/*
==============
GetToken
==============
*/
qboolean GetToken (qboolean crossline)
{
char *token_p;
if (tokenready) // is a token allready waiting?
{
tokenready = false;
return true;
}
// printf("script_p %x (%x)\n", script->script_p, script->end_p ); fflush( stdout );
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
tokenready = false;
// skip space, ctrl chars
skipspace:
while (*script->script_p <= 32)
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
if (*(script->script_p++) == '\n')
{
if (!crossline)
{
Error ("Line %i is incomplete\n",scriptline);
}
scriptline = ++script->line;
}
}
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
// strip single line comments
if (*script->script_p == ';' || *script->script_p == '#' || // semicolon and # is comment field
(*script->script_p == '/' && *((script->script_p)+1) == '/')) // also make // a comment field
{
if (!crossline)
Error ("Line %i is incomplete\n",scriptline);
while (*script->script_p++ != '\n')
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
}
scriptline = ++script->line;
goto skipspace;
}
// strip out matching /* */ comments
if (*script->script_p == '/' && *((script->script_p)+1) == '*')
{
script->script_p += 2;
while (*script->script_p != '*' || *((script->script_p)+1) != '/')
{
if (*script->script_p++ != '\n')
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
scriptline = ++script->line;
}
}
script->script_p += 2;
goto skipspace;
}
// copy token to buffer
token_p = token;
if (*script->script_p == '"')
{
// quoted token
script->script_p++;
while (*script->script_p != '"')
{
*token_p++ = *script->script_p++;
if (script->script_p == script->end_p)
break;
if (token_p == &token[MAXTOKEN])
Error ("Token too large on line %i\n",scriptline);
}
script->script_p++;
}
else // regular token
while ( *script->script_p > 32 && *script->script_p != ';')
{
if ( !ExpandMacroToken( token_p ) )
{
if ( !ExpandVariableToken( token_p ) )
{
*token_p++ = *script->script_p++;
if (script->script_p == script->end_p)
break;
if (token_p == &token[MAXTOKEN])
Error ("Token too large on line %i\n",scriptline);
}
}
}
// add null to end of token
*token_p = 0;
// check for other commands
if (!stricmp (token, "$include"))
{
GetToken (false);
AddScriptToStack (token);
return GetToken (crossline);
}
else if (!stricmp (token, "$definemacro"))
{
GetToken (false);
DefineMacro(token);
return GetToken (crossline);
}
else if (!stricmp (token, "$definevariable"))
{
GetToken (false);
DefineVariable(token);
return GetToken (crossline);
}
else if (AddMacroToStack( token ))
{
return GetToken (crossline);
}
return true;
}
/*
==============
GetToken
==============
*/
qboolean GetToken (qboolean crossline)
{
char *token_p;
if (tokenready) // is a token allready waiting?
{
tokenready = false;
return true;
}
// printf("script_p %x (%x)\n", script->script_p, script->end_p ); fflush( stdout );
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
tokenready = false;
// skip space, ctrl chars
skipspace:
while (*script->script_p <= 32)
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
if (*(script->script_p++) == '\n')
{
if (!crossline)
{
Error ("Line %i is incomplete\n",scriptline);
}
scriptline = ++script->line;
}
}
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
// strip single line comments
if (*script->script_p == ';' || *script->script_p == '#' || // semicolon and # is comment field
(*script->script_p == '/' && *((script->script_p)+1) == '/')) // also make // a comment field
{
if (!crossline)
Error ("Line %i is incomplete\n",scriptline);
while (*script->script_p++ != '\n')
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
}
scriptline = ++script->line;
goto skipspace;
}
// strip out matching /* */ comments
if (*script->script_p == '/' && *((script->script_p)+1) == '*')
{
script->script_p += 2;
while (*script->script_p != '*' || *((script->script_p)+1) != '/')
{
if (*script->script_p++ != '\n')
{
if (script->script_p >= script->end_p)
{
return EndOfScript (crossline);
}
scriptline = ++script->line;
}
}
script->script_p += 2;
goto skipspace;
}
// copy token to buffer
token_p = token;
if (*script->script_p == '"')
{
// quoted token
script->script_p++;
while (*script->script_p != '"')
{
*token_p++ = *script->script_p++;
if (script->script_p == script->end_p)
break;
if (token_p == &token[MAXTOKEN])
Error ("Token too large on line %i\n",scriptline);
}
script->script_p++;
}
else if ( g_bCheckSingleCharTokens && !g_sSingleCharTokens.IsEmpty() && strchr( g_sSingleCharTokens.String(), *script->script_p ) != NULL )
{
*token_p++ = *script->script_p++;
}
else // regular token
while ( *script->script_p > 32 && *script->script_p != ';')
{
if ( !ExpandMacroToken( token_p ) )
{
if ( !ExpandVariableToken( token_p ) )
{
*token_p++ = *script->script_p++;
if (script->script_p == script->end_p)
break;
if (token_p == &token[MAXTOKEN])
Error ("Token too large on line %i\n",scriptline);
}
}
}
// add null to end of token
