1 |
mmeineke |
10 |
#include <cstdlib> |
2 |
|
|
#include <cstdio> |
3 |
|
|
#include <cstring> |
4 |
|
|
|
5 |
|
|
#include <iostream> |
6 |
|
|
using namespace std; |
7 |
|
|
|
8 |
|
|
#include "ForceFields.hpp" |
9 |
|
|
#include "SRI.hpp" |
10 |
|
|
|
11 |
|
|
|
12 |
chuckv |
141 |
#ifdef IS_MPI |
13 |
|
|
|
14 |
mmeineke |
147 |
#include "mpiForceField.h" |
15 |
|
|
|
16 |
chuckv |
141 |
int myNode; |
17 |
|
|
|
18 |
|
|
// Declare the structures that will be passed by MPI |
19 |
|
|
|
20 |
|
|
typedef struct{ |
21 |
|
|
char name[15]; |
22 |
|
|
double mass; |
23 |
|
|
double epslon; |
24 |
|
|
double sigma; |
25 |
|
|
double dipole; |
26 |
|
|
int isDipole; |
27 |
|
|
int last; // 0 -> default |
28 |
|
|
// 1 -> tells nodes to stop listening |
29 |
|
|
// -1 -> an error has occured. (handled in mpiForceField) |
30 |
|
|
} atomStruct; |
31 |
|
|
MPI_Datatype mpiAtomStructType; |
32 |
|
|
|
33 |
mmeineke |
146 |
typedef struct{ |
34 |
|
|
char nameA[15]; |
35 |
|
|
char nameB[15]; |
36 |
|
|
char type[30]; |
37 |
|
|
double d0; |
38 |
|
|
int last; // 0 -> default |
39 |
|
|
// 1 -> tells nodes to stop listening |
40 |
|
|
// -1 -> an error has occured. (handled in mpiForceField) |
41 |
|
|
} bondStruct; |
42 |
|
|
MPI_Datatype mpiBondStructType; |
43 |
|
|
|
44 |
|
|
typedef struct{ |
45 |
|
|
char nameA[15]; |
46 |
|
|
char nameB[15]; |
47 |
|
|
char nameC[15]; |
48 |
|
|
char type[30]; |
49 |
|
|
double k1, k2, k3, t0; |
50 |
|
|
int last; // 0 -> default |
51 |
|
|
// 1 -> tells nodes to stop listening |
52 |
|
|
// -1 -> an error has occured. (handled in mpiForceField) |
53 |
|
|
} bendStruct; |
54 |
|
|
MPI_Datatype mpiBendStructType; |
55 |
|
|
|
56 |
|
|
typedef struct{ |
57 |
|
|
char nameA[15]; |
58 |
|
|
char nameB[15]; |
59 |
|
|
char nameC[15]; |
60 |
|
|
char nameD[15]; |
61 |
|
|
char type[30]; |
62 |
|
|
double k1, k2, k3, k4; |
63 |
|
|
int last; // 0 -> default |
64 |
|
|
// 1 -> tells nodes to stop listening |
65 |
|
|
// -1 -> an error has occured. (handled in mpiForceField) |
66 |
|
|
} TorsionStruct; |
67 |
|
|
MPI_Datatype mpiTorsionStructType; |
68 |
|
|
|
69 |
chuckv |
141 |
#endif |
70 |
|
|
|
71 |
|
|
|
72 |
|
|
|
73 |
mmeineke |
10 |
TraPPE_ExFF::TraPPE_ExFF(){ |
74 |
|
|
|
75 |
|
|
char fileName[200]; |
76 |
|
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
77 |
|
|
char* ffPath; |
78 |
|
|
char temp[200]; |
79 |
|
|
|
80 |
chuckv |
141 |
#ifdef IS_MPI |
81 |
|
|
int i; |
82 |
|
|
int mpiError; |
83 |
mmeineke |
147 |
|
84 |
chuckv |
141 |
mpiError = MPI_Comm_rank(MPI_COMM_WORLD,&myNode); |
85 |
mmeineke |
147 |
|
86 |
|
|
// ********************************************************************** |
87 |
|
|
// Init the atomStruct mpi type |
88 |
chuckv |
141 |
|
89 |
|
|
atomStruct atomProto; // mpiPrototype |
90 |
|
|
int atomBC[3] = {15,4,2}; // block counts |
91 |
|
|
MPI_Aint atomDspls[3]; // displacements |
92 |
|
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
93 |
|
|
|
94 |
chuckv |
137 |
|
95 |
|
|
|
96 |
chuckv |
141 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
97 |
|
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
98 |
|
|
MPI_Address(&atomProto.isDipole, &atomDspls[2]); |
99 |
mmeineke |
10 |
|
100 |
chuckv |
141 |
atomMbrTypes[0] = MPI_CHAR; |
101 |
|
|
atomMbrTypes[1] = MPI_DOUBLE; |
102 |
|
|
atomMbrTypes[2] = MPI_INT; |
103 |
mmeineke |
10 |
|
104 |
chuckv |
141 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
105 |
|
|
|
106 |
|
|
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
107 |
|
|
MPI_Type_commit(&mpiAtomStructType); |
108 |
mmeineke |
10 |
|
109 |
chuckv |
137 |
|
110 |
mmeineke |
147 |
// ********************************************************************** |
111 |
|
|
// Init the bondStruct mpi type |
112 |
|
|
|
113 |
|
|
bondStruct bondProto; // mpiPrototype |
114 |
|
|
int bondBC[3] = {60,1,1}; // block counts |
115 |
|
|
MPI_Aint bondDspls[3]; // displacements |
116 |
|
|
MPI_Datatype bondMbrTypes[3]; // member mpi types |
117 |
|
|
|
118 |
|
|
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
119 |
|
|
MPI_Address(&bondProto.d0, &bondDspls[1]); |
120 |
|
|
MPI_Address(&bondProto.last, &bondDspls[2]); |
121 |
|
|
|
122 |
|
|
bondMbrTypes[0] = MPI_CHAR; |
123 |
|
|
bondMbrTypes[1] = MPI_DOUBLE; |
124 |
|
|
bondMbrTypes[2] = MPI_INT; |
125 |
|
|
|
126 |
|
|
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
127 |
|
|
|
128 |
|
|
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
129 |
|
|
MPI_Type_commit(&mpiBondStructType); |
130 |
chuckv |
137 |
|
131 |
mmeineke |
10 |
|
132 |
mmeineke |
147 |
// ********************************************************************** |
133 |
|
|
// Init the bendStruct mpi type |
134 |
|
|
|
135 |
|
|
bendStruct bendProto; // mpiPrototype |
136 |
|
|
int bendBC[3] = {75,4,1}; // block counts |
137 |
|
|
MPI_Aint bendDspls[3]; // displacements |
138 |
|
|
MPI_Datatype bendMbrTypes[3]; // member mpi types |
139 |
|
|
|
140 |
|
|
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
141 |
|
|
MPI_Address(&bendProto.k1, &bendDspls[1]); |
