1 |
< |
#include <stdlib.h> |
2 |
< |
#include <stdio.h> |
3 |
< |
#include <string.h> |
1 |
> |
/* |
2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
> |
* |
4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
5 |
> |
* non-exclusive, royalty free, license to use, modify and |
6 |
> |
* redistribute this software in source and binary code form, provided |
7 |
> |
* that the following conditions are met: |
8 |
> |
* |
9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
10 |
> |
* publication of scientific results based in part on use of the |
11 |
> |
* program. An acceptable form of acknowledgement is citation of |
12 |
> |
* the article in which the program was described (Matthew |
13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
> |
* |
18 |
> |
* 2. Redistributions of source code must retain the above copyright |
19 |
> |
* notice, this list of conditions and the following disclaimer. |
20 |
> |
* |
21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
> |
* notice, this list of conditions and the following disclaimer in the |
23 |
> |
* documentation and/or other materials provided with the |
24 |
> |
* distribution. |
25 |
> |
* |
26 |
> |
* This software is provided "AS IS," without a warranty of any |
27 |
> |
* kind. All express or implied conditions, representations and |
28 |
> |
* warranties, including any implied warranty of merchantability, |
29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
> |
* be liable for any damages suffered by licensee as a result of |
32 |
> |
* using, modifying or distributing the software or its |
33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
36 |
> |
* damages, however caused and regardless of the theory of liability, |
37 |
> |
* arising out of the use of or inability to use software, even if the |
38 |
> |
* University of Notre Dame has been advised of the possibility of |
39 |
> |
* such damages. |
40 |
> |
*/ |
41 |
|
|
5 |
– |
#include <iostream> |
6 |
– |
using namespace std; |
42 |
|
|
43 |
< |
#include "UseTheForce/ForceFields.hpp" |
44 |
< |
#include "primitives/SRI.hpp" |
45 |
< |
#include "utils/simError.h" |
43 |
> |
#include "UseTheForce/DUFF.hpp" |
44 |
> |
#include "UseTheForce/DarkSide/lj_interface.h" |
45 |
> |
#include "UseTheForce/DarkSide/sticky_interface.h" |
46 |
> |
#include "UseTheForce/DarkSide/gb_interface.h" |
47 |
> |
#include "UseTheForce/ForceFieldFactory.hpp" |
48 |
> |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
49 |
> |
#include "io/AtomTypesSectionParser.hpp" |
50 |
> |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
51 |
> |
#include "io/ChargeAtomTypesSectionParser.hpp" |
52 |
> |
#include "io/MultipoleAtomTypesSectionParser.hpp" |
53 |
> |
#include "io/StickyAtomTypesSectionParser.hpp" |
54 |
> |
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
55 |
> |
#include "io/GayBerneAtomTypesSectionParser.hpp" |
56 |
> |
#include "io/BondTypesSectionParser.hpp" |
57 |
> |
#include "io/BendTypesSectionParser.hpp" |
58 |
> |
#include "io/TorsionTypesSectionParser.hpp" |
59 |
> |
#include "io/OptionSectionParser.hpp" |
60 |
> |
#include "UseTheForce/ForceFieldCreator.hpp" |
61 |
|
|
62 |
< |
#include "UseTheForce/fortranWrappers.hpp" |
62 |
> |
namespace oopse { |
63 |
> |
|
64 |
> |
DUFF::DUFF(){ |
65 |
|
|
66 |
< |
#ifdef IS_MPI |
67 |
< |
#include "UseTheForce/mpiForceField.h" |
16 |
< |
#endif // is_mpi |
66 |
> |
//set default force field filename |
67 |
> |
setForceFieldFileName("DUFF2.frc"); |
68 |
|
|
69 |
< |
|
70 |
< |
// define some bond Types |
71 |
< |
|
72 |
< |
#define FIXED_BOND 0 |
73 |
< |
#define HARMONIC_BOND 1 |
74 |
< |
|
75 |
< |
|
76 |
< |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
77 |
< |
|
78 |
< |
|
79 |
< |
// Declare the structures that will be passed by MPI |
80 |
< |
|
81 |
< |
typedef struct{ |
82 |
< |
char name[15]; |
83 |
< |
double mass; |
84 |
< |
double epslon; |
85 |
< |
double sigma; |
86 |
< |
double charge; |
87 |
< |
double dipole; |
88 |
< |
double w0; |
89 |
< |
double v0; |
90 |
< |
double v0p; |
91 |
< |
double rl; |
92 |
< |
double ru; |
42 |
< |
double rlp; |
43 |
< |
double rup; |
44 |
< |
int isSSD; |
45 |
< |
int isCharge; |
46 |
< |
int isDipole; |
47 |
< |
int ident; |
48 |
< |
int last; // 0 -> default |
49 |
< |
// 1 -> tells nodes to stop listening |
50 |
< |
} atomStruct; |
51 |
< |
|
52 |
< |
|
53 |
< |
typedef struct{ |
54 |
< |
char nameA[15]; |
55 |
< |
char nameB[15]; |
56 |
< |
double d0; |
57 |
< |
double k0; |
58 |
< |
int last; // 0 -> default |
59 |
< |
// 1 -> tells nodes to stop listening |
60 |
< |
int type; |
61 |
< |
} bondStruct; |
62 |
< |
|
63 |
< |
|
64 |
< |
typedef struct{ |
65 |
< |
char nameA[15]; |
66 |
< |
char nameB[15]; |
67 |
< |
char nameC[15]; |
68 |
< |
char type[30]; |
69 |
< |
double k1, k2, k3, t0; |
70 |
< |
int last; // 0 -> default |
71 |
< |
// 1 -> tells nodes to stop listening |
72 |
< |
} bendStruct; |
73 |
< |
|
74 |
< |
|
75 |
< |
typedef struct{ |
76 |
< |
char nameA[15]; |
77 |
< |
char nameB[15]; |
78 |
< |
char nameC[15]; |
79 |
< |
char nameD[15]; |
80 |
< |
char type[30]; |
81 |
< |
double k1, k2, k3, k4; |
82 |
< |
int last; // 0 -> default |
83 |
< |
// 1 -> tells nodes to stop listening |
84 |
< |
} torsionStruct; |
85 |
< |
|
86 |
< |
|
87 |
< |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
88 |
< |
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
89 |
< |
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
90 |
< |
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
91 |
< |
|
92 |
< |
|
93 |
< |
#ifdef IS_MPI |
94 |
< |
|
95 |
< |
MPI_Datatype mpiAtomStructType; |
96 |
< |
MPI_Datatype mpiBondStructType; |
97 |
< |
MPI_Datatype mpiBendStructType; |
98 |
< |
MPI_Datatype mpiTorsionStructType; |
99 |
< |
|
100 |
< |
#endif |
101 |
< |
|
102 |
< |
class LinkedAtomType { |
103 |
< |
public: |
104 |
< |
LinkedAtomType(){ |
105 |
< |
next = NULL; |
106 |
< |
name[0] = '\0'; |
107 |
< |
} |
108 |
< |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
109 |
< |
|
110 |
< |
LinkedAtomType* find(char* key){ |
111 |
< |
if( !strcmp(name, key) ) return this; |
112 |
< |
if( next != NULL ) return next->find(key); |
113 |
< |
return NULL; |
114 |
< |
} |
69 |
> |
//The order of adding section parsers is important. |
70 |
> |
//DirectionalAtomTypesSectionParser should be added before |
71 |
> |
//AtomTypesSectionParser, and these two section parsers will actually |
72 |
> |
//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and |
73 |
> |
//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which |
74 |
> |
//is a subclass of AtomType and should come first). Other AtomTypes Section |
75 |
> |
//Parser will not create the "real" AtomType, they only add and set some |
76 |
> |
//attribute of the AtomType. Thus their order are not important. |
77 |
> |
//AtomTypesSectionParser should be added before other atom type section |
78 |
> |
//parsers. Make sure they are added after DirectionalAtomTypesSectionParser |
79 |
> |
//and AtomTypesSectionParser. The order of BondTypesSectionParser, |
80 |
> |
//BendTypesSectionParser and TorsionTypesSectionParser are not important. |
81 |
> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
82 |
> |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
83 |
> |
spMan_.push_back(new AtomTypesSectionParser()); |
84 |
> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
85 |
> |
spMan_.push_back(new ChargeAtomTypesSectionParser()); |
86 |
> |
spMan_.push_back(new MultipoleAtomTypesSectionParser()); |
87 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
88 |
> |
