1 |
mmeineke |
270 |
#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 |
|
|
#include "simError.h" |
11 |
|
|
|
12 |
mmeineke |
294 |
#include <fortranWrappers.hpp> |
13 |
|
|
|
14 |
mmeineke |
291 |
#ifdef IS_MPI |
15 |
|
|
#include "mpiForceField.h" |
16 |
|
|
#endif // is_mpi |
17 |
mmeineke |
270 |
|
18 |
mmeineke |
291 |
namespace TPE { // restrict the access of the folowing to this file only. |
19 |
|
|
|
20 |
|
|
|
21 |
|
|
// Declare the structures that will be passed by MPI |
22 |
|
|
|
23 |
|
|
typedef struct{ |
24 |
|
|
char name[15]; |
25 |
|
|
double mass; |
26 |
|
|
double epslon; |
27 |
|
|
double sigma; |
28 |
|
|
double dipole; |
29 |
|
|
double w0; |
30 |
|
|
double v0; |
31 |
|
|
int isSSD; |
32 |
|
|
int isDipole; |
33 |
|
|
int ident; |
34 |
|
|
int last; // 0 -> default |
35 |
|
|
// 1 -> tells nodes to stop listening |
36 |
|
|
} atomStruct; |
37 |
|
|
|
38 |
|
|
|
39 |
|
|
typedef struct{ |
40 |
|
|
char nameA[15]; |
41 |
|
|
char nameB[15]; |
42 |
|
|
char type[30]; |
43 |
|
|
double d0; |
44 |
|
|
int last; // 0 -> default |
45 |
|
|
// 1 -> tells nodes to stop listening |
46 |
|
|
} bondStruct; |
47 |
|
|
|
48 |
|
|
|
49 |
|
|
typedef struct{ |
50 |
|
|
char nameA[15]; |
51 |
|
|
char nameB[15]; |
52 |
|
|
char nameC[15]; |
53 |
|
|
char type[30]; |
54 |
|
|
double k1, k2, k3, t0; |
55 |
|
|
int last; // 0 -> default |
56 |
|
|
// 1 -> tells nodes to stop listening |
57 |
|
|
} bendStruct; |
58 |
|
|
|
59 |
|
|
|
60 |
|
|
typedef struct{ |
61 |
|
|
char nameA[15]; |
62 |
|
|
char nameB[15]; |
63 |
|
|
char nameC[15]; |
64 |
|
|
char nameD[15]; |
65 |
|
|
char type[30]; |
66 |
|
|
double k1, k2, k3, k4; |
67 |
|
|
int last; // 0 -> default |
68 |
|
|
// 1 -> tells nodes to stop listening |
69 |
|
|
} torsionStruct; |
70 |
|
|
|
71 |
|
|
|
72 |
|
|
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
73 |
|
|
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ); |
74 |
|
|
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ); |
75 |
|
|
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ); |
76 |
|
|
|
77 |
|
|
|
78 |
mmeineke |
270 |
#ifdef IS_MPI |
79 |
|
|
|
80 |
mmeineke |
291 |
MPI_Datatype mpiAtomStructType; |
81 |
|
|
MPI_Datatype mpiBondStructType; |
82 |
|
|
MPI_Datatype mpiBendStructType; |
83 |
|
|
MPI_Datatype mpiTorsionStructType; |
84 |
mmeineke |
270 |
|
85 |
mmeineke |
291 |
#endif |
86 |
mmeineke |
270 |
|
87 |
mmeineke |
291 |
} // namespace |
88 |
mmeineke |
270 |
|
89 |
mmeineke |
291 |
using namespace TPE; |
90 |
|
|
|
91 |
|
|
|
92 |
|
|
//**************************************************************** |
93 |
|
|
// begins the actual forcefield stuff. |
94 |
|
|
//**************************************************************** |
95 |
|
|
|
96 |
|
|
|
97 |
mmeineke |
270 |
TraPPE_ExFF::TraPPE_ExFF(){ |
98 |
|
|
|
99 |
|
|
char fileName[200]; |
100 |
|
|
char* ffPath_env = "FORCE_PARAM_PATH"; |
101 |
|
|
char* ffPath; |
102 |
|
|
char temp[200]; |
103 |
|
|
char errMsg[1000]; |
104 |
|
|
|
105 |
mmeineke |
291 |
// do the funtion wrapping |
106 |
mmeineke |
294 |
wrapMeFF( this ); |
107 |
mmeineke |
291 |
|
108 |
|
|
|
109 |
mmeineke |
270 |
#ifdef IS_MPI |
110 |
|
|
int i; |
111 |
|
|
|
112 |
mmeineke |
291 |
// ********************************************************************** |
113 |
mmeineke |
270 |
// Init the atomStruct mpi type |
114 |
|
|
|
115 |
|
|
atomStruct atomProto; // mpiPrototype |
116 |
mmeineke |
291 |
int atomBC[3] = {15,6,4}; // block counts |
117 |
mmeineke |
270 |
MPI_Aint atomDspls[3]; // displacements |
118 |
|
|
MPI_Datatype atomMbrTypes[3]; // member mpi types |
119 |
|
|
|
120 |
|
|
MPI_Address(&atomProto.name, &atomDspls[0]); |
121 |
|
|
MPI_Address(&atomProto.mass, &atomDspls[1]); |
122 |
mmeineke |
291 |
MPI_Address(&atomProto.isSSD, &atomDspls[2]); |
123 |
mmeineke |
270 |
|
124 |
|
|
atomMbrTypes[0] = MPI_CHAR; |
125 |
|
|
atomMbrTypes[1] = MPI_DOUBLE; |
126 |
|
|
atomMbrTypes[2] = MPI_INT; |
127 |
|
|
|
128 |
|
|
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
129 |
|
|
|
130 |
|
|
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
131 |
|
|
MPI_Type_commit(&mpiAtomStructType); |
132 |
|
|
|
133 |
|
|
|
134 |
|
|
// ********************************************************************** |
135 |
|
|
// Init the bondStruct mpi type |
136 |
|
|
|
137 |
|
|
bondStruct bondProto; // mpiPrototype |
138 |
|
|
int bondBC[3] = {60,1,1}; // block counts |
139 |
|
|
MPI_Aint bondDspls[3]; // displacements |
140 |
|
|
MPI_Datatype bondMbrTypes[3]; // member mpi types |
141 |
|
|
|
142 |
|
|
MPI_Address(&bondProto.nameA, &bondDspls[0]); |
143 |
|
|
MPI_Address(&bondProto.d0, &bondDspls[1]); |
144 |
|
|
MPI_Address(&bondProto.last, &bondDspls[2]); |
145 |
|
|
|
146 |
|
|
bondMbrTypes[0] = MPI_CHAR; |
147 |
|
|
bondMbrTypes[1] = MPI_DOUBLE; |
148 |
|
|
bondMbrTypes[2] = MPI_INT; |
149 |
|
|
|
150 |
|
|
for (i=2; i >= 0; i--) bondDspls[i] -= bondDspls[0]; |
151 |
|
|
|
152 |
|
|
MPI_Type_struct(3, bondBC, bondDspls, bondMbrTypes, &mpiBondStructType); |
153 |
|
|
MPI_Type_commit(&mpiBondStructType); |
154 |
|
|
|
155 |
|
|
|
156 |
|
|
// ********************************************************************** |
157 |
|
|
// Init the bendStruct mpi type |
158 |
|
|
|
159 |
|
|
bendStruct bendProto; // mpiPrototype |
160 |
|
|
int bendBC[3] = {75,4,1}; // block counts |
161 |
|
|
MPI_Aint bendDspls[3]; // displacements |
162 |
|
|
MPI_Datatype bendMbrTypes[3]; // member mpi types |
163 |
|
|
|
164 |
|
|
MPI_Address(&bendProto.nameA, &bendDspls[0]); |
165 |
|
|
MPI_Address(&bendProto.k1, &bendDspls[1]); |
166 |
|
|
MPI_Address(&bendProto.last, &bendDspls[2]); |
167 |
|
|
|
168 |
|
|
bendMbrTypes[0] = MPI_CHAR; |
169 |
|
|
bendMbrTypes[1] = MPI_DOUBLE; |
170 |
|
|
bendMbrTypes[2] = MPI_INT; |
171 |
|
|
|
172 |
|
|
for (i=2; i >= 0; i--) bendDspls[i] -= bendDspls[0]; |
173 |
|
|
|
174 |
|
|
MPI_Type_struct(3, bendBC, bendDspls, bendMbrTypes, &mpiBendStructType); |
175 |
|
|
MPI_Type_commit(&mpiBendStructType); |
176 |
|
|
|
177 |
|
|
|
178 |
|
|
// ********************************************************************** |
179 |
|
|
// Init the torsionStruct mpi type |
180 |
|
|
|
181 |
|
|
torsionStruct torsionProto; // mpiPrototype |
182 |
|
|
int torsionBC[3] = {90,4,1}; // block counts |
183 |
|
|
MPI_Aint torsionDspls[3]; // displacements |
184 |
|
|
MPI_Datatype torsionMbrTypes[3]; // member mpi types |
185 |
|
|
|
186 |
|
|
MPI_Address(&torsionProto.nameA, &torsionDspls[0]); |
187 |
|
|
MPI_Address(&torsionProto.k1, &torsionDspls[1]); |
188 |
|
|
MPI_Address(&torsionProto.last, &torsionDspls[2]); |
189 |
|
|
|
190 |
|
|
torsionMbrTypes[0] = MPI_CHAR; |
191 |
|
|
torsionMbrTypes[1] = MPI_DOUBLE; |
192 |
|
|
torsionMbrTypes[2] = MPI_INT; |
193 |
|
|
|
194 |
|
|
for (i=2; i >= 0; i--) torsionDspls[i] -= torsionDspls[0]; |
195 |
|
|
|
196 |
|
|
MPI_Type_struct(3, torsionBC, torsionDspls, torsionMbrTypes, |
197 |
|
|
&mpiTorsionStructType); |
198 |
|
|
MPI_Type_commit(&mpiTorsionStructType); |
199 |
|
|
|
200 |
|
|
// *********************************************************************** |
201 |
|
|
|
202 |
|
|
if( worldRank == 0 ){ |
203 |
|
|
#endif |
204 |
|
|
|
205 |
|
|
// generate the force file name |
206 |
|
|
|
207 |