142 |
|
|
MPI_Address(&bendProto.last, &bendDspls[2]); |
143 |
|
|
|
144 |
|
|
bendMbrTypes[0] = MPI_CHAR; |
145 |
|
|
bendMbrTypes[1] = MPI_DOUBLE; |
146 |
|
|
bendMbrTypes[2] = MPI_INT; |
147 |
|
|
|
148 |
|
|
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
149 |
|
|
|
150 |
|
|
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
151 |
|
|
MPI_Type_commit(&mpiBendStructType); |
152 |
|
|
|
153 |
|
|
|
154 |
|
|
// ********************************************************************** |
155 |
|
|
// Init the torsionStruct mpi type |
156 |
|
|
|
157 |
|
|
torsionStruct torsionProto; // mpiPrototype |
158 |
|
|
int torsionBC[3] = {90,4,1}; // block counts |
159 |
|
|
MPI_Aint torsionDspls[3]; // displacements |
160 |
|
|
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
161 |
|
|
|
162 |
|
|
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
163 |
|
|
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
164 |
|
|
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
165 |
|
|
|
166 |
|
|
torsionMbrTypes[0] = MPI_CHAR; |
167 |
|
|
torsionMbrTypes[1] = MPI_DOUBLE; |
168 |
|
|
torsionMbrTypes[2] = MPI_INT; |
169 |
|
|
|
170 |
|
|
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
171 |
|
|
|
172 |
|
|
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
173 |
|
|
&mpiTorsionStructType); |
174 |
|
|
MPI_Type_commit(&mpiTorsionStructType); |
175 |
|
|
|
176 |
|
|
// *********************************************************************** |
177 |
|
|
|
178 |
chuckv |
141 |
if( myNode == 0 ){ |
179 |
|
|
#endif |
180 |
|
|
|
181 |
|
|
// generate the force file name |
182 |
|
|
|
183 |
|
|
strcpy( fileName, "TraPPE_Ex.frc" ); |
184 |
|
|
fprintf( stderr,"Trying to open %s\n", fileName ); |
185 |
|
|
|
186 |
|
|
// attempt to open the file in the current directory first. |
187 |
|
|
|
188 |
mmeineke |
10 |
frcFile = fopen( fileName, "r" ); |
189 |
|
|
|
190 |
|
|
if( frcFile == NULL ){ |
191 |
|
|
|
192 |
chuckv |
141 |
// next see if the force path enviorment variable is set |
193 |
|
|
|
194 |
|
|
ffPath = getenv( ffPath_env ); |
195 |
|
|
if( ffPath == NULL ) { |
196 |
|
|
fprintf( stderr, |
197 |
|
|
"Error opening the force field parameter file: %s\n" |
198 |
|
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
199 |
|
|
"vairable?\n", |
200 |
|
|
fileName ); |
201 |
|
|
exit( 8 ); |
202 |
|
|
} |
203 |
|
|
|
204 |
|
|
|
205 |
|
|
strcpy( temp, ffPath ); |
206 |
|
|
strcat( temp, "/" ); |
207 |
|
|
strcat( temp, fileName ); |
208 |
|
|
strcpy( fileName, temp ); |
209 |
|
|
|
210 |
|
|
frcFile = fopen( fileName, "r" ); |
211 |
|
|
|
212 |
|
|
if( frcFile == NULL ){ |
213 |
|
|
|
214 |
|
|
fprintf( stderr, |
215 |
|
|
"Error opening the force field parameter file: %s\n" |
216 |
|
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
217 |
|
|
"vairable?\n", |
218 |
|
|
fileName ); |
219 |
|
|
exit( 8 ); |
220 |
|
|
} |
221 |
mmeineke |
10 |
} |
222 |
chuckv |
141 |
#ifdef IS_MPI |
223 |
mmeineke |
10 |
} |
224 |
chuckv |
141 |
#endif |
225 |
mmeineke |
10 |
} |
226 |
|
|
|
227 |
chuckv |
141 |
|
228 |
mmeineke |
10 |
TraPPE_ExFF::~TraPPE_ExFF(){ |
229 |
|
|
|
230 |
|
|
fclose( frcFile ); |
231 |
|
|
} |
232 |
|
|
|
233 |
|
|
void TraPPE_ExFF::initializeAtoms( void ){ |
234 |
|
|
|
235 |
|
|
class LinkedType { |
236 |
|
|
public: |
237 |
|
|
LinkedType(){ |
238 |
|
|
next = NULL; |
239 |
|
|
name[0] = '\0'; |
240 |
|
|
} |
241 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
242 |
|
|
|
243 |
|
|
LinkedType* find(char* key){ |
244 |
|
|
if( !strcmp(name, key) ) return this; |
245 |
|
|
if( next != NULL ) return next->find(key); |
246 |
|
|
return NULL; |
247 |
|
|
} |
248 |
|
|
|
249 |
chuckv |
141 |
#ifdef IS_MPI |
250 |
|
|
void add( atomStruct &info ){ |
251 |
|
|
if( next != NULL ) next->add(info); |
252 |
|
|
else{ |
253 |
|
|
next = new LinkedType(); |
254 |
|
|
strcpy(next->name, info.name); |
255 |
|
|
next->isDipole = info.dipole; |
256 |
|
|
next->mass = info.mass; |
257 |
|
|
next->epslon = info.epslon; |
258 |
|
|
next->sigma = info.sigma; |
259 |
|
|
next->dipole = info.dipole; |
260 |
|
|
} |
261 |
|
|
} |
262 |
|
|
|
263 |
|
|
void duplicate( atomStruct &info ){ |
264 |
|
|
strcpy(info.name, name); |
265 |
|
|
info.isDipole = dipole; |
266 |
|
|
info.mass = mass; |
267 |
|
|
info.epslon = epslon; |
268 |
|
|
info.sigma = sigma; |
269 |
|
|
info.dipole = dipole; |
270 |
|
|
info.last = 0; |
271 |
|
|
} |
272 |
|
|
|
273 |
|
|
|
274 |
|
|
#endif |
275 |
|
|
|
276 |
mmeineke |
10 |
char name[15]; |
277 |
|
|
int isDipole; |
278 |
|
|
double mass; |
279 |
|
|
double epslon; |
280 |
|
|
double sigma; |
281 |
|
|
double dipole; |
282 |
|
|
LinkedType* next; |
283 |
|
|
}; |
284 |
|
|
|
285 |
|
|
LinkedType* headAtomType; |
286 |
|
|
LinkedType* currentAtomType; |
287 |
|
|
LinkedType* tempAtomType; |
288 |
|
|
|
289 |
|
|
char readLine[500]; |
290 |
|
|
char* the_token; |
291 |
|
|
char* eof_test; |
292 |
|
|
int foundAtom = 0; |
293 |
|
|
int lineNum = 0; |
294 |
|
|
int i; |
295 |
|
|
|
296 |
|
|
////////////////////////////////////////////////// |
