	sprintf( painCave.errMsg,
461	<	"Error parseing AtomTypes: line %d\n",
462	<	lineNum );
463	<	painCave.isFatal = 1;
464	<	simError();
465	<	}
466	<
467	<	sscanf( the_token, "%lf", &currentAtomType->dipole );
468	<	}
479	>	// the parser returns 0 if the line was blank
480	>	if( parseAtom( readLine, lineNum, info ) ){
481	>	info.ident = identNum;
482	>	headAtomType->add( info );;
483	>	identNum++;
484		}
485		}
471	–
472	–	tempAtomType = new LinkedType;
473	–	currentAtomType->next = tempAtomType;
474	–	currentAtomType = tempAtomType;
475	–
486		eof_test = fgets( readLine, sizeof(readLine), frcFile );
487		lineNum++;
488		}
#	Line 482 | Line 492 | void TraPPE_ExFF::initializeAtoms( void ){
492		// send out the linked list to all the other processes
493
494		sprintf( checkPointMsg,
495	<	"TraPPE_Ex atom structures read successfully." );
495	>	"TraPPE_ExFF atom structures read successfully." );
496		MPIcheckPoint();
497
498	<	currentAtomType = headAtomType;
498	>	currentAtomType = headAtomType->next; //skip the first element who is a place holder.
499		while( currentAtomType != NULL ){
500		currentAtomType->duplicate( info );
501	+
502	+
503	+
504		sendFrcStruct( &info, mpiAtomStructType );
505	+
506	+	sprintf( checkPointMsg,
507	+	"successfully sent TraPPE_Ex force type: \"%s\"\n",
508	+	info.name );
509	+	MPIcheckPoint();
510	+
511		currentAtomType = currentAtomType->next;
512		}
513		info.last = 1;
#	Line 504 | Line 523 | void TraPPE_ExFF::initializeAtoms( void ){
523
524		headAtomType = new LinkedType;
525		recieveFrcStruct( &info, mpiAtomStructType );
526	+
527		while( !info.last ){
528
529	+
530	+
531		headAtomType->add( info );
532	+
533	+	MPIcheckPoint();
534	+
535		recieveFrcStruct( &info, mpiAtomStructType );
536		}
537		}
538		#endif // is_mpi
539
540	+	// call new A_types in fortran
541
542	+	int isError;
543	+	currentAtomType = headAtomType;
544	+	while( currentAtomType != NULL ){
545	+
546	+	if( currentAtomType->name[0] != '\0' ){
547	+	isError = 0;
548	+	newTPEtype( &(currentAtomType->ident),
549	+	&(currentAtomType->mass),
550	+	&(currentAtomType->epslon),
551	+	&(currentAtomType->sigma),
552	+	&(currentAtomType->isDipole),
553	+	&(currentAtomType->isSSD),
554	+	&(currentAtomType->dipole),
555	+	&(currentAtomType->w0),
556	+	&(currentAtomType->v0),
557	+	&isError );
558	+	if( isError ){
559	+	sprintf( painCave.errMsg,
560	+	"Error initializing the \"%s\" atom type in fortran\n",
561	+	currentAtomType->name );
562	+	painCave.isFatal = 1;
563	+	simError();
564	+	}
565	+	}
566	+	currentAtomType = currentAtomType->next;
567	+	}
568	+
569	+	#ifdef IS_MPI
570	+	sprintf( checkPointMsg,
571	+	"TraPPE_ExFF atom structures successfully sent to fortran\n" );
572	+	MPIcheckPoint();
573	+	#endif // is_mpi
574	+
575	+
576		// initialize the atoms
577
578	+	double bigSigma = 0.0;
579		DirectionalAtom* dAtom;
580
581		for( i=0; i<nAtoms; i++ ){
#	Line 533 | Line 594 | void TraPPE_ExFF::initializeAtoms( void ){
594		the_atoms[i]->setSigma( currentAtomType->sigma );
595		the_atoms[i]->setLJ();
596
597	+	if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
598	+
599		if( currentAtomType->isDipole ){
600		if( the_atoms[i]->isDirectional() ){
601
#	Line 582 | Line 645 | void TraPPE_ExFF::initializeAtoms( void ){
645		}
646		}
647
648	+	#ifdef IS_MPI
649	+	double tempBig = bigSigma;
650	+	MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
651	+	#endif  //is_mpi
652
653	+	//calc rCut and rList
654	+
655	+	entry_plug->rCut = 2.5 * bigSigma;
656	+
657	+	if(entry_plug->rCut > (entry_plug->box_x / 2.0))
658	+	entry_plug->rCut = entry_plug->box_x / 2.0;