|
|
strcpy( fileName, "TraPPE_Ex.frc" ); |
208 |
|
|
// fprintf( stderr,"Trying to open %s\n", fileName ); |
209 |
|
|
|
210 |
|
|
// attempt to open the file in the current directory first. |
211 |
|
|
|
212 |
|
|
frcFile = fopen( fileName, "r" ); |
213 |
|
|
|
214 |
|
|
if( frcFile == NULL ){ |
215 |
|
|
|
216 |
|
|
// next see if the force path enviorment variable is set |
217 |
|
|
|
218 |
|
|
ffPath = getenv( ffPath_env ); |
219 |
|
|
if( ffPath == NULL ) { |
220 |
mmeineke |
321 |
STR_DEFINE(ffPath, FRC_PATH ); |
221 |
mmeineke |
270 |
} |
222 |
|
|
|
223 |
|
|
|
224 |
|
|
strcpy( temp, ffPath ); |
225 |
|
|
strcat( temp, "/" ); |
226 |
|
|
strcat( temp, fileName ); |
227 |
|
|
strcpy( fileName, temp ); |
228 |
|
|
|
229 |
|
|
frcFile = fopen( fileName, "r" ); |
230 |
|
|
|
231 |
|
|
if( frcFile == NULL ){ |
232 |
|
|
|
233 |
|
|
sprintf( painCave.errMsg, |
234 |
|
|
"Error opening the force field parameter file: %s\n" |
235 |
|
|
"Have you tried setting the FORCE_PARAM_PATH environment " |
236 |
|
|
"vairable?\n", |
237 |
|
|
fileName ); |
238 |
|
|
painCave.isFatal = 1; |
239 |
|
|
simError(); |
240 |
|
|
} |
241 |
|
|
} |
242 |
|
|
|
243 |
|
|
#ifdef IS_MPI |
244 |
|
|
} |
245 |
|
|
|
246 |
|
|
sprintf( checkPointMsg, "TraPPE_ExFF file opened sucessfully." ); |
247 |
|
|
MPIcheckPoint(); |
248 |
|
|
|
249 |
|
|
#endif // is_mpi |
250 |
|
|
} |
251 |
|
|
|
252 |
|
|
|
253 |
|
|
TraPPE_ExFF::~TraPPE_ExFF(){ |
254 |
|
|
|
255 |
|
|
#ifdef IS_MPI |
256 |
|
|
if( worldRank == 0 ){ |
257 |
|
|
#endif // is_mpi |
258 |
|
|
|
259 |
|
|
fclose( frcFile ); |
260 |
|
|
|
261 |
|
|
#ifdef IS_MPI |
262 |
|
|
} |
263 |
|
|
#endif // is_mpi |
264 |
|
|
} |
265 |
|
|
|
266 |
mmeineke |
296 |
void TraPPE_ExFF::doForces( int calcPot ){ |
267 |
mmeineke |
291 |
|
268 |
mmeineke |
296 |
int i, isError; |
269 |
|
|
double* frc; |
270 |
|
|
double* pos; |
271 |
|
|
double* tau; |
272 |
|
|
short int passedCalcPot = (short int)calcPot; |
273 |
|
|
|
274 |
|
|
// forces are zeroed here, before any are acumulated. |
275 |
|
|
// NOTE: do not rezero the forces in Fortran. |
276 |
|
|
|
277 |
|
|
for(i=0; i<entry_plug->n_atoms; i++){ |
278 |
|
|
entry_plug->atoms[i]->zeroForces(); |
279 |
|
|
} |
280 |
|
|
|
281 |
|
|
frc = Atom::getFrcArray(); |
282 |
|
|
pos = Atom::getPosArray(); |
283 |
|
|
tau = entry_plug->tau; |
284 |
|
|
|
285 |
|
|
isError = 0; |
286 |
|
|
fortranForceLoop( pos, frc, &(entry_plug->lrPot), tau, |
287 |
|
|
&passedCalcPot, &isError ); |
288 |
|
|
|
289 |
|
|
|
290 |
|
|
if( isError ){ |
291 |
|
|
sprintf( painCave.errMsg, |
292 |
|
|
"Error returned from the fortran force calculation.\n" ); |
293 |
|
|
painCave.isFatal = 1; |
294 |
|
|
simError(); |
295 |
|
|
} |
296 |
|
|
|
297 |
|
|
#ifdef IS_MPI |
298 |
|
|
sprintf( checkPointMsg, |
299 |
|
|
"successfully returned from the force calculation.\n" ); |
300 |
|
|
MPIcheckPoint(); |
301 |
|
|
#endif // is_mpi |
302 |
|
|
|
303 |
|
|
} |
304 |
|
|
|
305 |
|
|
|
306 |
mmeineke |
270 |
void TraPPE_ExFF::initializeAtoms( void ){ |
307 |
|
|
|
308 |
|
|
class LinkedType { |
309 |
|
|
public: |
310 |
|
|
LinkedType(){ |
311 |
|
|
next = NULL; |
312 |
|
|
name[0] = '\0'; |
313 |
|
|
} |
314 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
315 |
|
|
|
316 |
|
|
LinkedType* find(char* key){ |
317 |
|
|
if( !strcmp(name, key) ) return this; |
318 |
|
|
if( next != NULL ) return next->find(key); |
319 |
|
|
return NULL; |
320 |
|
|
} |
321 |
|
|
|
322 |
|
|
void add( atomStruct &info ){ |
323 |
mmeineke |
291 |
|
324 |
|
|
// check for duplicates |
325 |
|
|
|
326 |
|
|
if( !strcmp( info.name, name ) ){ |
327 |
|
|
sprintf( painCave.errMsg, |
328 |
|
|
"Duplicate TraPPE_Ex atom type \"%s\" found in " |
329 |
|
|
"the TraPPE_ExFF param file./n", |
330 |
|
|
name ); |
331 |
|
|
painCave.isFatal = 1; |
332 |
|
|
simError(); |
333 |
|
|
} |
334 |
|
|
|
335 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
336 |
|
|
else{ |
337 |
|
|
next = new LinkedType(); |
338 |
|
|
strcpy(next->name, info.name); |
339 |
mmeineke |
291 |
next->isDipole = info.isDipole; |
340 |
|
|
next->isSSD = info.isSSD; |
341 |
mmeineke |
270 |
next->mass = info.mass; |
342 |
|
|
next->epslon = info.epslon; |
343 |
|
|
next->sigma = info.sigma; |
344 |
|
|
next->dipole = info.dipole; |
345 |
mmeineke |
291 |
next->w0 = info.w0; |
346 |
|
|
next->v0 = info.v0; |
347 |
|
|
next->ident = info.ident; |
348 |
mmeineke |
270 |
} |
349 |
|
|
} |
350 |
mmeineke |
291 |
|
351 |
|
|
#ifdef IS_MPI |
352 |
mmeineke |
270 |
|
353 |
|
|
void duplicate( atomStruct &info ){ |
354 |
|
|
strcpy(info.name, name); |
355 |
mmeineke |
291 |
info.isDipole = isDipole; |
356 |
|
|
info.isSSD = isSSD; |
357 |
mmeineke |
270 |
info.mass = mass; |
358 |
|
|
info.epslon = epslon; |
359 |
|
|
info.sigma = sigma; |
360 |
|
|
info.dipole = dipole; |
361 |
mmeineke |
291 |
info.w0 = w0; |
362 |
|
|
info.v0 = v0; |
363 |
mmeineke |
270 |
info.last = 0; |
364 |
|
|
} |
365 |
|
|
|
366 |
|
|
|
367 |
|
|
#endif |
368 |
|
|
|
369 |
|
|
char name[15]; |
370 |
|
|
int isDipole; |
371 |
mmeineke |
291 |
int isSSD; |
372 |
mmeineke |
270 |
double mass; |
373 |
|
|
double epslon; |
374 |
|
|
double sigma; |
375 |
|
|
double dipole; |
376 |
mmeineke |
291 |
double w0; |
377 |
|
|
double v0; |
378 |
|
|
int ident; |
379 |
mmeineke |
270 |
LinkedType* next; |
380 |
|
|
}; |
381 |
|
|
|
382 |
|
|
LinkedType* headAtomType; |
383 |
|
|
LinkedType* currentAtomType; |
384 |
|
|
atomStruct info; |
385 |
|
|
info.last = 1; // initialize last to have the last set. |
386 |
|
|
// if things go well, last will be set to 0 |
387 |
mmeineke |
291 |
|
388 |
mmeineke |
270 |
|
389 |
|
|
|
390 |
|
|
int i; |
391 |
mmeineke |
291 |
int identNum; |
392 |
mmeineke |
270 |
|
393 |
mmeineke |
291 |
Atom** the_atoms; |
394 |
|
|
int nAtoms; |
395 |
|
|
the_atoms = entry_plug->atoms; |
396 |
|
|
nAtoms = entry_plug->n_atoms; |
397 |
|
|
|
398 |
|
|
|
399 |
mmeineke |
270 |
////////////////////////////////////////////////// |
400 |
|
|
// a quick water fix |
401 |
|
|
|
402 |
|
|
double waterI[3][3]; |
403 |
|
|
waterI[0][0] = 1.76958347772500; |
404 |
|
|
waterI[0][1] = 0.0; |
405 |
|
|
waterI[0][2] = 0.0; |
406 |
|
|
|
407 |
|
|
waterI[1][0] = 0.0; |
408 |
|
|
waterI[1][1] = 0.614537057924513; |
409 |
|
|
waterI[1][2] = 0.0; |
410 |
|
|
|
411 |
|
|
waterI[2][0] = 0.0; |
412 |
|
|
waterI[2][1] = 0.0; |
413 |
|
|
waterI[2][2] = 1.15504641980049; |
414 |
|
|
|
415 |
|
|
|
416 |
|
|
double headI[3][3]; |
417 |
|
|
headI[0][0] = 1125; |
418 |
|
|
headI[0][1] = 0.0; |
419 |
|
|
headI[0][2] = 0.0; |
420 |
|
|
|
421 |
|
|
headI[1][0] = 0.0; |
422 |
|
|
headI[1][1] = 1125; |
423 |
|
|
headI[1][2] = 0.0; |
424 |
|
|
|
425 |
|
|
headI[2][0] = 0.0; |
426 |
|
|
headI[2][1] = 0.0; |
427 |
|
|
headI[2][2] = 250; |
428 |
|
|
|
429 |
|
|
|
430 |
|
|
|
431 |
|
|
////////////////////////////////////////////////// |
432 |
|
|
|
433 |
mmeineke |
291 |
|
434 |
mmeineke |
270 |
#ifdef IS_MPI |
435 |
|
|
if( worldRank == 0 ){ |
436 |
|
|
#endif |
437 |
|
|
|
438 |
|
|
// read in the atom types. |
439 |
mmeineke |
291 |
|
440 |
mmeineke |
270 |
headAtomType = new LinkedType; |
441 |
|
|
|
442 |
mmeineke |
291 |
fastForward( "AtomTypes", "initializeAtoms" ); |
443 |
|
|
|
444 |