spMan_.push_back(new StickyPowerAtomTypesSectionParser()); |
89 |
> |
spMan_.push_back(new GayBerneAtomTypesSectionParser()); |
90 |
> |
spMan_.push_back(new BondTypesSectionParser()); |
91 |
> |
spMan_.push_back(new BendTypesSectionParser()); |
92 |
> |
spMan_.push_back(new TorsionTypesSectionParser()); |
93 |
|
|
94 |
< |
void printMe( void ){ |
117 |
< |
|
118 |
< |
std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; |
119 |
< |
// if( next != NULL ) next->printMe(); |
94 |
> |
} |
95 |
|
|
96 |
< |
} |
96 |
> |
void DUFF::parse(const std::string& filename) { |
97 |
> |
ifstrstream* ffStream; |
98 |
> |
ffStream = openForceFieldFile(filename); |
99 |
|
|
100 |
< |
void add( atomStruct &info ){ |
100 |
> |
spMan_.parse(*ffStream, *this); |
101 |
|
|
102 |
< |
// check for duplicates |
103 |
< |
|
127 |
< |
if( !strcmp( info.name, name ) ){ |
128 |
< |
sprintf( painCave.errMsg, |
129 |
< |
"Duplicate DUFF atom type \"%s\" found in " |
130 |
< |
"the DUFF param file./n", |
131 |
< |
name ); |
132 |
< |
painCave.isFatal = 1; |
133 |
< |
simError(); |
134 |
< |
} |
102 |
> |
ForceField::AtomTypeContainer::MapTypeIterator i; |
103 |
> |
AtomType* at; |
104 |
|
|
105 |
< |
if( next != NULL ) next->add(info); |
106 |
< |
else{ |
107 |
< |
next = new LinkedAtomType(); |
139 |
< |
strcpy(next->name, info.name); |
140 |
< |
next->isDipole = info.isDipole; |
141 |
< |
next->isSSD = info.isSSD; |
142 |
< |
next->mass = info.mass; |
143 |
< |
next->epslon = info.epslon; |
144 |
< |
next->sigma = info.sigma; |
145 |
< |
next->dipole = info.dipole; |
146 |
< |
next->w0 = info.w0; |
147 |
< |
next->v0 = info.v0; |
148 |
< |
next->v0p = info.v0p; |
149 |
< |
next->rl = info.rl; |
150 |
< |
next->ru = info.ru; |
151 |
< |
next->rlp = info.rlp; |
152 |
< |
next->rup = info.rup; |
153 |
< |
next->ident = info.ident; |
154 |
< |
} |
155 |
< |
} |
156 |
< |
|
157 |
< |
#ifdef IS_MPI |
158 |
< |
|
159 |
< |
void duplicate( atomStruct &info ){ |
160 |
< |
strcpy(info.name, name); |
161 |
< |
info.isDipole = isDipole; |
162 |
< |
info.isSSD = isSSD; |
163 |
< |
info.mass = mass; |
164 |
< |
info.epslon = epslon; |
165 |
< |
info.sigma = sigma; |
166 |
< |
info.dipole = dipole; |
167 |
< |
info.w0 = w0; |
168 |
< |
info.v0 = v0; |
169 |
< |
info.v0p = v0p; |
170 |
< |
info.rl = rl; |
171 |
< |
info.ru = ru; |
172 |
< |
info.rlp = rlp; |
173 |
< |
info.rup = rup; |
174 |
< |
info.ident = ident; |
175 |
< |
info.last = 0; |
105 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
106 |
> |
at = atomTypeCont_.nextType(i)) { |
107 |
> |
at->makeFortranAtomType(); |
108 |
|
} |
109 |
|
|
110 |
< |
|
111 |
< |
#endif |
112 |
< |
|
181 |
< |
char name[15]; |
182 |
< |
int isDipole; |
183 |
< |
int isSSD; |
184 |
< |
double mass; |
185 |
< |
double epslon; |
186 |
< |
double sigma; |
187 |
< |
double dipole; |
188 |
< |
double w0; |
189 |
< |
double v0; |
190 |
< |
double v0p; |
191 |
< |
double rl; |
192 |
< |
double ru; |
193 |
< |
double rlp; |
194 |
< |
double rup; |
195 |
< |
int ident; |
196 |
< |
LinkedAtomType* next; |
197 |
< |
}; |
198 |
< |
|
199 |
< |
class LinkedBondType { |
200 |
< |
public: |
201 |
< |
LinkedBondType(){ |
202 |
< |
next = NULL; |
203 |
< |
nameA[0] = '\0'; |
204 |
< |
nameB[0] = '\0'; |
110 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
111 |
> |
at = atomTypeCont_.nextType(i)) { |
112 |
> |
at->complete(); |
113 |
|
} |
206 |
– |
~LinkedBondType(){ if( next != NULL ) delete next; } |
114 |
|
|
115 |
< |
LinkedBondType* find(char* key1, char* key2){ |
209 |
< |
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
210 |
< |
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
211 |
< |
if( next != NULL ) return next->find(key1, key2); |
212 |
< |
return NULL; |
213 |
< |
} |
214 |
< |
|
215 |
< |
|
216 |
< |
void add( bondStruct &info ){ |
217 |
< |
|
218 |
< |
// check for duplicates |
219 |
< |
int dup = 0; |
220 |
< |
|
221 |
< |
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
222 |
< |
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
223 |
< |
|
224 |
< |
if(dup){ |
225 |
< |
sprintf( painCave.errMsg, |
226 |
< |
"Duplicate DUFF bond type \"%s - %s\" found in " |
227 |
< |
"the DUFF param file./n", |
228 |
< |
nameA, nameB ); |
229 |
< |
painCave.isFatal = 1; |
230 |
< |
simError(); |
231 |
< |
} |
232 |
< |
|
233 |
< |
|
234 |
< |
if( next != NULL ) next->add(info); |
235 |
< |
else{ |
236 |
< |
next = new LinkedBondType(); |
237 |
< |
strcpy(next->nameA, info.nameA); |
238 |
< |
strcpy(next->nameB, info.nameB); |
239 |
< |
next->type = info.type; |
240 |
< |
next->d0 = info.d0; |
241 |
< |
next->k0 = info.k0; |
242 |
< |
} |
243 |
< |
} |
244 |
< |
|
245 |
< |
#ifdef IS_MPI |
246 |
< |
void duplicate( bondStruct &info ){ |
247 |
< |
strcpy(info.nameA, nameA); |
248 |
< |
strcpy(info.nameB, nameB); |
249 |
< |
info.type = type; |
250 |
< |
info.d0 = d0; |
251 |
< |
info.k0 = k0; |
252 |
< |
info.last = 0; |
253 |
< |
} |
254 |
< |
|
255 |
< |
|
256 |
< |
#endif |
257 |
< |
|
258 |
< |
char nameA[15]; |
259 |
< |
char nameB[15]; |
260 |
< |
int type; |
261 |
< |
double d0; |
262 |
< |
double k0; |
263 |
< |
|
264 |
< |
LinkedBondType* next; |
265 |
< |
}; |
266 |
< |
|
267 |
< |
class LinkedBendType { |
268 |
< |
public: |
269 |
< |
LinkedBendType(){ |
270 |
< |
next = NULL; |
271 |
< |
nameA[0] = '\0'; |
272 |
< |
nameB[0] = '\0'; |
273 |
< |
nameC[0] = '\0'; |
274 |
< |
type[0] = '\0'; |
275 |
< |
} |
276 |
< |
~LinkedBendType(){ if( next != NULL ) delete next; } |
277 |
< |
|
278 |
< |
LinkedBendType* find( char* key1, char* key2, char* key3 ){ |
279 |
< |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
280 |
< |
&& !strcmp( nameC, key3 ) ) return this; |
281 |
< |
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
282 |
< |
&& !strcmp( nameC, key1 ) ) return this; |
283 |
< |
if( next != NULL ) return next->find(key1, key2, key3); |
284 |
< |
return NULL; |
285 |
< |
} |
286 |
< |
|
287 |
< |
void add( bendStruct &info ){ |
288 |
< |
|
289 |
< |
// check for duplicates |
290 |
< |
int dup = 0; |
291 |
< |
|
292 |
< |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
293 |
< |
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
294 |
< |
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
295 |
< |
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
296 |
< |
|
297 |
< |
if(dup){ |
298 |
< |
sprintf( painCave.errMsg, |
299 |
< |
"Duplicate DUFF bend type \"%s - %s - %s\" found in " |
300 |
< |
"the DUFF param file./n", |
301 |
< |
nameA, nameB, nameC ); |
302 |
< |
painCave.isFatal = 1; |
303 |
< |
simError(); |
304 |
< |
} |
305 |
< |
|
306 |
< |
if( next != NULL ) next->add(info); |
307 |
< |
else{ |
308 |
< |
next = new LinkedBendType(); |
309 |
< |
strcpy(next->nameA, info.nameA); |
310 |
< |
strcpy(next->nameB, info.nameB); |
311 |
< |
strcpy(next->nameC, info.nameC); |
312 |
< |
strcpy(next->type, info.type); |
313 |
< |
next->k1 = info.k1; |
314 |
< |
next->k2 = info.k2; |
315 |
< |
next->k3 = info.k3; |
316 |
< |
next->t0 = info.t0; |
317 |
< |
} |
318 |
< |
} |
319 |
< |
|
320 |
< |
#ifdef IS_MPI |
321 |
< |
|
322 |
< |
void duplicate( bendStruct &info ){ |
323 |
< |
strcpy(info.nameA, nameA); |
324 |
< |
strcpy(info.nameB, nameB); |
325 |
< |
strcpy(info.nameC, nameC); |
326 |
< |
strcpy(info.type, type); |
327 |
< |
info.k1 = k1; |
328 |
< |
info.k2 = k2; |
329 |
< |
info.k3 = k3; |
330 |
< |
info.t0 = t0; |
331 |
< |
info.last = 0; |
332 |
< |
} |
333 |
< |
|
334 |
< |
#endif // is_mpi |
335 |
< |
|
336 |
< |
char nameA[15]; |
337 |
< |
char nameB[15]; |
338 |
< |
char nameC[15]; |
339 |
< |
char type[30]; |
340 |
< |