659	+
660	+	if(entry_plug->rCut > (entry_plug->box_y / 2.0))
661	+	entry_plug->rCut = entry_plug->box_y / 2.0;
662	+
663	+	if(entry_plug->rCut > (entry_plug->box_z / 2.0))
664	+	entry_plug->rCut = entry_plug->box_z / 2.0;
665	+
666	+	entry_plug->rList = entry_plug->rCut + 1.0;
667	+
668	+
669		// clean up the memory
670
671		delete headAtomType;
#	Line 613 | Line 696 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
696		return NULL;
697		}
698
699	<	#ifdef IS_MPI
699	>
700		void add( bondStruct &info ){
701	+
702	+	// check for duplicates
703	+	int dup = 0;
704	+
705	+	if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1;
706	+	if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1;
707	+
708	+	if(dup){
709	+	sprintf( painCave.errMsg,
710	+	"Duplicate TraPPE_Ex bond type \"%s - %s\" found in "
711	+	"the TraPPE_ExFF param file./n",
712	+	nameA, nameB );
713	+	painCave.isFatal = 1;
714	+	simError();
715	+	}
716	+
717	+
718		if( next != NULL ) next->add(info);
719		else{
720		next = new LinkedType();
#	Line 625 | Line 725 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
725		}
726		}
727
728	+	#ifdef IS_MPI
729		void duplicate( bondStruct &info ){
730		strcpy(info.nameA, nameA);
731		strcpy(info.nameB, nameB);
#	Line 648 | Line 749 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
749
750		LinkedType* headBondType;
751		LinkedType* currentBondType;
651	–	LinkedType* tempBondType;
652	–
653	–	#ifdef IS_MPI
752		bondStruct info;
753		info.last = 1; // initialize last to have the last set.
754		// if things go well, last will be set to 0
657	–	#endif
755
659	–	char readLine[500];
660	–	char* the_token;
661	–	char* eof_test;
662	–	int foundBond = 0;
663	–	int lineNum = 0;
664	–	int i, a, b;
665	–	char* atomA;
666	–	char* atomB;
667	–
756		SRI **the_sris;
757		Atom** the_atoms;
758		int nBonds;
#	Line 672 | Line 760 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
760		the_atoms = entry_plug->atoms;
761		nBonds = entry_plug->n_bonds;
762
763	+	int i, a, b;
764	+	char* atomA;
765	+	char* atomB;
766
767		#ifdef IS_MPI
768		if( worldRank == 0 ){
#	Line 679 | Line 770 | void TraPPE_ExFF::initializeBonds( bond_pair* the_bond
770
771		// read in the bond types.
772
682	–	rewind( frcFile );
773		headBondType = new LinkedType;
684	–	currentBondType = headBondType;
774
775	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
775	>	fastForward( "BondTypes", "initializeBonds" );
776	>
777	>	// we are now at the bondTypes section
778	>
779	>	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
780		lineNum++;
688	–	if( eof_test == NULL ){
689	–	sprintf( painCave.errMsg, "Error in reading Bonds from force file.\n" );
690	–	painCave.isFatal = 1;
691	–	simError();
692	–	}
781
782
783	<	while( !foundBond ){
784	<	while( eof_test != NULL && readLine[0] != '#' ){
697	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
698	<	lineNum++;
699	<	}
700	<	if( eof_test == NULL ){
701	<	sprintf( painCave.errMsg,
702	<	"Error in reading Bonds from force file at line %d.\n",
703	<	lineNum );
704	<	painCave.isFatal = 1;
705	<	simError();
706	<	}
707	<
708	<	the_token = strtok( readLine, " ,;\t#\n" );
709	<	foundBond = !strcmp( "BondTypes", the_token );
710	<
711	<	if( !foundBond ){
712	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
713	<	lineNum++;
714	<
715	<	if( eof_test == NULL ){
716	<	sprintf( painCave.errMsg,
717	<	"Error in reading Bonds from force file at line %d.\n",
718	<	lineNum );
719	<	painCave.isFatal = 1;
720	<	simError();
721	<	}
722	<	}
723	<	}
724	<
725	<	// we are now at the BondTypes section.