mmeineke |
270 |
// we are now at the AtomTypes section. |
445 |
|
|
|
446 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
447 |
|
|
lineNum++; |
448 |
|
|
|
449 |
mmeineke |
291 |
|
450 |
|
|
// read a line, and start parseing out the atom types |
451 |
|
|
|
452 |
mmeineke |
270 |
if( eof_test == NULL ){ |
453 |
|
|
sprintf( painCave.errMsg, |
454 |
|
|
"Error in reading Atoms from force file at line %d.\n", |
455 |
|
|
lineNum ); |
456 |
|
|
painCave.isFatal = 1; |
457 |
|
|
simError(); |
458 |
|
|
} |
459 |
|
|
|
460 |
mmeineke |
291 |
identNum = 1; |
461 |
|
|
// stop reading at end of file, or at next section |
462 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
463 |
mmeineke |
291 |
|
464 |
|
|
// toss comment lines |
465 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
466 |
|
|
|
467 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
468 |
|
|
if( parseAtom( readLine, lineNum, info ) ){ |
469 |
|
|
info.ident = identNum; |
470 |
|
|
headAtomType->add( info );; |
471 |
|
|
identNum++; |
472 |
mmeineke |
270 |
} |
473 |
|
|
} |
474 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
475 |
|
|
lineNum++; |
476 |
|
|
} |
477 |
|
|
|
478 |
|
|
#ifdef IS_MPI |
479 |
|
|
|
480 |
|
|
// send out the linked list to all the other processes |
481 |
|
|
|
482 |
|
|
sprintf( checkPointMsg, |
483 |
mmeineke |
291 |
"TraPPE_ExFF atom structures read successfully." ); |
484 |
mmeineke |
270 |
MPIcheckPoint(); |
485 |
|
|
|
486 |
mmeineke |
291 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
487 |
mmeineke |
270 |
while( currentAtomType != NULL ){ |
488 |
|
|
currentAtomType->duplicate( info ); |
489 |
mmeineke |
291 |
|
490 |
|
|
|
491 |
|
|
|
492 |
mmeineke |
270 |
sendFrcStruct( &info, mpiAtomStructType ); |
493 |
mmeineke |
291 |
|
494 |
|
|
sprintf( checkPointMsg, |
495 |
|
|
"successfully sent TraPPE_Ex force type: \"%s\"\n", |
496 |
|
|
info.name ); |
497 |
|
|
MPIcheckPoint(); |
498 |
|
|
|
499 |
mmeineke |
270 |
currentAtomType = currentAtomType->next; |
500 |
|
|
} |
501 |
|
|
info.last = 1; |
502 |
|
|
sendFrcStruct( &info, mpiAtomStructType ); |
503 |
|
|
|
504 |
|
|
} |
505 |
|
|
|
506 |
|
|
else{ |
507 |
|
|
|
508 |
|
|
// listen for node 0 to send out the force params |
509 |
|
|
|
510 |
|
|
MPIcheckPoint(); |
511 |
|
|
|
512 |
|
|
headAtomType = new LinkedType; |
513 |
|
|
recieveFrcStruct( &info, mpiAtomStructType ); |
514 |
mmeineke |
291 |
|
515 |
mmeineke |
270 |
while( !info.last ){ |
516 |
|
|
|
517 |
mmeineke |
291 |
|
518 |
|
|
|
519 |
mmeineke |
270 |
headAtomType->add( info ); |
520 |
mmeineke |
291 |
|
521 |
|
|
MPIcheckPoint(); |
522 |
|
|
|
523 |
mmeineke |
270 |
recieveFrcStruct( &info, mpiAtomStructType ); |
524 |
|
|
} |
525 |
|
|
} |
526 |
|
|
#endif // is_mpi |
527 |
|
|
|
528 |
mmeineke |
291 |
// call new A_types in fortran |
529 |
mmeineke |
270 |
|
530 |
mmeineke |
291 |
int isError; |
531 |
mmeineke |
296 |
|
532 |
|
|
// dummy variables |
533 |
|
|
|
534 |
|
|
int isGB = 0; |
535 |
|
|
int isLJ = 1; |
536 |
|
|
|
537 |
|
|
|
538 |
mmeineke |
291 |
currentAtomType = headAtomType; |
539 |
|
|
while( currentAtomType != NULL ){ |
540 |
|
|
|
541 |
|
|
if( currentAtomType->name[0] != '\0' ){ |
542 |
|
|
isError = 0; |
543 |
|
|
newTPEtype( &(currentAtomType->ident), |
544 |
|
|
&(currentAtomType->mass), |
545 |
|
|
&(currentAtomType->epslon), |
546 |
|
|
&(currentAtomType->sigma), |
547 |
mmeineke |
296 |
&isLJ, |
548 |
|
|
&(currentAtomType->isSSD), |
549 |
mmeineke |
291 |
&(currentAtomType->isDipole), |
550 |
mmeineke |
296 |
&isGB, |
551 |
mmeineke |
291 |
&(currentAtomType->w0), |
552 |
|
|
&(currentAtomType->v0), |
553 |
mmeineke |
296 |
&(currentAtomType->dipole), |
554 |
mmeineke |
291 |
&isError ); |
555 |
|
|
if( isError ){ |
556 |
|
|
sprintf( painCave.errMsg, |
557 |
|
|
"Error initializing the \"%s\" atom type in fortran\n", |
558 |
|
|
currentAtomType->name ); |
559 |
|
|
painCave.isFatal = 1; |
560 |
|
|
simError(); |
561 |
|
|
} |
562 |
|
|
} |
563 |
|
|
currentAtomType = currentAtomType->next; |
564 |
|
|
} |
565 |
|
|
|
566 |
|
|
#ifdef IS_MPI |
567 |
|
|
sprintf( checkPointMsg, |
568 |
|
|
"TraPPE_ExFF atom structures successfully sent to fortran\n" ); |
569 |
|
|
MPIcheckPoint(); |
570 |
|
|
#endif // is_mpi |
571 |
|
|
|
572 |
|
|
|
573 |
mmeineke |
270 |
// initialize the atoms |
574 |
|
|
|
575 |
mmeineke |
291 |
double bigSigma = 0.0; |
576 |
mmeineke |
270 |
DirectionalAtom* dAtom; |
577 |
|
|
|
578 |
|
|
for( i=0; i<nAtoms; i++ ){ |
579 |
|
|
|
580 |
|
|
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
581 |
|
|
if( currentAtomType == NULL ){ |
582 |
|
|
sprintf( painCave.errMsg, |
583 |
|
|
"AtomType error, %s not found in force file.\n", |
584 |
|
|
the_atoms[i]->getType() ); |
585 |
|
|
painCave.isFatal = 1; |
586 |
|
|
simError(); |
587 |
|
|
} |
588 |
|
|
|
589 |
|
|
the_atoms[i]->setMass( currentAtomType->mass ); |
590 |
|
|
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
591 |
|
|
the_atoms[i]->setSigma( currentAtomType->sigma ); |
592 |
|
|
the_atoms[i]->setLJ(); |
593 |
|
|
|
594 |
mmeineke |
291 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
595 |
|
|
|
596 |
mmeineke |
270 |
if( currentAtomType->isDipole ){ |
597 |
|
|
if( the_atoms[i]->isDirectional() ){ |
598 |
|
|
|
599 |
|
|
dAtom = (DirectionalAtom *) the_atoms[i]; |
600 |
|
|
dAtom->setMu( currentAtomType->dipole ); |
601 |
|
|
dAtom->setHasDipole( 1 ); |
602 |
|
|
dAtom->setJx( 0.0 ); |
603 |
|
|
dAtom->setJy( 0.0 ); |
604 |
|
|
dAtom->setJz( 0.0 ); |
605 |
|
|
|
606 |
|
|
if(!strcmp("SSD",the_atoms[i]->getType())){ |
607 |
|
|
dAtom->setI( waterI ); |
608 |
|
|
dAtom->setSSD( 1 ); |
609 |
|
|
} |
610 |
|
|
else if(!strcmp("HEAD",the_atoms[i]->getType())){ |
611 |
|
|
dAtom->setI( headI ); |
612 |
|
|
dAtom->setSSD( 0 ); |
613 |
|
|
} |
614 |
|
|
else{ |
615 |
|
|
sprintf(painCave.errMsg, |
616 |
|
|
"AtmType error, %s does not have a moment of inertia set.\n", |
617 |
|
|
the_atoms[i]->getType() ); |
618 |
|
|
painCave.isFatal = 1; |
619 |
|
|
simError(); |
620 |
|
|
} |
621 |
|
|
entry_plug->n_dipoles++; |
622 |
|
|
} |
623 |
|
|
else{ |
624 |
|
|
|
625 |
|
|
sprintf( painCave.errMsg, |
626 |
|
|
"TraPPE_ExFF error: Atom \"%s\" is a dipole, yet no standard" |
627 |
|
|
" orientation was specifed in the BASS file.\n", |
628 |
|
|
currentAtomType->name ); |
629 |
|
|
painCave.isFatal = 1; |
630 |
|
|
simError(); |
631 |
|
|
} |
632 |
|
|
} |
633 |
|
|
else{ |
634 |
|
|
if( the_atoms[i]->isDirectional() ){ |
635 |
|
|
sprintf( painCave.errMsg, |
636 |
|
|
"TraPPE_ExFF error: Atom \"%s\" was given a standard" |
637 |
|
|
"orientation in the BASS file, yet it is not a dipole.\n", |
638 |
|
|
currentAtomType->name); |
639 |
|
|
painCave.isFatal = 1; |
640 |
|
|
simError(); |
641 |
|
|
} |
642 |
|
|
} |
643 |
|
|
} |
644 |
|
|
|
645 |
mmeineke |
291 |
#ifdef IS_MPI |
646 |
|
|
double tempBig = bigSigma; |
647 |
|
|
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
648 |
|
|
#endif //is_mpi |
649 |
mmeineke |
270 |
|
650 |
mmeineke |
291 |
//calc rCut and rList |
651 |
|
|
|
652 |
|
|
entry_plug->rCut = 2.5 * bigSigma; |
653 |
|
|
|
654 |
|
|
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) |
655 |
|
|
entry_plug->rCut = entry_plug->box_x / 2.0; |
