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root/group/branches/new_design/OOPSE-3.0/src/UseTheForce/DUFF.cpp

Comparing:
trunk/OOPSE-3.0/src/UseTheForce/DUFF.cpp (file contents), Revision 1636 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/new_design/OOPSE-3.0/src/UseTheForce/DUFF.cpp (file contents), Revision 1741 by tim, Tue Nov 16 02:07:14 2004 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <stdio.h>
3	<	#include <string.h>
1	>	/*
2	>	* Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3	>	*
4	>	* Contact: oopse@oopse.org
5	>	*
6	>	* This program is free software; you can redistribute it and/or
7	>	* modify it under the terms of the GNU Lesser General Public License
8	>	* as published by the Free Software Foundation; either version 2.1
9	>	* of the License, or (at your option) any later version.
10	>	* All we ask is that proper credit is given for our work, which includes
11	>	* - but is not limited to - adding the above copyright notice to the beginning
12	>	* of your source code files, and to any copyright notice that you may distribute
13	>	* with programs based on this work.
14	>	*
15	>	* This program is distributed in the hope that it will be useful,
16	>	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	>	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18	>	* GNU Lesser General Public License for more details.
19	>	*
20	>	* You should have received a copy of the GNU Lesser General Public License
21	>	* along with this program; if not, write to the Free Software
22	>	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
23	>	*
24	>	*/
25
26	<	#include <iostream>
6	<	using namespace std;
7	<
8	<	#include "UseTheForce/ForceFields.hpp"
9	<	#include "primitives/SRI.hpp"
10	<	#include "utils/simError.h"
11	<	#include "types/DirectionalAtomType.hpp"
26	>	#include "UseTheForce/DUFF.hpp"
27		#include "UseTheForce/DarkSide/lj_interface.h"
13	–	#include "UseTheForce/DarkSide/dipole_interface.h"
14	–	#include "UseTheForce/DarkSide/sticky_interface.h"
28
29	<	#ifdef IS_MPI
17	<	#include "UseTheForce/mpiForceField.h"
18	<	#endif // is_mpi
29	>	namespace oopse {
30
31	+	//definition of createDUFF
32	+	ForceField* createDUFF() {
33	+	return new DUFF();
34	+	}
35
36	<	// define some bond Types
36	>	//register createDUFF to ForceFieldCreator
37	>	ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
38
39	<	#define FIXED_BOND    0
40	<	#define HARMONIC_BOND 1
41	<
42	<
43	<	namespace DUFF_NS {  // restrict the access of the folowing to this file only.
44	<
45	<
30	<	// Declare the structures that will be passed by MPI
31	<
32	<	typedef struct{
33	<	char name[15];
39	>	void DUFF::parse(const std::string& filename) {
40	>	ifstrstream* ffStream;
41	>	ffStream = openForceFiledFile(filename);
42	>	const int bufferSize = 65535;
43	>	char line[bufferSize];
44	>	AtomType* atomType;
45	>	std::string atomTypeName;
46		double mass;
47	<	double epslon;
47	>	double epsilon;
48		double sigma;
49	<	double charge;
50	<	double dipole;
51	<	double w0;
40	<	double v0;
41	<	double v0p;
42	<	double rl;
43	<	double ru;
44	<	double rlp;
45	<	double rup;
46	<	int isSSD;
47	<	int isCharge;
48	<	int isDipole;
49	<	int ident;
50	<	int last;      //  0  -> default
51	<	//  1  -> tells nodes to stop listening
52	<	} atomStruct;
53	<
54	<
55	<	typedef struct{
56	<	char nameA[15];
57	<	char nameB[15];
58	<	double d0;
59	<	double k0;
60	<	int last;      //  0  -> default
61	<	//  1  -> tells nodes to stop listening
62	<	int type;
63	<	} bondStruct;
64	<
65	<
66	<	typedef struct{
67	<	char nameA[15];
68	<	char nameB[15];
69	<	char nameC[15];
70	<	char type[30];
71	<	double k1, k2, k3, t0;
72	<	int last;      //  0  -> default
73	<	//  1  -> tells nodes to stop listening
74	<	} bendStruct;
75	<
49	>	int status;
50	>	int ident = 1; //ident begins from 1 (fortran's index begins from 1)
51	>	int lineNo = 0;
52
53	<	typedef struct{
54	<	char nameA[15];
79	<	char nameB[15];
80	<	char nameC[15];
81	<	char nameD[15];
82	<	char type[30];
83	<	double k1, k2, k3, k4;
84	<	int last;      //  0  -> default
85	<	//  1  -> tells nodes to stop listening
86	<	} torsionStruct;
87	<
88	<
89	<	int parseAtom(    char *lineBuffer, int lineNum, atomStruct     &info );
90	<	int parseBond(    char *lineBuffer, int lineNum, bondStruct     &info );
91	<	int parseBend(    char *lineBuffer, int lineNum, bendStruct     &info );
92	<	int parseTorsion( char *lineBuffer, int lineNum, torsionStruct  &info );
93	<
94	<
95	<	#ifdef IS_MPI
53	>	while(ffStream.getline(line, bufferSize)){
54	>	++lineNo;
55
56	<	MPI_Datatype mpiAtomStructType;
57	<	MPI_Datatype mpiBondStructType;
58	<	MPI_Datatype mpiBendStructType;
59	<	MPI_Datatype mpiTorsionStructType;
56	>	//a line begins with '#' or '!' is comment which is skipped
57	>	if (line[0] != '#' ||line[0] != '!') {
58	>	StringTokenizer tokenizer(line);
59	>
60	>	if (tokenizer.countTokens() >= 4) {
61	>	atomTypeName = tokenizer.nextToken();
62	>	mass = tokenizer.nextTokenAsFloat();
63	>	epsilon = tokenizer.nextTokenAsFloat();
64	>	sigma = tokenizer.nextTokenAsFloat();
65
66	<	#endif
66	>	atomType = new AtomType();
67	>	atomType->setName(atomTypeName);
68	>	atomType->setMass(mass);
69	>
70	>	//by default, all of the properties in AtomTypeProperties is set to 0
71	>	//In  Lennard-Jones Force Field, we only need to set Lennard-Jones to true
72	>	atomType->setLennardJones();
73
74	<	class LinkedAtomType {
75	<	public:
76	<	LinkedAtomType(){
77	<	next = NULL;
78	<	name[0] = '\0';
79	<	}
110	<	~LinkedAtomType(){ if( next != NULL ) delete next; }
74	>	atomType->setIdent(ident);
75	>	atomType->addProperty(new DoubleGenericData("Epsilon", epsilon));
76	>	atomType->addProperty(new DoubleGenericData("Sigma", sigma));
77	>	atomType->complete();
78	>	//notify a new LJtype atom type is created
79	>	newLJtype(&ident, &sigma, &epsilon, &status);
80
81	<	LinkedAtomType* find(char* key){
82	<	if( !strcmp(name, key) ) return this;
83	<	if( next != NULL ) return next->find(key);
84	<	return NULL;
81	>	//add atom type to AtomTypeContainer
82	>	addAtomType(atomTypeName, atomType);
83	>	++ident;
84	>
85	>	} else {
86	>	sprintf( painCave.errMsg,
87	>	"Not enough tokens when parsing Lennard-Jones Force Field : %s\n"
88	>	"in line %d : %s\n",
89	>	filename.c_str(), lineNo, line);
90	>	painCave.severity = OOPSE_ERROR;
91	>	painCave.isFatal = 1;
92	>	simError();
93	>	}
94	>
95	>	}
96		}
97
98	<	void printMe( void ){
99	<
120	<	std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n";
121	<	//      if( next != NULL ) next->printMe();
98	>	delete ffStream;
99	>	}
100
123	–	}
101
102	<	void add( atomStruct &info ){
102	>	void DUFF::parseAtomType(){
103	>	}
104
105	<	// check for duplicates
106	<
129	<	if( !strcmp( info.name, name ) ){
130	<	sprintf( painCave.errMsg,
131	<	"Duplicate DUFF atom type \"%s\" found in "
132	<	"the DUFF param file./n",
133	<	name );
134	<	painCave.isFatal = 1;
135	<	simError();
136	<	}
137	<
138	<	if( next != NULL ) next->add(info);
139	<	else{
140	<	next = new LinkedAtomType();
141	<	strcpy(next->name, info.name);
142	<	next->isDipole = info.isDipole;
143	<	next->isSSD    = info.isSSD;
144	<	next->mass     = info.mass;
145	<	next->epslon   = info.epslon;
146	<	next->sigma    = info.sigma;
147	<	next->dipole   = info.dipole;
148	<	next->w0       = info.w0;
149	<	next->v0       = info.v0;
150	<	next->v0p      = info.v0p;
151	<	next->rl       = info.rl;
152	<	next->ru       = info.ru;
153	<	next->rlp      = info.rlp;
154	<	next->rup      = info.rup;
