15 |
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#include "mpiForceField.h" |
16 |
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#endif // is_mpi |
17 |
|
|
18 |
+ |
|
19 |
+ |
// define some bond Types |
20 |
+ |
|
21 |
+ |
#define FIXED_BOND 0 |
22 |
+ |
#define HARMONIC_BOND 1 |
23 |
+ |
|
24 |
+ |
|
25 |
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namespace TPE { // restrict the access of the folowing to this file only. |
26 |
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|
27 |
|
|
46 |
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typedef struct{ |
47 |
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char nameA[15]; |
48 |
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char nameB[15]; |
42 |
– |
char type[30]; |
49 |
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double d0; |
50 |
+ |
double k0; |
51 |
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int last; // 0 -> default |
52 |
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// 1 -> tells nodes to stop listening |
53 |
+ |
int type; |
54 |
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} bondStruct; |
55 |
|
|
56 |
|
|
180 |
|
next = NULL; |
181 |
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nameA[0] = '\0'; |
182 |
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nameB[0] = '\0'; |
175 |
– |
type[0] = '\0'; |
183 |
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} |
184 |
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~LinkedBondType(){ if( next != NULL ) delete next; } |
185 |
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|
214 |
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next = new LinkedBondType(); |
215 |
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strcpy(next->nameA, info.nameA); |
216 |
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strcpy(next->nameB, info.nameB); |
217 |
< |
strcpy(next->type, info.type); |
217 |
> |
next->type = info.type; |
218 |
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next->d0 = info.d0; |
219 |
+ |
next->k0 = info.k0; |
220 |
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} |
221 |
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} |
222 |
|
|
224 |
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void duplicate( bondStruct &info ){ |
225 |
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strcpy(info.nameA, nameA); |
226 |
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strcpy(info.nameB, nameB); |
227 |
< |
strcpy(info.type, type); |
227 |
> |
info.type = type; |
228 |
|
info.d0 = d0; |
229 |
+ |
info.k0 = k0; |
230 |
|
info.last = 0; |
231 |
|
} |
232 |
|
|
235 |
|
|
236 |
|
char nameA[15]; |
237 |
|
char nameB[15]; |
238 |
< |
char type[30]; |
238 |
> |
int type; |
239 |
|
double d0; |
240 |
+ |
double k0; |
241 |
|
|
242 |
|
LinkedBondType* next; |
243 |
|
}; |
478 |
|
// Init the bondStruct mpi type |
479 |
|
|
480 |
|
bondStruct bondProto; // mpiPrototype |
481 |
< |
int bondBC[3] = {60,1,1}; // block counts |
481 |
> |
int bondBC[3] = {30,2,2}; // block counts |
482 |
|
MPI_Aint bondDspls[3]; // displacements |
483 |
|
MPI_Datatype bondMbrTypes[3]; // member mpi types |
484 |
|
|
1199 |
|
simError(); |
1200 |
|
} |
1201 |
|
|
1202 |
< |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
1203 |
< |
|
1202 |
> |
switch( currentBondType->type ){ |
1203 |
> |
|
1204 |
> |
case FIXED_BOND: |
1205 |
> |
|
1206 |
|
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1207 |
|
*the_atoms[b], |
1208 |
|
currentBondType->d0 ); |
1209 |
|
entry_plug->n_constraints++; |
1210 |
+ |
break; |
1211 |
+ |
|
1212 |
+ |
case HARMONIC_BOND: |
1213 |
+ |
|
1214 |
+ |
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1215 |
+ |
*the_atoms[b], |
1216 |
+ |
currentBondType->d0, |
1217 |
+ |
currentBondType->k0 ); |
1218 |
+ |
break; |
1219 |
+ |
|
1220 |
+ |
default: |
1221 |
+ |
|
1222 |
+ |
break; |
1223 |
+ |
// do nothing |
1224 |
|
} |
1225 |
|
} |
1226 |
|
} |
1505 |
|
int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1506 |
|
|
1507 |
|
char* the_token; |
1508 |
+ |
char bondType[30]; |
1509 |
|
|
1510 |
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1511 |
|
if( the_token != NULL ){ |
1528 |
|
simError(); |
1529 |
|
} |
1530 |
|
|
1531 |
< |
strcpy( info.type, the_token ); |
1531 |
> |
strcpy( bondType, the_token ); |
1532 |
|
|
1533 |
< |
if( !strcmp( info.type, "fixed" ) ){ |
1533 |
> |
if( !strcmp( bondType, "fixed" ) ){ |
1534 |
> |
info.type = FIXED_BOND; |
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 |
> |
info.d0 = atof( the_token ); |
1544 |
> |
} |
1545 |
> |
else if( !strcmp( bondType, "harmonic" ) ){ |
1546 |
> |
info.type = HARMONIC_BOND; |
1547 |
> |
|
1548 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1549 |
|
sprintf( painCave.errMsg, |
1550 |
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1553 |
|
} |
1554 |
|
|
1555 |
|
info.d0 = atof( the_token ); |
1556 |
+ |
|
1557 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1558 |
+ |
sprintf( painCave.errMsg, |
1559 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1560 |
+ |
painCave.isFatal = 1; |
1561 |
+ |
simError(); |
1562 |
+ |
} |
1563 |
+ |
|
1564 |
+ |
info.k0 = atof( the_token ); |
1565 |
|
} |
1566 |
+ |
|
1567 |
|
else{ |
1568 |
|
sprintf( painCave.errMsg, |
1569 |
|
"Unknown DUFF bond type \"%s\" at line %d\n", |