656 |
|
|
|
657 |
|
|
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) |
658 |
|
|
entry_plug->rCut = entry_plug->box_y / 2.0; |
659 |
|
|
|
660 |
|
|
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) |
661 |
|
|
entry_plug->rCut = entry_plug->box_z / 2.0; |
662 |
|
|
|
663 |
|
|
entry_plug->rList = entry_plug->rCut + 1.0; |
664 |
|
|
|
665 |
|
|
|
666 |
mmeineke |
270 |
// clean up the memory |
667 |
|
|
|
668 |
|
|
delete headAtomType; |
669 |
|
|
|
670 |
|
|
#ifdef IS_MPI |
671 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex atoms initialized succesfully" ); |
672 |
|
|
MPIcheckPoint(); |
673 |
|
|
#endif // is_mpi |
674 |
|
|
|
675 |
mmeineke |
296 |
initFortran(); |
676 |
|
|
entry_plug->refreshSim(); |
677 |
|
|
|
678 |
mmeineke |
270 |
} |
679 |
|
|
|
680 |
|
|
void TraPPE_ExFF::initializeBonds( bond_pair* the_bonds ){ |
681 |
|
|
|
682 |
|
|
class LinkedType { |
683 |
|
|
public: |
684 |
|
|
LinkedType(){ |
685 |
|
|
next = NULL; |
686 |
|
|
nameA[0] = '\0'; |
687 |
|
|
nameB[0] = '\0'; |
688 |
|
|
type[0] = '\0'; |
689 |
|
|
} |
690 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
691 |
|
|
|
692 |
|
|
LinkedType* find(char* key1, char* key2){ |
693 |
|
|
if( !strcmp(nameA, key1 ) && !strcmp( nameB, key2 ) ) return this; |
694 |
|
|
if( !strcmp(nameA, key2 ) && !strcmp( nameB, key1 ) ) return this; |
695 |
|
|
if( next != NULL ) return next->find(key1, key2); |
696 |
|
|
return NULL; |
697 |
|
|
} |
698 |
|
|
|
699 |
mmeineke |
291 |
|
700 |
mmeineke |
270 |
void add( bondStruct &info ){ |
701 |
mmeineke |
291 |
|
702 |
|
|
// check for duplicates |
703 |
|
|
int dup = 0; |
704 |
|
|
|
705 |
|
|
if( !strcmp(nameA, info.nameA ) && !strcmp( nameB, info.nameB ) ) dup = 1; |
706 |
|
|
if( !strcmp(nameA, info.nameB ) && !strcmp( nameB, info.nameA ) ) dup = 1; |
707 |
|
|
|
708 |
|
|
if(dup){ |
709 |
|
|
sprintf( painCave.errMsg, |
710 |
|
|
"Duplicate TraPPE_Ex bond type \"%s - %s\" found in " |
711 |
|
|
"the TraPPE_ExFF param file./n", |
712 |
|
|
nameA, nameB ); |
713 |
|
|
painCave.isFatal = 1; |
714 |
|
|
simError(); |
715 |
|
|
} |
716 |
|
|
|
717 |
|
|
|
718 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
719 |
|
|
else{ |
720 |
|
|
next = new LinkedType(); |
721 |
|
|
strcpy(next->nameA, info.nameA); |
722 |
|
|
strcpy(next->nameB, info.nameB); |
723 |
|
|
strcpy(next->type, info.type); |
724 |
|
|
next->d0 = info.d0; |
725 |
|
|
} |
726 |
|
|
} |
727 |
|
|
|
728 |
mmeineke |
291 |
#ifdef IS_MPI |
729 |
mmeineke |
270 |
void duplicate( bondStruct &info ){ |
730 |
|
|
strcpy(info.nameA, nameA); |
731 |
|
|
strcpy(info.nameB, nameB); |
732 |
|
|
strcpy(info.type, type); |
733 |
|
|
info.d0 = d0; |
734 |
|
|
info.last = 0; |
735 |
|
|
} |
736 |
|
|
|
737 |
|
|
|
738 |
|
|
#endif |
739 |
|
|
|
740 |
|
|
char nameA[15]; |
741 |
|
|
char nameB[15]; |
742 |
|
|
char type[30]; |
743 |
|
|
double d0; |
744 |
|
|
|
745 |
|
|
LinkedType* next; |
746 |
|
|
}; |
747 |
|
|
|
748 |
|
|
|
749 |
|
|
|
750 |
|
|
LinkedType* headBondType; |
751 |
|
|
LinkedType* currentBondType; |
752 |
|
|
bondStruct info; |
753 |
|
|
info.last = 1; // initialize last to have the last set. |
754 |
|
|
// if things go well, last will be set to 0 |
755 |
|
|
|
756 |
|
|
SRI **the_sris; |
757 |
|
|
Atom** the_atoms; |
758 |
|
|
int nBonds; |
759 |
|
|
the_sris = entry_plug->sr_interactions; |
760 |
|
|
the_atoms = entry_plug->atoms; |
761 |
|
|
nBonds = entry_plug->n_bonds; |
762 |
|
|
|
763 |
mmeineke |
291 |
int i, a, b; |
764 |
|
|
char* atomA; |
765 |
|
|
char* atomB; |
766 |
mmeineke |
270 |
|
767 |
|
|
#ifdef IS_MPI |
768 |
|
|
if( worldRank == 0 ){ |
769 |
|
|
#endif |
770 |
|
|
|
771 |
|
|
// read in the bond types. |
772 |
|
|
|
773 |
|
|
headBondType = new LinkedType; |
774 |
|
|
|
775 |
mmeineke |
291 |
fastForward( "BondTypes", "initializeBonds" ); |
776 |
|
|
|
777 |
|
|
// we are now at the bondTypes section |
778 |
|
|
|
779 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
780 |
mmeineke |
270 |
lineNum++; |
781 |
|
|
|
782 |
|
|
|
783 |
mmeineke |
291 |
// read a line, and start parseing out the atom types |
784 |
|
|
|
785 |
mmeineke |
270 |
if( eof_test == NULL ){ |
786 |
|
|
sprintf( painCave.errMsg, |
787 |
mmeineke |
291 |
"Error in reading bonds from force file at line %d.\n", |
788 |
mmeineke |
270 |
lineNum ); |
789 |
|
|
painCave.isFatal = 1; |
790 |
|
|
simError(); |
791 |
|
|
} |
792 |
|
|
|
793 |
mmeineke |
291 |
// stop reading at end of file, or at next section |
794 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
795 |
mmeineke |
291 |
|
796 |
|
|
// toss comment lines |
797 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
798 |
|
|
|
799 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
800 |
|
|
if( parseBond( readLine, lineNum, info ) ){ |
801 |
|
|
headBondType->add( info ); |
802 |
mmeineke |
270 |
} |
803 |
|
|
} |
804 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
805 |
|
|
lineNum++; |
806 |
|
|
} |
807 |
mmeineke |
291 |
|
808 |
mmeineke |
270 |
#ifdef IS_MPI |
809 |
|
|
|
810 |
|
|
// send out the linked list to all the other processes |
811 |
|
|
|
812 |
|
|
sprintf( checkPointMsg, |
813 |
|
|
"TraPPE_Ex bond structures read successfully." ); |
814 |
|
|
MPIcheckPoint(); |
815 |
|
|
|
816 |
|
|
currentBondType = headBondType; |
817 |
|
|
while( currentBondType != NULL ){ |
818 |
|
|
currentBondType->duplicate( info ); |
819 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
820 |
|
|
currentBondType = currentBondType->next; |
821 |
|
|
} |
822 |
|
|
info.last = 1; |
823 |
|
|
sendFrcStruct( &info, mpiBondStructType ); |
824 |
|
|
|
825 |
|
|
} |
826 |
|
|
|
827 |
|
|
else{ |
828 |
|
|
|
829 |
|
|
// listen for node 0 to send out the force params |
830 |
|
|
|
831 |
|
|
MPIcheckPoint(); |
832 |
|
|
|
833 |
|
|
headBondType = new LinkedType; |
834 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
835 |
|
|
while( !info.last ){ |
836 |
|
|
|
837 |
|
|
headBondType->add( info ); |
838 |
|
|
recieveFrcStruct( &info, mpiBondStructType ); |
839 |
|
|
} |
840 |
|
|
} |
841 |
|
|
#endif // is_mpi |
842 |
|
|
|
843 |
|
|
|
844 |
|
|
// initialize the Bonds |
845 |
|
|
|
846 |
|
|
|
847 |
|
|
for( i=0; i<nBonds; i++ ){ |
848 |
|
|
|
849 |
|
|
a = the_bonds[i].a; |
850 |
|
|
b = the_bonds[i].b; |
851 |
|
|
|
852 |
|
|
atomA = the_atoms[a]->getType(); |
853 |
|
|
atomB = the_atoms[b]->getType(); |
854 |
|
|
currentBondType = headBondType->find( atomA, atomB ); |
855 |
|
|
if( currentBondType == NULL ){ |
856 |
|
|
sprintf( painCave.errMsg, |
857 |
|
|
"BondType error, %s - %s not found in force file.\n", |
858 |
|
|
atomA, atomB ); |
859 |
|
|
painCave.isFatal = 1; |
860 |
|
|
simError(); |
861 |
|
|
} |
862 |
|
|
|
863 |
|
|
if( !strcmp( currentBondType->type, "fixed" ) ){ |
864 |
|
|
|
865 |
|
|
the_sris[i] = new ConstrainedBond( *the_atoms[a], |
866 |
|
|
*the_atoms[b], |
867 |
|
|
currentBondType->d0 ); |
868 |
|
|
entry_plug->n_constraints++; |
869 |
|
|
} |
870 |
|
|
} |
871 |
|
|
|
872 |
|
|
|
873 |
|
|
// clean up the memory |
874 |
|
|
|
875 |
|
|
delete headBondType; |
876 |
|
|
|
877 |
|
|
#ifdef IS_MPI |
878 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bonds initialized succesfully" ); |
879 |
|
|