*token_p = 0;
// check for other commands
if ( !stricmp( token, "$include" ) )
{
GetToken( false );
bool bFallbackToToken = true;
CUtlVector< CUtlString > expandedPathList;
if ( CmdLib_ExpandWithBasePaths( expandedPathList, token ) > 0 )
{
for ( int i = 0; i < expandedPathList.Count(); ++i )
{
CUtlVector< CUtlString > findFileList;
FindFileAbsoluteList( findFileList, expandedPathList[i].String() );
if ( findFileList.Count() > 0 )
{
bFallbackToToken = false;
// Only add the first set of glob matches from the first base path
for ( int j = 0; j < findFileList.Count(); ++j )
{
AddScriptToStack( const_cast< char * >( findFileList[j].String() ) );
}
break;
}
}
}
if ( bFallbackToToken )
{
AddScriptToStack( token );
}
return GetToken( crossline );
}
else if (!stricmp (token, "$definemacro"))
{
GetToken (false);
DefineMacro(token);
return GetToken (crossline);
}
else if (!stricmp (token, "$definevariable"))
{
GetToken (false);
DefineVariable(token);
return GetToken (crossline);
}
else if (AddMacroToStack( token ))
{
return GetToken (crossline);
}
return true;
}
bool CNetCDFTraj::WriteHeader(CAmberTopology* p_top)
{
if( p_top == NULL ){
INVALID_ARGUMENT("p_top == NULL");
}
if( NCID < 0 ) {
ES_ERROR("file is not opened");
return(false);
}
int dimensionID[NC_MAX_VAR_DIMS];
NumOfTopologyAtoms = p_top->AtomList.GetNumberOfAtoms();
ActualAtoms = NumOfTopologyAtoms;
CurrentSnapshot = 0;
TotalSnapshots = 0;
if( Coordinates != NULL ) {
delete Coordinates;
}
Coordinates = new float[ActualAtoms*3];
// global dimmensions
DefineDimension(AMBER_NETCDF_FRAME, NC_UNLIMITED, &TimeDID);
DefineDimension(AMBER_NETCDF_SPATIAL, 3, &SpatialDID);
DefineDimension(AMBER_NETCDF_ATOM, ActualAtoms, &CoordinateDID);
DefineDimension(AMBER_NETCDF_LABEL, AMBER_NETCDF_LABELLEN, &LabelDID);
DefineDimension(AMBER_NETCDF_CELL_SPATIAL, 3, &CellSpatialDID);
DefineDimension(AMBER_NETCDF_CELL_ANGULAR, 3, &CellAngularDID);
// put global attributes
Conventions = "AMBER";
ConventionVersion = "1.0";
PutAttributeText(NC_GLOBAL, "title", Title);
PutAttributeText(NC_GLOBAL, "application", Application);
PutAttributeText(NC_GLOBAL, "program", Program);
PutAttributeText(NC_GLOBAL, "programVersion", Version);
PutAttributeText(NC_GLOBAL, "Conventions", Conventions);
PutAttributeText(NC_GLOBAL, "ConventionVersion", ConventionVersion);
// handle definition of non-optional variables
dimensionID[0] = SpatialDID;
DefineVariable(AMBER_NETCDF_SPATIAL, NC_CHAR, 1, dimensionID, &SpatialVID);
dimensionID[0] = TimeDID;
DefineVariable(AMBER_NETCDF_TIME, NC_FLOAT, 1, dimensionID, &TimeVID);
PutAttributeText(TimeVID, "units", "picosecond");
dimensionID[0] = TimeDID;
dimensionID[1] = CoordinateDID;
dimensionID[2] = SpatialDID;
DefineVariable(AMBER_NETCDF_COORDS, NC_FLOAT, 3, dimensionID, &CoordinateVID);
PutAttributeText(CoordinateVID, "units", "angstrom");
dimensionID[0] = CellSpatialDID;
DefineVariable(AMBER_NETCDF_CELL_SPATIAL, NC_CHAR, 1, dimensionID, &CellSpatialVID);
dimensionID[0] = CellAngularDID;
dimensionID[1] = LabelDID;
DefineVariable(AMBER_NETCDF_CELL_ANGULAR, NC_CHAR, 2, dimensionID, &CellAngularVID);
// set up box coords
HasBox = p_top->BoxInfo.GetType() != AMBER_BOX_NONE;
if( HasBox ) {
dimensionID[0] = TimeDID;
dimensionID[1] = CellSpatialDID;
DefineVariable("cell_lengths", NC_DOUBLE, 2, dimensionID, &CellLengthVID);
PutAttributeText(CellLengthVID, "units", "angstrom");
dimensionID[1] = CellAngularDID;
DefineVariable("cell_angles", NC_DOUBLE, 2, dimensionID, &CellAngleVID);
PutAttributeText(CellAngleVID, "units", "degree");
}
int err,oldMode;
// set fill mode
err = nc_set_fill(NCID, NC_NOFILL, &oldMode);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set fill value (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
// end definition
err = nc_enddef(NCID);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to end definitions (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
size_t start[3];
size_t count[3];
char xyz[3];
char abc[15] = { 'a', 'l', 'p', 'h', 'a',
'b', 'e', 't', 'a', ' ',
'g', 'a', 'm', 'm', 'a' };
// setup labels
start[0] = 0;
count[0] = 3;
xyz[0] = 'x';
xyz[1] = 'y';
xyz[2] = 'z';
err = nc_put_vara_text(NCID, SpatialVID, start, count, xyz);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set spatial VID 'x', 'y' and 'z' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
start[0] = 0;
count[0] = 3;
xyz[0] = 'a';
xyz[1] = 'b';
xyz[2] = 'c';
err = nc_put_vara_text(NCID, CellSpatialVID, start, count, xyz);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set spatial cell VID 'a', 'b' and 'c' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
start[0] = 0;
start[1] = 0;
count[0] = 3;
count[1] = 5;
err = nc_put_vara_text(NCID, CellAngularVID, start, count, abc);
if (err != NC_NOERR) {
CSmallString error;
error << "unable to set angular cell VID 'alpha', 'beta ' and 'gamma' (" << nc_strerror(err) << ")";
ES_ERROR(error);
return(false);
}
return(true);
}