726	<
727	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
728	<	lineNum++;
729	<
783	>	// read a line, and start parseing out the atom types
784	>
785		if( eof_test == NULL ){
786		sprintf( painCave.errMsg,
787	<	"Error in reading Bonds from force file at line %d.\n",
787	>	"Error in reading bonds from force file at line %d.\n",
788		lineNum );
789		painCave.isFatal = 1;
790		simError();
791		}
792
793	+	// stop reading at end of file, or at next section
794		while( readLine[0] != '#' && eof_test != NULL ){
795	<
795	>
796	>	// toss comment lines
797		if( readLine[0] != '!' ){
798
799	<	the_token = strtok( readLine, " \n\t,;" );
800	<	if( the_token != NULL ){
801	<
745	<	strcpy( currentBondType->nameA, the_token );
746	<
747	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
748	<	sprintf( painCave.errMsg,
749	<	"Error parseing BondTypes: line %d\n", lineNum );
750	<	painCave.isFatal = 1;
751	<	simError();
752	<	}
753	<
754	<	strcpy( currentBondType->nameB, the_token );
755	<
756	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
757	<	sprintf( painCave.errMsg,
758	<	"Error parseing BondTypes: line %d\n", lineNum );
759	<	painCave.isFatal = 1;
760	<	simError();
761	<	}
762	<
763	<	strcpy( currentBondType->type, the_token );
764	<
765	<	if( !strcmp( currentBondType->type, "fixed" ) ){
766	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
767	<	sprintf( painCave.errMsg,
768	<	"Error parseing BondTypes: line %d\n", lineNum );
769	<	painCave.isFatal = 1;
770	<	simError();
771	<	}
772	<
773	<	sscanf( the_token, "%lf", &currentBondType->d0 );
774	<	}
775	<
776	<	else{
777	<	sprintf( painCave.errMsg,
778	<	"Unknown TraPPE_Ex bond type \"%s\" at line %d\n",
779	<	currentBondType->type,
780	<	lineNum );
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
799	>	// the parser returns 0 if the line was blank
800	>	if( parseBond( readLine, lineNum, info ) ){
801	>	headBondType->add( info );
802		}
803		}
786	–
787	–	tempBondType = new LinkedType;
788	–	currentBondType->next = tempBondType;
789	–	currentBondType = tempBondType;
790	–
804		eof_test = fgets( readLine, sizeof(readLine), frcFile );
805		lineNum++;
806		}
807	<
807	>
808		#ifdef IS_MPI
809
810		// send out the linked list to all the other processes
#	Line 890 | Line 903 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
903		return NULL;
904		}
905
893	–	#ifdef IS_MPI
894	–
906		void add( bendStruct &info ){
907	+
908	+	// check for duplicates
909	+	int dup = 0;
910	+
911	+	if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB )
912	+	&& !strcmp( nameC, info.nameC ) ) dup = 1;
913	+	if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB )
914	+	&& !strcmp( nameC, info.nameA ) ) dup = 1;
915	+
916	+	if(dup){
917	+	sprintf( painCave.errMsg,
918	+	"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in "
919	+	"the TraPPE_ExFF param file./n",
920	+	nameA, nameB, nameC );
921	+	painCave.isFatal = 1;
922	+	simError();
923	+	}
924	+
925		if( next != NULL ) next->add(info);
926		else{
927		next = new LinkedType();
#	Line 906 | Line 935 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
935		next->t0 = info.t0;
936		}
937		}
938	<
938	>
939	>	#ifdef IS_MPI
940	>
941		void duplicate( bendStruct &info ){
942		strcpy(info.nameA, nameA);
943		strcpy(info.nameB, nameB);
#	Line 932 | Line 963 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
963
964		LinkedType* headBendType;
965		LinkedType* currentBendType;
935	–	LinkedType* tempBendType;
936	–
937	–	#ifdef IS_MPI
966		bendStruct info;
967		info.last = 1; // initialize last to have the last set.
968		// if things go well, last will be set to 0
941	–	#endif
969
943	–	char readLine[500];
944	–	char* the_token;
945	–	char* eof_test;
946	–	int foundBend = 0;
947	–	int lineNum = 0;
948	–	int i, a, b, c, index;
949	–	char* atomA;
950	–	char* atomB;
951	–	char* atomC;
970		QuadraticBend* qBend;
953	–
971		SRI **the_sris;
972		Atom** the_atoms;
973		int nBends;
#	Line 958 | Line 975 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
975		the_atoms = entry_plug->atoms;
976		nBends = entry_plug->n_bends;
977
978	+	int i, a, b, c;
979	+	char* atomA;
980	+	char* atomB;
981	+	char* atomC;
982
983	+
984		#ifdef IS_MPI
985		if( worldRank == 0 ){
986		#endif
987
988		// read in the bend types.
