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" |
9 |
< |
#include "primitives/SRI.hpp" |
10 |
< |
#include "utils/simError.h" |
11 |
< |
#include "types/DirectionalAtomType.hpp" |
43 |
> |
#include "UseTheForce/DUFF.hpp" |
44 |
|
#include "UseTheForce/DarkSide/lj_interface.h" |
13 |
– |
#include "UseTheForce/DarkSide/dipole_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 |
< |
#ifdef IS_MPI |
63 |
< |
#include "UseTheForce/mpiForceField.h" |
64 |
< |
#endif // is_mpi |
62 |
> |
namespace oopse { |
63 |
> |
|
64 |
> |
DUFF::DUFF(){ |
65 |
|
|
66 |
+ |
//set default force field filename |
67 |
+ |
setForceFieldFileName("DUFF2.frc"); |
68 |
|
|
69 |
< |
// define some bond Types |
69 |
> |
//The order of adding section parsers is important. |
70 |
> |
//OptionSectionParser must come first to set options for other parsers |
71 |
> |
//DirectionalAtomTypesSectionParser should be added before |
72 |
> |
//AtomTypesSectionParser, and these two section parsers will actually |
73 |
> |
//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and |
74 |
> |
//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which |
75 |
> |
//is a subclass of AtomType and should come first). Other AtomTypes Section |
76 |
> |
//Parser will not create the "real" AtomType, they only add and set some |
77 |
> |
//attribute of the AtomType. Thus their order are not important. |
78 |
> |
//AtomTypesSectionParser should be added before other atom type section |
79 |
> |
//parsers. Make sure they are added after DirectionalAtomTypesSectionParser |
80 |
> |
//and AtomTypesSectionParser. The order of BondTypesSectionParser, |
81 |
> |
//BendTypesSectionParser and TorsionTypesSectionParser are not important. |
82 |
> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
83 |
> |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
84 |
> |
spMan_.push_back(new AtomTypesSectionParser()); |
85 |
> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
86 |
> |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
87 |
> |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
88 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
89 |
> |
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
90 |
> |
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
91 |
> |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
92 |
> |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
93 |
> |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
94 |
> |
|
95 |
> |
} |
96 |
|
|
97 |
< |
#define FIXED_BOND 0 |
98 |
< |
#define HARMONIC_BOND 1 |
97 |
> |
void DUFF::parse(const std::string& filename) { |
98 |
> |
ifstrstream* ffStream; |
99 |
> |
bool hasGBtypes; |
100 |
|
|
101 |
+ |
ffStream = openForceFieldFile(filename); |
102 |
|
|
103 |
< |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
103 |
> |
spMan_.parse(*ffStream, *this); |
104 |
|
|
105 |
+ |
ForceField::AtomTypeContainer::MapTypeIterator i; |
106 |
+ |
AtomType* at; |
107 |
|
|
108 |
< |
// Declare the structures that will be passed by MPI |
109 |
< |
|
110 |
< |
typedef struct{ |
33 |
< |
char name[15]; |
34 |
< |
double mass; |
35 |
< |
double epslon; |
36 |
< |
double sigma; |
37 |
< |
double charge; |
38 |
< |
double dipole; |
39 |
< |
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 |
< |
|
76 |
< |
|
77 |
< |
typedef struct{ |
78 |
< |
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 |
96 |
< |
|
97 |
< |
MPI_Datatype mpiAtomStructType; |
98 |
< |
MPI_Datatype mpiBondStructType; |
99 |
< |
MPI_Datatype mpiBendStructType; |
100 |
< |
MPI_Datatype mpiTorsionStructType; |
101 |
< |
|
102 |
< |
#endif |
103 |
< |
|
104 |
< |
class LinkedAtomType { |
105 |
< |
public: |
106 |
< |
LinkedAtomType(){ |
107 |
< |
next = NULL; |
108 |
< |
name[0] = '\0'; |
108 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
109 |
> |
at = atomTypeCont_.nextType(i)) { |
110 |
> |
at->makeFortranAtomType(); |
111 |
|
} |
110 |
– |
~LinkedAtomType(){ if( next != NULL ) delete next; } |
112 |
|
|
113 |
< |
LinkedAtomType* find(char* key){ |
114 |
< |
if( !strcmp(name, key) ) return this; |
115 |
< |
if( next != NULL ) return next->find(key); |
115 |
< |
return NULL; |
113 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
114 |
> |
at = atomTypeCont_.nextType(i)) { |
115 |
> |
at->complete(); |
116 |
|
} |
117 |
– |
|
118 |
– |
void printMe( void ){ |
119 |
– |
|
120 |
– |
std::cerr << "LinkedAtype " << name << ": ident = " << ident << "\n"; |
121 |
– |
// if( next != NULL ) next->printMe(); |
117 |
|
|
118 |
+ |
hasGBtypes = false; |
119 |
+ |
for (at = atomTypeCont_.beginType(i); at != NULL; |
120 |
+ |
at = atomTypeCont_.nextType(i)) { |
121 |
+ |
if (at->isGayBerne()) |
122 |
+ |
hasGBtypes = true; |
123 |
|
} |
124 |
– |
|
125 |
– |
void add( atomStruct &info ){ |
126 |
– |
|
127 |
– |
// check for duplicates |
128 |
– |
|
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 |
124 |
|
|
125 |
< |
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 |
< |
} |
125 |
> |
int isError = 0; |
126 |
|
|
127 |
< |
|
128 |
< |
#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 |
< |
} |
127 |
> |
if (hasGBtypes) { |
128 |
> |
completeGBFF(&isError); |
129 |
|
} |
130 |
|
|
131 |
< |
#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 |
615 |
< |
} |
616 |
< |
|
617 |
< |
|
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 |
131 |
> |
delete ffStream; |
132 |
|
|
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 |
– |
|
133 |
|
} |
134 |
|
|
135 |
< |
else{ |
136 |
< |
|
137 |
< |
// listen for node 0 to send out the force params |
138 |
< |
|
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 |
< |
} |
135 |
> |
DUFF::~DUFF(){ |
136 |
> |
destroyLJTypes(); |
137 |
> |
destroyStickyTypes(); |
138 |
> |
destroyGayBerneTypes(); |
139 |
|
} |
140 |
< |
|
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->useLJ = 1; |
1113 |
< |
} |
1114 |
< |
|
1115 |
< |
|
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 |
< |
} |
140 |
> |
} //end namespace oopse |