297 |
|
|
// a quick water fix |
298 |
|
|
|
299 |
|
|
double waterI[3][3]; |
300 |
|
|
waterI[0][0] = 1.76958347772500; |
301 |
|
|
waterI[0][1] = 0.0; |
302 |
|
|
waterI[0][2] = 0.0; |
303 |
|
|
|
304 |
|
|
waterI[1][0] = 0.0; |
305 |
|
|
waterI[1][1] = 0.614537057924513; |
306 |
|
|
waterI[1][2] = 0.0; |
307 |
|
|
|
308 |
|
|
waterI[2][0] = 0.0; |
309 |
|
|
waterI[2][1] = 0.0; |
310 |
|
|
waterI[2][2] = 1.15504641980049; |
311 |
|
|
|
312 |
|
|
|
313 |
|
|
double headI[3][3]; |
314 |
|
|
headI[0][0] = 1125; |
315 |
|
|
headI[0][1] = 0.0; |
316 |
|
|
headI[0][2] = 0.0; |
317 |
|
|
|
318 |
|
|
headI[1][0] = 0.0; |
319 |
|
|
headI[1][1] = 1125; |
320 |
|
|
headI[1][2] = 0.0; |
321 |
|
|
|
322 |
|
|
headI[2][0] = 0.0; |
323 |
|
|
headI[2][1] = 0.0; |
324 |
|
|
headI[2][2] = 250; |
325 |
|
|
|
326 |
|
|
|
327 |
|
|
|
328 |
|
|
////////////////////////////////////////////////// |
329 |
|
|
|
330 |
|
|
Atom** the_atoms; |
331 |
|
|
int nAtoms; |
332 |
|
|
the_atoms = entry_plug->atoms; |
333 |
|
|
nAtoms = entry_plug->n_atoms; |
334 |
|
|
|
335 |
|
|
|
336 |
mmeineke |
147 |
#ifdef IS_MPI |
337 |
|
|
if( myNode == 0 ){ |
338 |
|
|
#endif |
339 |
|
|
|
340 |
|
|
// read in the atom types. |
341 |
|
|
|
342 |
|
|
rewind( frcFile ); |
343 |
|
|
headAtomType = new LinkedType; |
344 |
|
|
currentAtomType = headAtomType; |
345 |
|
|
|
346 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
347 |
|
|
lineNum++; |
348 |
mmeineke |
10 |
if( eof_test == NULL ){ |
349 |
mmeineke |
147 |
fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
350 |
mmeineke |
10 |
exit(8); |
351 |
|
|
} |
352 |
|
|
|
353 |
mmeineke |
147 |
|
354 |
|
|
while( !foundAtom ){ |
355 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
356 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
357 |
|
|
lineNum++; |
358 |
|
|
} |
359 |
mmeineke |
10 |
if( eof_test == NULL ){ |
360 |
|
|
fprintf( stderr, |
361 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
362 |
|
|
lineNum ); |
363 |
|
|
exit(8); |
364 |
mmeineke |
147 |
} |
365 |
|
|
|
366 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
367 |
|
|
foundAtom = !strcmp( "AtomTypes", the_token ); |
368 |
|
|
|
369 |
|
|
if( !foundAtom ){ |
370 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
371 |
|
|
lineNum++; |
372 |
|
|
|
373 |
|
|
if( eof_test == NULL ){ |
374 |
|
|
fprintf( stderr, |
375 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
376 |
|
|
lineNum ); |
377 |
|
|
exit(8); |
378 |
|
|
} |
379 |
|
|
} |
380 |
mmeineke |
10 |
} |
381 |
|
|
|
382 |
mmeineke |
147 |
// we are now at the AtomTypes section. |
383 |
|
|
|
384 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
385 |
|
|
lineNum++; |
386 |
|
|
|
387 |
|
|
if( eof_test == NULL ){ |
388 |
|
|
fprintf( stderr, |
389 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
390 |
|
|
lineNum ); |
391 |
|
|
exit(8); |
392 |
|
|
} |
393 |
|
|
|
394 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
395 |
mmeineke |
10 |
|
396 |
mmeineke |
147 |
if( readLine[0] != '!' ){ |
397 |
mmeineke |
10 |
|
398 |
mmeineke |
147 |
the_token = strtok( readLine, " \n\t,;" ); |
399 |
|
|
if( the_token != NULL ){ |
400 |
|
|
|
401 |
|
|
strcpy( currentAtomType->name, the_token ); |
402 |
|
|
|
403 |
mmeineke |
10 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
404 |
|
|
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
405 |
|
|
exit(8); |
406 |
|
|
} |
407 |
|
|
|
408 |
mmeineke |
147 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
409 |
|
|
|
410 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
411 |
|
|
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
412 |
|
|
exit(8); |
413 |
|
|
} |
414 |
|
|
|
415 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
416 |
|
|
|
417 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
418 |
|
|
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
419 |
|
|
exit(8); |
420 |
|
|
} |
421 |
|
|
|
422 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
423 |
|
|
|
424 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
425 |
|
|
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
426 |
|
|
exit(8); |
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
430 |
|
|
|
431 |
|
|
if( currentAtomType->isDipole ){ |
432 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
433 |
|
|
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
434 |
|
|
exit(8); |
435 |
|
|
} |
436 |
|
|
|
437 |
|
|
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
438 |
|
|
} |
439 |
mmeineke |
10 |
} |
440 |
|
|
} |
441 |
mmeineke |
147 |
|
442 |
|
|
tempAtomType = new LinkedType; |
443 |
|
|
currentAtomType->next = tempAtomType; |
444 |
|
|
currentAtomType = tempAtomType; |
445 |
|
|
|
446 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
447 |
|
|
lineNum++; |
448 |
mmeineke |
10 |
} |
449 |
mmeineke |
147 |
|
450 |
|
|
#ifdef IS_MPI |
451 |
|
|
} |
452 |
|
|
|
453 |
|
|
else{ |
454 |
mmeineke |
10 |
|
455 |
mmeineke |
147 |
// listen for the structs |
456 |
mmeineke |
10 |
|
457 |
|
|
} |
458 |
mmeineke |
147 |
#endif |
459 |
mmeineke |
10 |
|
