1 |
< |
#include <cstdlib> |
2 |
< |
#include <cstdio> |
3 |
< |
#include <cstring> |
1 |
> |
#include <stdlib.h> |
2 |
> |
#include <stdio.h> |
3 |
> |
#include <string.h> |
4 |
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|
5 |
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#include <iostream> |
6 |
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using namespace std; |
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#include "mpiForceField.h" |
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#endif // is_mpi |
17 |
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|
18 |
– |
namespace TPE { // restrict the access of the folowing to this file only. |
18 |
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|
19 |
+ |
// define some bond Types |
20 |
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|
21 |
+ |
#define FIXED_BOND 0 |
22 |
+ |
#define HARMONIC_BOND 1 |
23 |
+ |
|
24 |
+ |
|
25 |
+ |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
26 |
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|
27 |
+ |
|
28 |
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// Declare the structures that will be passed by MPI |
29 |
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|
30 |
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typedef struct{ |
32 |
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double mass; |
33 |
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double epslon; |
34 |
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double sigma; |
35 |
+ |
double charge; |
36 |
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double dipole; |
37 |
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double w0; |
38 |
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double v0; |
39 |
+ |
double v0p; |
40 |
+ |
double rl; |
41 |
+ |
double ru; |
42 |
+ |
double rlp; |
43 |
+ |
double rup; |
44 |
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int isSSD; |
45 |
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int isCharge; |
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int isDipole; |
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int ident; |
48 |
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int last; // 0 -> default |
53 |
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typedef struct{ |
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char nameA[15]; |
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char nameB[15]; |
42 |
– |
char type[30]; |
56 |
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double d0; |
57 |
+ |
double k0; |
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int last; // 0 -> default |
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// 1 -> tells nodes to stop listening |
60 |
+ |
int type; |
61 |
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} bondStruct; |
62 |
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|
63 |
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|
145 |
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next->dipole = info.dipole; |
146 |
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next->w0 = info.w0; |
147 |
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next->v0 = info.v0; |
148 |
+ |
next->v0p = info.v0p; |
149 |
+ |
next->rl = info.rl; |
150 |
+ |
next->ru = info.ru; |
151 |
+ |
next->rlp = info.rlp; |
152 |
+ |
next->rup = info.rup; |
153 |
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next->ident = info.ident; |
154 |
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} |
155 |
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} |
166 |
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info.dipole = dipole; |
167 |
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info.w0 = w0; |
168 |
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info.v0 = v0; |
169 |
+ |
info.v0p = v0p; |
170 |
+ |
info.rl = rl; |
171 |
+ |
info.ru = ru; |
172 |
+ |
info.rlp = rlp; |
173 |
+ |
info.rup = rup; |
174 |
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info.ident = ident; |
175 |
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info.last = 0; |
176 |
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} |
187 |
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double dipole; |
188 |
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double w0; |
189 |
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double v0; |
190 |
+ |
double v0p; |
191 |
+ |
double rl; |
192 |
+ |
double ru; |
193 |
+ |
double rlp; |
194 |
+ |
double rup; |
195 |
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int ident; |
196 |
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LinkedAtomType* next; |
197 |
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}; |
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next = NULL; |
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nameA[0] = '\0'; |
204 |
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nameB[0] = '\0'; |
175 |
– |
type[0] = '\0'; |
205 |
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} |
206 |
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~LinkedBondType(){ if( next != NULL ) delete next; } |
207 |
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|
236 |
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next = new LinkedBondType(); |
237 |
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strcpy(next->nameA, info.nameA); |
238 |
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strcpy(next->nameB, info.nameB); |
239 |
< |
strcpy(next->type, info.type); |
239 |
> |
next->type = info.type; |
240 |
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next->d0 = info.d0; |
241 |
+ |
next->k0 = info.k0; |
242 |
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} |
243 |
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} |
244 |
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|
246 |
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void duplicate( bondStruct &info ){ |
247 |
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strcpy(info.nameA, nameA); |
