zOPER_EXPORT zLONG OPERATION
AddRetCode( zVIEW vSubtask )
{
zLONG lIDNumber;
GetVariableID( &lIDNumber, "nZRetCode" );
if ( lIDNumber == -1 ) // an entity does not exist ... add it
{
lIDNumber = AddVariableEntityToPI( vSubtask, "nZRetCode", qTSHORT, 0, 0 );
}
return( lIDNumber );
}
bool CNetCDFTraj::ReadHeader(CAmberTopology* p_top)
{
if( p_top == NULL ){
INVALID_ARGUMENT("p_top == NULL");
}
if( NCID < 0 ) {
ES_ERROR("file is not opened");
return(false);
}
HasBox = p_top->BoxInfo.GetType() != AMBER_BOX_NONE;
NumOfTopologyAtoms = p_top->AtomList.GetNumberOfAtoms();
bool result = true;
result &= GetVariableAttribute(NC_GLOBAL,"title",Title);
result &= GetVariableAttribute(NC_GLOBAL,"application",Application);
result &= GetVariableAttribute(NC_GLOBAL,"program",Program);
result &= GetVariableAttribute(NC_GLOBAL,"programVersion",Version);
result &= GetVariableAttribute(NC_GLOBAL,"Conventions",Conventions);
result &= GetVariableAttribute(NC_GLOBAL,"ConventionVersion",ConventionVersion);
if( Conventions != "AMBER" ) {
CSmallString error;
error << "illegal conventions '" << Conventions << "', expecting 'AMBER'";
ES_ERROR(error);
return(false);
}
if( ConventionVersion != "1.0" ) {
CSmallString error;
error << "illegal convention version '" << ConventionVersion << "', expecting '1.0'";
ES_ERROR(error);
return(false);
}
GetDimensionInfo("frame", &TotalSnapshots);
GetDimensionInfo("spatial", &Spatial);
GetDimensionInfo("atom", &ActualAtoms);
if( Spatial != 3 ) {
CSmallString error;
error << "three dim expected but '" << Spatial << "' provided";
ES_ERROR(error);
return(false);
}
if( ActualAtoms != NumOfTopologyAtoms ) {
CSmallString error;
error << "number of atoms in the topology '" << ActualAtoms << "' is different than in topology '" << NumOfTopologyAtoms << "'";
ES_ERROR(error);
return(false);
}
// sanity check - spatial variable ---------------------
SpatialVID = GetVariableID("spatial");
if( SpatialVID < 0 ) {
return(false);
}
size_t start[3],count[3];
char xyz[3];
int err;
start[0] = 0;
count[0] = Spatial;
xyz[0] = (char) 0;
err = nc_get_vara_text(NCID,SpatialVID,start,count,xyz);
if( err != NC_NOERR ) {
CSmallString error;
error << "unable to get spatial names (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
if( (xyz[0] != 'x') || (xyz[1] != 'y') || (xyz[2] != 'z') ) {
CSmallString error;
error << "incorrect spatial labels (" << xyz[0] << "," << xyz[1] << "," << xyz[2] << ")";
ES_ERROR(error);
return(false);
}
// sanity check - time ---------------------------------
TimeVID = GetVariableID("time");
if( TimeVID < 0 ) {
return(false);
}
CSmallString unit;
if( GetVariableAttribute(TimeVID,"units",unit) == false ) {
return(false);
}
if( unit != "picosecond" ) {
CSmallString error;
error << "incorrect unit for time (" << unit << "), requested picosecond";
ES_ERROR(error);
return(false);
}
// sanity check - coordinates --------------------------
CoordinateVID = GetVariableID("coordinates");
if( CoordinateVID < 0 ) {
return(false);
}
if( GetVariableAttribute(CoordinateVID,"units",unit) == false ) {
return(false);
}
if( unit != "angstrom" ) {
CSmallString error;
error << "incorrect unit for coordinates (" << unit << "), requested angstrom";
ES_ERROR(error);
return(false);
}
CurrentSnapshot = 0;
if( Coordinates != NULL ) {
delete Coordinates;
}
Coordinates = new float[ActualAtoms*3];
// sanity check - box ----------------------------------
if( HasBox ){
// optional
CellLengthVID = GetVariableID("cell_lengths");
CellAngleVID = GetVariableID("cell_angles");
}
return(true);
}
//
// OPERATION: AddCompare
//
// DESCRIPTION: AddCompare
//
zOPER_EXPORT zLONG OPERATION
AddCompareToView( zVIEW vSubtask,
zVIEW vTargetView,
zPCHAR pchOperationName,
LPQEXPRSTRUCT sLeft,
zPCHAR pchLeftLiteral,
LPQEXPRSTRUCT sRight,
zPCHAR pchRightLiteral,