460 |
|
|
|
461 |
|
|
// initialize the atoms |
462 |
|
|
|
463 |
|
|
DirectionalAtom* dAtom; |
464 |
|
|
|
465 |
|
|
for( i=0; i<nAtoms; i++ ){ |
466 |
|
|
|
467 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
468 |
|
|
if( currentAtomType == NULL ){ |
469 |
|
|
fprintf( stderr, "AtomType error, %s not found in force file.\n", |
470 |
|
|
the_atoms[i]->getType() ); |
471 |
|
|
exit(8); |
472 |
|
|
} |
473 |
|
|
|
474 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
475 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
476 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
477 |
|
|
the_atoms[i]->setLJ(); |
478 |
|
|
|
479 |
|
|
if( currentAtomType->isDipole ){ |
480 |
|
|
if( the_atoms[i]->isDirectional() ){ |
481 |
|
|
|
482 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
483 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
484 |
|
|
dAtom->setHasDipole( 1 ); |
485 |
|
|
dAtom->setJx( 0.0 ); |
486 |
|
|
dAtom->setJy( 0.0 ); |
487 |
|
|
dAtom->setJz( 0.0 ); |
488 |
|
|
|
489 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
490 |
|
|
dAtom->setI( waterI ); |
491 |
|
|
dAtom->setSSD( 1 ); |
492 |
|
|
} |
493 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
494 |
|
|
dAtom->setI( headI ); |
495 |
|
|
dAtom->setSSD( 0 ); |
496 |
|
|
} |
497 |
|
|
else{ |
498 |
|
|
fprintf(stderr, |
499 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
500 |
|
|
the_atoms[i]->getType() ); |
501 |
|
|
exit(8); |
502 |
|
|
} |
503 |
|
|
entry_plug->n_dipoles++; |
504 |
|
|
} |
505 |
|
|
else{ |
506 |
|
|
std::cerr |
507 |
|
|
<< "TraPPE_ExFF error: Atom \"" |
508 |
|
|
<< currentAtomType->name << "\" is a dipole, yet no standard" |
509 |
|
|
<< " orientation was specifed in the BASS file.\n"; |
510 |
|
|
exit(8); |
511 |
|
|
} |
512 |
|
|
} |
513 |
|
|
else{ |
514 |
|
|
if( the_atoms[i]->isDirectional() ){ |
515 |
|
|
std::cerr |
516 |
|
|
<< "TraPPE_ExFF error: Atom \"" |
517 |
|
|
<< currentAtomType->name << "\" was given a standard orientation" |
518 |
|
|
<< " in the BASS file, yet it is not a dipole.\n"; |
519 |
|
|
exit(8); |
520 |
|
|
} |
521 |
|
|
} |
522 |
|
|
} |
523 |
|
|
|
524 |
|
|
|
525 |
|
|
// clean up the memory |
526 |
|
|
|
527 |
|
|
delete headAtomType; |
528 |
|
|
} |
529 |
|
|
|
530 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
531 |
|
|
|
532 |
|
|
class LinkedType { |
533 |
|
|
public: |
534 |
|
|
LinkedType(){ |
535 |
|
|
next = NULL; |
536 |
|
|
nameA[0] = '\0'; |
537 |
|
|
nameB[0] = '\0'; |
538 |
|
|
type[0] = '\0'; |
539 |
|
|
} |
540 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
541 |
|
|
|
542 |
|
|
LinkedType* find(char* key1, char* key2){ |
543 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
544 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
545 |
|
|
if( next != NULL ) return next->find(key1, key2); |
546 |
|
|
return NULL; |
547 |
|
|
} |
548 |
|
|
|
549 |
mmeineke |
146 |
#ifdef IS_MPI |
550 |
|
|
void add( bondStruct &info ){ |
551 |
|
|
if( next != NULL ) next->add(info); |
552 |
|
|
else{ |
553 |
|
|
next = new LinkedType(); |
554 |
|
|
strcpy(next->nameA, info.nameA); |
555 |
|
|
strcpy(next->nameB, info.nameB); |
556 |
|
|
strcpy(next->type, info.type); |
557 |
|
|
next->d0 = info.d0; |
558 |
|
|
} |
559 |
|
|
} |
560 |
|
|
|
561 |
|
|
void duplicate( bondStruct &info ){ |
562 |
|
|
strcpy(info.nameA, nameA); |
563 |
|
|
strcpy(info.nameB, nameB); |
564 |
|
|
strcpy(info.type, type); |
565 |
|
|
info.d0 = d0; |
566 |
|
|
info.last = 0; |
567 |
|
|
} |
568 |
|
|
|
569 |
|
|
|
570 |
|
|
#endif |
571 |
|
|
|
572 |
mmeineke |
10 |
char nameA[15]; |
573 |
|
|
char nameB[15]; |
574 |
|
|
char type[30]; |
575 |
|
|
double d0; |
576 |
|
|
|
577 |
|
|
LinkedType* next; |
578 |
|
|
}; |
579 |
|
|
|
580 |
|
|
|
581 |
|
|
|
582 |
|
|
LinkedType* headBondType; |
583 |
|
|
LinkedType* currentBondType; |
584 |
|
|
LinkedType* tempBondType; |
585 |
|
|
|
586 |
|
|
char readLine[500]; |
587 |
|
|
char* the_token; |
588 |
|
|
char* eof_test; |
589 |
|
|
int foundBond = 0; |
590 |
|
|
int lineNum = 0; |
591 |
|
|
int i, a, b; |
592 |
|
|
char* atomA; |
593 |
|
|
char* atomB; |
594 |
|
|
|
595 |
|
|
SRI **the_sris; |
596 |
|
|
Atom** the_atoms; |
597 |
|
|
int nBonds; |
598 |
|
|
the_sris = entry_plug->sr_interactions; |
599 |
|
|
the_atoms = entry_plug->atoms; |
600 |
|
|
nBonds = entry_plug->n_bonds; |
601 |
|
|
|
602 |
|
|
// read in the bond types. |
603 |
|
|
|
604 |
|
|
rewind( frcFile ); |
605 |
|
|
headBondType = new LinkedType; |
606 |
|
|
currentBondType = headBondType; |
607 |
|
|
|
608 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
609 |
|
|
lineNum++; |
610 |
|
|
if( eof_test == NULL ){ |
611 |
|
|
fprintf( stderr, "Error in reading Bonds from force file.\n" ); |
612 |
|
|
exit(8); |
613 |
|
|
} |
614 |
|
|
|
615 |
|
|
|
616 |
|
|
while( !foundBond ){ |
617 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
618 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
619 |
|
|
lineNum++; |
620 |
|
|
} |
621 |
|
|
if( eof_test == NULL ){ |
622 |
|
|
fprintf( stderr, |