989
968	–	rewind( frcFile );
990		headBendType = new LinkedType;
970	–	currentBendType = headBendType;
971	–
972	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
973	–	lineNum++;
974	–	if( eof_test == NULL ){
975	–	sprintf( painCave.errMsg, "Error in reading Bends from force file.\n" );
976	–	painCave.isFatal = 1;
977	–	simError();
978	–	}
979	–
980	–
981	–	while( !foundBend ){
982	–	while( eof_test != NULL && readLine[0] != '#' ){
983	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
984	–	lineNum++;
985	–	}
986	–	if( eof_test == NULL ){
987	–	sprintf( painCave.errMsg,
988	–	"Error in reading Bends from force file at line %d.\n",
989	–	lineNum );
990	–	painCave.isFatal = 1;
991	–	simError();
992	–	}
993	–
994	–	the_token = strtok( readLine, " ,;\t#\n" );
995	–	foundBend = !strcmp( "BendTypes", the_token );
991
992	<	if( !foundBend ){
998	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
999	<	lineNum++;
992	>	fastForward( "BendTypes", "initializeBends" );
993
994	<	if( eof_test == NULL ){
1002	<	sprintf( painCave.errMsg,
1003	<	"Error in reading Bends from force file at line %d.\n",
1004	<	lineNum );
1005	<	painCave.isFatal = 1;
1006	<	simError();
1007	<	}
1008	<	}
1009	<	}
994	>	// we are now at the bendTypes section
995
996	<	// we are now at the BendTypes section.
1012	<
1013	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
996	>	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
997		lineNum++;
998	<
998	>
999	>	// read a line, and start parseing out the bend types
1000	>
1001		if( eof_test == NULL ){
1002		sprintf( painCave.errMsg,
1003	<	"Error in reading Bends from force file at line %d.\n",
1003	>	"Error in reading bends from force file at line %d.\n",
1004		lineNum );
1005		painCave.isFatal = 1;
1006		simError();
1007		}
1023	–
1024	–	while( readLine[0] != '#' && eof_test != NULL ){
1008
1009	<	if( readLine[0] != '!' ){
1009	>	// stop reading at end of file, or at next section
1010	>	while( readLine[0] != '#' && eof_test != NULL ){
1011
1012	<	the_token = strtok( readLine, " \n\t,;" );
1013	<	if( the_token != NULL ){
1012	>	// toss comment lines
1013	>	if( readLine[0] != '!' ){
1014
1015	<	strcpy( currentBendType->nameA, the_token );
1016	<
1017	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1034	<	sprintf( painCave.errMsg,
1035	<	"Error parseing BendTypes: line %d\n", lineNum );
1036	<	painCave.isFatal = 1;
1037	<	simError();
1038	<	}
1039	<
1040	<	strcpy( currentBendType->nameB, the_token );
1041	<
1042	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1043	<	sprintf( painCave.errMsg,
1044	<	"Error parseing BendTypes: line %d\n", lineNum );
1045	<	painCave.isFatal = 1;
1046	<	simError();
1047	<	}
1048	<
1049	<	strcpy( currentBendType->nameC, the_token );
1050	<
1051	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1052	<	sprintf( painCave.errMsg,
1053	<	"Error parseing BendTypes: line %d\n", lineNum );
1054	<	painCave.isFatal = 1;
1055	<	simError();
1056	<	}
1057	<
1058	<	strcpy( currentBendType->type, the_token );
1059	<
1060	<	if( !strcmp( currentBendType->type, "quadratic" ) ){
1061	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1062	<	sprintf( painCave.errMsg,
1063	<	"Error parseing BendTypes: line %d\n", lineNum );
1064	<	painCave.isFatal = 1;
1065	<	simError();
1066	<	}
1067	<
1068	<	sscanf( the_token, "%lf", &currentBendType->k1 );
1069	<
1070	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1071	<	sprintf( painCave.errMsg,
1072	<	"Error parseing BendTypes: line %d\n", lineNum );
1073	<	painCave.isFatal = 1;
1074	<	simError();
1075	<	}
1076	<
1077	<	sscanf( the_token, "%lf", &currentBendType->k2 );
1078	<
1079	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1080	<	sprintf( painCave.errMsg,
1081	<	"Error parseing BendTypes: line %d\n", lineNum );
1082	<	painCave.isFatal = 1;
1083	<	simError();
1084	<	}
1085	<
1086	<	sscanf( the_token, "%lf", &currentBendType->k3 );
1087	<
1088	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1089	<	sprintf( painCave.errMsg,
1090	<	"Error parseing BendTypes: line %d\n", lineNum );
1091	<	painCave.isFatal = 1;
1092	<	simError();
1093	<	}
1094	<
1095	<	sscanf( the_token, "%lf", &currentBendType->t0 );
1096	<	}
1097	<
1098	<	else{
1099	<	sprintf( painCave.errMsg,
1100	<	"Unknown TraPPE_Ex bend type \"%s\" at line %d\n",