double k1, k2, k3, t0; |
341 |
< |
|
342 |
< |
LinkedBendType* next; |
343 |
< |
}; |
344 |
< |
|
345 |
< |
class LinkedTorsionType { |
346 |
< |
public: |
347 |
< |
LinkedTorsionType(){ |
348 |
< |
next = NULL; |
349 |
< |
nameA[0] = '\0'; |
350 |
< |
nameB[0] = '\0'; |
351 |
< |
nameC[0] = '\0'; |
352 |
< |
type[0] = '\0'; |
353 |
< |
} |
354 |
< |
~LinkedTorsionType(){ if( next != NULL ) delete next; } |
355 |
< |
|
356 |
< |
LinkedTorsionType* find( char* key1, char* key2, char* key3, char* key4 ){ |
357 |
< |
|
358 |
< |
|
359 |
< |
|
360 |
< |
|
361 |
< |
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
362 |
< |
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
363 |
< |
|
364 |
< |
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
365 |
< |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
366 |
< |
|
367 |
< |
if( next != NULL ) return next->find(key1, key2, key3, key4); |
368 |
< |
return NULL; |
369 |
< |
} |
370 |
< |
|
371 |
< |
void add( torsionStruct &info ){ |
372 |
< |
|
373 |
< |
// check for duplicates |
374 |
< |
int dup = 0; |
375 |
< |
|
376 |
< |
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
377 |
< |
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
378 |
< |
|
379 |
< |
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
380 |
< |
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
381 |
< |
|
382 |
< |
if(dup){ |
383 |
< |
sprintf( painCave.errMsg, |
384 |
< |
"Duplicate DUFF torsion type \"%s - %s - %s - %s\" found in " |
385 |
< |
"the DUFF param file./n", nameA, nameB, nameC, nameD ); |
386 |
< |
painCave.isFatal = 1; |
387 |
< |
simError(); |
388 |
< |
} |
389 |
< |
|
390 |
< |
if( next != NULL ) next->add(info); |
391 |
< |
else{ |
392 |
< |
next = new LinkedTorsionType(); |
393 |
< |
strcpy(next->nameA, info.nameA); |
394 |
< |
strcpy(next->nameB, info.nameB); |
395 |
< |
strcpy(next->nameC, info.nameC); |
396 |
< |
strcpy(next->nameD, info.nameD); |
397 |
< |
strcpy(next->type, info.type); |
398 |
< |
next->k1 = info.k1; |
399 |
< |
next->k2 = info.k2; |
400 |
< |
next->k3 = info.k3; |
401 |
< |
next->k4 = info.k4; |
115 |
> |
int isError = 0; |
116 |
|
|
117 |
< |
} |
404 |
< |
} |
405 |
< |
|
406 |
< |
#ifdef IS_MPI |
117 |
> |
delete ffStream; |
118 |
|
|
408 |
– |
void duplicate( torsionStruct &info ){ |
409 |
– |
strcpy(info.nameA, nameA); |
410 |
– |
strcpy(info.nameB, nameB); |
411 |
– |
strcpy(info.nameC, nameC); |
412 |
– |
strcpy(info.nameD, nameD); |
413 |
– |
strcpy(info.type, type); |
414 |
– |
info.k1 = k1; |
415 |
– |
info.k2 = k2; |
416 |
– |
info.k3 = k3; |
417 |
– |
info.k4 = k4; |
418 |
– |
info.last = 0; |
419 |
– |
} |
420 |
– |
|
421 |
– |
#endif |
422 |
– |
|
423 |
– |
char nameA[15]; |
424 |
– |
char nameB[15]; |
425 |
– |
char nameC[15]; |
426 |
– |
char nameD[15]; |
427 |
– |
char type[30]; |
428 |
– |
double k1, k2, k3, k4; |
429 |
– |
|
430 |
– |
LinkedTorsionType* next; |
431 |
– |
}; |
432 |
– |
|
433 |
– |
|
434 |
– |
LinkedAtomType* headAtomType; |
435 |
– |
LinkedAtomType* currentAtomType; |
436 |
– |
LinkedBondType* headBondType; |
437 |
– |
LinkedBondType* currentBondType; |
438 |
– |
LinkedBendType* headBendType; |
439 |
– |
LinkedBendType* currentBendType; |
440 |
– |
LinkedTorsionType* headTorsionType; |
441 |
– |
LinkedTorsionType* currentTorsionType; |
442 |
– |
|
443 |
– |
} // namespace |
444 |
– |
|
445 |
– |
using namespace DUFF_NS; |
446 |
– |
|
447 |
– |
|
448 |
– |
//**************************************************************** |
449 |
– |
// begins the actual forcefield stuff. |
450 |
– |
//**************************************************************** |
451 |
– |
|
452 |
– |
|
453 |
– |
DUFF::DUFF(){ |
454 |
– |
|
455 |
– |
char fileName[200]; |
456 |
– |
char* ffPath_env = "FORCE_PARAM_PATH"; |
457 |
– |
char* ffPath; |
458 |
– |
char temp[200]; |
459 |
– |
|
460 |
– |
headAtomType = NULL; |
461 |
– |
currentAtomType = NULL; |
462 |
– |
headBondType = NULL; |
463 |
– |
currentBondType = NULL; |
464 |
– |
headBendType = NULL; |
465 |
– |
currentBendType = NULL; |
466 |
– |
headTorsionType = NULL; |
467 |
– |
currentTorsionType = NULL; |
468 |
– |
|
469 |
– |
// do the funtion wrapping |
470 |
– |
wrapMeFF( this ); |
471 |
– |
|
472 |
– |
|
473 |
– |
#ifdef IS_MPI |
474 |
– |
int i; |
475 |
– |
|
476 |
– |
// ********************************************************************** |
477 |
– |
// Init the atomStruct mpi type |
478 |
– |
|
479 |
– |
atomStruct atomProto; // mpiPrototype |
480 |
– |
int atomBC[3] = {15,12,5}; // block counts |
481 |
– |
MPI_Aint atomDspls[3]; // displacements |
482 |
– |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
483 |
– |
|
484 |
– |
MPI_Address(&atomProto.name, &atomDspls[0]); |
485 |
– |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
486 |
– |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
487 |
– |
|
488 |
– |
atomMbrTypes[0] = MPI_CHAR; |
489 |
– |
atomMbrTypes[1] = MPI_DOUBLE; |
490 |
– |
atomMbrTypes[2] = MPI_INT; |
491 |
– |
|
492 |
– |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
493 |
– |
|
494 |
– |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
495 |
– |
MPI_Type_commit(&mpiAtomStructType); |
496 |
– |
|
497 |
– |
|
498 |
– |
// ********************************************************************** |
499 |
– |
// Init the bondStruct mpi type |
500 |
– |
|
501 |
– |
bondStruct bondProto; // mpiPrototype |
502 |
– |
int bondBC[3] = {30,2,2}; // block counts |
503 |
– |
MPI_Aint bondDspls[3]; // displacements |
504 |
– |
MPI_Datatype bondMbrTypes[3]; // member mpi types |
505 |
– |
|
506 |
– |
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
507 |
– |
MPI_Address(&bondProto.d0, &bondDspls[1]); |
508 |
– |
MPI_Address(&bondProto.last, &bondDspls[2]); |
509 |
– |
|
510 |
– |
bondMbrTypes[0] = MPI_CHAR; |
511 |
– |
bondMbrTypes[1] = MPI_DOUBLE; |
512 |
– |
bondMbrTypes[2] = MPI_INT; |
513 |
– |
|
514 |
– |
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
515 |
– |
|
516 |
– |
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
517 |
– |
MPI_Type_commit(&mpiBondStructType); |
518 |
– |
|
519 |
– |
|
520 |
– |
// ********************************************************************** |
521 |
– |
// Init the bendStruct mpi type |
522 |
– |
|
523 |
– |
bendStruct bendProto; // mpiPrototype |
524 |
– |
int bendBC[3] = {75,4,1}; // block counts |
525 |
– |
MPI_Aint bendDspls[3]; // displacements |
526 |
– |
MPI_Datatype bendMbrTypes[3]; // member mpi types |
527 |
– |
|
528 |
– |
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
529 |
– |
MPI_Address(&bendProto.k1, &bendDspls[1]); |
530 |
– |
MPI_Address(&bendProto.last, &bendDspls[2]); |
531 |
– |
|
532 |
– |
bendMbrTypes[0] = MPI_CHAR; |
533 |
– |
bendMbrTypes[1] = MPI_DOUBLE; |
534 |
– |
bendMbrTypes[2] = MPI_INT; |
535 |
– |
|
536 |
– |
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
537 |
– |
|
538 |
– |
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
539 |
– |
MPI_Type_commit(&mpiBendStructType); |
540 |
– |
|
541 |
– |
|
542 |
– |
// ********************************************************************** |
543 |
– |
// Init the torsionStruct mpi type |
544 |
– |
|
545 |
– |
torsionStruct torsionProto; // mpiPrototype |
546 |
– |
int torsionBC[3] = {90,4,1}; // block counts |
547 |
– |
MPI_Aint torsionDspls[3]; // displacements |
548 |
– |
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
549 |
– |
|
550 |
– |
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
551 |
– |
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
552 |
– |
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
553 |
– |
|
554 |
