#include "cddefines.h"
#include "cddrive.h"
#include "trace.h"
#include "conv.h"
#include "init.h"
#include "lines.h"
#include "pressure.h"
#include "dense.h"
#include "radius.h"
#include "struc.h"
#include "mole.h"
#include "elementnames.h"
#include "mean.h"
#include "phycon.h"
#include "called.h"
#include "parse.h"
#include "input.h"
#include "taulines.h"
#include "version.h"
#include "thermal.h"
#include "grid.h"
#include "timesc.h"
#include "cloudy.h"
#include "warnings.h"
#include "broke.h"
#include "iso.h"
#include "save.h"
#include "rfield.h"
#include "lines_service.h"
#include "service.h"
#include "parser.h"
#include "generic_state.h"
#include "prt.h"
#include "noexec.h"
#include <sys/time.h>
#include <sys/resource.h>

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Functions
int	cdDrive ()

void	cdReasonGeo (FILE *ioOUT)

void	cdWarnings (FILE *ioOUT)

void	cdCautions (FILE *ioOUT)

void	cdTimescales (double TTherm, double THRecom, double *TH2)

void	cdSurprises (FILE *ioOUT)

void	cdNotes (FILE *ioOUT)

double	cdCooling_last ()

void	cdVersion (char chString[])

void	cdDate (char chString[])

double	cdHeating_last ()

double	cdEDEN_last ()

void	cdNoExec ()

STATIC void	cdClock (struct timeval *clock_dat)

void	cdSetExecTime ()

double	cdExecTime ()

long	cdMemory ()

void	cdPrintCommands (FILE *ioOUT)

void	cdEmis (const char chLabel, realnum wavelength, double emiss, bool lgEmergent)

void	cdEmis (const LineID &line, double *emiss, bool lgEmergent)

void	cdEmis_ip (long int ipLine, double *emiss, bool lgEmergent)

int	cdColm (const char chLabel, long int ion, double theocl)

void	cdErrors (FILE *ioOUT)

void	cdDepth_depth (double cdDepth[])

void	cdPressure_depth (double TotalPressure[], double GasPressure[], double RadiationPressure[])

void	cdPressure_last (double PresTotal, double PresGas, double *PresRad)

long int	cdnZone ()

double	cdTemp_last ()

STATIC bool	set_weighting (const char chCaller, const char chWeight, int &dim)

int	cdIonFrac (const char chLabel, long int IonStage, double fracin, const char *chWeight, bool lgDensity)

long	debugLine (realnum wavelength)

long int	cdLine (const string &chLabel, realnum wavelength, double relint, double absint, int LineType)

long int	cdLine (const LineID &line, double relint, double absint, int LineType)

void	cdLine_ip (long int ipLine, double relint, double absint, int LineType)

void	cdNwcns (long int NumberWarnings, long int NumberCautions, long int NumberNotes, long int NumberSurprises, long int NumberTempFailures, long int NumberPresFailures, long int NumberIonFailures, long int NumberNeFailures)

void	cdOutput (const string &filename, const char *mode)

void	cdOutput (const string &filename, FILE *fp)

void	cdInput (const string &filename, const char *mode)

void	cdTalk (bool lgTOn)

double	cdB21cm ()

int	cdTemp (const char chLabel, long int IonStage, double TeMean, const char *chWeight)

int	cdTemp (const string &chLabel, double TeMean, const char chWeight)

void	test_cdTemp_molecules ()

int	cdRead (const string &chInputLine)

void	cdClosePunchFiles ()

Variables
static bool	lgCalled =false

static struct timeval	before

Function Documentation

double cdB21cm ( )

cdB21cm returns B as measured by 21 cm assumes tangled field weighted by n(H0)/T

References DEBUG_ENTRY, mean, SMALLFLOAT, and t_mean::TempB_HarMean.

Referenced by PrtFinal().

void cdCautions ( FILE * )

produces list of cautions

References t_warnings::chCaunln, DEBUG_ENTRY, fprintf(), and warnings.

Referenced by cdErrors(), PrtComment(), SaveLineIntensity(), SaveResults(), and ShowMe().

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STATIC void cdClock ( struct timeval * clock_dat )

References cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), and ioQQQ.

Referenced by cdExecTime(), and cdSetExecTime().