155	<	next->ident    = info.ident;
156	<	}
157	<	}
158	<
159	<	#ifdef IS_MPI
160	<
161	<	void duplicate( atomStruct &info ){
162	<	strcpy(info.name, name);
163	<	info.isDipole = isDipole;
164	<	info.isSSD    = isSSD;
165	<	info.mass     = mass;
166	<	info.epslon   = epslon;
167	<	info.sigma    = sigma;
168	<	info.dipole   = dipole;
169	<	info.w0       = w0;
170	<	info.v0       = v0;
171	<	info.v0p      = v0p;
172	<	info.rl       = rl;
173	<	info.ru       = ru;
174	<	info.rlp      = rlp;
175	<	info.rup      = rup;
176	<	info.ident    = ident;
177	<	info.last     = 0;
178	<	}
105	>	void DUFF::parseBondType(){
106	>	}
107
108	<
181	<	#endif
182	<
183	<	char name[15];
184	<	int isDipole;
185	<	int isSSD;
186	<	double mass;
187	<	double epslon;
188	<	double sigma;
189	<	double dipole;
190	<	double w0;
191	<	double v0;
192	<	double v0p;
193	<	double rl;
194	<	double ru;
195	<	double rlp;
196	<	double rup;
197	<	int ident;
198	<	LinkedAtomType* next;
199	<	};
200	<
201	<	class LinkedBondType {
202	<	public:
203	<	LinkedBondType(){
204	<	next = NULL;
205	<	nameA[0] = '\0';
206	<	nameB[0] = '\0';
207	<	}
208	<	~LinkedBondType(){ if( next != NULL ) delete next; }
209	<
210	<	LinkedBondType* find(char* key1, char* key2){
211	<	if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this;
212	<	if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this;
213	<	if( next != NULL ) return next->find(key1, key2);
214	<	return NULL;
215	<	}
216	<
217	<
218	<	void add( bondStruct &info ){
219	<
220	<	// check for duplicates
221	<	int dup = 0;
222	<
223	<	if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1;
224	<	if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1;
225	<
226	<	if(dup){
227	<	sprintf( painCave.errMsg,
228	<	"Duplicate DUFF bond type \"%s - %s\" found in "
229	<	"the DUFF param file./n",
230	<	nameA, nameB );
231	<	painCave.isFatal = 1;
232	<	simError();
233	<	}
234	<
235	<
236	<	if( next != NULL ) next->add(info);
237	<	else{
238	<	next = new LinkedBondType();
239	<	strcpy(next->nameA, info.nameA);
240	<	strcpy(next->nameB, info.nameB);
241	<	next->type = info.type;
242	<	next->d0 = info.d0;
243	<	next->k0 = info.k0;
244	<	}
245	<	}
246	<
247	<	#ifdef IS_MPI
248	<	void duplicate( bondStruct &info ){
249	<	strcpy(info.nameA, nameA);
250	<	strcpy(info.nameB, nameB);
251	<	info.type = type;
252	<	info.d0   = d0;
253	<	info.k0   = k0;
254	<	info.last = 0;
255	<	}
256	<
257	<
258	<	#endif
259	<
260	<	char nameA[15];
261	<	char nameB[15];
262	<	int type;
263	<	double d0;
264	<	double k0;
265	<
266	<	LinkedBondType* next;
267	<	};
268	<
269	<	class LinkedBendType {
270	<	public:
271	<	LinkedBendType(){
272	<	next = NULL;
273	<	nameA[0] = '\0';
274	<	nameB[0] = '\0';
275	<	nameC[0] = '\0';
276	<	type[0] = '\0';
277	<	}
278	<	~LinkedBendType(){ if( next != NULL ) delete next; }
279	<
280	<	LinkedBendType* find( char* key1, char* key2, char* key3 ){
281	<	if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 )
282	<	&& !strcmp( nameC, key3 ) ) return this;
283	<	if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 )
284	<	&& !strcmp( nameC, key1 ) ) return this;
285	<	if( next != NULL ) return next->find(key1, key2, key3);
286	<	return NULL;
287	<	}
288	<
289	<	void add( bendStruct &info ){
290	<
291	<	// check for duplicates
292	<	int dup = 0;
293	<
294	<	if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB )
295	<	&& !strcmp( nameC, info.nameC ) ) dup = 1;
296	<	if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB )
297	<	&& !strcmp( nameC, info.nameA ) ) dup = 1;
298	<
299	<	if(dup){
300	<	sprintf( painCave.errMsg,
301	<	"Duplicate DUFF bend type \"%s - %s - %s\" found in "
302	<	"the DUFF param file./n",
303	<	nameA, nameB, nameC );
304	<	painCave.isFatal = 1;
305	<	simError();
306	<	}
307	<
308	<	if( next != NULL ) next->add(info);
309	<	else{
310	<	next = new LinkedBendType();
311	<	strcpy(next->nameA, info.nameA);
312	<	strcpy(next->nameB, info.nameB);
313	<	strcpy(next->nameC, info.nameC);
314	<	strcpy(next->type,  info.type);
315	<	next->k1 = info.k1;
316	<	next->k2 = info.k2;
317	<	next->k3 = info.k3;
318	<	next->t0 = info.t0;
319	<	}
320	<	}
321	<
322	<	#ifdef IS_MPI
323	<
324	<	void duplicate( bendStruct &info ){
325	<	strcpy(info.nameA, nameA);
326	<	strcpy(info.nameB, nameB);
327	<	strcpy(info.nameC, nameC);
328	<	strcpy(info.type,  type);
329	<	info.k1   = k1;
330	<	info.k2   = k2;
331	<	info.k3   = k3;
332	<	info.t0   = t0;
333	<	info.last = 0;
334	<	}
335	<
336	<	#endif // is_mpi
337	<
338	<	char nameA[15];
339	<	char nameB[15];
340	<	char nameC[15];
341	<	char type[30];
342	<	double k1, k2, k3, t0;
343	<
344	<	LinkedBendType* next;
345	<	};
346	<
347	<	class LinkedTorsionType {
348	<	public:
349	<	LinkedTorsionType(){
350	<	next = NULL;
351	<	nameA[0] = '\0';
352	<	nameB[0] = '\0';
353	<	nameC[0] = '\0';
354	<	type[0] = '\0';
355	<	}
356	<	~LinkedTorsionType(){ if( next != NULL ) delete next; }
357	<
358	<	LinkedTorsionType* find( char* key1, char* key2, char* key3, char* key4 ){
359	<
360	<
361	<
362	<
363	<	if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) &&
364	<	!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this;
365	<
366	<	if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) &&
367	<	!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this;
368	<
369	<	if( next != NULL ) return next->find(key1, key2, key3, key4);
370	<	return NULL;
371	<	}
372	<
373	<	void add( torsionStruct &info ){
374	<
375	<	// check for duplicates
376	<	int dup = 0;
377	<
378	<	if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) &&
379	<	!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1;
380	<
381	<	if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) &&
382	<	!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1;
383	<
384	<	if(dup){
385	<	sprintf( painCave.errMsg,
386	<	"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in "
387	<	"the DUFF param file./n", nameA, nameB, nameC, nameD );
388	<	painCave.isFatal = 1;
389	<	simError();
390	<	}
391	<
392	<	if( next != NULL ) next->add(info);
393	<	else{
394	<	next = new LinkedTorsionType();
395	<	strcpy(next->nameA, info.nameA);
396	<	strcpy(next->nameB, info.nameB);
397	<	strcpy(next->nameC, info.nameC);
398	<	strcpy(next->nameD, info.nameD);
399	<	strcpy(next->type,  info.type);
400	<	next->k1 = info.k1;
401	<	next->k2 = info.k2;
402	<	next->k3 = info.k3;
403	<	next->k4 = info.k4;
404	<
405	<	}
406	<	}
407	<
408	<	#ifdef IS_MPI
409	<
410	<	void duplicate( torsionStruct &info ){
411	<	strcpy(info.nameA, nameA);
412	<	strcpy(info.nameB, nameB);
413	<	strcpy(info.nameC, nameC);
414	<	strcpy(info.nameD, nameD);
415	<	strcpy(info.type,  type);
416	<	info.k1   = k1;
417	<	info.k2   = k2;
418	<	info.k3   = k3;
419	<	info.k4   = k4;
420	<	info.last = 0;
421	<	}
422	<
423	<	#endif
424	<
425	<	char nameA[15];
426	<	char nameB[15];
427	<	char nameC[15];
428	<	char nameD[15];
429	<	char type[30];
430	<	double k1, k2, k3, k4;
431	<
432	<	LinkedTorsionType* next;
433	<	};
434	<
435	<
436	<	LinkedAtomType* headAtomType;
437	<	LinkedAtomType* currentAtomType;
438	<	LinkedBondType* headBondType;
439	<	LinkedBondType* currentBondType;
440	<	LinkedBendType* headBendType;
441	<	LinkedBendType* currentBendType;
442	<	LinkedTorsionType* headTorsionType;
443	<	LinkedTorsionType* currentTorsionType;
444	<
445	<	} // namespace
446	<
447	<	using namespace DUFF_NS;
448	<
449	<
450	<	//****************************************************************
451	<	// begins the actual forcefield stuff.