MPIcheckPoint(); |
880 |
|
|
#endif // is_mpi |
881 |
|
|
|
882 |
|
|
} |
883 |
|
|
|
884 |
|
|
void TraPPE_ExFF::initializeBends( bend_set* the_bends ){ |
885 |
|
|
|
886 |
|
|
class LinkedType { |
887 |
|
|
public: |
888 |
|
|
LinkedType(){ |
889 |
|
|
next = NULL; |
890 |
|
|
nameA[0] = '\0'; |
891 |
|
|
nameB[0] = '\0'; |
892 |
|
|
nameC[0] = '\0'; |
893 |
|
|
type[0] = '\0'; |
894 |
|
|
} |
895 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
896 |
|
|
|
897 |
|
|
LinkedType* find( char* key1, char* key2, char* key3 ){ |
898 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) |
899 |
|
|
&& !strcmp( nameC, key3 ) ) return this; |
900 |
|
|
if( !strcmp( nameA, key3 ) && !strcmp( nameB, key2 ) |
901 |
|
|
&& !strcmp( nameC, key1 ) ) return this; |
902 |
|
|
if( next != NULL ) return next->find(key1, key2, key3); |
903 |
|
|
return NULL; |
904 |
|
|
} |
905 |
|
|
|
906 |
mmeineke |
291 |
void add( bendStruct &info ){ |
907 |
mmeineke |
270 |
|
908 |
mmeineke |
291 |
// check for duplicates |
909 |
|
|
int dup = 0; |
910 |
|
|
|
911 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) |
912 |
|
|
&& !strcmp( nameC, info.nameC ) ) dup = 1; |
913 |
|
|
if( !strcmp( nameA, info.nameC ) && !strcmp( nameB, info.nameB ) |
914 |
|
|
&& !strcmp( nameC, info.nameA ) ) dup = 1; |
915 |
|
|
|
916 |
|
|
if(dup){ |
917 |
|
|
sprintf( painCave.errMsg, |
918 |
|
|
"Duplicate TraPPE_Ex bend type \"%s - %s - %s\" found in " |
919 |
|
|
"the TraPPE_ExFF param file./n", |
920 |
|
|
nameA, nameB, nameC ); |
921 |
|
|
painCave.isFatal = 1; |
922 |
|
|
simError(); |
923 |
|
|
} |
924 |
|
|
|
925 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
926 |
|
|
else{ |
927 |
|
|
next = new LinkedType(); |
928 |
|
|
strcpy(next->nameA, info.nameA); |
929 |
|
|
strcpy(next->nameB, info.nameB); |
930 |
|
|
strcpy(next->nameC, info.nameC); |
931 |
|
|
strcpy(next->type, info.type); |
932 |
|
|
next->k1 = info.k1; |
933 |
|
|
next->k2 = info.k2; |
934 |
|
|
next->k3 = info.k3; |
935 |
|
|
next->t0 = info.t0; |
936 |
|
|
} |
937 |
|
|
} |
938 |
mmeineke |
291 |
|
939 |
|
|
#ifdef IS_MPI |
940 |
|
|
|
941 |
mmeineke |
270 |
void duplicate( bendStruct &info ){ |
942 |
|
|
strcpy(info.nameA, nameA); |
943 |
|
|
strcpy(info.nameB, nameB); |
944 |
|
|
strcpy(info.nameC, nameC); |
945 |
|
|
strcpy(info.type, type); |
946 |
|
|
info.k1 = k1; |
947 |
|
|
info.k2 = k2; |
948 |
|
|
info.k3 = k3; |
949 |
|
|
info.t0 = t0; |
950 |
|
|
info.last = 0; |
951 |
|
|
} |
952 |
|
|
|
953 |
|
|
#endif // is_mpi |
954 |
|
|
|
955 |
|
|
char nameA[15]; |
956 |
|
|
char nameB[15]; |
957 |
|
|
char nameC[15]; |
958 |
|
|
char type[30]; |
959 |
|
|
double k1, k2, k3, t0; |
960 |
|
|
|
961 |
|
|
LinkedType* next; |
962 |
|
|
}; |
963 |
|
|
|
964 |
|
|
LinkedType* headBendType; |
965 |
|
|
LinkedType* currentBendType; |
966 |
|
|
bendStruct info; |
967 |
|
|
info.last = 1; // initialize last to have the last set. |
968 |
|
|
// if things go well, last will be set to 0 |
969 |
|
|
|
970 |
|
|
QuadraticBend* qBend; |
971 |
mmeineke |
311 |
GhostBend* gBend; |
972 |
mmeineke |
270 |
SRI **the_sris; |
973 |
|
|
Atom** the_atoms; |
974 |
|
|
int nBends; |
975 |
|
|
the_sris = entry_plug->sr_interactions; |
976 |
|
|
the_atoms = entry_plug->atoms; |
977 |
|
|
nBends = entry_plug->n_bends; |
978 |
|
|
|
979 |
mmeineke |
291 |
int i, a, b, c; |
980 |
|
|
char* atomA; |
981 |
|
|
char* atomB; |
982 |
|
|
char* atomC; |
983 |
mmeineke |
270 |
|
984 |
mmeineke |
291 |
|
985 |
mmeineke |
270 |
#ifdef IS_MPI |
986 |
|
|
if( worldRank == 0 ){ |
987 |
|
|
#endif |
988 |
|
|
|
989 |
|
|
// read in the bend types. |
990 |
|
|
|
991 |
|
|
headBendType = new LinkedType; |
992 |
|
|
|
993 |
mmeineke |
291 |
fastForward( "BendTypes", "initializeBends" ); |
994 |
mmeineke |
270 |
|
995 |
mmeineke |
291 |
// we are now at the bendTypes section |
996 |
mmeineke |
270 |
|
997 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
998 |
|
|
lineNum++; |
999 |
|
|
|
1000 |
|
|
// read a line, and start parseing out the bend types |
1001 |
mmeineke |
270 |
|
1002 |
|
|
if( eof_test == NULL ){ |
1003 |
|
|
sprintf( painCave.errMsg, |
1004 |
mmeineke |
291 |
"Error in reading bends from force file at line %d.\n", |
1005 |
mmeineke |
270 |
lineNum ); |
1006 |
|
|
painCave.isFatal = 1; |
1007 |
|
|
simError(); |
1008 |
|
|
} |
1009 |
mmeineke |
291 |
|
1010 |
|
|
// stop reading at end of file, or at next section |
1011 |
mmeineke |
270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
1012 |
mmeineke |
291 |
|
1013 |
|
|
// toss comment lines |
1014 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
1015 |
|
|
|
1016 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
1017 |
|
|
if( parseBend( readLine, lineNum, info ) ){ |
1018 |
|
|
headBendType->add( info ); |
1019 |
mmeineke |
270 |
} |
1020 |
|
|
} |
1021 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1022 |
|
|
lineNum++; |
1023 |
|
|
} |
1024 |
mmeineke |
291 |
|
1025 |
mmeineke |
270 |
#ifdef IS_MPI |
1026 |
|
|
|
1027 |
|
|
// send out the linked list to all the other processes |
1028 |
|
|
|
1029 |
|
|
sprintf( checkPointMsg, |
1030 |
|
|
"TraPPE_Ex bend structures read successfully." ); |
1031 |
|
|
MPIcheckPoint(); |
1032 |
|
|
|
1033 |
|
|
currentBendType = headBendType; |
1034 |
|
|
while( currentBendType != NULL ){ |
1035 |
|
|
currentBendType->duplicate( info ); |
1036 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1037 |
|
|
currentBendType = currentBendType->next; |
1038 |
|
|
} |
1039 |
|
|
info.last = 1; |
1040 |
|
|
sendFrcStruct( &info, mpiBendStructType ); |
1041 |
|
|
|
1042 |
|
|
} |
1043 |
|
|
|
1044 |
|
|
else{ |
1045 |
|
|
|
1046 |
|
|
// listen for node 0 to send out the force params |
1047 |
|
|
|
1048 |
|
|
MPIcheckPoint(); |
1049 |
|
|
|
1050 |
|
|
headBendType = new LinkedType; |
1051 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1052 |
|
|
while( !info.last ){ |
1053 |
|
|
|
1054 |
|
|
headBendType->add( info ); |
1055 |
|
|
recieveFrcStruct( &info, mpiBendStructType ); |
1056 |
|
|
} |
1057 |
|
|
} |
1058 |
|
|
#endif // is_mpi |
1059 |
|
|
|
1060 |
|
|
// initialize the Bends |
1061 |
mmeineke |
291 |
|
1062 |
|
|
int index; |
1063 |
mmeineke |
270 |
|
1064 |
|
|
for( i=0; i<nBends; i++ ){ |
1065 |
|
|
|
1066 |
|
|
a = the_bends[i].a; |
1067 |
|
|
b = the_bends[i].b; |
1068 |
|
|
c = the_bends[i].c; |
1069 |
|
|
|
1070 |
|
|
atomA = the_atoms[a]->getType(); |
1071 |
|
|
atomB = the_atoms[b]->getType(); |
1072 |
mmeineke |
311 |
|
1073 |
|
|
if( the_bends[i].isGhost ) atomC = "GHOST"; |
1074 |
|
|
else atomC = the_atoms[c]->getType(); |
1075 |
|
|
|
1076 |
mmeineke |
270 |
currentBendType = headBendType->find( atomA, atomB, atomC ); |
1077 |
|
|
if( currentBendType == NULL ){ |
1078 |
|
|
sprintf( painCave.errMsg, "BendType error, %s - %s - %s not found" |
1079 |
|
|
" in force file.\n", |
1080 |
|
|
atomA, atomB, atomC ); |
1081 |
|
|
painCave.isFatal = 1; |
1082 |
|
|
simError(); |
1083 |
|
|
} |
1084 |
|
|
|
1085 |
|
|
if( !strcmp( currentBendType->type, "quadratic" ) ){ |
1086 |
|
|
|
1087 |
|
|
index = i + entry_plug->n_bonds; |
1088 |
mmeineke |
311 |
|
1089 |
|
|
if( the_bends[i].isGhost){ |
1090 |
|
|
|
1091 |
|
|
if( the_bends[i].ghost == b ){ |
1092 |
|
|
// do nothing |