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void cdClosePunchFiles ( )

wrapper to close all save files

References CloseSaveFiles(), and DEBUG_ENTRY.

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int cdColm	(	const char *	chLabel,
		long int	ion,
		double *	theocl
	)

References caps(), cdH2_colden(), t_elementnames::chElementNameShort, column(), molezone::column, DEBUG_ENTRY, dense, elementnames, findspecieslocal(), fprintf(), ioQQQ, ipHe2s3S, ipHE_LIKE, ipHELIUM, ipHYDROGEN, iso_sp, t_dense::lgElmtOn, LIMELM, matchGeneric(), MAX2, mean, NCHLAB, genericState::q, genericState::sp, t_iso_sp::st, trimTrailingWhiteSpace(), and t_mean::xIonMean.

Referenced by lgCheckMonitors(), optimize_func(), PrtColumns(), save_average(), and SaveDo().

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double cdCooling_last ( )

cdCooling_last The returns the total cooling (erg cm^-3 s^-1) for the last computed zone

References t_thermal::ctot, and thermal.

void cdDate ( char chString[] )

cdDate The argument is a string with at least 8 char that will receive a null terminated string with the date of the current version of the code.

References Singleton< t_version >::Inst().

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void cdDepth_depth ( double cdDepth[] )

returns depth structure of previous model

Parameters

cdDepth[]

References DEBUG_ENTRY, t_struc::depth, nzone, and struc.

int cdDrive ( )

cdDrive This command actually computes a model. It returns 0 if the calculation was successful, and 1 if an error condition was encountered

References cdEXIT, cloudy(), t_input::crd, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), grid, grid_do(), InitCoreload(), t_mesh::InitMesh(), input, ioQQQ, lgcdInitCalled, t_prt::lgIncludeBlends, t_grid::lgInsideGrid, t_optimize::lgNoVary, t_optimize::lgOptimr, t_trace::lgTrace, t_optimize::lgVaryOn, t_mesh::ncells(), t_rfield::nflux, t_rfield::nflux_with_check, t_rfield::nPositive, optimize, ParseInitFile(), prt, rfield, and trace.

Referenced by cdMain().

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double cdEDEN_last ( )

cdEDEN_last return electron density of last zone

References dense, and t_dense::eden.

void cdEmis	(	const char *	chLabel,
		realnum	wavelength,
		double *	emiss,
		bool	lgEmergent
	)

cdEms obtain the local emissivity for a line, for the last computed zone

References cdEmis(), and DEBUG_ENTRY.

Referenced by cdEmis(), and cdEmis_ip().

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void cdEmis	(	const LineID &	line,
		double *	emiss,
		bool	lgEmergent
	)

References cdEmis(), DEBUG_ENTRY, t_LineSave::findline(), t_LineSave::lines, and LineSave.

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void cdEmis_ip	(	long int	ipLine,
		double *	emiss,
		bool	lgEmergent
	)

cdEms_ip obtain the local emissivity for a line with known index

Parameters

ipLine	index of the line in the stack
*emiss	the vol emissivity of this line in last computed zone
lgEmergent	intrinsic or emergent emissivities

References ASSERT, cdEmis(), DEBUG_ENTRY, t_LineSave::lines, LineSave, and t_LineSave::nsum.

Referenced by save_line().

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void cdErrors ( FILE * )

cdErrors After the calculation is completed, a summary of all error messages can be be generated by calling this routine. The argument is the output file

Parameters

[out] *ioOUT output file

References cdCautions(), cdNwcns(), cdWarnings(), t_input::chTitle, DEBUG_ENTRY, fprintf(), and input.

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double cdExecTime ( )

cdExecTime returns the elapsed time cpu time (sec) that has elapsed since cdInit called cdSetExecTime.

References before, cdClock(), cdEXIT, DEBUG_ENTRY, EXIT_FAILURE, fprintf(), ioQQQ, and lgCalled.

Referenced by cdMain(), PrtFinal(), and SaveDo().

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double cdHeating_last ( )

cdHeating_last returns the total heating (erg cm^-3 s^-1) for the last computed zone

References t_thermal::htot, and thermal.

void cdInput	(	const string &	filename = `""`,
		const char *	mode = `"r"`
	)

cdInput This tells the code where to get input. The arguments are as for the stdio.h fopen call, but the resulting file pointer is checked for validity. All further input will come from this file. If filename = "", input is switched to stdin (and mode is ignored). If this routine is not called then all input will come from stdin, the standard c input

References AS_LOCAL_ONLY_TRY, cdEXIT, DEBUG_ENTRY, ES_FAILURE, fprintf(), ioQQQ, ioStdin, NULL, and open_data().