452	<	//****************************************************************
453	<
454	<
455	<	DUFF::DUFF(){
456	<
457	<	char fileName[200];
458	<	char* ffPath_env = "FORCE_PARAM_PATH";
459	<	char* ffPath;
460	<	char temp[200];
461	<
462	<	headAtomType       = NULL;
463	<	currentAtomType    = NULL;
464	<	headBondType       = NULL;
465	<	currentBondType    = NULL;
466	<	headBendType       = NULL;
467	<	currentBendType    = NULL;
468	<	headTorsionType    = NULL;
469	<	currentTorsionType = NULL;
470	<
471	<
472	<	#ifdef IS_MPI
473	<	int i;
474	<
475	<	// **********************************************************************
476	<	// Init the atomStruct mpi type
477	<
478	<	atomStruct atomProto; // mpiPrototype
479	<	int atomBC[3] = {15,12,5};  // block counts
480	<	MPI_Aint atomDspls[3];           // displacements
481	<	MPI_Datatype atomMbrTypes[3];    // member mpi types
482	<
483	<	MPI_Address(&atomProto.name, &atomDspls[0]);
484	<	MPI_Address(&atomProto.mass, &atomDspls[1]);
485	<	MPI_Address(&atomProto.isSSD, &atomDspls[2]);
486	<
487	<	atomMbrTypes[0] = MPI_CHAR;
488	<	atomMbrTypes[1] = MPI_DOUBLE;
489	<	atomMbrTypes[2] = MPI_INT;
490	<
491	<	for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
492	<
493	<	MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
494	<	MPI_Type_commit(&mpiAtomStructType);
495	<
496	<
497	<	// **********************************************************************
498	<	// Init the bondStruct mpi type
499	<
500	<	bondStruct bondProto; // mpiPrototype
501	<	int bondBC[3] = {30,2,2};  // block counts
502	<	MPI_Aint bondDspls[3];           // displacements
503	<	MPI_Datatype bondMbrTypes[3];    // member mpi types
504	<
505	<	MPI_Address(&bondProto.nameA, &bondDspls[0]);
506	<	MPI_Address(&bondProto.d0,    &bondDspls[1]);
507	<	MPI_Address(&bondProto.last,  &bondDspls[2]);
508	<
509	<	bondMbrTypes[0] = MPI_CHAR;
510	<	bondMbrTypes[1] = MPI_DOUBLE;
511	<	bondMbrTypes[2] = MPI_INT;
512	<
513	<	for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0];
514	<
515	<	MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType);
516	<	MPI_Type_commit(&mpiBondStructType);
517	<
518	<
519	<	// **********************************************************************
520	<	// Init the bendStruct mpi type
521	<
522	<	bendStruct bendProto; // mpiPrototype
523	<	int bendBC[3] = {75,4,1};  // block counts
524	<	MPI_Aint bendDspls[3];           // displacements
525	<	MPI_Datatype bendMbrTypes[3];    // member mpi types
526	<
527	<	MPI_Address(&bendProto.nameA, &bendDspls[0]);
528	<	MPI_Address(&bendProto.k1,    &bendDspls[1]);
529	<	MPI_Address(&bendProto.last,  &bendDspls[2]);
530	<
531	<	bendMbrTypes[0] = MPI_CHAR;
532	<	bendMbrTypes[1] = MPI_DOUBLE;
533	<	bendMbrTypes[2] = MPI_INT;
534	<
535	<	for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0];
536	<
537	<	MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType);
538	<	MPI_Type_commit(&mpiBendStructType);
539	<
540	<
541	<	// **********************************************************************
542	<	// Init the torsionStruct mpi type
543	<
544	<	torsionStruct torsionProto; // mpiPrototype
545	<	int torsionBC[3] = {90,4,1};  // block counts
546	<	MPI_Aint torsionDspls[3];           // displacements
547	<	MPI_Datatype torsionMbrTypes[3];    // member mpi types
548	<
549	<	MPI_Address(&torsionProto.nameA, &torsionDspls[0]);
550	<	MPI_Address(&torsionProto.k1,    &torsionDspls[1]);
551	<	MPI_Address(&torsionProto.last,  &torsionDspls[2]);
552	<
553	<	torsionMbrTypes[0] = MPI_CHAR;
554	<	torsionMbrTypes[1] = MPI_DOUBLE;
555	<	torsionMbrTypes[2] = MPI_INT;
556	<
557	<	for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0];
558	<
559	<	MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes,
560	<	&mpiTorsionStructType);
561	<	MPI_Type_commit(&mpiTorsionStructType);
562	<
563	<	// ***********************************************************************
564	<
565	<	if( worldRank == 0 ){
566	<	#endif
567	<
568	<	// generate the force file name
569	<
570	<	strcpy( fileName, "DUFF.frc" );
571	<	//    fprintf( stderr,"Trying to open %s\n", fileName );
572	<
573	<	// attempt to open the file in the current directory first.
