| 98 |
|
|
| 99 |
|
// gather all of the information from the Bass file |
| 100 |
|
|
| 101 |
– |
std::cerr << "gathering info\n"; |
| 102 |
– |
|
| 101 |
|
gatherInfo(); |
| 102 |
|
|
| 103 |
|
// creation of complex system objects |
| 104 |
|
|
| 107 |
– |
std::cerr << "creating system objects\n"; |
| 108 |
– |
|
| 105 |
|
sysObjectsCreation(); |
| 106 |
|
|
| 107 |
|
// check on the post processing info |
| 112 |
– |
|
| 113 |
– |
std::cerr << "performing final info check.\n"; |
| 108 |
|
|
| 109 |
|
finalInfoCheck(); |
| 110 |
|
|
| 111 |
|
// initialize the system coordinates |
| 118 |
– |
|
| 119 |
– |
std::cerr << "about to init coords\n"; |
| 112 |
|
|
| 113 |
|
if( !isInfoArray ) initSystemCoords(); |
| 114 |
|
|
| 891 |
|
|
| 892 |
|
char* inName; |
| 893 |
|
|
| 902 |
– |
std::cerr << "Setting atom Coords\n"; |
| 894 |
|
|
| 895 |
|
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
| 896 |
|
|
| 903 |
|
if( worldRank == 0 ){ |
| 904 |
|
#endif //is_mpi |
| 905 |
|
inName = globals->getInitialConfig(); |
| 906 |
+ |
double* tempDouble = new double[1000000]; |
| 907 |
|
fileInit = new InitializeFromFile( inName ); |
| 908 |
|
#ifdef IS_MPI |
| 909 |
|
}else fileInit = new InitializeFromFile( NULL ); |
| 1612 |
|
" , you must set sample time.\n"); |
| 1613 |
|
painCave.isFatal = 1; |
| 1614 |
|
simError(); |
| 1623 |
– |
} |
| 1624 |
– |
|
| 1625 |
– |
// |
| 1626 |
– |
nZConstraints = globals->getNzConstraints(); |
| 1627 |
– |
zconStamp = globals->getZconStamp(); |
| 1628 |
– |
ZConsParaItem tempParaItem; |
| 1629 |
– |
|
| 1630 |
– |
ZConsParaData* zconsParaData = new ZConsParaData(); |
| 1631 |
– |
zconsParaData->setID(ZCONSPARADATA_ID); |
| 1632 |
– |
|
| 1633 |
– |
for(int i = 0; i < nZConstraints; i++){ |
| 1634 |
– |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
| 1635 |
– |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
| 1636 |
– |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
| 1637 |
– |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
| 1638 |
– |
|
| 1639 |
– |
zconsParaData->addItem(tempParaItem); |
| 1615 |
|
} |
| 1616 |
|
|
| 1642 |
– |
//sort the parameters by index of molecules |
| 1643 |
– |
zconsParaData->sortByIndex(); |
| 1644 |
– |
|
| 1645 |
– |
//push data into siminfo, therefore, we can retrieve later |
| 1646 |
– |
theInfo.addProperty(zconsParaData); |
| 1647 |
– |
|
| 1617 |
|
//push zconsTol into siminfo, if user does not specify |
| 1618 |
|
//value for zconsTol, a default value will be used |
| 1619 |
|
DoubleData* zconsTol = new DoubleData(); |
| 1622 |
|
zconsTol->setData(globals->getZconsTol()); |
| 1623 |
|
} |
| 1624 |
|
else{ |
| 1625 |
< |
double defaultZConsTol = 1E-6; |
| 1625 |
> |
double defaultZConsTol = 0.01; |
| 1626 |
|
sprintf( painCave.errMsg, |
| 1627 |
|
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
| 1628 |
|
" , default value %f is used.\n", defaultZConsTol); |
| 1632 |
|
zconsTol->setData(defaultZConsTol); |
| 1633 |
|
} |
| 1634 |
|
theInfo.addProperty(zconsTol); |
| 1635 |
+ |
|
| 1636 |
+ |
//set Force Substraction Policy |
| 1637 |
+ |
StringData* zconsForcePolicy = new StringData(); |
| 1638 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
| 1639 |
+ |
|
| 1640 |
+ |
if(globals->haveZconsForcePolicy()){ |
| 1641 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
| 1642 |
+ |
} |
| 1643 |
+ |
else{ |
| 1644 |
+ |
sprintf( painCave.errMsg, |
| 1645 |
+ |
"ZConstraint Warning: User does not set force substraction policy, " |
| 1646 |
+ |
"average force substraction policy is used\n"); |
| 1647 |
+ |
painCave.isFatal = 0; |
| 1648 |
+ |
simError(); |
| 1649 |
+ |
zconsForcePolicy->setData("BYNUMBER"); |
| 1650 |
+ |
} |
| 1651 |
|
|
| 1652 |
+ |
theInfo.addProperty(zconsForcePolicy); |
| 1653 |
+ |
|
| 1654 |
|
//Determine the name of ouput file and add it into SimInfo's property list |
| 1655 |
|
//Be careful, do not use inFileName, since it is a pointer which |
| 1656 |
|
//point to a string at master node, and slave nodes do not contain that string |
| 1663 |
|
zconsFilename->setID(ZCONSFILENAME_ID); |
| 1664 |
|
zconsFilename->setData(zconsOutput); |
| 1665 |
|
|
| 1666 |
< |
theInfo.addProperty(zconsFilename); |
| 1666 |
> |
theInfo.addProperty(zconsFilename); |
| 1667 |
> |
|
| 1668 |
> |
//setup index, pos and other parameters of z-constraint molecules |
| 1669 |
> |
nZConstraints = globals->getNzConstraints(); |
| 1670 |
> |
theInfo.nZconstraints = nZConstraints; |
| 1671 |
> |
|
| 1672 |
> |
zconStamp = globals->getZconStamp(); |
| 1673 |
> |
ZConsParaItem tempParaItem; |
| 1674 |
> |
|
| 1675 |
> |
ZConsParaData* zconsParaData = new ZConsParaData(); |
| 1676 |
> |
zconsParaData->setID(ZCONSPARADATA_ID); |
| 1677 |
> |
|
| 1678 |
> |
for(int i = 0; i < nZConstraints; i++){ |
| 1679 |
> |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
| 1680 |
> |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
| 1681 |
> |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
| 1682 |
> |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
| 1683 |
> |
|
| 1684 |
> |
zconsParaData->addItem(tempParaItem); |
| 1685 |
> |
} |
| 1686 |
> |
|
| 1687 |
> |
//sort the parameters by index of molecules |
| 1688 |
> |
zconsParaData->sortByIndex(); |
| 1689 |
> |
|
| 1690 |
> |
//push data into siminfo, therefore, we can retrieve later |
| 1691 |
> |
theInfo.addProperty(zconsParaData); |
| 1692 |
> |
|
| 1693 |
|
} |