– |
torsionMbrTypes[0] = MPI_CHAR; |
555 |
– |
torsionMbrTypes[1] = MPI_DOUBLE; |
556 |
– |
torsionMbrTypes[2] = MPI_INT; |
557 |
– |
|
558 |
– |
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
559 |
– |
|
560 |
– |
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
561 |
– |
&mpiTorsionStructType); |
562 |
– |
MPI_Type_commit(&mpiTorsionStructType); |
563 |
– |
|
564 |
– |
// *********************************************************************** |
565 |
– |
|
566 |
– |
if( worldRank == 0 ){ |
567 |
– |
#endif |
568 |
– |
|
569 |
– |
// generate the force file name |
570 |
– |
|
571 |
– |
strcpy( fileName, "DUFF.frc" ); |
572 |
– |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
573 |
– |
|
574 |
– |
// attempt to open the file in the current directory first. |
575 |
– |
|
576 |
– |
frcFile = fopen( fileName, "r" ); |
577 |
– |
|
578 |
– |
if( frcFile == NULL ){ |
579 |
– |
|
580 |
– |
// next see if the force path enviorment variable is set |
581 |
– |
|
582 |
– |
ffPath = getenv( ffPath_env ); |
583 |
– |
if( ffPath == NULL ) { |
584 |
– |
STR_DEFINE(ffPath, FRC_PATH ); |
585 |
– |
} |
586 |
– |
|
587 |
– |
|
588 |
– |
strcpy( temp, ffPath ); |
589 |
– |
strcat( temp, "/" ); |
590 |
– |
strcat( temp, fileName ); |
591 |
– |
strcpy( fileName, temp ); |
592 |
– |
|
593 |
– |
frcFile = fopen( fileName, "r" ); |
594 |
– |
|
595 |
– |
if( frcFile == NULL ){ |
596 |
– |
|
597 |
– |
sprintf( painCave.errMsg, |
598 |
– |
"Error opening the force field parameter file:\n" |
599 |
– |
"\t%s\n" |
600 |
– |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
601 |
– |
"variable?\n", |
602 |
– |
fileName ); |
603 |
– |
painCave.severity = OOPSE_ERROR; |
604 |
– |
painCave.isFatal = 1; |
605 |
– |
simError(); |
606 |
– |
} |
607 |
– |
} |
608 |
– |
|
609 |
– |
#ifdef IS_MPI |
119 |
|
} |
611 |
– |
|
612 |
– |
sprintf( checkPointMsg, "DUFF file opened sucessfully." ); |
613 |
– |
MPIcheckPoint(); |
614 |
– |
|
615 |
– |
#endif // is_mpi |
616 |
– |
} |
120 |
|
|
121 |
< |
|
122 |
< |
DUFF::~DUFF(){ |
123 |
< |
|
124 |
< |
if( headAtomType != NULL ) delete headAtomType; |
622 |
< |
if( headBondType != NULL ) delete headBondType; |
623 |
< |
if( headBendType != NULL ) delete headBendType; |
624 |
< |
if( headTorsionType != NULL ) delete headTorsionType; |
625 |
< |
|
626 |
< |
#ifdef IS_MPI |
627 |
< |
if( worldRank == 0 ){ |
628 |
< |
#endif // is_mpi |
629 |
< |
|
630 |
< |
fclose( frcFile ); |
631 |
< |
|
632 |
< |
#ifdef IS_MPI |
633 |
< |
} |
634 |
< |
#endif // is_mpi |
635 |
< |
} |
636 |
< |
|
637 |
< |
void DUFF::cleanMe( void ){ |
638 |
< |
|
639 |
< |
#ifdef IS_MPI |
640 |
< |
|
641 |
< |
// keep the linked lists in the mpi version |
642 |
< |
|
643 |
< |
#else // is_mpi |
644 |
< |
|
645 |
< |
// delete the linked lists in the single processor version |
646 |
< |
|
647 |
< |
if( headAtomType != NULL ) delete headAtomType; |
648 |
< |
if( headBondType != NULL ) delete headBondType; |
649 |
< |
if( headBendType != NULL ) delete headBendType; |
650 |
< |
if( headTorsionType != NULL ) delete headTorsionType; |
651 |
< |
|
652 |
< |
#endif // is_mpi |
653 |
< |
} |
654 |
< |
|
655 |
< |
|
656 |
< |
void DUFF::initForceField( int ljMixRule ){ |
657 |
< |
|
658 |
< |
initFortran( ljMixRule, entry_plug->useReactionField ); |
659 |
< |
} |
660 |
< |
|
661 |
< |
double DUFF::getAtomTypeMass (char* atomType) { |
662 |
< |
|
663 |
< |
currentAtomType = headAtomType->find( atomType ); |
664 |
< |
if( currentAtomType == NULL ){ |
665 |
< |
sprintf( painCave.errMsg, |
666 |
< |
"AtomType error, %s not found in force file.\n", |
667 |
< |
atomType ); |
668 |
< |
painCave.isFatal = 1; |
669 |
< |
simError(); |
670 |
< |
} |
671 |
< |
|
672 |
< |
return currentAtomType->mass; |
673 |
< |
} |
674 |
< |
|
675 |
< |
void DUFF::readParams( void ){ |
676 |
< |
|
677 |
< |
int identNum; |
678 |
< |
|
679 |
< |
atomStruct atomInfo; |
680 |
< |
bondStruct bondInfo; |
681 |
< |
bendStruct bendInfo; |
682 |
< |
torsionStruct torsionInfo; |
683 |
< |
|
684 |
< |
bigSigma = 0.0; |
685 |
< |
|
686 |
< |
atomInfo.last = 1; |
687 |
< |
bondInfo.last = 1; |
688 |
< |
bendInfo.last = 1; |
689 |
< |
torsionInfo.last = 1; |
690 |
< |
|
691 |
< |
// read in the atom info |
692 |
< |
|
693 |
< |
#ifdef IS_MPI |
694 |
< |
if( worldRank == 0 ){ |
695 |
< |
#endif |
696 |
< |
|
697 |
< |
// read in the atom types. |
698 |
< |
|
699 |
< |
headAtomType = new LinkedAtomType; |
700 |
< |
|
701 |
< |
fastForward( "AtomTypes", "initializeAtoms" ); |
702 |
< |
|
703 |
< |
// we are now at the AtomTypes section. |
704 |
< |
|
705 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
706 |
< |
lineNum++; |
707 |
< |
|
708 |
< |
|
709 |
< |
// read a line, and start parseing out the atom types |
710 |
< |
|
711 |
< |
if( eof_test == NULL ){ |
712 |
< |
sprintf( painCave.errMsg, |
713 |
< |
"Error in reading Atoms from force file at line %d.\n", |
714 |
< |
lineNum ); |
715 |
< |
painCave.isFatal = 1; |
716 |
< |
simError(); |
717 |
< |
} |
718 |
< |
|
719 |
< |
identNum = 1; |
720 |
< |
// stop reading at end of file, or at next section |
721 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
722 |
< |
|
723 |
< |
// toss comment lines |
724 |
< |
if( readLine[0] != '!' ){ |
725 |
< |
|
726 |
< |
// the parser returns 0 if the line was blank |
727 |
< |
if( parseAtom( readLine, lineNum, atomInfo ) ){ |
728 |
< |
atomInfo.ident = identNum; |
729 |
< |
headAtomType->add( atomInfo );; |
730 |
< |
identNum++; |
731 |
< |
} |
732 |
< |
} |
733 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
734 |
< |
lineNum++; |
735 |
< |
} |
736 |
< |
|
737 |
< |
#ifdef IS_MPI |
738 |
< |
|
739 |
< |
// send out the linked list to all the other processes |
740 |
< |
|
741 |
< |
sprintf( checkPointMsg, |
742 |
< |
"DUFF atom structures read successfully." ); |
743 |
< |
MPIcheckPoint(); |
744 |
< |
|
745 |
< |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
746 |
< |
while( currentAtomType != NULL ){ |
747 |
< |
currentAtomType->duplicate( atomInfo ); |
748 |
< |
|
749 |
< |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
750 |
< |
|
751 |
< |
sprintf( checkPointMsg, |
752 |
< |
"successfully sent DUFF force type: \"%s\"\n", |
753 |
< |
atomInfo.name ); |
754 |
< |
MPIcheckPoint(); |
755 |
< |
|
756 |
< |
currentAtomType = currentAtomType->next; |
757 |
< |
} |
758 |
< |
atomInfo.last = 1; |
759 |
< |
sendFrcStruct( &atomInfo, mpiAtomStructType ); |
760 |
< |
|
761 |
< |
} |
762 |
< |
|
763 |
< |
else{ |
764 |
< |
|
765 |
< |
// listen for node 0 to send out the force params |
766 |
< |
|
767 |
< |
MPIcheckPoint(); |
768 |
< |
|
769 |
< |
headAtomType = new LinkedAtomType; |
770 |
< |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
771 |
< |
|
772 |
< |
while( !atomInfo.last ){ |
773 |
< |
|
774 |
< |
headAtomType->add( atomInfo ); |
775 |
< |
|
776 |
< |
MPIcheckPoint(); |
777 |
< |
|
778 |
< |
receiveFrcStruct( &atomInfo, mpiAtomStructType ); |
779 |
< |
} |
780 |
< |
} |
781 |
< |
|
782 |
< |
#endif // is_mpi |
783 |
< |
|
784 |
< |
|
785 |
< |
|
786 |
< |
// call new A_types in fortran |
787 |
< |
|
788 |
< |
int isError; |
789 |
< |
|
790 |
< |
// dummy variables |
791 |
< |
|
792 |
< |
int isGB = 0; |
793 |
< |
int isLJ = 1; |
794 |
< |
int isEAM =0; |
795 |
< |
int isCharge = 0; |
796 |
< |
double charge=0.0; |
797 |
< |
|
798 |
< |
currentAtomType = headAtomType->next;; |
799 |
< |
while( currentAtomType != NULL ){ |
800 |
< |
|
801 |
< |
if(currentAtomType->isDipole) entry_plug->useDipoles = 1; |
802 |
< |
if(currentAtomType->isSSD) { |
803 |
< |
entry_plug->useSticky = 1; |
804 |