574	<
575	<	frcFile = fopen( fileName, "r" );
576	<
577	<	if( frcFile == NULL ){
578	<
579	<	// next see if the force path enviorment variable is set
580	<
581	<	ffPath = getenv( ffPath_env );
582	<	if( ffPath == NULL ) {
583	<	STR_DEFINE(ffPath, FRC_PATH );
584	<	}
585	<
586	<
587	<	strcpy( temp, ffPath );
588	<	strcat( temp, "/" );
589	<	strcat( temp, fileName );
590	<	strcpy( fileName, temp );
591	<
592	<	frcFile = fopen( fileName, "r" );
593	<
594	<	if( frcFile == NULL ){
595	<
596	<	sprintf( painCave.errMsg,
597	<	"Error opening the force field parameter file:\n"
598	<	"\t%s\n"
599	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
600	<	"variable?\n",
601	<	fileName );
602	<	painCave.severity = OOPSE_ERROR;
603	<	painCave.isFatal = 1;
604	<	simError();
605	<	}
606	<	}
607	<
608	<	#ifdef IS_MPI
609	<	}
610	<
611	<	sprintf( checkPointMsg, "DUFF file opened sucessfully." );
612	<	MPIcheckPoint();
613	<
614	<	#endif // is_mpi
108	>	void DUFF::parseBendType(){
109		}
110
111	<
618	<	DUFF::~DUFF(){
619	<
620	<	if( headAtomType != NULL ) delete headAtomType;
621	<	if( headBondType != NULL ) delete headBondType;
622	<	if( headBendType != NULL ) delete headBendType;
623	<	if( headTorsionType != NULL ) delete headTorsionType;
624	<
625	<	#ifdef IS_MPI
626	<	if( worldRank == 0 ){
627	<	#endif // is_mpi
628	<
629	<	fclose( frcFile );
630	<
631	<	#ifdef IS_MPI
632	<	}
633	<	#endif // is_mpi
634	<	}
635	<
636	<	void DUFF::cleanMe( void ){
637	<
638	<	#ifdef IS_MPI
639	<
640	<	// keep the linked lists in the mpi version
641	<
642	<	#else // is_mpi
643	<
644	<	// delete the linked lists in the single processor version
645	<
646	<	if( headAtomType != NULL ) delete headAtomType;
647	<	if( headBondType != NULL ) delete headBondType;
648	<	if( headBendType != NULL ) delete headBendType;
649	<	if( headTorsionType != NULL ) delete headTorsionType;
650	<
651	<	#endif // is_mpi
652	<	}
653	<
654	<
655	<	void DUFF::initForceField(){
656	<
657	<	initFortran( entry_plug->useReactionField );
658	<	}
659	<
660	<	double DUFF::getAtomTypeMass (char* atomType) {
661	<
662	<	currentAtomType = headAtomType->find( atomType );
663	<	if( currentAtomType == NULL ){
664	<	sprintf( painCave.errMsg,
665	<	"AtomType error, %s not found in force file.\n",
666	<	atomType );
667	<	painCave.isFatal = 1;
668	<	simError();
669	<	}
670	<
671	<	return currentAtomType->mass;
672	<	}
673	<
674	<	void DUFF::readParams( void ){
675	<
676	<	int identNum, isError;
677	<
678	<	atomStruct atomInfo;
679	<	bondStruct bondInfo;
680	<	bendStruct bendInfo;
681	<	torsionStruct torsionInfo;
682	<
683	<	AtomType* at;
684	<
685	<	bigSigma = 0.0;
686	<
687	<	atomInfo.last = 1;
688	<	bondInfo.last = 1;
689	<	bendInfo.last = 1;
690	<	torsionInfo.last = 1;
691	<
692	<	// read in the atom info
693	<
694	<	#ifdef IS_MPI
695	<	if( worldRank == 0 ){
696	<	#endif
697	<
698	<	// read in the atom types.
699	<
700	<	headAtomType = new LinkedAtomType;
701	<
702	<	fastForward( "AtomTypes", "initializeAtoms" );
703	<
704	<	// we are now at the AtomTypes section.
705	<
706	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
707	<	lineNum++;
708	<
709	<
710	<	// read a line, and start parseing out the atom types
711	<
712	<	if( eof_test == NULL ){
713	<	sprintf( painCave.errMsg,
714	<	"Error in reading Atoms from force file at line %d.\n",
715	<	lineNum );
716	<	painCave.isFatal = 1;
717	<	simError();
718	<	}
719	<
720	<	identNum = 1;
721	<	// stop reading at end of file, or at next section
722	<	while( readLine[0] != '#' && eof_test != NULL ){
723	<
724	<	// toss comment lines
725	<	if( readLine[0] != '!' ){
726	<
727	<	// the parser returns 0 if the line was blank
728	<	if( parseAtom( readLine, lineNum, atomInfo ) ){
729	<	atomInfo.ident = identNum;
730	<	headAtomType->add( atomInfo );;
731	<	identNum++;
732	<	}
733	<	}
734	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
735	<	lineNum++;
736	<	}
737	<
738	<	#ifdef IS_MPI
739	<
740	<	// send out the linked list to all the other processes
741	<
742	<	sprintf( checkPointMsg,
743	<	"DUFF atom structures read successfully." );
744	<	MPIcheckPoint();
745	<
746	<	currentAtomType = headAtomType->next; //skip the first element who is a place holder.
747	<	while( currentAtomType != NULL ){
748	<	currentAtomType->duplicate( atomInfo );
749	<
750	<	sendFrcStruct( &atomInfo, mpiAtomStructType );
751	<
752	<	sprintf( checkPointMsg,
753	<	"successfully sent DUFF force type: \"%s\"\n",
754	<	atomInfo.name );
755	<	MPIcheckPoint();
756	<
757	<	currentAtomType = currentAtomType->next;
758	<	}
759	<	atomInfo.last = 1;
760	<	sendFrcStruct( &atomInfo, mpiAtomStructType );
761	<
762	<	}
763	<
764	<	else{
765	<
766	<	// listen for node 0 to send out the force params
767	<
768	<	MPIcheckPoint();
769	<
770	<	headAtomType = new LinkedAtomType;
771	<	receiveFrcStruct( &atomInfo, mpiAtomStructType );
772	<
773	<	while( !atomInfo.last ){
774	<
775	<	headAtomType->add( atomInfo );
776	<
777	<	MPIcheckPoint();
778	<
779	<	receiveFrcStruct( &atomInfo, mpiAtomStructType );
780	<	}
781	<	}
782	<
783	<	#endif // is_mpi
784	<
785	<	// dummy variables
786	<
787	<	currentAtomType = headAtomType->next;;
788	<	while( currentAtomType != NULL ){
789	<
790	<	if( currentAtomType->name[0] != '\0' ){
791	<
792	<	if (currentAtomType->isSSD || currentAtomType->isDipole)
793	<	DirectionalAtomType* at = new DirectionalAtomType();
794	<	else
795	<	AtomType* at = new AtomType();
796	<
797	<	if (currentAtomType->isSSD) {
798	<	((DirectionalAtomType*)at)->setSticky();
799	<	entry_plug->useSticky = 1;
800	<	}
801	<
802	<	if (currentAtomType->isDipole) {
803	<	((DirectionalAtomType*)at)->setDipole();
804	<	entry_plug->useDipoles = 1;
805	<	}
806	<
807	<	at->setIdent(currentAtomType->ident);
808	<	at->setName(currentAtomType->name);
809	<	at->setLennardJones();
810	<	at->complete();
811	<	}
812	<	currentAtomType = currentAtomType->next;
813	<	}
814	<
815	<	currentAtomType = headAtomType->next;;
816	<	while( currentAtomType != NULL ){
817	<
818	<	if( currentAtomType->name[0] != '\0' ){
819	<	isError = 0;
820	<	newLJtype( &(currentAtomType->ident), &(currentAtomType->sigma),
821	<	&(currentAtomType->epslon), &isError);
822	<	if( isError ){
823	<	sprintf( painCave.errMsg,
824	<	"Error initializing the \"%s\" LJ type in fortran\n",
825	<	currentAtomType->name );
826	<	painCave.isFatal = 1;
827	<	simError();
828	<	}
829	<
830	<	if (currentAtomType->isDipole) {
831	<	newDipoleType(&(currentAtomType->ident), &(currentAtomType->dipole),
832	<	&isError);
833	<	if( isError ){
834	<	sprintf( painCave.errMsg,
835	<	"Error initializing the \"%s\" dipole type in fortran\n",
836	<	currentAtomType->name );
837	<	painCave.isFatal = 1;
838	<	simError();
839	<	}
840	<	}
841	<
842	<	if(currentAtomType->isSSD) {
843	<	makeStickyType( &(currentAtomType->w0), &(currentAtomType->v0),
844	<	&(currentAtomType->v0p),
845	<	&(currentAtomType->rl), &(currentAtomType->ru),
846	<	&(currentAtomType->rlp), &(currentAtomType->rup));
847	<	}
848	<
849	<	}
850	<	currentAtomType = currentAtomType->next;
851	<	}
852	<
853	<	#ifdef IS_MPI
854	<	sprintf( checkPointMsg,
855	<	"DUFF atom structures successfully sent to fortran\n" );
856	<	MPIcheckPoint();
857	<	#endif // is_mpi
858	<
859	<
860	<
861	<	// read in the bonds
862	<
863	<	#ifdef IS_MPI
864	<	if( worldRank == 0 ){
865	<	#endif
866	<
867	<	// read in the bond types.