1093 |
|
|
} |
1094 |
|
|
else if( the_bends[i].ghost == a ){ |
1095 |
|
|
c = a; |
1096 |
|
|
a = b; |
1097 |
|
|
b = a; |
1098 |
|
|
} |
1099 |
|
|
else{ |
1100 |
|
|
sprintf( painCave.errMsg, |
1101 |
|
|
"BendType error, %s - %s - %s,\n" |
1102 |
|
|
" --> central atom is not " |
1103 |
|
|
"correctly identified with the " |
1104 |
|
|
"\"ghostVectorSource = \" tag.\n", |
1105 |
|
|
atomA, atomB, atomC ); |
1106 |
|
|
painCave.isFatal = 1; |
1107 |
|
|
simError(); |
1108 |
|
|
} |
1109 |
|
|
|
1110 |
|
|
gBend = new GhostBend( *the_atoms[a], |
1111 |
|
|
*the_atoms[b] ); |
1112 |
|
|
gBend->setConstants( currentBendType->k1, |
1113 |
|
|
currentBendType->k2, |
1114 |
|
|
currentBendType->k3, |
1115 |
|
|
currentBendType->t0 ); |
1116 |
|
|
the_sris[index] = gBend; |
1117 |
|
|
} |
1118 |
|
|
else{ |
1119 |
|
|
qBend = new QuadraticBend( *the_atoms[a], |
1120 |
|
|
*the_atoms[b], |
1121 |
|
|
*the_atoms[c] ); |
1122 |
|
|
qBend->setConstants( currentBendType->k1, |
1123 |
|
|
currentBendType->k2, |
1124 |
|
|
currentBendType->k3, |
1125 |
|
|
currentBendType->t0 ); |
1126 |
|
|
the_sris[index] = qBend; |
1127 |
|
|
} |
1128 |
mmeineke |
270 |
} |
1129 |
|
|
} |
1130 |
|
|
|
1131 |
|
|
|
1132 |
|
|
// clean up the memory |
1133 |
|
|
|
1134 |
|
|
delete headBendType; |
1135 |
|
|
|
1136 |
|
|
#ifdef IS_MPI |
1137 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex bends initialized succesfully" ); |
1138 |
|
|
MPIcheckPoint(); |
1139 |
|
|
#endif // is_mpi |
1140 |
|
|
|
1141 |
|
|
} |
1142 |
|
|
|
1143 |
|
|
void TraPPE_ExFF::initializeTorsions( torsion_set* the_torsions ){ |
1144 |
|
|
|
1145 |
|
|
class LinkedType { |
1146 |
|
|
public: |
1147 |
|
|
LinkedType(){ |
1148 |
|
|
next = NULL; |
1149 |
|
|
nameA[0] = '\0'; |
1150 |
|
|
nameB[0] = '\0'; |
1151 |
|
|
nameC[0] = '\0'; |
1152 |
|
|
type[0] = '\0'; |
1153 |
|
|
} |
1154 |
|
|
~LinkedType(){ if( next != NULL ) delete next; } |
1155 |
|
|
|
1156 |
|
|
LinkedType* find( char* key1, char* key2, char* key3, char* key4 ){ |
1157 |
|
|
if( !strcmp( nameA, key1 ) && !strcmp( nameB, key2 ) && |
1158 |
|
|
!strcmp( nameC, key3 ) && !strcmp( nameD, key4 ) ) return this; |
1159 |
|
|
|
1160 |
|
|
if( !strcmp( nameA, key4 ) && !strcmp( nameB, key3 ) && |
1161 |
mmeineke |
291 |
!strcmp( nameC, key2 ) && !strcmp( nameD, key1 ) ) return this; |
1162 |
mmeineke |
270 |
|
1163 |
|
|
if( next != NULL ) return next->find(key1, key2, key3, key4); |
1164 |
|
|
return NULL; |
1165 |
|
|
} |
1166 |
|
|
|
1167 |
|
|
void add( torsionStruct &info ){ |
1168 |
mmeineke |
291 |
|
1169 |
|
|
// check for duplicates |
1170 |
|
|
int dup = 0; |
1171 |
|
|
|
1172 |
|
|
if( !strcmp( nameA, info.nameA ) && !strcmp( nameB, info.nameB ) && |
1173 |
|
|
!strcmp( nameC, info.nameC ) && !strcmp( nameD, info.nameD ) ) dup = 1; |
1174 |
|
|
|
1175 |
|
|
if( !strcmp( nameA, info.nameD ) && !strcmp( nameB, info.nameC ) && |
1176 |
|
|
!strcmp( nameC, info.nameB ) && !strcmp( nameD, info.nameA ) ) dup = 1; |
1177 |
|
|
|
1178 |
|
|
if(dup){ |
1179 |
|
|
sprintf( painCave.errMsg, |
1180 |
|
|
"Duplicate TraPPE_Ex torsion type \"%s - %s - %s - %s\" found in " |
1181 |
|
|
"the TraPPE_ExFF param file./n", nameA, nameB, nameC, nameD ); |
1182 |
|
|
painCave.isFatal = 1; |
1183 |
|
|
simError(); |
1184 |
|
|
} |
1185 |
|
|
|
1186 |
mmeineke |
270 |
if( next != NULL ) next->add(info); |
1187 |
|
|
else{ |
1188 |
|
|
next = new LinkedType(); |
1189 |
|
|
strcpy(next->nameA, info.nameA); |
1190 |
|
|
strcpy(next->nameB, info.nameB); |
1191 |
|
|
strcpy(next->nameC, info.nameC); |
1192 |
|
|
strcpy(next->type, info.type); |
1193 |
|
|
next->k1 = info.k1; |
1194 |
|
|
next->k2 = info.k2; |
1195 |
|
|
next->k3 = info.k3; |
1196 |
|
|
next->k4 = info.k4; |
1197 |
|
|
} |
1198 |
|
|
} |
1199 |
mmeineke |
291 |
|
1200 |
|
|
#ifdef IS_MPI |
1201 |
mmeineke |
270 |
|
1202 |
|
|
void duplicate( torsionStruct &info ){ |
1203 |
|
|
strcpy(info.nameA, nameA); |
1204 |
|
|
strcpy(info.nameB, nameB); |
1205 |
|
|
strcpy(info.nameC, nameC); |
1206 |
|
|
strcpy(info.nameD, nameD); |
1207 |
|
|
strcpy(info.type, type); |
1208 |
|
|
info.k1 = k1; |
1209 |
|
|
info.k2 = k2; |
1210 |
|
|
info.k3 = k3; |
1211 |
|
|
info.k4 = k4; |
1212 |
|
|
info.last = 0; |
1213 |
|
|
} |
1214 |
|
|
|
1215 |
|
|
#endif |
1216 |
|
|
|
1217 |
|
|
char nameA[15]; |
1218 |
|
|
char nameB[15]; |
1219 |
|
|
char nameC[15]; |
1220 |
|
|
char nameD[15]; |
1221 |
|
|
char type[30]; |
1222 |
|
|
double k1, k2, k3, k4; |
1223 |
|
|
|
1224 |
|
|
LinkedType* next; |
1225 |
|
|
}; |
1226 |
|
|
|
1227 |
|
|
LinkedType* headTorsionType; |
1228 |
|
|
LinkedType* currentTorsionType; |
1229 |
|
|
torsionStruct info; |
1230 |
|
|
info.last = 1; // initialize last to have the last set. |
1231 |
|
|
// if things go well, last will be set to 0 |
1232 |
|
|
|
1233 |
|
|
int i, a, b, c, d, index; |
1234 |
|
|
char* atomA; |
1235 |
|
|
char* atomB; |
1236 |
|
|
char* atomC; |
1237 |
|
|
char* atomD; |
1238 |
|
|
CubicTorsion* cTors; |
1239 |
|
|
|
1240 |
|
|
SRI **the_sris; |
1241 |
|
|
Atom** the_atoms; |
1242 |
|
|
int nTorsions; |
1243 |
|
|
the_sris = entry_plug->sr_interactions; |
1244 |
|
|
the_atoms = entry_plug->atoms; |
1245 |
|
|
nTorsions = entry_plug->n_torsions; |
1246 |
|
|
|
1247 |
|
|
#ifdef IS_MPI |
1248 |
|
|
if( worldRank == 0 ){ |
1249 |
|
|
#endif |
1250 |
|
|
|
1251 |
|
|
// read in the torsion types. |
1252 |
|
|
|
1253 |
|
|
headTorsionType = new LinkedType; |
1254 |
mmeineke |
291 |
|
1255 |
|
|
fastForward( "TorsionTypes", "initializeTorsions" ); |
1256 |
mmeineke |
270 |
|
1257 |
mmeineke |
291 |
// we are now at the torsionTypes section |
1258 |
mmeineke |
270 |
|
1259 |
mmeineke |
291 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1260 |
|
|
lineNum++; |
1261 |
mmeineke |
270 |
|
1262 |
mmeineke |
291 |
|
1263 |
|
|
// read a line, and start parseing out the atom types |
1264 |
mmeineke |
270 |
|
1265 |
|
|
if( eof_test == NULL ){ |
1266 |
|
|
sprintf( painCave.errMsg, |
1267 |
mmeineke |
291 |
"Error in reading torsions from force file at line %d.\n", |
1268 |
mmeineke |
270 |
lineNum ); |
1269 |
|
|
painCave.isFatal = 1; |
1270 |
|
|
simError(); |
1271 |
|
|
} |
1272 |
mmeineke |
291 |
|
1273 |
|
|
// stop reading at end of file, or at next section |
1274 |
|
|
while( readLine[0] != '#' && eof_test != NULL ){ |
1275 |
mmeineke |
270 |
|
1276 |
mmeineke |
291 |
// toss comment lines |
1277 |
mmeineke |
270 |
if( readLine[0] != '!' ){ |
1278 |
|
|
|
1279 |
mmeineke |
291 |
// the parser returns 0 if the line was blank |
1280 |
|
|
if( parseTorsion( readLine, lineNum, info ) ){ |
1281 |
|
|
headTorsionType->add( info ); |
1282 |
mmeineke |
270 |
} |
1283 |
|
|
} |
1284 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1285 |
|
|
lineNum++; |
1286 |
|
|
} |
1287 |
|
|
|
1288 |
|
|
#ifdef IS_MPI |
1289 |
|
|
|
1290 |
|
|
// send out the linked list to all the other processes |
1291 |
|
|
|
1292 |
|
|
sprintf( checkPointMsg, |
1293 |
|
|
"TraPPE_Ex torsion structures read successfully." ); |
1294 |
|
|
MPIcheckPoint(); |
1295 |
|
|
|
1296 |
|
|
currentTorsionType = headTorsionType; |
1297 |
|
|
while( currentTorsionType != NULL ){ |
1298 |
|
|
currentTorsionType->duplicate( info ); |