623 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
624 |
|
|
lineNum ); |
625 |
|
|
exit(8); |
626 |
|
|
} |
627 |
|
|
|
628 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
629 |
|
|
foundBond = !strcmp( "BondTypes", the_token ); |
630 |
|
|
|
631 |
|
|
if( !foundBond ){ |
632 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
633 |
|
|
lineNum++; |
634 |
|
|
|
635 |
|
|
if( eof_test == NULL ){ |
636 |
|
|
fprintf( stderr, |
637 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
638 |
|
|
lineNum ); |
639 |
|
|
exit(8); |
640 |
|
|
} |
641 |
|
|
} |
642 |
|
|
} |
643 |
|
|
|
644 |
|
|
// we are now at the BondTypes section. |
645 |
|
|
|
646 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
647 |
|
|
lineNum++; |
648 |
|
|
|
649 |
|
|
if( eof_test == NULL ){ |
650 |
|
|
fprintf( stderr, |
651 |
|
|
"Error in reading Bonds from force file at line %d.\n", |
652 |
|
|
lineNum ); |
653 |
|
|
exit(8); |
654 |
|
|
} |
655 |
|
|
|
656 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
657 |
|
|
|
658 |
|
|
if( readLine[0] != '!' ){ |
659 |
|
|
|
660 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
661 |
|
|
if( the_token != NULL ){ |
662 |
|
|
|
663 |
|
|
strcpy( currentBondType->nameA, the_token ); |
664 |
|
|
|
665 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
666 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
667 |
|
|
exit(8); |
668 |
|
|
} |
669 |
|
|
|
670 |
|
|
strcpy( currentBondType->nameB, the_token ); |
671 |
|
|
|
672 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
673 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
674 |
|
|
exit(8); |
675 |
|
|
} |
676 |
|
|
|
677 |
|
|
strcpy( currentBondType->type, the_token ); |
678 |
|
|
|
679 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
680 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
681 |
|
|
fprintf( stderr, "Error parseing BondTypes: line %d\n", lineNum ); |
682 |
|
|
exit(8); |
683 |
|
|
} |
684 |
|
|
|
685 |
|
|
sscanf( the_token, "%lf", ¤tBondType->d0 ); |
686 |
|
|
} |
687 |
|
|
|
688 |
|
|
else{ |
689 |
|
|
fprintf(stderr, |
690 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
691 |
|
|
currentBondType->type, |
692 |
|
|
lineNum ); |
693 |
|
|
exit(8); |
694 |
|
|
} |
695 |
|
|
} |
696 |
|
|
} |
697 |
|
|
|
698 |
|
|
tempBondType = new LinkedType; |
699 |
|
|
currentBondType->next = tempBondType; |
700 |
|
|
currentBondType = tempBondType; |
701 |
|
|
|
702 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
703 |
|
|
lineNum++; |
704 |
|
|
} |
705 |
|
|
|
706 |
|
|
|
707 |
|
|
// initialize the Bonds |
708 |
|
|
|
709 |
|
|
|
710 |
|
|
for( i=0; i<nBonds; i++ ){ |
711 |
|
|
|
712 |
|
|
a = the_bonds[i].a; |
713 |
|
|
b = the_bonds[i].b; |
714 |
|
|
|
715 |
|
|
atomA = the_atoms[a]->getType(); |
716 |
|
|
atomB = the_atoms[b]->getType(); |
717 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
718 |
|
|
if( currentBondType == NULL ){ |
719 |
|
|
fprintf( stderr, "BondType error, %s - %s not found in force file.\n", |
720 |
|
|
atomA, atomB ); |
721 |
|
|
exit(8); |
722 |
|
|
} |
723 |
|
|
|
724 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
725 |
|
|
|
726 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
727 |
|
|
*the_atoms[b], |
728 |
|
|
currentBondType->d0 ); |
729 |
|
|
entry_plug->n_constraints++; |
730 |
|
|
} |
731 |
|
|
} |
732 |
|
|
|
733 |
|
|
|
734 |
|
|
// clean up the memory |
735 |
|
|
|
736 |
|
|
delete headBondType; |
737 |
|
|
|
738 |
|
|
} |
739 |
|
|
|
740 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
741 |
|
|
|
742 |
|
|
class LinkedType { |
743 |
|
|
public: |
744 |
|
|
LinkedType(){ |
745 |
|
|
next = NULL; |
746 |
|
|
nameA[0] = '\0'; |
747 |
|
|
nameB[0] = '\0'; |
748 |
|
|
nameC[0] = '\0'; |
749 |
|
|
type[0] = '\0'; |
750 |
|
|
} |
751 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
752 |
|
|
|
753 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
754 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
755 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
756 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
757 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
758 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
759 |
|
|
return NULL; |
760 |
|
|
} |
761 |
|
|
|
762 |
mmeineke |
146 |
#ifdef IS_MPI |
763 |
|
|
|
764 |
|
|
void add( bendStruct &info ){ |
765 |
|
|
if( next != NULL ) next->add(info); |
766 |
|
|
else{ |
767 |
|
|
next = new LinkedType(); |
768 |
|
|
strcpy(next->nameA, info.nameA); |
769 |
|
|
strcpy(next->nameB, info.nameB); |
770 |
|
|
strcpy(next->nameC, info.nameC); |
771 |
|
|
strcpy(next->type, info.type); |
772 |
|
|
next->k1 = info.k1; |
773 |
|
|
next->k2 = info.k2; |
774 |
|
|
next->k3 = info.k3; |
775 |
|
|
next->t0 = info.t0; |
776 |
|
|
} |
777 |
|
|
} |
778 |
|
|
|
779 |
|
|
void duplicate( bendStruct &info ){ |
780 |
|
|
strcpy(info.nameA, nameA); |
781 |
|
|
strcpy(info.nameB, nameB); |
782 |
|
|
strcpy(info.nameC, nameC); |
783 |
|
|
strcpy(info.type, type); |
784 |
|
|
info.k1 = k1; |
785 |
|
|
info.k2 = k2; |
786 |
|
|
info.k3 = k3; |
787 |
|
|
info.t0 = t0; |