< |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
805 |
< |
&(currentAtomType->v0p), |
806 |
< |
&(currentAtomType->rl), &(currentAtomType->ru), |
807 |
< |
&(currentAtomType->rlp), &(currentAtomType->rup)); |
808 |
< |
} |
809 |
< |
|
810 |
< |
if( currentAtomType->name[0] != '\0' ){ |
811 |
< |
isError = 0; |
812 |
< |
makeAtype( &(currentAtomType->ident), |
813 |
< |
&isLJ, |
814 |
< |
&(currentAtomType->isSSD), |
815 |
< |
&(currentAtomType->isDipole), |
816 |
< |
&isGB, |
817 |
< |
&isEAM, |
818 |
< |
&isCharge, |
819 |
< |
&(currentAtomType->epslon), |
820 |
< |
&(currentAtomType->sigma), |
821 |
< |
&charge, |
822 |
< |
&(currentAtomType->dipole), |
823 |
< |
&isError ); |
824 |
< |
if( isError ){ |
825 |
< |
sprintf( painCave.errMsg, |
826 |
< |
"Error initializing the \"%s\" atom type in fortran\n", |
827 |
< |
currentAtomType->name ); |
828 |
< |
painCave.isFatal = 1; |
829 |
< |
simError(); |
830 |
< |
} |
831 |
< |
} |
832 |
< |
currentAtomType = currentAtomType->next; |
833 |
< |
} |
834 |
< |
|
835 |
< |
#ifdef IS_MPI |
836 |
< |
sprintf( checkPointMsg, |
837 |
< |
"DUFF atom structures successfully sent to fortran\n" ); |
838 |
< |
MPIcheckPoint(); |
839 |
< |
#endif // is_mpi |
840 |
< |
|
841 |
< |
|
842 |
< |
|
843 |
< |
// read in the bonds |
844 |
< |
|
845 |
< |
#ifdef IS_MPI |
846 |
< |
if( worldRank == 0 ){ |
847 |
< |
#endif |
848 |
< |
|
849 |
< |
// read in the bond types. |
850 |
< |
|
851 |
< |
headBondType = new LinkedBondType; |
852 |
< |
|
853 |
< |
fastForward( "BondTypes", "initializeBonds" ); |
854 |
< |
|
855 |
< |
// we are now at the bondTypes section |
856 |
< |
|
857 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
858 |
< |
lineNum++; |
859 |
< |
|
860 |
< |
|
861 |
< |
// read a line, and start parseing out the atom types |
862 |
< |
|
863 |
< |
if( eof_test == NULL ){ |
864 |
< |
sprintf( painCave.errMsg, |
865 |
< |
"Error in reading bonds from force file at line %d.\n", |
866 |
< |
lineNum ); |
867 |
< |
painCave.isFatal = 1; |
868 |
< |
simError(); |
869 |
< |
} |
870 |
< |
|
871 |
< |
// stop reading at end of file, or at next section |
872 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
873 |
< |
|
874 |
< |
// toss comment lines |
875 |
< |
if( readLine[0] != '!' ){ |
876 |
< |
|
877 |
< |
// the parser returns 0 if the line was blank |
878 |
< |
if( parseBond( readLine, lineNum, bondInfo ) ){ |
879 |
< |
headBondType->add( bondInfo ); |
880 |
< |
} |
881 |
< |
} |
882 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
883 |
< |
lineNum++; |
884 |
< |
} |
885 |
< |
|
886 |
< |
#ifdef IS_MPI |
887 |
< |
|
888 |
< |
// send out the linked list to all the other processes |
889 |
< |
|
890 |
< |
sprintf( checkPointMsg, |
891 |
< |
"DUFF bond structures read successfully." ); |
892 |
< |
MPIcheckPoint(); |
893 |
< |
|
894 |
< |
currentBondType = headBondType->next; |
895 |
< |
while( currentBondType != NULL ){ |
896 |
< |
currentBondType->duplicate( bondInfo ); |
897 |
< |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
898 |
< |
currentBondType = currentBondType->next; |
899 |
< |
} |
900 |
< |
bondInfo.last = 1; |
901 |
< |
sendFrcStruct( &bondInfo, mpiBondStructType ); |
902 |
< |
|
903 |
< |
} |
904 |
< |
|
905 |
< |
else{ |
906 |
< |
|
907 |
< |
// listen for node 0 to send out the force params |
908 |
< |
|
909 |
< |
MPIcheckPoint(); |
910 |
< |
|
911 |
< |
headBondType = new LinkedBondType; |
912 |
< |
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
913 |
< |
while( !bondInfo.last ){ |
914 |
< |
|
915 |
< |
headBondType->add( bondInfo ); |
916 |
< |
receiveFrcStruct( &bondInfo, mpiBondStructType ); |
917 |
< |
} |
918 |
< |
} |
919 |
< |
|
920 |
< |
sprintf( checkPointMsg, |
921 |
< |
"DUFF bond structures broadcast successfully." ); |
922 |
< |
MPIcheckPoint(); |
923 |
< |
|
924 |
< |
#endif // is_mpi |
925 |
< |
|
926 |
< |
|
927 |
< |
// read in the bends |
928 |
< |
|
929 |
< |
#ifdef IS_MPI |
930 |
< |
if( worldRank == 0 ){ |
931 |
< |
#endif |
932 |
< |
|
933 |
< |
// read in the bend types. |
934 |
< |
|
935 |
< |
headBendType = new LinkedBendType; |
936 |
< |
|
937 |
< |
fastForward( "BendTypes", "initializeBends" ); |
938 |
< |
|
939 |
< |
// we are now at the bendTypes section |
940 |
< |
|
941 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
942 |
< |
lineNum++; |
943 |
< |
|
944 |
< |
// read a line, and start parseing out the bend types |
945 |
< |
|
946 |
< |
if( eof_test == NULL ){ |
947 |
< |
sprintf( painCave.errMsg, |
948 |
< |
"Error in reading bends from force file at line %d.\n", |
949 |
< |
lineNum ); |
950 |
< |
painCave.isFatal = 1; |
951 |
< |
simError(); |
952 |
< |
} |
953 |
< |
|
954 |
< |
// stop reading at end of file, or at next section |
955 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
956 |
< |
|
957 |
< |
// toss comment lines |
958 |
< |
if( readLine[0] != '!' ){ |
959 |
< |
|
960 |
< |
// the parser returns 0 if the line was blank |
961 |
< |
if( parseBend( readLine, lineNum, bendInfo ) ){ |
962 |
< |
headBendType->add( bendInfo ); |
963 |
< |
} |
964 |
< |
} |
965 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
966 |
< |
lineNum++; |
967 |
< |
} |
968 |
< |
|
969 |
< |
#ifdef IS_MPI |
970 |
< |
|
971 |
< |
// send out the linked list to all the other processes |
972 |
< |
|
973 |
< |
sprintf( checkPointMsg, |
974 |
< |
"DUFF bend structures read successfully." ); |
975 |
< |
MPIcheckPoint(); |
976 |
< |
|
977 |
< |
currentBendType = headBendType->next; |
978 |
< |
while( currentBendType != NULL ){ |
979 |
< |
currentBendType->duplicate( bendInfo ); |
980 |
< |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
981 |
< |
currentBendType = currentBendType->next; |
982 |
< |
} |
983 |
< |
bendInfo.last = 1; |
984 |
< |
sendFrcStruct( &bendInfo, mpiBendStructType ); |
985 |
< |
|
986 |
< |
} |
987 |
< |
|
988 |
< |
else{ |
989 |
< |
|
990 |
< |
// listen for node 0 to send out the force params |
991 |
< |
|
992 |
< |
MPIcheckPoint(); |
993 |
< |
|
994 |
< |
headBendType = new LinkedBendType; |
995 |
< |
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
996 |
< |
while( !bendInfo.last ){ |
997 |
< |
|
998 |
< |
headBendType->add( bendInfo ); |
999 |
< |
receiveFrcStruct( &bendInfo, mpiBendStructType ); |
1000 |
< |
} |
1001 |
< |
} |
1002 |
< |
|
1003 |
< |
sprintf( checkPointMsg, |
1004 |
< |
"DUFF bend structures broadcast successfully." ); |
1005 |
< |
MPIcheckPoint(); |
1006 |
< |
|
1007 |
< |
#endif // is_mpi |
1008 |
< |
|
1009 |
< |
|
1010 |
< |
// read in the torsions |
1011 |
< |
|
1012 |
< |
#ifdef IS_MPI |
1013 |
< |
if( worldRank == 0 ){ |
1014 |
< |
#endif |
1015 |
< |
|
1016 |
< |
// read in the torsion types. |
1017 |
< |
|
1018 |
< |
headTorsionType = new LinkedTorsionType; |
1019 |
< |
|
1020 |
< |
fastForward( "TorsionTypes", "initializeTorsions" ); |
1021 |
< |
|
1022 |
< |
// we are now at the torsionTypes section |
1023 |
< |
|
1024 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1025 |
< |
lineNum++; |
1026 |
< |
|
1027 |
< |
|
1028 |
< |
// read a line, and start parseing out the atom types |
1029 |
< |
|
1030 |
< |
if( eof_test == NULL ){ |
1031 |
< |
sprintf( painCave.errMsg, |
1032 |
< |
"Error in reading torsions from force file at line %d.\n", |
1033 |
< |
lineNum ); |
1034 |
< |
painCave.isFatal = 1; |
1035 |
< |
simError(); |
1036 |
< |
} |
1037 |
< |
|
1038 |
< |
// stop reading at end of file, or at next section |
1039 |
< |
while( readLine[0] != '#' && eof_test != NULL ){ |
1040 |
< |
|
1041 |
< |
// toss comment lines |
1042 |
< |
if( readLine[0] != '!' ){ |
1043 |
< |
|
1044 |
< |