868	<
869	<	headBondType = new LinkedBondType;
870	<
871	<	fastForward( "BondTypes", "initializeBonds" );
872	<
873	<	// we are now at the bondTypes section
874	<
875	<	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
876	<	lineNum++;
877	<
878	<
879	<	// read a line, and start parseing out the atom types
880	<
881	<	if( eof_test == NULL ){
882	<	sprintf( painCave.errMsg,
883	<	"Error in reading bonds from force file at line %d.\n",
884	<	lineNum );
885	<	painCave.isFatal = 1;
886	<	simError();
887	<	}
888	<
889	<	// stop reading at end of file, or at next section
890	<	while( readLine[0] != '#' && eof_test != NULL ){
891	<
892	<	// toss comment lines
893	<	if( readLine[0] != '!' ){
894	<
895	<	// the parser returns 0 if the line was blank
896	<	if( parseBond( readLine, lineNum, bondInfo ) ){
897	<	headBondType->add( bondInfo );
898	<	}
899	<	}
900	<	eof_test = fgets( readLine, sizeof(readLine), frcFile );
901	<	lineNum++;
902	<	}
903	<
904	<	#ifdef IS_MPI
905	<
906	<	// send out the linked list to all the other processes
907	<
908	<	sprintf( checkPointMsg,
909	<	"DUFF bond structures read successfully." );
910	<	MPIcheckPoint();
911	<
912	<	currentBondType = headBondType->next;
913	<	while( currentBondType != NULL ){
914	<	currentBondType->duplicate( bondInfo );
915	<	sendFrcStruct( &bondInfo, mpiBondStructType );
916	<	currentBondType = currentBondType->next;
917	<	}
918	<	bondInfo.last = 1;
919	<	sendFrcStruct( &bondInfo, mpiBondStructType );
920	<
921	<	}
111	>	void DUFF::parseTorsionType(){
112
923	–	else{
924	–
925	–	// listen for node 0 to send out the force params
926	–
927	–	MPIcheckPoint();
928	–
929	–	headBondType = new LinkedBondType;
930	–	receiveFrcStruct( &bondInfo, mpiBondStructType );
931	–	while( !bondInfo.last ){
932	–
933	–	headBondType->add( bondInfo );
934	–	receiveFrcStruct( &bondInfo, mpiBondStructType );
935	–	}
936	–	}
937	–
938	–	sprintf( checkPointMsg,
939	–	"DUFF bond structures broadcast successfully." );
940	–	MPIcheckPoint();
941	–
942	–	#endif // is_mpi
943	–
944	–
945	–	// read in the bends
946	–
947	–	#ifdef IS_MPI
948	–	if( worldRank == 0 ){
949	–	#endif
950	–
951	–	// read in the bend types.
952	–
953	–	headBendType = new LinkedBendType;
954	–
955	–	fastForward( "BendTypes", "initializeBends" );
956	–
957	–	// we are now at the bendTypes section
958	–
959	–	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
960	–	lineNum++;
961	–
962	–	// read a line, and start parseing out the bend types
963	–
964	–	if( eof_test == NULL ){
965	–	sprintf( painCave.errMsg,
966	–	"Error in reading bends from force file at line %d.\n",
967	–	lineNum );
968	–	painCave.isFatal = 1;
969	–	simError();
970	–	}
971	–
972	–	// stop reading at end of file, or at next section
973	–	while( readLine[0] != '#' && eof_test != NULL ){
974	–
975	–	// toss comment lines
976	–	if( readLine[0] != '!' ){
977	–
978	–	// the parser returns 0 if the line was blank
979	–	if( parseBend( readLine, lineNum, bendInfo ) ){
980	–	headBendType->add( bendInfo );
981	–	}
982	–	}
983	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
984	–	lineNum++;
985	–	}
986	–
987	–	#ifdef IS_MPI
988	–
989	–	// send out the linked list to all the other processes
990	–
991	–	sprintf( checkPointMsg,
992	–	"DUFF bend structures read successfully." );
993	–	MPIcheckPoint();
994	–
995	–	currentBendType = headBendType->next;
996	–	while( currentBendType != NULL ){
997	–	currentBendType->duplicate( bendInfo );
998	–	sendFrcStruct( &bendInfo, mpiBendStructType );
999	–	currentBendType = currentBendType->next;
1000	–	}
1001	–	bendInfo.last = 1;
1002	–	sendFrcStruct( &bendInfo, mpiBendStructType );
1003	–
1004	–	}
1005	–
1006	–	else{
1007	–
1008	–	// listen for node 0 to send out the force params
1009	–
1010	–	MPIcheckPoint();
1011	–
1012	–	headBendType = new LinkedBendType;
1013	–	receiveFrcStruct( &bendInfo, mpiBendStructType );
1014	–	while( !bendInfo.last ){
1015	–
1016	–	headBendType->add( bendInfo );
1017	–	receiveFrcStruct( &bendInfo, mpiBendStructType );
1018	–	}
1019	–	}
1020	–
1021	–	sprintf( checkPointMsg,
1022	–	"DUFF bend structures broadcast successfully." );
1023	–	MPIcheckPoint();
1024	–
1025	–	#endif // is_mpi
1026	–
1027	–
1028	–	// read in the torsions
1029	–
1030	–	#ifdef IS_MPI
1031	–	if( worldRank == 0 ){
1032	–	#endif
1033	–
1034	–	// read in the torsion types.
1035	–
1036	–	headTorsionType = new LinkedTorsionType;
1037	–
1038	–	fastForward( "TorsionTypes", "initializeTorsions" );
1039	–
1040	–	// we are now at the torsionTypes section
1041	–
1042	–	eof_test =  fgets( readLine, sizeof(readLine), frcFile );
1043	–	lineNum++;
1044	–
1045	–
1046	–	// read a line, and start parseing out the atom types
1047	–
1048	–	if( eof_test == NULL ){
1049	–	sprintf( painCave.errMsg,
1050	–	"Error in reading torsions from force file at line %d.\n",
1051	–	lineNum );
1052	–	painCave.isFatal = 1;
1053	–	simError();
1054	–	}
1055	–
1056	–	// stop reading at end of file, or at next section
1057	–	while( readLine[0] != '#' && eof_test != NULL ){
1058	–
1059	–	// toss comment lines
1060	–	if( readLine[0] != '!' ){
1061	–
1062	–	// the parser returns 0 if the line was blank
1063	–	if( parseTorsion( readLine, lineNum, torsionInfo ) ){
1064	–	headTorsionType->add( torsionInfo );
1065	–
1066	–	}
1067	–	}
1068	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1069	–	lineNum++;
1070	–	}
1071	–
1072	–	#ifdef IS_MPI
1073	–
1074	–	// send out the linked list to all the other processes
1075	–
1076	–	sprintf( checkPointMsg,
1077	–	"DUFF torsion structures read successfully." );
1078	–	MPIcheckPoint();
1079	–
1080	–	currentTorsionType = headTorsionType->next;
1081	–	while( currentTorsionType != NULL ){
1082	–	currentTorsionType->duplicate( torsionInfo );
1083	–	sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1084	–	currentTorsionType = currentTorsionType->next;
1085	–	}
1086	–	torsionInfo.last = 1;
1087	–	sendFrcStruct( &torsionInfo, mpiTorsionStructType );
1088	–
1089	–	}
1090	–
1091	–	else{
1092	–
1093	–	// listen for node 0 to send out the force params
1094	–
1095	–	MPIcheckPoint();
1096	–
1097	–	headTorsionType = new LinkedTorsionType;
1098	–	receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1099	–	while( !torsionInfo.last ){
1100	–
1101	–	headTorsionType->add( torsionInfo );
1102	–	receiveFrcStruct( &torsionInfo, mpiTorsionStructType );
1103	–	}
1104	–	}
1105	–
1106	–	sprintf( checkPointMsg,
1107	–	"DUFF torsion structures broadcast successfully." );
1108	–	MPIcheckPoint();
1109	–
1110	–	#endif // is_mpi
1111	–
1112	–	entry_plug->useLennardJones = 1;
113		}
114
115	+	} //end namespace oopse
116
1116	–