248 |
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strcpy(info.nameB, nameB); |
249 |
< |
strcpy(info.type, type); |
249 |
> |
info.type = type; |
250 |
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info.d0 = d0; |
251 |
+ |
info.k0 = k0; |
252 |
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info.last = 0; |
253 |
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} |
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|
257 |
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|
258 |
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char nameA[15]; |
259 |
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char nameB[15]; |
260 |
< |
char type[30]; |
260 |
> |
int type; |
261 |
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double d0; |
262 |
+ |
double k0; |
263 |
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|
264 |
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LinkedBondType* next; |
265 |
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}; |
442 |
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|
443 |
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} // namespace |
444 |
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|
445 |
< |
using namespace TPE; |
445 |
> |
using namespace DUFF_NS; |
446 |
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|
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|
448 |
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//**************************************************************** |
456 |
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char* ffPath_env = "FORCE_PARAM_PATH"; |
457 |
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char* ffPath; |
458 |
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char temp[200]; |
427 |
– |
char errMsg[1000]; |
459 |
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|
460 |
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headAtomType = NULL; |
461 |
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currentAtomType = NULL; |
477 |
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// Init the atomStruct mpi type |
478 |
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|
479 |
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atomStruct atomProto; // mpiPrototype |
480 |
< |
int atomBC[3] = {15,6,4}; // block counts |
480 |
> |
int atomBC[3] = {15,11,4}; // block counts |
481 |
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MPI_Aint atomDspls[3]; // displacements |
482 |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
483 |
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|
499 |
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// Init the bondStruct mpi type |
500 |
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|
501 |
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bondStruct bondProto; // mpiPrototype |
502 |
< |
int bondBC[3] = {60,1,1}; // block counts |
502 |
> |
int bondBC[3] = {30,2,2}; // block counts |
503 |
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MPI_Aint bondDspls[3]; // displacements |
504 |
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MPI_Datatype bondMbrTypes[3]; // member mpi types |
505 |
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|
659 |
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|
660 |
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void DUFF::readParams( void ){ |
661 |
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|
631 |
– |
int i, a, b, c, d; |
662 |
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int identNum; |
633 |
– |
char* atomA; |
634 |
– |
char* atomB; |
635 |
– |
char* atomC; |
636 |
– |
char* atomD; |
663 |
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|
664 |
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atomStruct atomInfo; |
665 |
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bondStruct bondInfo; |
780 |
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|
781 |
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int isGB = 0; |
782 |
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int isLJ = 1; |
783 |
< |
double GB_dummy = 0.0; |
784 |
< |
|
785 |
< |
|
783 |
> |
int isEAM =0; |
784 |
> |
int isCharge = 0; |
785 |
> |
double charge=0.0; |
786 |
> |
|
787 |
|
currentAtomType = headAtomType->next;; |
788 |
|
while( currentAtomType != NULL ){ |
789 |
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|
790 |
< |
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
790 |
> |
if(currentAtomType->isDipole) entry_plug->useDipoles = 1; |
791 |
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if(currentAtomType->isSSD) { |
792 |
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entry_plug->useSticky = 1; |
793 |
< |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); |
793 |
> |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
794 |
> |
&(currentAtomType->v0p), |
795 |
> |
&(currentAtomType->rl), &(currentAtomType->ru), |
796 |
> |
&(currentAtomType->rlp), &(currentAtomType->rup)); |
797 |
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} |
798 |
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|
799 |
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if( currentAtomType->name[0] != '\0' ){ |
803 |
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&(currentAtomType->isSSD), |
804 |
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&(currentAtomType->isDipole), |
805 |
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&isGB, |
806 |
+ |
&isEAM, |
807 |
+ |
&isCharge, |
808 |
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&(currentAtomType->epslon), |
809 |
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&(currentAtomType->sigma), |
810 |
+ |
&charge, |
811 |
|
&(currentAtomType->dipole), |
812 |
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&isError ); |
813 |
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if( isError ){ |
1222 |
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simError(); |
1223 |
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} |