1299 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1300 |
|
|
currentTorsionType = currentTorsionType->next; |
1301 |
|
|
} |
1302 |
|
|
info.last = 1; |
1303 |
|
|
sendFrcStruct( &info, mpiTorsionStructType ); |
1304 |
|
|
|
1305 |
|
|
} |
1306 |
|
|
|
1307 |
|
|
else{ |
1308 |
|
|
|
1309 |
|
|
// listen for node 0 to send out the force params |
1310 |
|
|
|
1311 |
|
|
MPIcheckPoint(); |
1312 |
|
|
|
1313 |
|
|
headTorsionType = new LinkedType; |
1314 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1315 |
|
|
while( !info.last ){ |
1316 |
|
|
|
1317 |
|
|
headTorsionType->add( info ); |
1318 |
|
|
recieveFrcStruct( &info, mpiTorsionStructType ); |
1319 |
|
|
} |
1320 |
|
|
} |
1321 |
|
|
#endif // is_mpi |
1322 |
|
|
|
1323 |
|
|
// initialize the Torsions |
1324 |
|
|
|
1325 |
|
|
for( i=0; i<nTorsions; i++ ){ |
1326 |
|
|
|
1327 |
|
|
a = the_torsions[i].a; |
1328 |
|
|
b = the_torsions[i].b; |
1329 |
|
|
c = the_torsions[i].c; |
1330 |
|
|
d = the_torsions[i].d; |
1331 |
|
|
|
1332 |
|
|
atomA = the_atoms[a]->getType(); |
1333 |
|
|
atomB = the_atoms[b]->getType(); |
1334 |
|
|
atomC = the_atoms[c]->getType(); |
1335 |
|
|
atomD = the_atoms[d]->getType(); |
1336 |
|
|
currentTorsionType = headTorsionType->find( atomA, atomB, atomC, atomD ); |
1337 |
|
|
if( currentTorsionType == NULL ){ |
1338 |
|
|
sprintf( painCave.errMsg, |
1339 |
|
|
"TorsionType error, %s - %s - %s - %s not found" |
1340 |
|
|
" in force file.\n", |
1341 |
|
|
atomA, atomB, atomC, atomD ); |
1342 |
|
|
painCave.isFatal = 1; |
1343 |
|
|
simError(); |
1344 |
|
|
} |
1345 |
|
|
|
1346 |
|
|
if( !strcmp( currentTorsionType->type, "cubic" ) ){ |
1347 |
|
|
index = i + entry_plug->n_bonds + entry_plug->n_bends; |
1348 |
|
|
|
1349 |
|
|
cTors = new CubicTorsion( *the_atoms[a], *the_atoms[b], |
1350 |
|
|
*the_atoms[c], *the_atoms[d] ); |
1351 |
|
|
cTors->setConstants( currentTorsionType->k1, currentTorsionType->k2, |
1352 |
|
|
currentTorsionType->k3, currentTorsionType->k4 ); |
1353 |
|
|
the_sris[index] = cTors; |
1354 |
|
|
} |
1355 |
|
|
} |
1356 |
|
|
|
1357 |
|
|
|
1358 |
|
|
// clean up the memory |
1359 |
|
|
|
1360 |
|
|
delete headTorsionType; |
1361 |
|
|
|
1362 |
|
|
#ifdef IS_MPI |
1363 |
|
|
sprintf( checkPointMsg, "TraPPE_Ex torsions initialized succesfully" ); |
1364 |
|
|
MPIcheckPoint(); |
1365 |
|
|
#endif // is_mpi |
1366 |
|
|
|
1367 |
|
|
} |
1368 |
mmeineke |
291 |
|
1369 |
|
|
void TraPPE_ExFF::fastForward( char* stopText, char* searchOwner ){ |
1370 |
|
|
|
1371 |
|
|
int foundText = 0; |
1372 |
|
|
char* the_token; |
1373 |
|
|
|
1374 |
|
|
rewind( frcFile ); |
1375 |
|
|
lineNum = 0; |
1376 |
|
|
|
1377 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1378 |
|
|
lineNum++; |
1379 |
|
|
if( eof_test == NULL ){ |
1380 |
|
|
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
1381 |
|
|
" file is empty.\n", |
1382 |
|
|
searchOwner ); |
1383 |
|
|
painCave.isFatal = 1; |
1384 |
|
|
simError(); |
1385 |
|
|
} |
1386 |
|
|
|
1387 |
|
|
|
1388 |
|
|
while( !foundText ){ |
1389 |
|
|
while( eof_test != NULL && readLine[0] != '#' ){ |
1390 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1391 |
|
|
lineNum++; |
1392 |
|
|
} |
1393 |
|
|
if( eof_test == NULL ){ |
1394 |
|
|
sprintf( painCave.errMsg, |
1395 |
|
|
"Error fast forwarding force file for %s at " |
1396 |
|
|
"line %d: file ended unexpectedly.\n", |
1397 |
|
|
searchOwner, |
1398 |
|
|
lineNum ); |
1399 |
|
|
painCave.isFatal = 1; |
1400 |
|
|
simError(); |
1401 |
|
|
} |
1402 |
|
|
|
1403 |
|
|
the_token = strtok( readLine, " ,;\t#\n" ); |
1404 |
|
|
foundText = !strcmp( stopText, the_token ); |
1405 |
|
|
|
1406 |
|
|
if( !foundText ){ |
1407 |
|
|
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
1408 |
|
|
lineNum++; |
1409 |
|
|
|
1410 |
|
|
if( eof_test == NULL ){ |
1411 |
|
|
sprintf( painCave.errMsg, |
1412 |
|
|
"Error fast forwarding force file for %s at " |
1413 |
|
|
"line %d: file ended unexpectedly.\n", |
1414 |
|
|
searchOwner, |
1415 |
|
|
lineNum ); |
1416 |
|
|
painCave.isFatal = 1; |
1417 |
|
|
simError(); |
1418 |
|
|
} |
1419 |
|
|
} |
1420 |
|
|
} |
1421 |
|
|
} |
1422 |
|
|
|
1423 |
|
|
|
1424 |
|
|
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1425 |
|
|
|
1426 |
|
|
char* the_token; |
1427 |
|
|
|
1428 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1429 |
|
|
if( the_token != NULL ){ |
1430 |
|
|
|
1431 |
|
|
strcpy( info.name, the_token ); |
1432 |
|
|
|
1433 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1434 |
|
|
sprintf( painCave.errMsg, |
1435 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1436 |
|
|
painCave.isFatal = 1; |
1437 |
|
|
simError(); |
1438 |
|
|
} |
1439 |
|
|
|
1440 |
|
|
info.isDipole = atoi( the_token ); |
1441 |
|
|
|
1442 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1443 |
|
|
sprintf( painCave.errMsg, |
1444 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1445 |
|
|
painCave.isFatal = 1; |
1446 |
|
|
simError(); |
1447 |
|
|
} |
1448 |
|
|
|
1449 |
|
|
info.isSSD = atoi( the_token ); |
1450 |
|
|
|
1451 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1452 |
|
|
sprintf( painCave.errMsg, |
1453 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1454 |
|
|
painCave.isFatal = 1; |
1455 |
|
|
simError(); |
1456 |
|
|
} |
1457 |
|
|
|
1458 |
|
|
info.mass = atof( the_token ); |
1459 |
|
|
|
1460 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1461 |
|
|
sprintf( painCave.errMsg, |
1462 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1463 |
|
|
painCave.isFatal = 1; |
1464 |
|
|
simError(); |
1465 |
|
|
} |
1466 |
|
|
|
1467 |
|
|
info.epslon = atof( the_token ); |
1468 |
|
|
|
1469 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1470 |
|
|
sprintf( painCave.errMsg, |
1471 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1472 |
|
|
painCave.isFatal = 1; |
1473 |
|
|
simError(); |
1474 |
|
|
} |
1475 |
|
|
|
1476 |
|
|
info.sigma = atof( the_token ); |
1477 |
|
|
|
1478 |
|
|
if( info.isDipole ){ |
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.dipole = atof( the_token ); |
1488 |
|
|
} |
1489 |
|
|
else info.dipole = 0.0; |
1490 |
|
|
|
1491 |
|
|
if( info.isSSD ){ |
1492 |
|
|
|
1493 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1494 |
|
|
sprintf( painCave.errMsg, |
1495 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1496 |
|
|
painCave.isFatal = 1; |
1497 |
|
|
simError(); |
1498 |
|
|
} |
1499 |
|
|
|
1500 |
|
|
info.w0 = atof( the_token ); |
1501 |
|
|
|
1502 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1503 |
|
|
sprintf( painCave.errMsg, |
1504 |
|
|
"Error parseing AtomTypes: line %d\n", lineNum ); |
1505 |
|
|
painCave.isFatal = 1; |
1506 |
|
|
simError(); |
1507 |
|
|
} |
1508 |
|
|
|
1509 |
|
|
info.v0 = atof( the_token ); |
1510 |
|
|
} |
1511 |
|
|
else info.v0 = info.w0 = 0.0; |
1512 |
|
|
|
1513 |
|
|
return 1; |
1514 |
|
|
} |
1515 |
|
|
else return 0; |
1516 |
|
|
} |
1517 |
|
|
|
1518 |
|
|
int parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1519 |
|
|
|
1520 |
|
|
char* the_token; |
1521 |
|
|
|
1522 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1523 |
|
|
if( the_token != NULL ){ |
1524 |
|
|
|
1525 |
|
|
strcpy( info.nameA, the_token ); |
1526 |
|
|
|
1527 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1528 |