1101	<	currentBendType->type,
1102	<	lineNum );
1103	<	painCave.isFatal = 1;
1104	<	simError();
1105	<	}
1015	>	// the parser returns 0 if the line was blank
1016	>	if( parseBend( readLine, lineNum, info ) ){
1017	>	headBendType->add( info );
1018		}
1019		}
1108	–
1109	–	tempBendType = new LinkedType;
1110	–	currentBendType->next = tempBendType;
1111	–	currentBendType = tempBendType;
1112	–
1020		eof_test = fgets( readLine, sizeof(readLine), frcFile );
1021		lineNum++;
1022		}
1023	<
1023	>
1024		#ifdef IS_MPI
1025
1026		// send out the linked list to all the other processes
#	Line 1150 | Line 1057 | void TraPPE_ExFF::initializeBends( bend_set* the_bends
1057		#endif // is_mpi
1058
1059		// initialize the Bends
1060	+
1061	+	int index;
1062
1063		for( i=0; i<nBends; i++ ){
1064
#	Line 1213 | Line 1122 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1122		!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this;
1123
1124		if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) &&
1125	<	!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this;
1125	>	!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this;
1126
1127		if( next != NULL ) return next->find(key1, key2, key3, key4);
1128		return NULL;
1129		}
1221	–
1222	–	#ifdef IS_MPI
1130
1131		void add( torsionStruct &info ){
1132	+
1133	+	// check for duplicates
1134	+	int dup = 0;
1135	+
1136	+	if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) &&
1137	+	!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1;
1138	+
1139	+	if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) &&
1140	+	!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1;
1141	+
1142	+	if(dup){
1143	+	sprintf( painCave.errMsg,
1144	+	"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in "
1145	+	"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD );
1146	+	painCave.isFatal = 1;
1147	+	simError();
1148	+	}
1149	+
1150		if( next != NULL ) next->add(info);
1151		else{
1152		next = new LinkedType();
#	Line 1235 | Line 1160 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1160		next->k4 = info.k4;
1161		}
1162		}
1163	+
1164	+	#ifdef IS_MPI
1165
1166		void duplicate( torsionStruct &info ){
1167		strcpy(info.nameA, nameA);
#	Line 1263 | Line 1190 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1190
1191		LinkedType* headTorsionType;
1192		LinkedType* currentTorsionType;
1266	–	LinkedType* tempTorsionType;
1267	–
1268	–	#ifdef IS_MPI
1193		torsionStruct info;
1194		info.last = 1; // initialize last to have the last set.
1195		// if things go well, last will be set to 0
1272	–	#endif
1196
1274	–	char readLine[500];
1275	–	char* the_token;
1276	–	char* eof_test;
1277	–	int foundTorsion = 0;
1278	–	int lineNum = 0;
1197		int i, a, b, c, d, index;
1198		char* atomA;
1199		char* atomB;
#	Line 1296 | Line 1214 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1214
1215		// read in the torsion types.
1216
1299	–	rewind( frcFile );
1217		headTorsionType = new LinkedType;
1301	–	currentTorsionType = headTorsionType;
1302	–
1303	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1304	–	lineNum++;
1305	–	if( eof_test == NULL ){
1306	–	sprintf( painCave.errMsg,
1307	–	"Error in reading Torsions from force file.\n" );
1308	–	painCave.isFatal = 1;
1309	–	simError();
1310	–	}
1311	–
1312	–
1313	–	while( !foundTorsion ){
1314	–	while( eof_test != NULL && readLine[0] != '#' ){
1315	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1316	–	lineNum++;
1317	–	}
1318	–	if( eof_test == NULL ){
1319	–	sprintf( painCave.errMsg,
1320	–	"Error in reading Torsions from force file at line %d.\n",
1321	–	lineNum );
1322	–	painCave.isFatal = 1;
1323	–	simError();
1324	–	}
1325	–
1326	–	the_token = strtok( readLine, " ,;\t#\n" );
1327	–	foundTorsion = !strcmp( "TorsionTypes", the_token );
1218
1219	<	if( !foundTorsion ){
1330	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1331	<	lineNum++;
1219	>	fastForward( "TorsionTypes", "initializeTorsions" );
1220
1221	<	if( eof_test == NULL ){
1334	<	sprintf( painCave.errMsg,
1335	<	"Error in reading Torsions from force file at line %d.\n",
1336	<	lineNum );
1337	<	painCave.isFatal = 1;
1338	<	simError();
1339	<	}
1340	<	}
1341	<	}
1221	>	// we are now at the torsionTypes section
1222
1223	<	// we are now at the TorsionTypes section.