1117	–	void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
1118	–
1119	–
1120	–	//////////////////////////////////////////////////
1121	–	// a quick water fix
1122	–
1123	–	double waterI[3][3];
1124	–	waterI[0][0] = 1.76958347772500;
1125	–	waterI[0][1] = 0.0;
1126	–	waterI[0][2] = 0.0;
1127	–
1128	–	waterI[1][0] = 0.0;
1129	–	waterI[1][1] = 0.614537057924513;
1130	–	waterI[1][2] = 0.0;
1131	–
1132	–	waterI[2][0] = 0.0;
1133	–	waterI[2][1] = 0.0;
1134	–	waterI[2][2] = 1.15504641980049;
1135	–
1136	–
1137	–	double headI[3][3];
1138	–	headI[0][0] = 1125;
1139	–	headI[0][1] = 0.0;
1140	–	headI[0][2] = 0.0;
1141	–
1142	–	headI[1][0] = 0.0;
1143	–	headI[1][1] = 1125;
1144	–	headI[1][2] = 0.0;
1145	–
1146	–	headI[2][0] = 0.0;
1147	–	headI[2][1] = 0.0;
1148	–	headI[2][2] = 250;
1149	–
1150	–	//////////////////////////////////////////////////
1151	–
1152	–
1153	–	// initialize the atoms
1154	–
1155	–	DirectionalAtom* dAtom;
1156	–	double ji[3];
1157	–
1158	–	for(int i=0; i<nAtoms; i++ ){
1159	–
1160	–	currentAtomType = headAtomType->find( the_atoms[i]->getType() );
1161	–	if( currentAtomType == NULL ){
1162	–	sprintf( painCave.errMsg,
1163	–	"AtomType error, %s not found in force file.\n",
1164	–	the_atoms[i]->getType() );
1165	–	painCave.isFatal = 1;
1166	–	simError();
1167	–	}
1168	–
1169	–	the_atoms[i]->setMass( currentAtomType->mass );
1170	–	the_atoms[i]->setIdent( currentAtomType->ident );
1171	–
1172	–	if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
1173	–
1174	–	if( currentAtomType->isDipole ){
1175	–	if( the_atoms[i]->isDirectional() ){
1176	–
1177	–	dAtom = (DirectionalAtom *) the_atoms[i];
1178	–	dAtom->setHasDipole( 1 );
1179	–
1180	–	ji[0] = 0.0;
1181	–	ji[1] = 0.0;
1182	–	ji[2] = 0.0;
1183	–
1184	–	dAtom->setJ( ji );
1185	–
1186	–	if(!strcmp("SSD",the_atoms[i]->getType())){
1187	–	dAtom->setI( waterI );
1188	–	}
1189	–	else if(!strcmp("HEAD",the_atoms[i]->getType())){
1190	–	dAtom->setI( headI );
1191	–	}
1192	–	else{
1193	–	sprintf(painCave.errMsg,
1194	–	"AtmType error, %s does not have a moment of inertia set.\n",
1195	–	the_atoms[i]->getType() );
1196	–	painCave.isFatal = 1;
1197	–	simError();
1198	–	}
1199	–	entry_plug->n_dipoles++;
1200	–	}
1201	–	else{
1202	–
1203	–	sprintf( painCave.errMsg,
1204	–	"DUFF error: Atom \"%s\" is a dipole, yet no standard"
1205	–	" orientation was specifed in the meta-data file.\n",
1206	–	currentAtomType->name );
1207	–	painCave.isFatal = 1;
1208	–	simError();
1209	–	}
1210	–	}
1211	–	else{
1212	–	if( the_atoms[i]->isDirectional() ){
1213	–	sprintf( painCave.errMsg,
1214	–	"DUFF error: Atom \"%s\" was given a standard "
1215	–	"orientation in the meta-data file, yet it is not a dipole.\n",
1216	–	currentAtomType->name);
1217	–	painCave.isFatal = 1;
1218	–	simError();
1219	–	}
1220	–	}
1221	–	}
1222	–	}
1223	–
1224	–	void DUFF::initializeBonds( int nBonds, Bond** bondArray,
1225	–	bond_pair* the_bonds ){
1226	–	int i,a,b;
1227	–	char* atomA;
1228	–	char* atomB;
1229	–
1230	–	Atom** the_atoms;
1231	–	the_atoms = entry_plug->atoms;
1232	–
1233	–
1234	–	// initialize the Bonds
1235	–
1236	–	for( i=0; i<nBonds; i++ ){
1237	–
1238	–	a = the_bonds[i].a;
1239	–	b = the_bonds[i].b;
1240	–
1241	–	atomA = the_atoms[a]->getType();
1242	–	atomB = the_atoms[b]->getType();
1243	–	currentBondType = headBondType->find( atomA, atomB );
1244	–	if( currentBondType == NULL ){
1245	–	sprintf( painCave.errMsg,
1246	–	"BondType error, %s - %s not found in force file.\n",
1247	–	atomA, atomB );
1248	–	painCave.isFatal = 1;
1249	–	simError();
1250	–	}
1251	–
1252	–	switch( currentBondType->type ){
1253	–
1254	–	case FIXED_BOND:
1255	–
1256	–	bondArray[i] = new ConstrainedBond( *the_atoms[a],
1257	–	*the_atoms[b],
1258	–	currentBondType->d0 );
1259	–	entry_plug->n_constraints++;
1260	–	break;
1261	–
1262	–	case HARMONIC_BOND:
1263	–
1264	–	bondArray[i] = new HarmonicBond( *the_atoms[a],
1265	–	*the_atoms[b],
1266	–	currentBondType->d0,
1267	–	currentBondType->k0 );
1268	–	break;
1269	–
1270	–	default:
1271	–
1272	–	break;
1273	–	// do nothing
1274	–	}
1275	–	}
1276	–	}
1277	–
1278	–	void DUFF::initializeBends( int nBends, Bend** bendArray,
1279	–	bend_set* the_bends ){
1280	–
1281	–	QuadraticBend* qBend;
1282	–	GhostBend* gBend;
1283	–	Atom** the_atoms;
1284	–	the_atoms = entry_plug->atoms;
1285	–
1286	–	int i, a, b, c;
1287	–	char* atomA;
1288	–	char* atomB;
1289	–	char* atomC;
1290	–
1291	–	// initialize the Bends
1292	–
1293	–	for( i=0; i<nBends; i++ ){
1294	–
1295	–	a = the_bends[i].a;
1296	–	b = the_bends[i].b;
1297	–	c = the_bends[i].c;
1298	–
1299	–	atomA = the_atoms[a]->getType();
1300	–	atomB = the_atoms[b]->getType();
1301	–
1302	–	if( the_bends[i].isGhost ) atomC = "GHOST";
1303	–	else atomC = the_atoms[c]->getType();
1304	–
1305	–	currentBendType = headBendType->find( atomA, atomB, atomC );
1306	–	if( currentBendType == NULL ){
1307	–	sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found"
1308	–	" in force file.\n",
1309	–	atomA, atomB, atomC );
1310	–	painCave.isFatal = 1;
1311	–	simError();
1312	–	}
1313	–
1314	–	if( !strcmp( currentBendType->type, "quadratic" ) ){
1315	–
1316	–	if( the_bends[i].isGhost){
1317	–
1318	–	if( the_bends[i].ghost == b ){
1319	–	// do nothing
1320	–	}
1321	–	else if( the_bends[i].ghost == a ){
1322	–	c = a;
1323	–	a = b;
1324	–	b = c;
1325	–	}
1326	–	else{
1327	–	sprintf( painCave.errMsg,
1328	–	"BendType error, %s - %s - %s,\n"
1329	–	"  --> central atom is not "
1330	–	"correctly identified with the "
1331	–	"\"ghostVectorSource = \" tag.\n",
1332	–	atomA, atomB, atomC );
1333	–	painCave.isFatal = 1;
1334	–	simError();
1335	–	}
1336	–
1337	–	gBend = new GhostBend( *the_atoms[a],
1338	–	*the_atoms[b]);
1339	–
1340	–	gBend->setConstants( currentBendType->k1,
1341	–	currentBendType->k2,
1342	–	currentBendType->k3,
1343	–	currentBendType->t0 );
1344	–	bendArray[i] = gBend;
1345	–	}
1346	–	else{
1347	–	qBend = new QuadraticBend( *the_atoms[a],
1348	–	*the_atoms[b],
1349	–	*the_atoms[c] );
1350	–	qBend->setConstants( currentBendType->k1,
1351	–	currentBendType->k2,
1352	–	currentBendType->k3,
1353	–	currentBendType->t0 );
1354	–	bendArray[i] = qBend;
1355	–	}
1356	–	}
1357	–	}
1358	–	}
1359	–
1360	–	void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
1361	–	torsion_set* the_torsions ){
1362	–
1363	–	int i, a, b, c, d;
1364	–	char* atomA;
1365	–	char* atomB;
1366	–	char* atomC;
1367	–	char* atomD;
1368	–
1369	–	CubicTorsion* cTors;
1370	–	Atom** the_atoms;
1371	–	the_atoms = entry_plug->atoms;
1372	–
1373	–	// initialize the Torsions
1374	–
1375	–	for( i=0; i<nTorsions; i++ ){
1376	–
1377	–	a = the_torsions[i].a;
1378	–	b = the_torsions[i].b;