// the parser returns 0 if the line was blank |
1045 |
< |
if( parseTorsion( readLine, lineNum, torsionInfo ) ){ |
1046 |
< |
headTorsionType->add( torsionInfo ); |
1047 |
< |
|
1048 |
< |
} |
1049 |
< |
} |
1050 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1051 |
< |
lineNum++; |
1052 |
< |
} |
1053 |
< |
|
1054 |
< |
#ifdef IS_MPI |
1055 |
< |
|
1056 |
< |
// send out the linked list to all the other processes |
1057 |
< |
|
1058 |
< |
sprintf( checkPointMsg, |
1059 |
< |
"DUFF torsion structures read successfully." ); |
1060 |
< |
MPIcheckPoint(); |
1061 |
< |
|
1062 |
< |
currentTorsionType = headTorsionType->next; |
1063 |
< |
while( currentTorsionType != NULL ){ |
1064 |
< |
currentTorsionType->duplicate( torsionInfo ); |
1065 |
< |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1066 |
< |
currentTorsionType = currentTorsionType->next; |
1067 |
< |
} |
1068 |
< |
torsionInfo.last = 1; |
1069 |
< |
sendFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1070 |
< |
|
1071 |
< |
} |
1072 |
< |
|
1073 |
< |
else{ |
1074 |
< |
|
1075 |
< |
// listen for node 0 to send out the force params |
1076 |
< |
|
1077 |
< |
MPIcheckPoint(); |
1078 |
< |
|
1079 |
< |
headTorsionType = new LinkedTorsionType; |
1080 |
< |
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1081 |
< |
while( !torsionInfo.last ){ |
1082 |
< |
|
1083 |
< |
headTorsionType->add( torsionInfo ); |
1084 |
< |
receiveFrcStruct( &torsionInfo, mpiTorsionStructType ); |
1085 |
< |
} |
1086 |
< |
} |
1087 |
< |
|
1088 |
< |
sprintf( checkPointMsg, |
1089 |
< |
"DUFF torsion structures broadcast successfully." ); |
1090 |
< |
MPIcheckPoint(); |
1091 |
< |
|
1092 |
< |
#endif // is_mpi |
1093 |
< |
|
1094 |
< |
entry_plug->useLJ = 1; |
1095 |
< |
} |
1096 |
< |
|
1097 |
< |
|
1098 |
< |
|
1099 |
< |
void DUFF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
1100 |
< |
|
1101 |
< |
|
1102 |
< |
////////////////////////////////////////////////// |
1103 |
< |
// a quick water fix |
1104 |
< |
|
1105 |
< |
double waterI[3][3]; |
1106 |
< |
waterI[0][0] = 1.76958347772500; |
1107 |
< |
waterI[0][1] = 0.0; |
1108 |
< |
waterI[0][2] = 0.0; |
1109 |
< |
|
1110 |
< |
waterI[1][0] = 0.0; |
1111 |
< |
waterI[1][1] = 0.614537057924513; |
1112 |
< |
waterI[1][2] = 0.0; |
1113 |
< |
|
1114 |
< |
waterI[2][0] = 0.0; |
1115 |
< |
waterI[2][1] = 0.0; |
1116 |
< |
waterI[2][2] = 1.15504641980049; |
1117 |
< |
|
1118 |
< |
|
1119 |
< |
double headI[3][3]; |
1120 |
< |
headI[0][0] = 1125; |
1121 |
< |
headI[0][1] = 0.0; |
1122 |
< |
headI[0][2] = 0.0; |
1123 |
< |
|
1124 |
< |
headI[1][0] = 0.0; |
1125 |
< |
headI[1][1] = 1125; |
1126 |
< |
headI[1][2] = 0.0; |
1127 |
< |
|
1128 |
< |
headI[2][0] = 0.0; |
1129 |
< |
headI[2][1] = 0.0; |
1130 |
< |
headI[2][2] = 250; |
1131 |
< |
|
1132 |
< |
////////////////////////////////////////////////// |
1133 |
< |
|
1134 |
< |
|
1135 |
< |
// initialize the atoms |
1136 |
< |
|
1137 |
< |
DirectionalAtom* dAtom; |
1138 |
< |
double ji[3]; |
1139 |
< |
|
1140 |
< |
for(int i=0; i<nAtoms; i++ ){ |
1141 |
< |
|
1142 |
< |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
1143 |
< |
if( currentAtomType == NULL ){ |
1144 |
< |
sprintf( painCave.errMsg, |
1145 |
< |
"AtomType error, %s not found in force file.\n", |
1146 |
< |
the_atoms[i]->getType() ); |
1147 |
< |
painCave.isFatal = 1; |
1148 |
< |
simError(); |
1149 |
< |
} |
1150 |
< |
|
1151 |
< |
the_atoms[i]->setMass( currentAtomType->mass ); |
1152 |
< |
the_atoms[i]->setIdent( currentAtomType->ident ); |
1153 |
< |
|
1154 |
< |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
1155 |
< |
|
1156 |
< |
if( currentAtomType->isDipole ){ |
1157 |
< |
if( the_atoms[i]->isDirectional() ){ |
1158 |
< |
|
1159 |
< |
dAtom = (DirectionalAtom *) the_atoms[i]; |
1160 |
< |
dAtom->setHasDipole( 1 ); |
1161 |
< |
|
1162 |
< |
ji[0] = 0.0; |
1163 |
< |
ji[1] = 0.0; |
1164 |
< |
ji[2] = 0.0; |
1165 |
< |
|
1166 |
< |
dAtom->setJ( ji ); |
1167 |
< |
|
1168 |
< |
if(!strcmp("SSD",the_atoms[i]->getType())){ |
1169 |
< |
dAtom->setI( waterI ); |
1170 |
< |
} |
1171 |
< |
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
1172 |
< |
dAtom->setI( headI ); |
1173 |
< |
} |
1174 |
< |
else{ |
1175 |
< |
sprintf(painCave.errMsg, |
1176 |
< |
"AtmType error, %s does not have a moment of inertia set.\n", |
1177 |
< |
the_atoms[i]->getType() ); |
1178 |
< |
painCave.isFatal = 1; |
1179 |
< |
simError(); |
1180 |
< |
} |
1181 |
< |
entry_plug->n_dipoles++; |
1182 |
< |
} |
1183 |
< |
else{ |
1184 |
< |
|
1185 |
< |
sprintf( painCave.errMsg, |
1186 |
< |
"DUFF error: Atom \"%s\" is a dipole, yet no standard" |
1187 |
< |
" orientation was specifed in the meta-data file.\n", |
1188 |
< |
currentAtomType->name ); |
1189 |
< |
painCave.isFatal = 1; |
1190 |
< |
simError(); |
1191 |
< |
} |
1192 |
< |
} |
1193 |
< |
else{ |
1194 |
< |
if( the_atoms[i]->isDirectional() ){ |
1195 |
< |
sprintf( painCave.errMsg, |
1196 |
< |
"DUFF error: Atom \"%s\" was given a standard " |
1197 |
< |
"orientation in the meta-data file, yet it is not a dipole.\n", |
1198 |
< |
currentAtomType->name); |
1199 |
< |
painCave.isFatal = 1; |
1200 |
< |
simError(); |
1201 |
< |
} |
1202 |
< |
} |
1203 |
< |
} |
1204 |
< |
} |
1205 |
< |
|
1206 |
< |
void DUFF::initializeBonds( int nBonds, Bond** bondArray, |
1207 |
< |
bond_pair* the_bonds ){ |
1208 |
< |
int i,a,b; |
1209 |
< |
char* atomA; |
1210 |
< |
char* atomB; |
1211 |
< |
|
1212 |
< |
Atom** the_atoms; |
1213 |
< |
the_atoms = entry_plug->atoms; |
1214 |
< |
|
1215 |
< |
|
1216 |
< |
// initialize the Bonds |
1217 |
< |
|
1218 |
< |
for( i=0; i<nBonds; i++ ){ |
1219 |
< |
|
1220 |
< |
a = the_bonds[i].a; |
1221 |
< |
b = the_bonds[i].b; |
1222 |
< |
|
1223 |
< |
atomA = the_atoms[a]->getType(); |
1224 |
< |
atomB = the_atoms[b]->getType(); |
1225 |
< |
currentBondType = headBondType->find( atomA, atomB ); |
1226 |
< |
if( currentBondType == NULL ){ |
1227 |
< |
sprintf( painCave.errMsg, |
1228 |
< |
"BondType error, %s - %s not found in force file.\n", |
1229 |
< |
atomA, atomB ); |
1230 |
< |
painCave.isFatal = 1; |
1231 |
< |
simError(); |
1232 |
< |
} |
1233 |
< |
|
1234 |
< |
switch( currentBondType->type ){ |
1235 |
< |
|
1236 |
< |
case FIXED_BOND: |
1237 |
< |
|
1238 |
< |
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1239 |
< |
*the_atoms[b], |
1240 |
< |
currentBondType->d0 ); |
1241 |
< |
entry_plug->n_constraints++; |
1242 |
< |
break; |
1243 |
< |
|
1244 |
< |
case HARMONIC_BOND: |
1245 |
< |
|
1246 |
< |
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1247 |
< |
*the_atoms[b], |
1248 |
< |
currentBondType->d0, |
1249 |
< |
currentBondType->k0 ); |
1250 |
< |
break; |
1251 |
< |
|
1252 |
< |
default: |
1253 |
< |
|
1254 |
< |
break; |
1255 |
< |
// do nothing |
1256 |
< |
} |
1257 |
< |
} |
1258 |
< |
} |
1259 |
< |
|
1260 |
< |
void DUFF::initializeBends( int nBends, Bend** bendArray, |
1261 |
< |
bend_set* the_bends ){ |
1262 |
< |
|
1263 |
< |
QuadraticBend* qBend; |
1264 |
< |
GhostBend* gBend; |
1265 |
< |
Atom** the_atoms; |
1266 |
< |
the_atoms = entry_plug->atoms; |
1267 |
< |
|
1268 |
< |
int i, a, b, c; |
1269 |
< |
char* atomA; |
1270 |
< |
char* atomB; |
1271 |
< |
char* atomC; |
1272 |
< |
|
1273 |
< |
// initialize the Bends |
1274 |
< |
|
1275 |
< |
for( i=0; i<nBends; i++ ){ |
1276 |
< |
|
1277 |
< |
a = the_bends[i].a; |
1278 |
< |
b = the_bends[i].b; |
1279 |
< |
c = the_bends[i].c; |
1280 |
< |
|
1281 |
< |
atomA = the_atoms[a]->getType(); |
1282 |
< |
atomB = the_atoms[b]->getType(); |
1283 |
< |
|
1284 |
< |
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1285 |
< |
