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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; |
35 |
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double dipole; |
36 |
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double w0; |
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double v0; |
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double v0p; |
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double rl; |
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double ru; |
41 |
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double rlp; |
42 |
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double rup; |
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int isSSD; |
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int isDipole; |
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int ident; |
143 |
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next->dipole = info.dipole; |
144 |
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next->w0 = info.w0; |
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next->v0 = info.v0; |
146 |
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next->v0p = info.v0p; |
147 |
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next->rl = info.rl; |
148 |
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next->ru = info.ru; |
149 |
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next->rlp = info.rlp; |
150 |
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next->rup = info.rup; |
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next->ident = info.ident; |
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} |
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} |
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info.dipole = dipole; |
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info.w0 = w0; |
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info.v0 = v0; |
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info.v0p = v0p; |
168 |
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info.rl = rl; |
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info.ru = ru; |
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info.rlp = rlp; |
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info.rup = rup; |
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info.ident = ident; |
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info.last = 0; |
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} |
185 |
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double dipole; |
186 |
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double w0; |
187 |
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double v0; |
188 |
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double v0p; |
189 |
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double rl; |
190 |
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double ru; |
191 |
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double rlp; |
192 |
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double rup; |
193 |
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int ident; |
194 |
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LinkedAtomType* next; |
195 |
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}; |
454 |
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char* ffPath_env = "FORCE_PARAM_PATH"; |
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char* ffPath; |
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char temp[200]; |
437 |
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char errMsg[1000]; |
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headAtomType = NULL; |
459 |
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currentAtomType = NULL; |
475 |
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// Init the atomStruct mpi type |
476 |
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|
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atomStruct atomProto; // mpiPrototype |
478 |
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int atomBC[3] = {15,6,4}; // block counts |
478 |
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int atomBC[3] = {15,11,4}; // block counts |
479 |
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MPI_Aint atomDspls[3]; // displacements |
480 |
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MPI_Datatype atomMbrTypes[3]; // member mpi types |
481 |
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657 |
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658 |
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void DUFF::readParams( void ){ |
659 |
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641 |
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int i, a, b, c, d; |
660 |
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int identNum; |
643 |
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char* atomA; |
644 |
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char* atomB; |
645 |
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char* atomC; |
646 |
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char* atomD; |
661 |
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662 |
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atomStruct atomInfo; |
663 |
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bondStruct bondInfo; |
778 |
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779 |
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int isGB = 0; |
780 |
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int isLJ = 1; |
781 |
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double GB_dummy = 0.0; |
782 |
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769 |
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|
781 |
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int isEAM =0; |
782 |
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|
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currentAtomType = headAtomType->next;; |
784 |
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while( currentAtomType != NULL ){ |
785 |
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|
786 |
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if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
787 |
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if(currentAtomType->isSSD) { |
788 |
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entry_plug->useSticky = 1; |
789 |
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set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); |
789 |
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set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
790 |
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&(currentAtomType->v0p), |
791 |
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&(currentAtomType->rl), &(currentAtomType->ru), |
792 |
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&(currentAtomType->rlp), &(currentAtomType->rup)); |
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} |
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|
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if( currentAtomType->name[0] != '\0' ){ |
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&(currentAtomType->isSSD), |
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&(currentAtomType->isDipole), |
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&isGB, |
802 |
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&isEAM, |
803 |
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&(currentAtomType->epslon), |
804 |
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&(currentAtomType->sigma), |
805 |
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&(currentAtomType->dipole), |
1302 |
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} |
1303 |
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|
1304 |
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gBend = new GhostBend( *the_atoms[a], |
1305 |
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*the_atoms[b] ); |
1305 |
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*the_atoms[b]); |
1306 |
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|
1307 |
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gBend->setConstants( currentBendType->k1, |
1308 |
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currentBendType->k2, |
1309 |
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currentBendType->k3, |
1319 |
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currentBendType->k3, |
1320 |
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currentBendType->t0 ); |
1321 |
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bendArray[i] = qBend; |
1322 |
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} |
1322 |
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} |
1323 |
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} |
1324 |
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} |
1325 |
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} |
1512 |
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} |
1513 |
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1514 |
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info.v0 = atof( the_token ); |
1515 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1516 |
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sprintf( painCave.errMsg, |
1517 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1518 |
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painCave.isFatal = 1; |
1519 |
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simError(); |
1520 |
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} |
1521 |
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|
1522 |
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info.v0p = atof( the_token ); |
1523 |
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|
1524 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1525 |
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sprintf( painCave.errMsg, |
1526 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1527 |
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painCave.isFatal = 1; |
1528 |
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simError(); |
1529 |
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} |
1530 |
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|
1531 |
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info.rl = atof( the_token ); |
1532 |
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|
1533 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1534 |
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sprintf( painCave.errMsg, |
1535 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1536 |
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painCave.isFatal = 1; |
1537 |
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simError(); |
1538 |
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} |
1539 |
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|
1540 |
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info.ru = atof( the_token ); |
1541 |
+ |
|
1542 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1543 |
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sprintf( painCave.errMsg, |
1544 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1545 |
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painCave.isFatal = 1; |
1546 |
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simError(); |
1547 |
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} |
1548 |
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|
1549 |
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info.rlp = atof( the_token ); |
1550 |
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|
1551 |
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if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1552 |
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sprintf( painCave.errMsg, |
1553 |
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"Error parseing AtomTypes: line %d\n", lineNum ); |
1554 |
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painCave.isFatal = 1; |
1555 |
+ |
simError(); |
1556 |
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} |
1557 |
+ |
|
1558 |
+ |
info.rup = atof( the_token ); |
1559 |
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} |
1560 |
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else info.v0 = info.w0 = 0.0; |
1560 |
> |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1561 |
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|
1562 |
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return 1; |
1563 |
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} |
1603 |
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} |
1604 |
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|
1605 |
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info.d0 = atof( the_token ); |
1606 |
+ |
|
1607 |
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info.k0=0.0; |
1608 |
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} |
1609 |
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else if( !strcmp( bondType, "harmonic" ) ){ |
1610 |
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info.type = HARMONIC_BOND; |
1631 |
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else{ |
1632 |
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sprintf( painCave.errMsg, |
1633 |
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"Unknown DUFF bond type \"%s\" at line %d\n", |
1634 |
< |
info.type, |
1634 |
> |
bondType, |
1635 |
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lineNum ); |
1636 |
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painCave.isFatal = 1; |
1637 |
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simError(); |