1379	–	c = the_torsions[i].c;
1380	–	d = the_torsions[i].d;
1381	–
1382	–	atomA = the_atoms[a]->getType();
1383	–	atomB = the_atoms[b]->getType();
1384	–	atomC = the_atoms[c]->getType();
1385	–	atomD = the_atoms[d]->getType();
1386	–	currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD );
1387	–	if( currentTorsionType == NULL ){
1388	–	sprintf( painCave.errMsg,
1389	–	"TorsionType error, %s - %s - %s - %s not found"
1390	–	" in force file.\n",
1391	–	atomA, atomB, atomC, atomD );
1392	–	painCave.isFatal = 1;
1393	–	simError();
1394	–	}
1395	–
1396	–	if( !strcmp( currentTorsionType->type, "cubic" ) ){
1397	–
1398	–	cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b],
1399	–	*the_atoms[c], *the_atoms[d] );
1400	–	cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2,
1401	–	currentTorsionType->k3, currentTorsionType->k4 );
1402	–	torsionArray[i] = cTors;
1403	–	}
1404	–	}
1405	–	}
1406	–
1407	–	void DUFF::fastForward( char* stopText, char* searchOwner ){
1408	–
1409	–	int foundText = 0;
1410	–	char* the_token;
1411	–
1412	–	rewind( frcFile );
1413	–	lineNum = 0;
1414	–
1415	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1416	–	lineNum++;
1417	–	if( eof_test == NULL ){
1418	–	sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
1419	–	" file is empty.\n",
1420	–	searchOwner );
1421	–	painCave.isFatal = 1;
1422	–	simError();
1423	–	}
1424	–
1425	–
1426	–	while( !foundText ){
1427	–	while( eof_test != NULL && readLine[0] != '#' ){
1428	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1429	–	lineNum++;
1430	–	}
1431	–	if( eof_test == NULL ){
1432	–	sprintf( painCave.errMsg,
1433	–	"Error fast forwarding force file for %s at "
1434	–	"line %d: file ended unexpectedly.\n",
1435	–	searchOwner,
1436	–	lineNum );
1437	–	painCave.isFatal = 1;
1438	–	simError();
1439	–	}
1440	–
1441	–	the_token = strtok( readLine, " ,;\t#\n" );
1442	–	foundText = !strcmp( stopText, the_token );
1443	–
1444	–	if( !foundText ){
1445	–	eof_test = fgets( readLine, sizeof(readLine), frcFile );
1446	–	lineNum++;
1447	–
1448	–	if( eof_test == NULL ){
1449	–	sprintf( painCave.errMsg,
1450	–	"Error fast forwarding force file for %s at "
1451	–	"line %d: file ended unexpectedly.\n",
1452	–	searchOwner,
1453	–	lineNum );
1454	–	painCave.isFatal = 1;
1455	–	simError();
1456	–	}
1457	–	}
1458	–	}
1459	–	}
1460	–
1461	–
1462	–	int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
1463	–
1464	–	char* the_token;
1465	–
1466	–	the_token = strtok( lineBuffer, " \n\t,;" );
1467	–	if( the_token != NULL ){
1468	–
1469	–	strcpy( info.name, the_token );
1470	–
1471	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1472	–	sprintf( painCave.errMsg,
1473	–	"Error parseing AtomTypes: line %d\n", lineNum );
1474	–	painCave.isFatal = 1;
1475	–	simError();
1476	–	}
1477	–
1478	–	info.isDipole = atoi( the_token );
1479	–
1480	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1481	–	sprintf( painCave.errMsg,
1482	–	"Error parseing AtomTypes: line %d\n", lineNum );
1483	–	painCave.isFatal = 1;
1484	–	simError();
1485	–	}
1486	–
1487	–	info.isSSD = atoi( the_token );
1488	–
1489	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1490	–	sprintf( painCave.errMsg,
1491	–	"Error parseing AtomTypes: line %d\n", lineNum );
1492	–	painCave.isFatal = 1;
1493	–	simError();
1494	–	}
1495	–
1496	–	info.mass = atof( the_token );
1497	–
1498	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1499	–	sprintf( painCave.errMsg,
1500	–	"Error parseing AtomTypes: line %d\n", lineNum );
1501	–	painCave.isFatal = 1;
1502	–	simError();
1503	–	}
1504	–
1505	–	info.epslon = atof( the_token );
1506	–
1507	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1508	–	sprintf( painCave.errMsg,
1509	–	"Error parseing AtomTypes: line %d\n", lineNum );
1510	–	painCave.isFatal = 1;
1511	–	simError();
1512	–	}
1513	–
1514	–	info.sigma = atof( the_token );
1515	–
1516	–	if( info.isDipole ){
1517	–
1518	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1519	–	sprintf( painCave.errMsg,
1520	–	"Error parseing AtomTypes: line %d\n", lineNum );
1521	–	painCave.isFatal = 1;
1522	–	simError();
1523	–	}
1524	–
1525	–	info.dipole = atof( the_token );
1526	–	}
1527	–	else info.dipole = 0.0;
1528	–
1529	–	if( info.isSSD ){
1530	–
1531	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1532	–	sprintf( painCave.errMsg,
1533	–	"Error parseing AtomTypes: line %d\n", lineNum );
1534	–	painCave.isFatal = 1;
1535	–	simError();
1536	–	}
1537	–
1538	–	info.w0 = atof( the_token );
1539	–
1540	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1541	–	sprintf( painCave.errMsg,
1542	–	"Error parseing AtomTypes: line %d\n", lineNum );
1543	–	painCave.isFatal = 1;
1544	–	simError();
1545	–	}
1546	–
1547	–	info.v0 = atof( the_token );
1548	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1549	–	sprintf( painCave.errMsg,
1550	–	"Error parseing AtomTypes: line %d\n", lineNum );
1551	–	painCave.isFatal = 1;
1552	–	simError();
1553	–	}
1554	–
1555	–	info.v0p = atof( the_token );
1556	–
1557	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1558	–	sprintf( painCave.errMsg,
1559	–	"Error parseing AtomTypes: line %d\n", lineNum );
1560	–	painCave.isFatal = 1;
1561	–	simError();
1562	–	}
1563	–
1564	–	info.rl = atof( the_token );
1565	–
1566	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1567	–	sprintf( painCave.errMsg,
1568	–	"Error parseing AtomTypes: line %d\n", lineNum );
1569	–	painCave.isFatal = 1;
1570	–	simError();
1571	–	}
1572	–
1573	–	info.ru = atof( the_token );
1574	–
1575	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1576	–	sprintf( painCave.errMsg,
1577	–	"Error parseing AtomTypes: line %d\n", lineNum );
1578	–	painCave.isFatal = 1;
1579	–	simError();
1580	–	}
1581	–
1582	–	info.rlp = atof( the_token );
1583	–
1584	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1585	–	sprintf( painCave.errMsg,
1586	–	"Error parseing AtomTypes: line %d\n", lineNum );
1587	–	painCave.isFatal = 1;
1588	–	simError();
1589	–	}
1590	–
1591	–	info.rup = atof( the_token );
1592	–	}
1593	–	else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0;
1594	–
1595	–	return 1;
1596	–	}
1597	–	else return 0;
1598	–	}
1599	–
1600	–	int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){
1601	–
1602	–	char* the_token;
1603	–	char bondType[30];
1604	–
1605	–	the_token = strtok( lineBuffer, " \n\t,;" );
1606	–	if( the_token != NULL ){
1607	–
1608	–	strcpy( info.nameA, the_token );
1609	–
1610	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1611	–	sprintf( painCave.errMsg,
1612	–	"Error parseing BondTypes: line %d\n", lineNum );
1613	–	painCave.isFatal = 1;
1614	–	simError();