788 |
|
|
info.last = 0; |
789 |
|
|
} |
790 |
|
|
|
791 |
|
|
#endif |
792 |
|
|
|
793 |
mmeineke |
10 |
char nameA[15]; |
794 |
|
|
char nameB[15]; |
795 |
|
|
char nameC[15]; |
796 |
|
|
char type[30]; |
797 |
|
|
double k1, k2, k3, t0; |
798 |
|
|
|
799 |
|
|
LinkedType* next; |
800 |
|
|
}; |
801 |
|
|
|
802 |
|
|
LinkedType* headBendType; |
803 |
|
|
LinkedType* currentBendType; |
804 |
|
|
LinkedType* tempBendType; |
805 |
|
|
|
806 |
|
|
char readLine[500]; |
807 |
|
|
char* the_token; |
808 |
|
|
char* eof_test; |
809 |
|
|
int foundBend = 0; |
810 |
|
|
int lineNum = 0; |
811 |
|
|
int i, a, b, c, index; |
812 |
|
|
char* atomA; |
813 |
|
|
char* atomB; |
814 |
|
|
char* atomC; |
815 |
|
|
QuadraticBend* qBend; |
816 |
|
|
|
817 |
|
|
SRI **the_sris; |
818 |
|
|
Atom** the_atoms; |
819 |
|
|
int nBends; |
820 |
|
|
the_sris = entry_plug->sr_interactions; |
821 |
|
|
the_atoms = entry_plug->atoms; |
822 |
|
|
nBends = entry_plug->n_bends; |
823 |
|
|
|
824 |
|
|
// read in the bend types. |
825 |
|
|
|
826 |
|
|
rewind( frcFile ); |
827 |
|
|
headBendType = new LinkedType; |
828 |
|
|
currentBendType = headBendType; |
829 |
|
|
|
830 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
831 |
|
|
lineNum++; |
832 |
|
|
if( eof_test == NULL ){ |
833 |
|
|
fprintf( stderr, "Error in reading Bends from force file.\n" ); |
834 |
|
|
exit(8); |
835 |
|
|
} |
836 |
|
|
|
837 |
|
|
|
838 |
|
|
while( !foundBend ){ |
839 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
840 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
841 |
|
|
lineNum++; |
842 |
|
|
} |
843 |
|
|
if( eof_test == NULL ){ |
844 |
|
|
fprintf( stderr, |
845 |
|
|
"Error in reading Bends from force file at line %d.\n", |
846 |
|
|
lineNum ); |
847 |
|
|
exit(8); |
848 |
|
|
} |
849 |
|
|
|
850 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
851 |
|
|
foundBend = !strcmp( "BendTypes", the_token ); |
852 |
|
|
|
853 |
|
|
if( !foundBend ){ |
854 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
855 |
|
|
lineNum++; |
856 |
|
|
|
857 |
|
|
if( eof_test == NULL ){ |
858 |
|
|
fprintf( stderr, |
859 |
|
|
"Error in reading Bends from force file at line %d.\n", |
860 |
|
|
lineNum ); |
861 |
|
|
exit(8); |
862 |
|
|
} |
863 |
|
|
} |
864 |
|
|
} |
865 |
|
|
|
866 |
|
|
// we are now at the BendTypes section. |
867 |
|
|
|
868 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
869 |
|
|
lineNum++; |
870 |
|
|
|
871 |
|
|
if( eof_test == NULL ){ |
872 |
|
|
fprintf( stderr, |
873 |
|
|
"Error in reading Bends from force file at line %d.\n", |
874 |
|
|
lineNum ); |
875 |
|
|
exit(8); |
876 |
|
|
} |
877 |
|
|
|
878 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
879 |
|
|
|
880 |
|
|
if( readLine[0] != '!' ){ |
881 |
|
|
|
882 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
883 |
|
|
if( the_token != NULL ){ |
884 |
|
|
|
885 |
|
|
strcpy( currentBendType->nameA, the_token ); |
886 |
|
|
|
887 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
888 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
889 |
|
|
exit(8); |
890 |
|
|
} |
891 |
|
|
|
892 |
|
|
strcpy( currentBendType->nameB, the_token ); |
893 |
|
|
|
894 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
895 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
896 |
|
|
exit(8); |
897 |
|
|
} |
898 |
|
|
|
899 |
|
|
strcpy( currentBendType->nameC, the_token ); |
900 |
|
|
|
901 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
902 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
903 |
|
|
exit(8); |
904 |
|
|
} |
905 |
|
|
|
906 |
|
|
strcpy( currentBendType->type, the_token ); |
907 |
|
|
|
908 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
909 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
910 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
911 |
|
|
exit(8); |
912 |
|
|
} |
913 |
|
|
|
914 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k1 ); |
915 |
|
|
|
916 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
917 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
918 |
|
|
exit(8); |
919 |
|
|
} |
920 |
|
|
|
921 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k2 ); |
922 |
|
|
|
923 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
924 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
925 |
|
|
exit(8); |
926 |
|
|
} |
927 |
|
|
|
928 |
|
|
sscanf( the_token, "%lf", ¤tBendType->k3 ); |
929 |
|
|
|
930 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
931 |
|
|
fprintf( stderr, "Error parseing BendTypes: line %d\n", lineNum ); |
932 |
|
|
exit(8); |
933 |
|
|
} |
934 |
|
|
|
935 |
|
|
sscanf( the_token, "%lf", ¤tBendType->t0 ); |
936 |
|
|
} |
937 |
|
|
|
938 |
|
|
else{ |
939 |
|
|
fprintf(stderr, |
940 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
941 |
|
|
currentBendType->type, |
942 |
|
|
lineNum ); |
943 |
|
|
exit(8); |
944 |
|
|
} |
945 |
|
|
} |
946 |
|
|
} |
947 |
|
|
|
948 |
|
|
tempBendType = new LinkedType; |
949 |
|
|
currentBendType->next = tempBendType; |
950 |
|
|
currentBendType = tempBendType; |
951 |
|
|
|