1344	<
1345	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1223	>	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
1224		lineNum++;
1225	<
1225	>
1226	>
1227	>	// read a line, and start parseing out the atom types
1228	>
1229		if( eof_test == NULL ){
1230		sprintf( painCave.errMsg,
1231	<	"Error in reading Torsions from force file at line %d.\n",
1231	>	"Error in reading torsions from force file at line %d.\n",
1232		lineNum );
1233		painCave.isFatal = 1;
1234		simError();
1235		}
1355	–
1356	–	while( readLine[0] != '#' && eof_test != NULL ){
1236
1237	+	// stop reading at end of file, or at next section
1238	+	while( readLine[0] != '#' && eof_test != NULL ){
1239	+
1240	+	// toss comment lines
1241		if( readLine[0] != '!' ){
1359	–
1360	–	the_token = strtok( readLine, " \n\t,;" );
1361	–	if( the_token != NULL ){
1242
1243	<	strcpy( currentTorsionType->nameA, the_token );
1244	<
1245	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1366	<	sprintf( painCave.errMsg,
1367	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1368	<	painCave.isFatal = 1;
1369	<	simError();
1370	<	}
1371	<
1372	<	strcpy( currentTorsionType->nameB, the_token );
1373	<
1374	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1375	<	sprintf( painCave.errMsg,
1376	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1377	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<
1381	<	strcpy( currentTorsionType->nameC, the_token );
1382	<
1383	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1384	<	sprintf( painCave.errMsg,
1385	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1386	<	painCave.isFatal = 1;
1387	<	simError();
1388	<	}
1389	<
1390	<	strcpy( currentTorsionType->nameD, the_token );
1391	<
1392	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1393	<	sprintf( painCave.errMsg,
1394	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1395	<	painCave.isFatal = 1;
1396	<	simError();
1397	<	}
1398	<
1399	<	strcpy( currentTorsionType->type, the_token );
1400	<
1401	<	if( !strcmp( currentTorsionType->type, "cubic" ) ){
1402	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1403	<	sprintf( painCave.errMsg,
1404	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1405	<	painCave.isFatal = 1;
1406	<	simError();
1407	<	}
1408	<
1409	<	sscanf( the_token, "%lf", &currentTorsionType->k1 );
1410	<
1411	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1412	<	sprintf( painCave.errMsg,
1413	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1414	<	painCave.isFatal = 1;
1415	<	simError();
1416	<	}
1417	<
1418	<	sscanf( the_token, "%lf", &currentTorsionType->k2 );
1419	<
1420	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1421	<	sprintf( painCave.errMsg,
1422	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1423	<	painCave.isFatal = 1;
1424	<	simError();
1425	<	}
1426	<
1427	<	sscanf( the_token, "%lf", &currentTorsionType->k3 );
1428	<
1429	<	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1430	<	sprintf( painCave.errMsg,
1431	<	"Error parseing TorsionTypes: line %d\n", lineNum );
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<
1436	<	sscanf( the_token, "%lf", &currentTorsionType->k4 );
1437	<	}
1438	<
1439	<	else{
1440	<	sprintf( painCave.errMsg,
1441	<	"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n",
1442	<	currentTorsionType->type,
1443	<	lineNum );
1444	<	painCave.isFatal = 1;
1445	<	simError();
1446	<	}
1243	>	// the parser returns 0 if the line was blank
1244	>	if( parseTorsion( readLine, lineNum, info ) ){
1245	>	headTorsionType->add( info );
1246		}
1247		}
1449	–
1450	–	tempTorsionType = new LinkedType;
1451	–	currentTorsionType->next = tempTorsionType;
1452	–	currentTorsionType = tempTorsionType;
1453	–
1248		eof_test = fgets( readLine, sizeof(readLine), frcFile );
1249		lineNum++;
1250		}
#	Line 1533 | Line 1327 | void TraPPE_ExFF::initializeTorsions( torsion_set* the
1327		sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" );
1328		MPIcheckPoint();
1329		#endif // is_mpi
1330	+
1331	+	}
1332	+
1333	+	void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){
1334	+
1335	+	int foundText = 0;
1336	+	char* the_token;
1337	+
1338	+	rewind( frcFile );
1339	+	lineNum = 0;
1340	+
1341	+	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1342	+	lineNum++;
1343	+	if( eof_test == NULL ){
1344	+	sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
1345	+	" file is empty.\n",
1346	+	searchOwner );
1347	+	painCave.isFatal = 1;
1348	+	simError();
1349	+	}
1350	+
1351	+
1352	+	while( !foundText ){
1353	+	while( eof_test != NULL && readLine[0] != '#' ){
1354	+	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1355	+	lineNum++;
1356	+	}
1357	+	if( eof_test == NULL ){
1358	+	sprintf( painCave.errMsg,