1615	–	}
1616	–
1617	–	strcpy( info.nameB, the_token );
1618	–
1619	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1620	–	sprintf( painCave.errMsg,
1621	–	"Error parseing BondTypes: line %d\n", lineNum );
1622	–	painCave.isFatal = 1;
1623	–	simError();
1624	–	}
1625	–
1626	–	strcpy( bondType, the_token );
1627	–
1628	–	if( !strcmp( bondType, "fixed" ) ){
1629	–	info.type = FIXED_BOND;
1630	–
1631	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1632	–	sprintf( painCave.errMsg,
1633	–	"Error parseing BondTypes: line %d\n", lineNum );
1634	–	painCave.isFatal = 1;
1635	–	simError();
1636	–	}
1637	–
1638	–	info.d0 = atof( the_token );
1639	–
1640	–	info.k0=0.0;
1641	–	}
1642	–	else if( !strcmp( bondType, "harmonic" ) ){
1643	–	info.type = HARMONIC_BOND;
1644	–
1645	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1646	–	sprintf( painCave.errMsg,
1647	–	"Error parseing BondTypes: line %d\n", lineNum );
1648	–	painCave.isFatal = 1;
1649	–	simError();
1650	–	}
1651	–
1652	–	info.d0 = atof( the_token );
1653	–
1654	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1655	–	sprintf( painCave.errMsg,
1656	–	"Error parseing BondTypes: line %d\n", lineNum );
1657	–	painCave.isFatal = 1;
1658	–	simError();
1659	–	}
1660	–
1661	–	info.k0 = atof( the_token );
1662	–	}
1663	–
1664	–	else{
1665	–	sprintf( painCave.errMsg,
1666	–	"Unknown DUFF bond type \"%s\" at line %d\n",
1667	–	bondType,
1668	–	lineNum );
1669	–	painCave.isFatal = 1;
1670	–	simError();
1671	–	}
1672	–
1673	–	return 1;
1674	–	}
1675	–	else return 0;
1676	–	}
1677	–
1678	–
1679	–	int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){
1680	–
1681	–	char* the_token;
1682	–
1683	–	the_token = strtok( lineBuffer, " \n\t,;" );
1684	–	if( the_token != NULL ){
1685	–
1686	–	strcpy( info.nameA, the_token );
1687	–
1688	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1689	–	sprintf( painCave.errMsg,
1690	–	"Error parseing BendTypes: line %d\n", lineNum );
1691	–	painCave.isFatal = 1;
1692	–	simError();
1693	–	}
1694	–
1695	–	strcpy( info.nameB, the_token );
1696	–
1697	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1698	–	sprintf( painCave.errMsg,
1699	–	"Error parseing BendTypes: line %d\n", lineNum );
1700	–	painCave.isFatal = 1;
1701	–	simError();
1702	–	}
1703	–
1704	–	strcpy( info.nameC, the_token );
1705	–
1706	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1707	–	sprintf( painCave.errMsg,
1708	–	"Error parseing BendTypes: line %d\n", lineNum );
1709	–	painCave.isFatal = 1;
1710	–	simError();
1711	–	}
1712	–
1713	–	strcpy( info.type, the_token );
1714	–
1715	–	if( !strcmp( info.type, "quadratic" ) ){
1716	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1717	–	sprintf( painCave.errMsg,
1718	–	"Error parseing BendTypes: line %d\n", lineNum );
1719	–	painCave.isFatal = 1;
1720	–	simError();
1721	–	}
1722	–
1723	–	info.k1 = atof( the_token );
1724	–
1725	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1726	–	sprintf( painCave.errMsg,
1727	–	"Error parseing BendTypes: line %d\n", lineNum );
1728	–	painCave.isFatal = 1;
1729	–	simError();
1730	–	}
1731	–
1732	–	info.k2 = atof( the_token );
1733	–
1734	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1735	–	sprintf( painCave.errMsg,
1736	–	"Error parseing BendTypes: line %d\n", lineNum );
1737	–	painCave.isFatal = 1;
1738	–	simError();
1739	–	}
1740	–
1741	–	info.k3 = atof( the_token );
1742	–
1743	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1744	–	sprintf( painCave.errMsg,
1745	–	"Error parseing BendTypes: line %d\n", lineNum );
1746	–	painCave.isFatal = 1;
1747	–	simError();
1748	–	}
1749	–
1750	–	info.t0 = atof( the_token );
1751	–	}
1752	–
1753	–	else{
1754	–	sprintf( painCave.errMsg,
1755	–	"Unknown DUFF bend type \"%s\" at line %d\n",
1756	–	info.type,
1757	–	lineNum );
1758	–	painCave.isFatal = 1;
1759	–	simError();
1760	–	}
1761	–
1762	–	return 1;
1763	–	}
1764	–	else return 0;
1765	–	}
1766	–
1767	–	int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){
1768	–
1769	–	char*  the_token;
1770	–
1771	–	the_token = strtok( lineBuffer, " \n\t,;" );
1772	–	if( the_token != NULL ){
1773	–
1774	–	strcpy( info.nameA, the_token );
1775	–
1776	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1777	–	sprintf( painCave.errMsg,
1778	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1779	–	painCave.isFatal = 1;
1780	–	simError();
1781	–	}
1782	–
1783	–	strcpy( info.nameB, the_token );
1784	–
1785	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1786	–	sprintf( painCave.errMsg,
1787	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1788	–	painCave.isFatal = 1;
1789	–	simError();
1790	–	}
1791	–
1792	–	strcpy( info.nameC, the_token );
1793	–
1794	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1795	–	sprintf( painCave.errMsg,
1796	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1797	–	painCave.isFatal = 1;
1798	–	simError();
1799	–	}
1800	–
1801	–	strcpy( info.nameD, the_token );
1802	–
1803	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1804	–	sprintf( painCave.errMsg,
1805	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1806	–	painCave.isFatal = 1;
1807	–	simError();
1808	–	}
1809	–
1810	–	strcpy( info.type, the_token );
1811	–
1812	–	if( !strcmp( info.type, "cubic" ) ){
1813	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1814	–	sprintf( painCave.errMsg,
1815	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1816	–	painCave.isFatal = 1;
1817	–	simError();
1818	–	}
1819	–
1820	–	info.k1 = atof( the_token );
1821	–
1822	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1823	–	sprintf( painCave.errMsg,
1824	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1825	–	painCave.isFatal = 1;
1826	–	simError();
1827	–	}
1828	–
1829	–	info.k2 = atof( the_token );
1830	–
1831	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1832	–	sprintf( painCave.errMsg,
1833	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1834	–	painCave.isFatal = 1;
1835	–	simError();
1836	–	}
1837	–
1838	–	info.k3 = atof( the_token );
1839	–
1840	–	if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
1841	–	sprintf( painCave.errMsg,
1842	–	"Error parseing TorsionTypes: line %d\n", lineNum );
1843	–	painCave.isFatal = 1;
1844	–	simError();
1845	–	}
1846	–
1847	–	info.k4 = atof( the_token );
1848	–
1849	–	}
1850	–
1851	–	else{
1852	–	sprintf( painCave.errMsg,
1853	–	"Unknown DUFF torsion type \"%s\" at line %d\n",
1854	–	info.type,
1855	–	lineNum );
1856	–	painCave.isFatal = 1;
1857	–	simError();
1858	–	}
1859	–
1860	–	return 1;
1861	–	}
1862	–
1863	–	else return 0;
1864	–	}

Diff Legend

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