952 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
953 |
|
|
lineNum++; |
954 |
|
|
} |
955 |
|
|
|
956 |
|
|
|
957 |
|
|
// initialize the Bends |
958 |
|
|
|
959 |
|
|
for( i=0; i<nBends; i++ ){ |
960 |
|
|
|
961 |
|
|
a = the_bends[i].a; |
962 |
|
|
b = the_bends[i].b; |
963 |
|
|
c = the_bends[i].c; |
964 |
|
|
|
965 |
|
|
atomA = the_atoms[a]->getType(); |
966 |
|
|
atomB = the_atoms[b]->getType(); |
967 |
|
|
atomC = the_atoms[c]->getType(); |
968 |
|
|
currentBendType = headBendType->find( atomA, atomB, atomC ); |
969 |
|
|
if( currentBendType == NULL ){ |
970 |
|
|
fprintf( stderr, "BendType error, %s - %s - %s not found" |
971 |
|
|
" in force file.\n", |
972 |
|
|
atomA, atomB, atomC ); |
973 |
|
|
exit(8); |
974 |
|
|
} |
975 |
|
|
|
976 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
977 |
|
|
|
978 |
|
|
index = i + entry_plug->n_bonds; |
979 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
980 |
|
|
*the_atoms[b], |
981 |
|
|
*the_atoms[c] ); |
982 |
|
|
qBend->setConstants( currentBendType->k1, |
983 |
|
|
currentBendType->k2, |
984 |
|
|
currentBendType->k3, |
985 |
|
|
currentBendType->t0 ); |
986 |
|
|
the_sris[index] = qBend; |
987 |
|
|
} |
988 |
|
|
} |
989 |
|
|
|
990 |
|
|
|
991 |
|
|
// clean up the memory |
992 |
|
|
|
993 |
|
|
delete headBendType; |
994 |
|
|
|
995 |
|
|
} |
996 |
|
|
|
997 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
998 |
|
|
|
999 |
|
|
class LinkedType { |
1000 |
|
|
public: |
1001 |
|
|
LinkedType(){ |
1002 |
|
|
next = NULL; |
1003 |
|
|
nameA[0] = '\0'; |
1004 |
|
|
nameB[0] = '\0'; |
1005 |
|
|
nameC[0] = '\0'; |
1006 |
|
|
type[0] = '\0'; |
1007 |
|
|
} |
1008 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1009 |
|
|
|
1010 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1011 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1012 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1013 |
|
|
|
1014 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1015 |
|
|
!strcmp( nameC, key2 ) && !strcmp( nameD, key4 ) ) return this; |
1016 |
|
|
|
1017 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1018 |
|
|
return NULL; |
1019 |
|
|
} |
1020 |
|
|
|
1021 |
mmeineke |
146 |
#ifdef IS_MPI |
1022 |
|
|
|
1023 |
|
|
void add( torsionStruct &info ){ |
1024 |
|
|
if( next != NULL ) next->add(info); |
1025 |
|
|
else{ |
1026 |
|
|
next = new LinkedType(); |
1027 |
|
|
strcpy(next->nameA, info.nameA); |
1028 |
|
|
strcpy(next->nameB, info.nameB); |
1029 |
|
|
strcpy(next->nameC, info.nameC); |
1030 |
|
|
strcpy(next->type, info.type); |
1031 |
|
|
next->k1 = info.k1; |
1032 |
|
|
next->k2 = info.k2; |
1033 |
|
|
next->k3 = info.k3; |
1034 |
|
|
next->k4 = info.k4; |
1035 |
|
|
} |
1036 |
|
|
} |
1037 |
|
|
|
1038 |
|
|
void duplicate( torsionStruct &info ){ |
1039 |
|
|
strcpy(info.nameA, nameA); |
1040 |
|
|
strcpy(info.nameB, nameB); |
1041 |
|
|
strcpy(info.nameC, nameC); |
1042 |
|
|
strcpy(info.nameD, nameD); |
1043 |
|
|
strcpy(info.type, type); |
1044 |
|
|
info.k1 = k1; |
1045 |
|
|
info.k2 = k2; |
1046 |
|
|
info.k3 = k3; |
1047 |
|
|
info.k4 = k4; |
1048 |
|
|
info.last = 0; |
1049 |
|
|
} |
1050 |
|
|
|
1051 |
|
|
#endif |
1052 |
|
|
|
1053 |
mmeineke |
10 |
char nameA[15]; |
1054 |
|
|
char nameB[15]; |
1055 |
|
|
char nameC[15]; |
1056 |
|
|
char nameD[15]; |
1057 |
|
|
char type[30]; |
1058 |
|
|
double k1, k2, k3, k4; |
1059 |
|
|
|
1060 |
|
|
LinkedType* next; |
1061 |
|
|
}; |
1062 |
|
|
|
1063 |
|
|
LinkedType* headTorsionType; |
1064 |
|
|
LinkedType* currentTorsionType; |
1065 |
|
|
LinkedType* tempTorsionType; |
1066 |
|
|
|
1067 |
|
|
char readLine[500]; |
1068 |
|
|
char* the_token; |
1069 |
|
|
char* eof_test; |
1070 |
|
|
int foundTorsion = 0; |
1071 |
|
|
int lineNum = 0; |
1072 |
|
|
int i, a, b, c, d, index; |
1073 |
|
|
char* atomA; |
1074 |
|
|
char* atomB; |
1075 |
|
|
char* atomC; |
1076 |
|
|
char* atomD; |
1077 |
|
|
CubicTorsion* cTors; |
1078 |
|
|
|
1079 |
|
|
SRI **the_sris; |
1080 |
|
|
Atom** the_atoms; |
1081 |
|
|
int nTorsions; |
1082 |
|
|
the_sris = entry_plug->sr_interactions; |
1083 |
|
|
the_atoms = entry_plug->atoms; |
1084 |
|
|
nTorsions = entry_plug->n_torsions; |
1085 |
|
|
|
1086 |
|
|
// read in the torsion types. |
1087 |
|
|
|
1088 |
|
|
rewind( frcFile ); |
1089 |
|
|
headTorsionType = new LinkedType; |
1090 |
|
|
currentTorsionType = headTorsionType; |
1091 |
|
|
|
1092 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1093 |
|
|
lineNum++; |
1094 |
|
|
if( eof_test == NULL ){ |
1095 |
|
|
fprintf( stderr, "Error in reading Torsions from force file.\n" ); |
1096 |
|
|
exit(8); |
1097 |
|
|
} |
1098 |
|
|
|
1099 |
|
|
|
1100 |
|
|
while( !foundTorsion ){ |
1101 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1102 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1103 |
|
|
lineNum++; |
1104 |
|
|
} |
1105 |
|
|
if( eof_test == NULL ){ |
1106 |
|
|
fprintf( stderr, |
1107 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1108 |
|
|
lineNum ); |
1109 |
|
|
exit(8); |
1110 |
|
|
} |
1111 |
|
|
|
1112 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1113 |