else atomC = the_atoms[c]->getType(); |
1286 |
< |
|
1287 |
< |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1288 |
< |
if( currentBendType == NULL ){ |
1289 |
< |
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1290 |
< |
" in force file.\n", |
1291 |
< |
atomA, atomB, atomC ); |
1292 |
< |
painCave.isFatal = 1; |
1293 |
< |
simError(); |
1294 |
< |
} |
1295 |
< |
|
1296 |
< |
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1297 |
< |
|
1298 |
< |
if( the_bends[i].isGhost){ |
1299 |
< |
|
1300 |
< |
if( the_bends[i].ghost == b ){ |
1301 |
< |
// do nothing |
1302 |
< |
} |
1303 |
< |
else if( the_bends[i].ghost == a ){ |
1304 |
< |
c = a; |
1305 |
< |
a = b; |
1306 |
< |
b = c; |
1307 |
< |
} |
1308 |
< |
else{ |
1309 |
< |
sprintf( painCave.errMsg, |
1310 |
< |
"BendType error, %s - %s - %s,\n" |
1311 |
< |
" --> central atom is not " |
1312 |
< |
"correctly identified with the " |
1313 |
< |
"\"ghostVectorSource = \" tag.\n", |
1314 |
< |
atomA, atomB, atomC ); |
1315 |
< |
painCave.isFatal = 1; |
1316 |
< |
simError(); |
1317 |
< |
} |
1318 |
< |
|
1319 |
< |
gBend = new GhostBend( *the_atoms[a], |
1320 |
< |
*the_atoms[b]); |
1321 |
< |
|
1322 |
< |
gBend->setConstants( currentBendType->k1, |
1323 |
< |
currentBendType->k2, |
1324 |
< |
currentBendType->k3, |
1325 |
< |
currentBendType->t0 ); |
1326 |
< |
bendArray[i] = gBend; |
1327 |
< |
} |
1328 |
< |
else{ |
1329 |
< |
qBend = new QuadraticBend( *the_atoms[a], |
1330 |
< |
*the_atoms[b], |
1331 |
< |
*the_atoms[c] ); |
1332 |
< |
qBend->setConstants( currentBendType->k1, |
1333 |
< |
currentBendType->k2, |
1334 |
< |
currentBendType->k3, |
1335 |
< |
currentBendType->t0 ); |
1336 |
< |
bendArray[i] = qBend; |
1337 |
< |
} |
1338 |
< |
} |
1339 |
< |
} |
1340 |
< |
} |
1341 |
< |
|
1342 |
< |
void DUFF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
1343 |
< |
torsion_set* the_torsions ){ |
1344 |
< |
|
1345 |
< |
int i, a, b, c, d; |
1346 |
< |
char* atomA; |
1347 |
< |
char* atomB; |
1348 |
< |
char* atomC; |
1349 |
< |
char* atomD; |
1350 |
< |
|
1351 |
< |
CubicTorsion* cTors; |
1352 |
< |
Atom** the_atoms; |
1353 |
< |
the_atoms = entry_plug->atoms; |
1354 |
< |
|
1355 |
< |
// initialize the Torsions |
1356 |
< |
|
1357 |
< |
for( i=0; i<nTorsions; i++ ){ |
1358 |
< |
|
1359 |
< |
a = the_torsions[i].a; |
1360 |
< |
b = the_torsions[i].b; |
1361 |
< |
c = the_torsions[i].c; |
1362 |
< |
d = the_torsions[i].d; |
1363 |
< |
|
1364 |
< |
atomA = the_atoms[a]->getType(); |
1365 |
< |
atomB = the_atoms[b]->getType(); |
1366 |
< |
atomC = the_atoms[c]->getType(); |
1367 |
< |
atomD = the_atoms[d]->getType(); |
1368 |
< |
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1369 |
< |
if( currentTorsionType == NULL ){ |
1370 |
< |
sprintf( painCave.errMsg, |
1371 |
< |
"TorsionType error, %s - %s - %s - %s not found" |
1372 |
< |
" in force file.\n", |
1373 |
< |
atomA, atomB, atomC, atomD ); |
1374 |
< |
painCave.isFatal = 1; |
1375 |
< |
simError(); |
1376 |
< |
} |
1377 |
< |
|
1378 |
< |
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1379 |
< |
|
1380 |
< |
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1381 |
< |
*the_atoms[c], *the_atoms[d] ); |
1382 |
< |
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1383 |
< |
currentTorsionType->k3, currentTorsionType->k4 ); |
1384 |
< |
torsionArray[i] = cTors; |
1385 |
< |
} |
121 |
> |
DUFF::~DUFF(){ |
122 |
> |
destroyLJTypes(); |
123 |
> |
destroyStickyTypes(); |
124 |
> |
destroyGayBerneTypes(); |
125 |
|
} |
126 |
< |
} |
1388 |
< |
|
1389 |
< |
void DUFF::fastForward( char* stopText, char* searchOwner ){ |
1390 |
< |
|
1391 |
< |
int foundText = 0; |
1392 |
< |
char* the_token; |
1393 |
< |
|
1394 |
< |
rewind( frcFile ); |
1395 |
< |
lineNum = 0; |
1396 |
< |
|
1397 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1398 |
< |
lineNum++; |
1399 |
< |
if( eof_test == NULL ){ |
1400 |
< |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1401 |
< |
" file is empty.\n", |
1402 |
< |
searchOwner ); |
1403 |
< |
painCave.isFatal = 1; |
1404 |
< |
simError(); |
1405 |
< |
} |
1406 |
< |
|
1407 |
< |
|
1408 |
< |
while( !foundText ){ |
1409 |
< |
while( eof_test != NULL && readLine[0] != '#' ){ |
1410 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1411 |
< |
lineNum++; |
1412 |
< |
} |
1413 |
< |
if( eof_test == NULL ){ |
1414 |
< |
sprintf( painCave.errMsg, |
1415 |
< |
"Error fast forwarding force file for %s at " |
1416 |
< |
"line %d: file ended unexpectedly.\n", |
1417 |
< |
searchOwner, |
1418 |
< |
lineNum ); |
1419 |
< |
painCave.isFatal = 1; |
1420 |
< |
simError(); |
1421 |
< |
} |
1422 |
< |
|
1423 |
< |
the_token = strtok( readLine, " ,;\t#\n" ); |
1424 |
< |
foundText = !strcmp( stopText, the_token ); |
1425 |
< |
|
1426 |
< |
if( !foundText ){ |
1427 |
< |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1428 |
< |
lineNum++; |
1429 |
< |
|
1430 |
< |
if( eof_test == NULL ){ |
1431 |
< |
sprintf( painCave.errMsg, |
1432 |
< |
"Error fast forwarding force file for %s at " |
1433 |
< |
"line %d: file ended unexpectedly.\n", |
1434 |
< |
searchOwner, |
1435 |
< |
lineNum ); |
1436 |
< |
painCave.isFatal = 1; |
1437 |
< |
simError(); |
1438 |
< |
} |
1439 |
< |
} |
1440 |
< |
} |
1441 |
< |
} |
1442 |
< |
|
1443 |
< |
|
1444 |
< |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1445 |
< |
|
1446 |
< |
char* the_token; |
1447 |
< |
|
1448 |
< |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1449 |
< |
if( the_token != NULL ){ |
1450 |
< |
|
1451 |
< |
strcpy( info.name, the_token ); |
1452 |
< |
|
1453 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1454 |
< |
sprintf( painCave.errMsg, |
1455 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1456 |
< |
painCave.isFatal = 1; |
1457 |
< |
simError(); |
1458 |
< |
} |
1459 |
< |
|
1460 |
< |
info.isDipole = atoi( the_token ); |
1461 |
< |
|
1462 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1463 |
< |
sprintf( painCave.errMsg, |
1464 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1465 |
< |
painCave.isFatal = 1; |
1466 |
< |
simError(); |
1467 |
< |
} |
1468 |
< |
|
1469 |
< |
info.isSSD = atoi( 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.mass = atof( 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.epslon = atof( 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.sigma = atof( the_token ); |
1497 |
< |
|
1498 |
< |
if( info.isDipole ){ |
1499 |
< |
|
1500 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1501 |
< |
sprintf( painCave.errMsg, |
1502 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1503 |
< |
painCave.isFatal = 1; |
1504 |
< |
simError(); |
1505 |
< |
} |
1506 |
< |
|
1507 |
< |
info.dipole = atof( the_token ); |
1508 |
< |
} |
1509 |
< |
else info.dipole = 0.0; |
1510 |
< |
|
1511 |
< |
if( info.isSSD ){ |
1512 |
< |
|
1513 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1514 |
< |
sprintf( painCave.errMsg, |
1515 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1516 |
< |
painCave.isFatal = 1; |
1517 |
< |
simError(); |
1518 |
< |
} |
1519 |
< |
|
1520 |
< |
info.w0 = atof( the_token ); |
1521 |
< |
|
1522 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1523 |
< |
sprintf( painCave.errMsg, |
1524 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1525 |
< |
painCave.isFatal = 1; |
1526 |
< |
simError(); |
1527 |
< |
} |
1528 |
< |
|
1529 |
< |
info.v0 = atof( the_token ); |
1530 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1531 |
< |
sprintf( painCave.errMsg, |
1532 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1533 |
< |
painCave.isFatal = 1; |
1534 |
< |
simError(); |
