22 |
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#define HARMONIC_BOND 1 |
23 |
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|
24 |
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|
25 |
< |
namespace TPE { // restrict the access of the folowing to this file only. |
25 |
> |
namespace DUFF_NS { // restrict the access of the folowing to this file only. |
26 |
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|
27 |
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|
28 |
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// Declare the structures that will be passed by MPI |
35 |
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double dipole; |
36 |
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double w0; |
37 |
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double v0; |
38 |
+ |
double v0p; |
39 |
+ |
double rl; |
40 |
+ |
double ru; |
41 |
+ |
double rlp; |
42 |
+ |
double rup; |
43 |
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int isSSD; |
44 |
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int isDipole; |
45 |
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int ident; |
143 |
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next->dipole = info.dipole; |
144 |
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next->w0 = info.w0; |
145 |
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next->v0 = info.v0; |
146 |
+ |
next->v0p = info.v0p; |
147 |
+ |
next->rl = info.rl; |
148 |
+ |
next->ru = info.ru; |
149 |
+ |
next->rlp = info.rlp; |
150 |
+ |
next->rup = info.rup; |
151 |
|
next->ident = info.ident; |
152 |
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} |
153 |
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} |
164 |
|
info.dipole = dipole; |
165 |
|
info.w0 = w0; |
166 |
|
info.v0 = v0; |
167 |
+ |
info.v0p = v0p; |
168 |
+ |
info.rl = rl; |
169 |
+ |
info.ru = ru; |
170 |
+ |
info.rlp = rlp; |
171 |
+ |
info.rup = rup; |
172 |
|
info.ident = ident; |
173 |
|
info.last = 0; |
174 |
|
} |
185 |
|
double dipole; |
186 |
|
double w0; |
187 |
|
double v0; |
188 |
+ |
double v0p; |
189 |
+ |
double rl; |
190 |
+ |
double ru; |
191 |
+ |
double rlp; |
192 |
+ |
double rup; |
193 |
|
int ident; |
194 |
|
LinkedAtomType* next; |
195 |
|
}; |
440 |
|
|
441 |
|
} // namespace |
442 |
|
|
443 |
< |
using namespace TPE; |
443 |
> |
using namespace DUFF_NS; |
444 |
|
|
445 |
|
|
446 |
|
//**************************************************************** |
784 |
|
|
785 |
|
int isGB = 0; |
786 |
|
int isLJ = 1; |
787 |
+ |
int isEAM =0; |
788 |
|
double GB_dummy = 0.0; |
789 |
|
|
790 |
|
|
794 |
|
if(currentAtomType->isDipole) entry_plug->useDipole = 1; |
795 |
|
if(currentAtomType->isSSD) { |
796 |
|
entry_plug->useSticky = 1; |
797 |
< |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0)); |
797 |
> |
set_sticky_params( &(currentAtomType->w0), &(currentAtomType->v0), |
798 |
> |
&(currentAtomType->v0p), |
799 |
> |
&(currentAtomType->rl), &(currentAtomType->ru), |
800 |
> |
&(currentAtomType->rlp), &(currentAtomType->rup)); |
801 |
|
} |
802 |
|
|
803 |
|
if( currentAtomType->name[0] != '\0' ){ |
807 |
|
&(currentAtomType->isSSD), |
808 |
|
&(currentAtomType->isDipole), |
809 |
|
&isGB, |
810 |
+ |
&isEAM, |
811 |
|
&(currentAtomType->epslon), |
812 |
|
&(currentAtomType->sigma), |
813 |
|
&(currentAtomType->dipole), |
1433 |
|
} |
1434 |
|
|
1435 |
|
|
1436 |
< |
int TPE::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1436 |
> |
int DUFF_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
1437 |
|
|
1438 |
|
char* the_token; |
1439 |
|
|
1519 |
|
} |
1520 |
|
|
1521 |
|
info.v0 = atof( the_token ); |
1522 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1523 |
+ |
sprintf( painCave.errMsg, |
1524 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1525 |
+ |
painCave.isFatal = 1; |
1526 |
+ |
simError(); |
1527 |
+ |
} |
1528 |
+ |
|
1529 |
+ |
info.v0p = atof( the_token ); |
1530 |
+ |
|
1531 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1532 |
+ |
sprintf( painCave.errMsg, |
1533 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1534 |
+ |
painCave.isFatal = 1; |
1535 |
+ |
simError(); |
1536 |
+ |
} |
1537 |
+ |
|
1538 |
+ |
info.rl = atof( the_token ); |
1539 |
+ |
|
1540 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1541 |
+ |
sprintf( painCave.errMsg, |
1542 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1543 |
+ |
painCave.isFatal = 1; |
1544 |
+ |
simError(); |
1545 |
+ |
} |
1546 |
+ |
|
1547 |
+ |
info.ru = atof( the_token ); |
1548 |
+ |
|
1549 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1550 |
+ |
sprintf( painCave.errMsg, |
1551 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1552 |
+ |
painCave.isFatal = 1; |
1553 |
+ |
simError(); |
1554 |
+ |
} |
1555 |
+ |
|
1556 |
+ |
info.rlp = atof( the_token ); |
1557 |
+ |
|
1558 |
+ |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
1559 |
+ |
sprintf( painCave.errMsg, |
1560 |
+ |
"Error parseing AtomTypes: line %d\n", lineNum ); |
1561 |
+ |
painCave.isFatal = 1; |
1562 |
+ |
simError(); |
1563 |
+ |
} |
1564 |
+ |
|
1565 |
+ |
info.rup = atof( the_token ); |
1566 |
|
} |
1567 |
< |
else info.v0 = info.w0 = 0.0; |
1567 |
> |
else info.v0 = info.w0 = info.v0p = info.rl = info.ru = info.rlp = info.rup = 0.0; |
1568 |
|
|
1569 |
|
return 1; |
1570 |
|
} |
1571 |
|
else return 0; |
1572 |
|
} |
1573 |
|
|
1574 |
< |
int TPE::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1574 |
> |
int DUFF_NS::parseBond( char *lineBuffer, int lineNum, bondStruct &info ){ |
1575 |
|
|
1576 |
|
char* the_token; |
1577 |
|
char bondType[30]; |
1648 |
|
} |
1649 |
|
|
1650 |
|
|
1651 |
< |
int TPE::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1651 |
> |
int DUFF_NS::parseBend( char *lineBuffer, int lineNum, bendStruct &info ){ |
1652 |
|
|
1653 |
|
char* the_token; |
1654 |
|
|
1736 |
|
else return 0; |
1737 |
|
} |
1738 |
|
|
1739 |
< |
int TPE::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1739 |
> |
int DUFF_NS::parseTorsion( char *lineBuffer, int lineNum, torsionStruct &info ){ |
1740 |
|
|
1741 |
|
char* the_token; |
1742 |
|
|