|
|
sprintf( painCave.errMsg, |
1529 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1530 |
|
|
painCave.isFatal = 1; |
1531 |
|
|
simError(); |
1532 |
|
|
} |
1533 |
|
|
|
1534 |
|
|
strcpy( info.nameB, the_token ); |
1535 |
|
|
|
1536 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1537 |
|
|
sprintf( painCave.errMsg, |
1538 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1539 |
|
|
painCave.isFatal = 1; |
1540 |
|
|
simError(); |
1541 |
|
|
} |
1542 |
|
|
|
1543 |
|
|
strcpy( info.type, the_token ); |
1544 |
|
|
|
1545 |
|
|
if( !strcmp( info.type, "fixed" ) ){ |
1546 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1547 |
|
|
sprintf( painCave.errMsg, |
1548 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1549 |
|
|
painCave.isFatal = 1; |
1550 |
|
|
simError(); |
1551 |
|
|
} |
1552 |
|
|
|
1553 |
|
|
info.d0 = atof( the_token ); |
1554 |
|
|
} |
1555 |
|
|
else{ |
1556 |
|
|
sprintf( painCave.errMsg, |
1557 |
|
|
"Unknown TraPPE_Ex bond type \"%s\" at line %d\n", |
1558 |
|
|
info.type, |
1559 |
|
|
lineNum ); |
1560 |
|
|
painCave.isFatal = 1; |
1561 |
|
|
simError(); |
1562 |
|
|
} |
1563 |
|
|
|
1564 |
|
|
return 1; |
1565 |
|
|
} |
1566 |
|
|
else return 0; |
1567 |
|
|
} |
1568 |
|
|
|
1569 |
|
|
|
1570 |
|
|
int parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1571 |
|
|
|
1572 |
|
|
char* the_token; |
1573 |
|
|
|
1574 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1575 |
|
|
if( the_token != NULL ){ |
1576 |
|
|
|
1577 |
|
|
strcpy( info.nameA, the_token ); |
1578 |
|
|
|
1579 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1580 |
|
|
sprintf( painCave.errMsg, |
1581 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1582 |
|
|
painCave.isFatal = 1; |
1583 |
|
|
simError(); |
1584 |
|
|
} |
1585 |
|
|
|
1586 |
|
|
strcpy( info.nameB, the_token ); |
1587 |
|
|
|
1588 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1589 |
|
|
sprintf( painCave.errMsg, |
1590 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1591 |
|
|
painCave.isFatal = 1; |
1592 |
|
|
simError(); |
1593 |
|
|
} |
1594 |
|
|
|
1595 |
|
|
strcpy( info.nameC, the_token ); |
1596 |
|
|
|
1597 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1598 |
|
|
sprintf( painCave.errMsg, |
1599 |
|
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1600 |
|
|
painCave.isFatal = 1; |
1601 |
|
|
simError(); |
1602 |
|
|
} |
1603 |
|
|
|
1604 |
|
|
strcpy( info.type, the_token ); |
1605 |
|
|
|
1606 |
|
|
if( !strcmp( info.type, "quadratic" ) ){ |
1607 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1608 |
|
|
sprintf( painCave.errMsg, |
1609 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1610 |
|
|
painCave.isFatal = 1; |
1611 |
|
|
simError(); |
1612 |
|
|
} |
1613 |
|
|
|
1614 |
|
|
info.k1 = atof( the_token ); |
1615 |
|
|
|
1616 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1617 |
|
|
sprintf( painCave.errMsg, |
1618 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1619 |
|
|
painCave.isFatal = 1; |
1620 |
|
|
simError(); |
1621 |
|
|
} |
1622 |
|
|
|
1623 |
|
|
info.k2 = atof( the_token ); |
1624 |
|
|
|
1625 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1626 |
|
|
sprintf( painCave.errMsg, |
1627 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1628 |
|
|
painCave.isFatal = 1; |
1629 |
|
|
simError(); |
1630 |
|
|
} |
1631 |
|
|
|
1632 |
|
|
info.k3 = atof( the_token ); |
1633 |
|
|
|
1634 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1635 |
|
|
sprintf( painCave.errMsg, |
1636 |
|
|
"Error parseing BendTypes: line %d\n", lineNum ); |
1637 |
|
|
painCave.isFatal = 1; |
1638 |
|
|
simError(); |
1639 |
|
|
} |
1640 |
|
|
|
1641 |
|
|
info.t0 = atof( the_token ); |
1642 |
|
|
} |
1643 |
|
|
|
1644 |
|
|
else{ |
1645 |
|
|
sprintf( painCave.errMsg, |
1646 |
|
|
"Unknown TraPPE_Ex bend type \"%s\" at line %d\n", |
1647 |
|
|
info.type, |
1648 |
|
|
lineNum ); |
1649 |
|
|
painCave.isFatal = 1; |
1650 |
|
|
simError(); |
1651 |
|
|
} |
1652 |
|
|
|
1653 |
|
|
return 1; |
1654 |
|
|
} |
1655 |
|
|
else return 0; |
1656 |
|
|
} |
1657 |
|
|
|
1658 |
|
|
int parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1659 |
|
|
|
1660 |
|
|
char* the_token; |
1661 |
|
|
|
1662 |
|
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1663 |
|
|
if( the_token != NULL ){ |
1664 |
|
|
|
1665 |
|
|
strcpy( info.nameA, the_token ); |
1666 |
|
|
|
1667 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1668 |
|
|
sprintf( painCave.errMsg, |
1669 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1670 |
|
|
painCave.isFatal = 1; |
1671 |
|
|
simError(); |
1672 |
|
|
} |
1673 |
|
|
|
1674 |
|
|
strcpy( info.nameB, the_token ); |
1675 |
|
|
|
1676 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1677 |
|
|
sprintf( painCave.errMsg, |
1678 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1679 |
|
|
painCave.isFatal = 1; |
1680 |
|
|
simError(); |
1681 |
|
|
} |
1682 |
|
|
|
1683 |
|
|
strcpy( info.nameC, the_token ); |
1684 |
|
|
|
1685 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1686 |
|
|
sprintf( painCave.errMsg, |
1687 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1688 |
|
|
painCave.isFatal = 1; |
1689 |
|
|
simError(); |
1690 |
|
|
} |
1691 |
|
|
|
1692 |
|
|
strcpy( info.nameD, the_token ); |
1693 |
|
|
|
1694 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1695 |
|
|
sprintf( painCave.errMsg, |
1696 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1697 |
|
|
painCave.isFatal = 1; |
1698 |
|
|
simError(); |
1699 |
|
|
} |
1700 |
|
|
|
1701 |
|
|
strcpy( info.type, the_token ); |
1702 |
|
|
|
1703 |
|
|
if( !strcmp( info.type, "cubic" ) ){ |
1704 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1705 |
|
|
sprintf( painCave.errMsg, |
1706 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1707 |
|
|
painCave.isFatal = 1; |
1708 |
|
|
simError(); |
1709 |
|
|
} |
1710 |
|
|
|
1711 |
|
|
info.k1 = atof( the_token ); |
1712 |
|
|
|
1713 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1714 |
|
|
sprintf( painCave.errMsg, |
1715 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1716 |
|
|
painCave.isFatal = 1; |
1717 |
|
|
simError(); |
1718 |
|
|
} |
1719 |
|
|
|
1720 |
|
|
info.k2 = atof( the_token ); |
1721 |
|
|
|
1722 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1723 |
|
|
sprintf( painCave.errMsg, |
1724 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1725 |
|
|
painCave.isFatal = 1; |
1726 |
|
|
simError(); |
1727 |
|
|
} |
1728 |
|
|
|
1729 |
|
|
info.k3 = atof( the_token ); |
1730 |
|
|
|
1731 |
|
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1732 |
|
|
sprintf( painCave.errMsg, |
1733 |
|
|
"Error parseing TorsionTypes: line %d\n", lineNum ); |
1734 |
|
|
painCave.isFatal = 1; |
1735 |
|
|
simError(); |
1736 |
|
|
} |
1737 |
|
|
|
1738 |
|
|
info.k4 = atof( the_token ); |
1739 |
|
|
|
1740 |
|
|
} |
1741 |
|
|
|
1742 |
|
|
else{ |
1743 |
|
|
sprintf( painCave.errMsg, |
1744 |
|
|
"Unknown TraPPE_Ex torsion type \"%s\" at line %d\n", |
1745 |
|
|
info.type, |
1746 |
|
|
lineNum ); |
1747 |
|
|
painCave.isFatal = 1; |
1748 |
|
|
simError(); |
1749 |
|
|
} |
1750 |
|
|
|
1751 |
|
|
return 1; |
1752 |
|
|
} |
1753 |
|
|
|
1754 |
|
|
else return 0; |
1755 |
|
|
} |