|
|
foundTorsion = !strcmp( "TorsionTypes", the_token ); |
1114 |
|
|
|
1115 |
|
|
if( !foundTorsion ){ |
1116 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1117 |
|
|
lineNum++; |
1118 |
|
|
|
1119 |
|
|
if( eof_test == NULL ){ |
1120 |
|
|
fprintf( stderr, |
1121 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1122 |
|
|
lineNum ); |
1123 |
|
|
exit(8); |
1124 |
|
|
} |
1125 |
|
|
} |
1126 |
|
|
} |
1127 |
|
|
|
1128 |
|
|
// we are now at the TorsionTypes section. |
1129 |
|
|
|
1130 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1131 |
|
|
lineNum++; |
1132 |
|
|
|
1133 |
|
|
if( eof_test == NULL ){ |
1134 |
|
|
fprintf( stderr, |
1135 |
|
|
"Error in reading Torsions from force file at line %d.\n", |
1136 |
|
|
lineNum ); |
1137 |
|
|
exit(8); |
1138 |
|
|
} |
1139 |
|
|
|
1140 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1141 |
|
|
|
1142 |
|
|
if( readLine[0] != '!' ){ |
1143 |
|
|
|
1144 |
|
|
the_token = strtok( readLine, " \n\t,;" ); |
1145 |
|
|
if( the_token != NULL ){ |
1146 |
|
|
|
1147 |
|
|
strcpy( currentTorsionType->nameA, the_token ); |
1148 |
|
|
|
1149 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1150 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1151 |
|
|
exit(8); |
1152 |
|
|
} |
1153 |
|
|
|
1154 |
|
|
strcpy( currentTorsionType->nameB, the_token ); |
1155 |
|
|
|
1156 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1157 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1158 |
|
|
exit(8); |
1159 |
|
|
} |
1160 |
|
|
|
1161 |
|
|
strcpy( currentTorsionType->nameC, the_token ); |
1162 |
|
|
|
1163 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1164 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1165 |
|
|
exit(8); |
1166 |
|
|
} |
1167 |
|
|
|
1168 |
|
|
strcpy( currentTorsionType->nameD, the_token ); |
1169 |
|
|
|
1170 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1171 |
|
|
fprintf( stderr, "Error parseing TorsionTypes: line %d\n", lineNum ); |
1172 |
|
|
exit(8); |
1173 |
|
|
} |
1174 |
|
|
|
1175 |
|
|
strcpy( currentTorsionType->type, the_token ); |
1176 |
|
|
|
1177 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1178 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1179 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1180 |
|
|
exit(8); |
1181 |
|
|
} |
1182 |
|
|
|
1183 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k1 ); |
1184 |
|
|
|
1185 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1186 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1187 |
|
|
exit(8); |
1188 |
|
|
} |
1189 |
|
|
|
1190 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k2 ); |
1191 |
|
|
|
1192 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1193 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1194 |
|
|
exit(8); |
1195 |
|
|
} |
1196 |
|
|
|
1197 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k3 ); |
1198 |
|
|
|
1199 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1200 |
|
|
fprintf(stderr,"Error parseing TorsionTypes: line %d\n", lineNum ); |
1201 |
|
|
exit(8); |
1202 |
|
|
} |
1203 |
|
|
|
1204 |
|
|
sscanf( the_token, "%lf", ¤tTorsionType->k4 ); |
1205 |
|
|
} |
1206 |
|
|
|
1207 |
|
|
else{ |
1208 |
|
|
fprintf(stderr, |
1209 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1210 |
|
|
currentTorsionType->type, |
1211 |
|
|
lineNum ); |
1212 |
|
|
exit(8); |
1213 |
|
|
} |
1214 |
|
|
} |
1215 |
|
|
} |
1216 |
|
|
|
1217 |
|
|
tempTorsionType = new LinkedType; |
1218 |
|
|
currentTorsionType->next = tempTorsionType; |
1219 |
|
|
currentTorsionType = tempTorsionType; |
1220 |
|
|
|
1221 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1222 |
|
|
lineNum++; |
1223 |
|
|
} |
1224 |
|
|
|
1225 |
|
|
|
1226 |
|
|
// initialize the Torsions |
1227 |
|
|
|
1228 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1229 |
|
|
|
1230 |
|
|
a = the_torsions[i].a; |
1231 |
|
|
b = the_torsions[i].b; |
1232 |
|
|
c = the_torsions[i].c; |
1233 |
|
|
d = the_torsions[i].d; |
1234 |
|
|
|
1235 |
|
|
atomA = the_atoms[a]->getType(); |
1236 |
|
|
atomB = the_atoms[b]->getType(); |
1237 |
|
|
atomC = the_atoms[c]->getType(); |
1238 |
|
|
atomD = the_atoms[d]->getType(); |
1239 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1240 |
|
|
if( currentTorsionType == NULL ){ |
1241 |
|
|
fprintf( stderr, "TorsionType error, %s - %s - %s - %s not found" |
1242 |
|
|
" in force file.\n", |
1243 |
|
|
atomA, atomB, atomC, atomD ); |
1244 |
|
|
exit(8); |
1245 |
|
|
} |
1246 |
|
|
|
1247 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1248 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1249 |
|
|
|
1250 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1251 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1252 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1253 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1254 |
|
|
the_sris[index] = cTors; |
1255 |
|
|
} |
1256 |
|
|
} |
1257 |
|
|
|
1258 |
|
|
|
1259 |
|
|
// clean up the memory |
1260 |
|
|
|
1261 |
|
|
delete headTorsionType; |
1262 |
|
|
|
1263 |
|
|
} |