1359	+	"Error fast forwarding force file for %s at "
1360	+	"line %d: file ended unexpectedly.\n",
1361	+	searchOwner,
1362	+	lineNum );
1363	+	painCave.isFatal = 1;
1364	+	simError();
1365	+	}
1366	+
1367	+	the_token = strtok( readLine, " ,;\t#\n" );
1368	+	foundText = !strcmp( stopText, the_token );
1369	+
1370	+	if( !foundText ){
1371	+	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1372	+	lineNum++;
1373	+
1374	+	if( eof_test == NULL ){
1375	+	sprintf( painCave.errMsg,
1376	+	"Error fast forwarding force file for %s at "
1377	+	"line %d: file ended unexpectedly.\n",
1378	+	searchOwner,
1379	+	lineNum );
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+	}
1384	+	}
1385	+	}
1386	+
1387	+
1388	+	int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1389	+
1390	+	char* the_token;
1391	+
1392	+	the_token = strtok( lineBuffer, " \n\t,;" );
1393	+	if( the_token != NULL ){
1394	+
1395	+	strcpy( info.name, the_token );
1396
1397	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1398	+	sprintf( painCave.errMsg,
1399	+	"Error parseing AtomTypes: line %d\n", lineNum );
1400	+	painCave.isFatal = 1;
1401	+	simError();
1402	+	}
1403	+
1404	+	info.isDipole = atoi( the_token );
1405	+
1406	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1407	+	sprintf( painCave.errMsg,
1408	+	"Error parseing AtomTypes: line %d\n", lineNum );
1409	+	painCave.isFatal = 1;
1410	+	simError();
1411	+	}
1412	+
1413	+	info.isSSD = atoi( the_token );
1414	+
1415	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1416	+	sprintf( painCave.errMsg,
1417	+	"Error parseing AtomTypes: line %d\n", lineNum );
1418	+	painCave.isFatal = 1;
1419	+	simError();
1420	+	}
1421	+
1422	+	info.mass = atof( the_token );
1423	+
1424	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1425	+	sprintf( painCave.errMsg,
1426	+	"Error parseing AtomTypes: line %d\n", lineNum );
1427	+	painCave.isFatal = 1;
1428	+	simError();
1429	+	}
1430	+
1431	+	info.epslon = atof( the_token );
1432	+
1433	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1434	+	sprintf( painCave.errMsg,
1435	+	"Error parseing AtomTypes: line %d\n", lineNum );
1436	+	painCave.isFatal = 1;
1437	+	simError();
1438	+	}
1439	+
1440	+	info.sigma = atof( the_token );
1441	+
1442	+	if( info.isDipole ){
1443	+
1444	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1445	+	sprintf( painCave.errMsg,
1446	+	"Error parseing AtomTypes: line %d\n", lineNum );
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+
1451	+	info.dipole = atof( the_token );
1452	+	}
1453	+	else info.dipole = 0.0;
1454	+
1455	+	if( info.isSSD ){
1456	+
1457	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1458	+	sprintf( painCave.errMsg,
1459	+	"Error parseing AtomTypes: line %d\n", lineNum );
1460	+	painCave.isFatal = 1;
1461	+	simError();
1462	+	}
1463	+
1464	+	info.w0 = atof( the_token );
1465	+
1466	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1467	+	sprintf( painCave.errMsg,
1468	+	"Error parseing AtomTypes: line %d\n", lineNum );
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+
1473	+	info.v0 = atof( the_token );
1474	+	}
1475	+	else info.v0 = info.w0 = 0.0;
1476	+
1477	+	return 1;
1478	+	}
1479	+	else return 0;
1480		}
1481	+
1482	+	int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1483	+
1484	+	char* the_token;
1485	+
1486	+	the_token = strtok( lineBuffer, " \n\t,;" );
1487	+	if( the_token != NULL ){
1488	+
1489	+	strcpy( info.nameA, the_token );
1490	+
1491	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1492	+	sprintf( painCave.errMsg,
1493	+	"Error parseing BondTypes: line %d\n", lineNum );
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+	strcpy( info.nameB, the_token );
1499	+
1500	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1501	+	sprintf( painCave.errMsg,
1502	+	"Error parseing BondTypes: line %d\n", lineNum );
1503	+	painCave.isFatal = 1;
1504	+	simError();
1505	+	}
1506	+
1507	+	strcpy( info.type, the_token );
1508	+
1509	+	if( !strcmp( info.type, "fixed" ) ){
1510	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1511	+	sprintf( painCave.errMsg,
1512	+	"Error parseing BondTypes: line %d\n", lineNum );
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	info.d0 = atof( the_token );
1518	+	}
1519	+	else{
1520	+	sprintf( painCave.errMsg,
1521	+	"Unknown TraPPE_Ex bond type \"%s\" at line %d\n",
1522	+	info.type,
1523	+	lineNum );
1524	+	painCave.isFatal = 1;
1525	+	simError();
1526	+	}
1527	+
1528	+	return 1;
1529	+	}
1530	+	else return 0;
1531	+	}
1532	+
1533	+
1534	+	int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1535	+
1536	+	char* the_token;
1537	+
1538	+	the_token = strtok( lineBuffer, " \n\t,;" );
1539	+	if( the_token != NULL ){
1540	+
1541	+	strcpy( info.nameA, the_token );
1542	+
