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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <iostream> |
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using namespace std; |
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 |
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double v0p; |
40 |
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double rl; |
41 |
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double ru; |
42 |
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double rlp; |
43 |
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double rup; |
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int isSSD; |
45 |
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int isCharge; |
46 |
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int isDipole; |
47 |
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int ident; |
48 |
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int last; // 0 -> default |
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 |
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next->v0p = info.v0p; |
149 |
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next->rl = info.rl; |
150 |
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next->ru = info.ru; |
151 |
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next->rlp = info.rlp; |
152 |
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next->rup = info.rup; |
153 |
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next->ident = info.ident; |
154 |
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} |
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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 |
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info.v0p = v0p; |
170 |
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info.rl = rl; |
171 |
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info.ru = ru; |
172 |
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info.rlp = rlp; |
173 |
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info.rup = rup; |
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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 |
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double v0p; |
191 |
+ |
double rl; |
192 |
+ |
double ru; |
193 |
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double rlp; |
194 |
+ |
double rup; |
195 |
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int ident; |
196 |
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LinkedAtomType* next; |
197 |
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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]; |
437 |
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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 |
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int atomBC[3] = {15,6,4}; // block counts |
480 |
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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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|
659 |
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|
660 |
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void DUFF::readParams( void ){ |
661 |
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|
641 |
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int i, a, b, c, d; |
662 |
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int identNum; |
643 |
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char* atomA; |
644 |
– |
char* atomB; |
645 |
– |
char* atomC; |
646 |
– |
char* atomD; |
663 |
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|
664 |
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atomStruct atomInfo; |
665 |
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bondStruct bondInfo; |
781 |
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int isGB = 0; |
782 |
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int isLJ = 1; |
783 |
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int isEAM =0; |
784 |
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double GB_dummy = 0.0; |
785 |
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|
786 |
< |
|
784 |
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int isCharge = 0; |
785 |
> |
double charge=0.0; |
786 |
> |
|
787 |
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currentAtomType = headAtomType->next;; |
788 |
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while( currentAtomType != NULL ){ |
789 |
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|
790 |
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if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
790 |
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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 |
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set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); |
793 |
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set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
794 |
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&(currentAtomType->v0p), |
795 |
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&(currentAtomType->rl), &(currentAtomType->ru), |
796 |
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&(currentAtomType->rlp), &(currentAtomType->rup)); |
797 |
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} |
798 |
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|
799 |
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if( currentAtomType->name[0] != '\0' ){ |
804 |
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&(currentAtomType->isDipole), |
805 |
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&isGB, |
806 |
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&isEAM, |
807 |
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&isCharge, |
808 |
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&(currentAtomType->epslon), |
809 |
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&(currentAtomType->sigma), |
810 |
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&charge, |
811 |
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&(currentAtomType->dipole), |
812 |
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&isError ); |
813 |
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if( isError ){ |
1308 |
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} |
1309 |
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|
1310 |
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gBend = new GhostBend( *the_atoms[a], |
1311 |
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*the_atoms[b] ); |
1311 |
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*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 |
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} |
1328 |
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} |
1329 |
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} |
1330 |
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} |
1331 |
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} |
1518 |
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} |
1519 |
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|
1520 |
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info.v0 = atof( the_token ); |
1521 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1522 |
+ |
sprintf( painCave.errMsg, |
1523 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1524 |
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painCave.isFatal = 1; |
1525 |
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simError(); |
1526 |
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} |
1527 |
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|
1528 |
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info.v0p = atof( the_token ); |
1529 |
+ |
|
1530 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1531 |
+ |
sprintf( painCave.errMsg, |
1532 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1533 |
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painCave.isFatal = 1; |
1534 |
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simError(); |
1535 |
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} |
1536 |
+ |
|
1537 |
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info.rl = atof( the_token ); |
1538 |
+ |
|
1539 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1540 |
+ |
sprintf( painCave.errMsg, |
1541 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1542 |
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painCave.isFatal = 1; |
1543 |
+ |
simError(); |
1544 |
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} |
1545 |
+ |
|
1546 |
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info.ru = atof( the_token ); |
1547 |
+ |
|
1548 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1549 |
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sprintf( painCave.errMsg, |
1550 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1551 |
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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 |
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} |
1566 |
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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 |
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|
1568 |
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return 1; |
1569 |
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} |
1609 |
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} |
1610 |
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|
1611 |
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info.d0 = atof( the_token ); |
1612 |
+ |
|
1613 |
+ |
info.k0=0.0; |
1614 |
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} |
1615 |
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else if( !strcmp( bondType, "harmonic" ) ){ |
1616 |
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info.type = HARMONIC_BOND; |
1637 |
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else{ |
1638 |
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sprintf( painCave.errMsg, |
1639 |
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"Unknown DUFF bond type \"%s\" at line %d\n", |
1640 |
< |
info.type, |
1640 |
> |
bondType, |
1641 |
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lineNum ); |
1642 |
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painCave.isFatal = 1; |
1643 |
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simError(); |