zLONG lOperator )
{
zLONG lIDNumber;
zLONG lZKeyNumber;
zCHAR szViewName[ 33 ];
zLONG lViewID;
zCHAR szEntityName[ 33 ];
zLONG lEntityID;
zCHAR szAttributeName[ 33 ];
zLONG lAttributeID;
GetOperationClass( vSubtask, &lIDNumber, pchOperationName );
lZKeyNumber = GetOperationZKey( vSubtask, qZEIDONOPERATION, pchOperationName );
if ( lZKeyNumber < 0 )
return( -1 ); // this is an error situation
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATIONCALL, lIDNumber,
qTSHORT, pchOperationName, lZKeyNumber, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, "(", qOPENOPER, 0 );
SplitQualifier( pchLeftLiteral, szViewName, szEntityName, szAttributeName );
GetVariableID( &lViewID, szViewName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qNUMERIC, qTVIEW, "", lViewID, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC, qTINTEGER, ",", qCOMMA, 0 );
// was a variable entity name
if ( sLeft->lDataClass == qENTITYISUNKNOWN ||
sLeft->lDataClass == qENTITYANDATTRIBUTEAREUNKNOWN )
{
GetVariableID( &lEntityID, szEntityName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qTEXT,
qTENTITYNAME, szEntityName, lEntityID, 0 );
}
else // was a constant
{
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qTEXT,
qTENTITYNAME, szEntityName, 0, 0 );
}
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ",", qCOMMA, 0 );
// was a variable attribute name
if ( sLeft->lDataClass == qATTRIBUTEISUNKNOWN ||
sLeft->lDataClass == qENTITYANDATTRIBUTEAREUNKNOWN )
{
GetVariableID( &lAttributeID, szAttributeName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qTEXT,
qTATTRIBUTENAME, szAttributeName, lAttributeID, 0 );
}
else // was a constant
{
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qTEXT,
qTATTRIBUTENAME, szAttributeName, 0, 0 );
}
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ",", qCOMMA, 0 );
if ( sRight->lElementClass == qVARIABLE || sRight->lElementClass == qCONSTANT )
{
AddExprNodeEntityToView( vSubtask, vTargetView, sRight->lElementClass, sRight->lDataClass,
sRight->lDataType, pchRightLiteral, sRight->lOffset, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ")", qCLOSEOPER, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, "", lOperator, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qNUMERIC,
qTINTEGER, "0", 0, 0 );
return( 0 );
}
SplitQualifier( pchRightLiteral, szViewName, szEntityName, szAttributeName );
GetVariableID( &lViewID, szViewName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qNUMERIC,
qTVIEW, "", lViewID, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ",", qCOMMA, 0 );
// was a variable entity name
if ( sRight->lDataClass == qENTITYISUNKNOWN ||
sRight->lDataClass == qENTITYANDATTRIBUTEAREUNKNOWN )
{
GetVariableID( &lEntityID, szEntityName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qTEXT,
qTENTITYNAME, szEntityName, lEntityID, 0 );
}
else // was a constant
{
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qTEXT,
qTENTITYNAME, szEntityName, 0, 0 );
}
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ",", qCOMMA, 0 );
// was a variable attribute name
if ( sRight->lDataClass == qATTRIBUTEISUNKNOWN ||
sRight->lDataClass == qENTITYANDATTRIBUTEAREUNKNOWN )
{
GetVariableID( &lAttributeID, szAttributeName );
AddExprNodeEntityToView( vSubtask, vTargetView, qVARIABLE, qTEXT,
qTATTRIBUTENAME, szAttributeName, lAttributeID, 0 );
}
else // was a constant
{
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qTEXT,
qTATTRIBUTENAME, szAttributeName, 0, 0 );
}
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, ")", qCLOSEOPER, 0 );
if ( lOperator > 0 )
{
AddExprNodeEntityToView( vSubtask, vTargetView, qOPERATOR, qNUMERIC,
qTINTEGER, "", lOperator, 0 );
AddExprNodeEntityToView( vSubtask, vTargetView, qCONSTANT, qNUMERIC,
qTINTEGER, "0", 0, 0 );
}
return( 0 );
}