1535 |
< |
} |
1536 |
< |
|
1537 |
< |
info.v0p = atof( the_token ); |
1538 |
< |
|
1539 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1540 |
< |
sprintf( painCave.errMsg, |
1541 |
< |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1542 |
< |
painCave.isFatal = 1; |
1543 |
< |
simError(); |
1544 |
< |
} |
1545 |
< |
|
1546 |
< |
info.rl = atof( the_token ); |
1547 |
< |
|
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.ru = 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.rlp = 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.rup = atof( the_token ); |
1574 |
< |
} |
1575 |
< |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1576 |
< |
|
1577 |
< |
return 1; |
1578 |
< |
} |
1579 |
< |
else return 0; |
1580 |
< |
} |
1581 |
< |
|
1582 |
< |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1583 |
< |
|
1584 |
< |
char* the_token; |
1585 |
< |
char bondType[30]; |
1586 |
< |
|
1587 |
< |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1588 |
< |
if( the_token != NULL ){ |
1589 |
< |
|
1590 |
< |
strcpy( info.nameA, the_token ); |
1591 |
< |
|
1592 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1593 |
< |
sprintf( painCave.errMsg, |
1594 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1595 |
< |
painCave.isFatal = 1; |
1596 |
< |
simError(); |
1597 |
< |
} |
1598 |
< |
|
1599 |
< |
strcpy( info.nameB, the_token ); |
1600 |
< |
|
1601 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1602 |
< |
sprintf( painCave.errMsg, |
1603 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1604 |
< |
painCave.isFatal = 1; |
1605 |
< |
simError(); |
1606 |
< |
} |
1607 |
< |
|
1608 |
< |
strcpy( bondType, the_token ); |
1609 |
< |
|
1610 |
< |
if( !strcmp( bondType, "fixed" ) ){ |
1611 |
< |
info.type = FIXED_BOND; |
1612 |
< |
|
1613 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1614 |
< |
sprintf( painCave.errMsg, |
1615 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1616 |
< |
painCave.isFatal = 1; |
1617 |
< |
simError(); |
1618 |
< |
} |
1619 |
< |
|
1620 |
< |
info.d0 = atof( the_token ); |
1621 |
< |
|
1622 |
< |
info.k0=0.0; |
1623 |
< |
} |
1624 |
< |
else if( !strcmp( bondType, "harmonic" ) ){ |
1625 |
< |
info.type = HARMONIC_BOND; |
1626 |
< |
|
1627 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1628 |
< |
sprintf( painCave.errMsg, |
1629 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1630 |
< |
painCave.isFatal = 1; |
1631 |
< |
simError(); |
1632 |
< |
} |
1633 |
< |
|
1634 |
< |
info.d0 = atof( the_token ); |
1635 |
< |
|
1636 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1637 |
< |
sprintf( painCave.errMsg, |
1638 |
< |
"Error parseing BondTypes: line %d\n", lineNum ); |
1639 |
< |
painCave.isFatal = 1; |
1640 |
< |
simError(); |
1641 |
< |
} |
1642 |
< |
|
1643 |
< |
info.k0 = atof( the_token ); |
1644 |
< |
} |
1645 |
< |
|
1646 |
< |
else{ |
1647 |
< |
sprintf( painCave.errMsg, |
1648 |
< |
"Unknown DUFF bond type \"%s\" at line %d\n", |
1649 |
< |
bondType, |
1650 |
< |
lineNum ); |
1651 |
< |
painCave.isFatal = 1; |
1652 |
< |
simError(); |
1653 |
< |
} |
1654 |
< |
|
1655 |
< |
return 1; |
1656 |
< |
} |
1657 |
< |
else return 0; |
1658 |
< |
} |
1659 |
< |
|
1660 |
< |
|
1661 |
< |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1662 |
< |
|
1663 |
< |
char* the_token; |
1664 |
< |
|
1665 |
< |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1666 |
< |
if( the_token != NULL ){ |
1667 |
< |
|
1668 |
< |
strcpy( info.nameA, the_token ); |
1669 |
< |
|
1670 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1671 |
< |
sprintf( painCave.errMsg, |
1672 |
< |
"Error parseing BendTypes: line %d\n", lineNum ); |
1673 |
< |
painCave.isFatal = 1; |
1674 |
< |
simError(); |
1675 |
< |
} |
1676 |
< |
|
1677 |
< |
strcpy( info.nameB, the_token ); |
1678 |
< |
|
1679 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1680 |
< |
sprintf( painCave.errMsg, |
1681 |
< |
"Error parseing BendTypes: line %d\n", lineNum ); |
1682 |
< |
painCave.isFatal = 1; |
1683 |
< |
simError(); |
1684 |
< |
} |
1685 |
< |
|
1686 |
< |
strcpy( info.nameC, 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.type, the_token ); |
1696 |
< |
|
1697 |
< |
if( !strcmp( info.type, "quadratic" ) ){ |
1698 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1699 |
< |
sprintf( painCave.errMsg, |
1700 |
< |
"Error parseing BendTypes: line %d\n", lineNum ); |
1701 |
< |
painCave.isFatal = 1; |
1702 |
< |
simError(); |
1703 |
< |
} |
1704 |
< |
|
1705 |
< |
info.k1 = atof( the_token ); |
1706 |
< |
|
1707 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1708 |
< |
sprintf( painCave.errMsg, |
1709 |
< |
"Error parseing BendTypes: line %d\n", lineNum ); |
1710 |
< |
painCave.isFatal = 1; |
1711 |
< |
simError(); |
1712 |
< |
} |
1713 |
< |
|
1714 |
< |
info.k2 = atof( the_token ); |
1715 |
< |
|
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.k3 = 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.t0 = atof( the_token ); |
1733 |
< |
} |
1734 |
< |
|
1735 |
< |
else{ |
1736 |
< |
sprintf( painCave.errMsg, |
1737 |
< |
"Unknown DUFF bend type \"%s\" at line %d\n", |
1738 |
< |
info.type, |
1739 |
< |
lineNum ); |
1740 |
< |
painCave.isFatal = 1; |
1741 |
< |
simError(); |
1742 |
< |
} |
1743 |
< |
|
1744 |
< |
return 1; |
1745 |
< |
} |
1746 |
< |
else return 0; |
1747 |
< |
} |
1748 |
< |
|
1749 |
< |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1750 |
< |
|
1751 |
< |
char* the_token; |
1752 |
< |
|
1753 |
< |
the_token = strtok( lineBuffer, " \n\t,;" ); |
1754 |
< |
if( the_token != NULL ){ |
1755 |
< |
|
1756 |
< |
strcpy( info.nameA, the_token ); |
1757 |
< |
|
1758 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1759 |
< |
sprintf( painCave.errMsg, |
1760 |
< |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1761 |
< |
painCave.isFatal = 1; |
1762 |
< |
simError(); |
1763 |
< |
} |
1764 |
< |
|
1765 |
< |
strcpy( info.nameB, the_token ); |
1766 |
< |
|
1767 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1768 |
< |
sprintf( painCave.errMsg, |
1769 |
< |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1770 |
< |
painCave.isFatal = 1; |
1771 |
< |
simError(); |
1772 |
< |
} |
1773 |
< |
|
1774 |
< |
strcpy( info.nameC, 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.nameD, 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.type, the_token ); |
1793 |
< |
|
1794 |
< |
if( !strcmp( info.type, "cubic" ) ){ |
1795 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1796 |
< |
sprintf( painCave.errMsg, |
1797 |
< |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1798 |
< |
painCave.isFatal = 1; |
1799 |
< |
simError(); |
1800 |
< |
} |
1801 |
< |
|
1802 |
< |
info.k1 = atof( the_token ); |
1803 |
< |
|
1804 |
< |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1805 |
< |
sprintf( painCave.errMsg, |
1806 |
< |
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1807 |
< |
painCave.isFatal = 1; |
1808 |
< |
simError(); |
1809 |
< |
} |
1810 |
< |
|
1811 |
< |
info.k2 = atof( the_token ); |
1812 |
< |
|
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.k3 = 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.k4 = atof( the_token ); |
1830 |
< |
|
1831 |
< |
} |
1832 |
< |
|
1833 |
< |
else{ |
1834 |
< |
sprintf( painCave.errMsg, |
1835 |
< |
"Unknown DUFF torsion type \"%s\" at line %d\n", |
1836 |
< |
info.type, |
1837 |
< |
lineNum ); |
1838 |
< |
painCave.isFatal = 1; |
1839 |
< |
simError(); |
1840 |
< |
} |
1841 |
< |
|
1842 |
< |
return 1; |
1843 |
< |
} |
1844 |
< |
|
1845 |
< |
else return 0; |
1846 |
< |
} |
126 |
> |
} //end namespace oopse |