1543	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1544	+	sprintf( painCave.errMsg,
1545	+	"Error parseing BondTypes: line %d\n", lineNum );
1546	+	painCave.isFatal = 1;
1547	+	simError();
1548	+	}
1549	+
1550	+	strcpy( info.nameB, the_token );
1551	+
1552	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1553	+	sprintf( painCave.errMsg,
1554	+	"Error parseing BondTypes: line %d\n", lineNum );
1555	+	painCave.isFatal = 1;
1556	+	simError();
1557	+	}
1558	+
1559	+	strcpy( info.nameC, the_token );
1560	+
1561	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1562	+	sprintf( painCave.errMsg,
1563	+	"Error parseing BondTypes: line %d\n", lineNum );
1564	+	painCave.isFatal = 1;
1565	+	simError();
1566	+	}
1567	+
1568	+	strcpy( info.type, the_token );
1569	+
1570	+	if( !strcmp( info.type, "quadratic" ) ){
1571	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1572	+	sprintf( painCave.errMsg,
1573	+	"Error parseing BendTypes: line %d\n", lineNum );
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+	info.k1 = atof( the_token );
1579	+
1580	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1581	+	sprintf( painCave.errMsg,
1582	+	"Error parseing BendTypes: line %d\n", lineNum );
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+	info.k2 = atof( the_token );
1588	+
1589	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1590	+	sprintf( painCave.errMsg,
1591	+	"Error parseing BendTypes: line %d\n", lineNum );
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+	info.k3 = atof( the_token );
1597	+
1598	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1599	+	sprintf( painCave.errMsg,
1600	+	"Error parseing BendTypes: line %d\n", lineNum );
1601	+	painCave.isFatal = 1;
1602	+	simError();
1603	+	}
1604	+
1605	+	info.t0 = atof( the_token );
1606	+	}
1607	+
1608	+	else{
1609	+	sprintf( painCave.errMsg,
1610	+	"Unknown TraPPE_Ex bend type \"%s\" at line %d\n",
1611	+	info.type,
1612	+	lineNum );
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	return 1;
1618	+	}
1619	+	else return 0;
1620	+	}
1621	+
1622	+	int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1623	+
1624	+	char*  the_token;
1625	+
1626	+	the_token = strtok( lineBuffer, " \n\t,;" );
1627	+	if( the_token != NULL ){
1628	+
1629	+	strcpy( info.nameA, the_token );
1630	+
1631	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1632	+	sprintf( painCave.errMsg,
1633	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1634	+	painCave.isFatal = 1;
1635	+	simError();
1636	+	}
1637	+
1638	+	strcpy( info.nameB, the_token );
1639	+
1640	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1641	+	sprintf( painCave.errMsg,
1642	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1643	+	painCave.isFatal = 1;
1644	+	simError();
1645	+	}
1646	+
1647	+	strcpy( info.nameC, the_token );
1648	+
1649	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1650	+	sprintf( painCave.errMsg,
1651	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1652	+	painCave.isFatal = 1;
1653	+	simError();
1654	+	}
1655	+
1656	+	strcpy( info.nameD, the_token );
1657	+
1658	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1659	+	sprintf( painCave.errMsg,
1660	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1661	+	painCave.isFatal = 1;
1662	+	simError();
1663	+	}
1664	+
1665	+	strcpy( info.type, the_token );
1666	+
1667	+	if( !strcmp( info.type, "cubic" ) ){
1668	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1669	+	sprintf( painCave.errMsg,
1670	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1671	+	painCave.isFatal = 1;
1672	+	simError();
1673	+	}
1674	+
1675	+	info.k1 = atof( the_token );
1676	+
1677	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1678	+	sprintf( painCave.errMsg,
1679	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1680	+	painCave.isFatal = 1;
1681	+	simError();
1682	+	}
1683	+
1684	+	info.k2 = atof( the_token );
1685	+
1686	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1687	+	sprintf( painCave.errMsg,
1688	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1689	+	painCave.isFatal = 1;
1690	+	simError();
1691	+	}
1692	+
1693	+	info.k3 = atof( the_token );
1694	+
1695	+	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1696	+	sprintf( painCave.errMsg,
1697	+	"Error parseing TorsionTypes: line %d\n", lineNum );
1698	+	painCave.isFatal = 1;
1699	+	simError();
1700	+	}
1701	+
1702	+	info.k4 = atof( the_token );
1703	+
1704	+	}
1705	+
1706	+	else{
1707	+	sprintf( painCave.errMsg,
1708	+	"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n",
1709	+	info.type,
1710	+	lineNum );
1711	+	painCave.isFatal = 1;
1712	+	simError();
1713	+	}
1714	+
1715	+	return 1;
1716	+	}
1717	+
1718	+	else return 0;
1719	+	}

Diff Legend

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