1224 |
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|
1225 |
< |
if( !strcmp( currentBondType->type, "fixed" ) ){ |
1226 |
< |
|
1225 |
> |
switch( currentBondType->type ){ |
1226 |
> |
|
1227 |
> |
case FIXED_BOND: |
1228 |
> |
|
1229 |
|
bondArray[i] = new ConstrainedBond( *the_atoms[a], |
1230 |
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*the_atoms[b], |
1231 |
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currentBondType->d0 ); |
1232 |
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entry_plug->n_constraints++; |
1233 |
+ |
break; |
1234 |
+ |
|
1235 |
+ |
case HARMONIC_BOND: |
1236 |
+ |
|
1237 |
+ |
bondArray[i] = new HarmonicBond( *the_atoms[a], |
1238 |
+ |
*the_atoms[b], |
1239 |
+ |
currentBondType->d0, |
1240 |
+ |
currentBondType->k0 ); |
1241 |
+ |
break; |
1242 |
+ |
|
1243 |
+ |
default: |
1244 |
+ |
|
1245 |
+ |
break; |
1246 |
+ |
// do nothing |
1247 |
|
} |
1248 |
|
} |
1249 |
|
} |
1308 |
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} |
1309 |
|
|
1310 |
|
gBend = new GhostBend( *the_atoms[a], |
1311 |
< |
*the_atoms[b] ); |
1311 |
> |
*the_atoms[b]); |
1312 |
> |
|
1313 |
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gBend->setConstants( currentBendType->k1, |
1314 |
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currentBendType->k2, |
1315 |
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currentBendType->k3, |
1325 |
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currentBendType->k3, |
1326 |
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currentBendType->t0 ); |
1327 |
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bendArray[i] = qBend; |
1328 |
< |
} |
1328 |
> |
} |
1329 |
|
} |
1330 |
|
} |
1331 |
|
} |
1432 |
|
} |
1433 |
|
|
1434 |
|
|
1435 |
< |
int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1435 |
> |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1436 |
|
|
1437 |
|
char* the_token; |
1438 |
|
|
1518 |
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} |
1519 |
|
|
1520 |
|
info.v0 = atof( the_token ); |
1521 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1522 |
+ |
sprintf( painCave.errMsg, |
1523 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1524 |
+ |
painCave.isFatal = 1; |
1525 |
+ |
simError(); |
1526 |
+ |
} |
1527 |
+ |
|
1528 |
+ |
info.v0p = atof( the_token ); |
1529 |
+ |
|
1530 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1531 |
+ |
sprintf( painCave.errMsg, |
1532 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1533 |
+ |
painCave.isFatal = 1; |
1534 |
+ |
simError(); |
1535 |
+ |
} |
1536 |
+ |
|
1537 |
+ |
info.rl = atof( the_token ); |
1538 |
+ |
|
1539 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1540 |
+ |
sprintf( painCave.errMsg, |
1541 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1542 |
+ |
painCave.isFatal = 1; |
1543 |
+ |
simError(); |
1544 |
+ |
} |
1545 |
+ |
|
1546 |
+ |
info.ru = atof( the_token ); |
1547 |
+ |
|
1548 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1549 |
+ |
sprintf( painCave.errMsg, |
1550 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1551 |
+ |
painCave.isFatal = 1; |
1552 |
+ |
simError(); |
1553 |
+ |
} |
1554 |
+ |
|
1555 |
+ |
info.rlp = atof( the_token ); |
1556 |
+ |
|
1557 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1558 |
+ |
sprintf( painCave.errMsg, |
1559 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1560 |
+ |
painCave.isFatal = 1; |
1561 |
+ |
simError(); |
1562 |
+ |
} |
1563 |
+ |
|
1564 |
+ |
info.rup = atof( the_token ); |
1565 |
|
} |
1566 |
< |
else info.v0 = info.w0 = 0.0; |
1566 |
> |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1567 |
|
|
1568 |
|
return 1; |
1569 |
|
} |
1570 |
|
else return 0; |
1571 |
|
} |
1572 |
|
|
1573 |
< |
int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1573 |
> |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1574 |
|
|
1575 |
|
char* the_token; |
1576 |
+ |
char bondType[30]; |
1577 |
|
|
1578 |
|
the_token = strtok( lineBuffer, " \n\t,;" ); |
1579 |
|
if( the_token != NULL ){ |
1596 |
|
simError(); |
1597 |
|
} |
1598 |
|
|
1599 |
< |
strcpy( info.type, the_token ); |
1599 |
> |
strcpy( bondType, the_token ); |
1600 |
|
|
1601 |
< |
if( !strcmp( info.type, "fixed" ) ){ |
1601 |
> |
if( !strcmp( bondType, "fixed" ) ){ |
1602 |
> |
info.type = FIXED_BOND; |
1603 |
> |
|
1604 |
|
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1605 |
|
sprintf( painCave.errMsg, |
1606 |
|
"Error parseing BondTypes: line %d\n", lineNum ); |
1609 |
|
} |
1610 |
|
|
1611 |
|
info.d0 = atof( the_token ); |
1612 |
+ |
|
1613 |
+ |
info.k0=0.0; |
1614 |
|
} |
1615 |
+ |
else if( !strcmp( bondType, "harmonic" ) ){ |
1616 |
+ |
info.type = HARMONIC_BOND; |
1617 |
+ |
|
1618 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1619 |
+ |
sprintf( painCave.errMsg, |
1620 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1621 |
+ |
painCave.isFatal = 1; |
1622 |
+ |
simError(); |
1623 |
+ |
} |
1624 |
+ |
|
1625 |
+ |
info.d0 = atof( the_token ); |
1626 |
+ |
|
1627 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1628 |
+ |
sprintf( painCave.errMsg, |
1629 |
+ |
"Error parseing BondTypes: line %d\n", lineNum ); |
1630 |
+ |
painCave.isFatal = 1; |
1631 |
+ |
simError(); |
1632 |
+ |
} |
1633 |
+ |
|
1634 |
+ |
info.k0 = atof( the_token ); |
1635 |
+ |
} |
1636 |
+ |
|
1637 |
|
else{ |
1638 |
|
sprintf( painCave.errMsg, |
1639 |
|
"Unknown DUFF bond type \"%s\" at line %d\n", |
1640 |
< |
info.type, |
1640 |
> |
bondType, |
1641 |
|
lineNum ); |
1642 |
|
painCave.isFatal = 1; |
1643 |
|
simError(); |
1649 |
|
} |
1650 |
|
|
1651 |
|
|
1652 |
< |
int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1652 |
> |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1653 |
|
|
1654 |
|
char* the_token; |
1655 |
|
|
1737 |
|
else return 0; |
1738 |
|
} |
1739 |
|
|
1740 |
< |
int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1740 |
> |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1741 |
|
|
1742 |
|
char* the_token; |
1743 |
|
|