Referenced by cdMain(), and cdPrepareExit().

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int cdIonFrac	(	const char *	chLabel,
		long int	IonStage,
		double *	fracin,
		const char *	chWeight,
		bool	lgDensity
	)

 * cdIonFrac
 * This returns the ionization fraction for any element included in the calculation. 
 * The first parameter is 4 char null terminated string giving the first 4 letters of
 * element name as spelled by Cloudy.  
 * The second parameter is an integer giving the ionization stage, 
 * 1 for atom, 2 for first ion, etc.
 * The third parameter returns the predicted ionization fraction of that ion stage.
 * The last parameter is an 8 character + null string that says either "volume" or "radius",
 * to specify whether the average should be weighted by volume or radius.
 * The return value is 0 if the routine could find the species and
 * non-zero if it failed to find the element

Parameters

*chLabel	four char string, null terminated, giving the element name
IonStage	IonStage is ionization stage, 1 for atom, up to N+1 where N is atomic number
*fracin	will be fractional ionization
*chWeight	how to weight the average, must be "VOLUME" or "RADIUS"
lgDensity	if true then weighting also has electron density, if false then only volume or radius

References caps(), t_elementnames::chElementNameShort, DEBUG_ENTRY, elementnames, exp10(), fprintf(), ioQQQ, ipHYDROGEN, LIMELM, mean, t_mean::MeanIon(), set_weighting(), and trimTrailingWhiteSpace().

Referenced by DynaPunchTimeDep(), lgCheckMonitors(), and save_average().

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long int cdLine	(	const string &	chLabel,
		realnum	wavelength,
		double *	relint,
		double *	absint,
		int	LineType = `0`
	)

cdLine This routine finds the predicted intensity of any line in the standard output.

Parameters

*chLabel	1st parameter is the species label, as it appears in the output.
wavelength	2nd parameter is the float wavelength in Angstroms, not how it appears in printout. The digits must agree with the number in the printout, but the units must be Angstroms. 3rd parameter is the predicted intensity relative to the normalization line. 4th par is the log of the predicted luminosity or intensity of the line (ergs).
*relint	5th is pointer to relative intensity, a double that is returned
*absint	6th is pointer to log of absolute intensity
LineType	- emergent or intrinsic intensity

Returns: return value: The routine returns an index (>0) of the array element within stack if it finds the line, It returns the negative of the total number of lines if it could not find the line. (this is a debugging aid) note that this returns a long int since there are LOTS of lines this also IS NOT the standard C convention for success or failure

References cdLine(), and DEBUG_ENTRY.

Referenced by cdLine(), ConvIterCheck(), IterStart(), lgCheckMonitors(), lines(), PrtComment(), PrtFinal(), and SaveDo().

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long int cdLine	(	const LineID &	line,
		double *	relint,
		double *	absint,
		int	LineType = `0`
	)

cdLine get the predicted line intensity, using LineID

Parameters

line	the line we are looking for
*relint	linear intensity relative to normalization line
*absint	log of luminosity or intensity of line
LineType	- intrinsic or emergent intensity

References cdLine_ip(), DEBUG_ENTRY, t_LineSave::findline(), and LineSave.

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void cdLine_ip	(	long int	ipLine,
		double *	relint,
		double *	absint,
		int	LineType = `0`
	)

cdLine_ip get the predicted line intensity, using index for line in stack

Parameters

ipLine
*relint	linear intensity relative to normalization line
*absint	log of luminosity or intensity of line
LineType	- intrinsic or emergent intensity

References ASSERT, t_radius::Conv2PrtInten, DEBUG_ENTRY, fprintf(), ioQQQ, t_LineSave::ipNormWavL, t_LineSave::lines, LineSave, t_LineSave::nsum, radius, and t_LineSave::ScaleNormLine.

Referenced by cdLine(), lgCheckMonitors(), PrtLineSum(), and save_line().

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long cdMemory ( )

References cdEXIT, EXIT_FAILURE, fprintf(), and ioQQQ.

Referenced by cdMain().

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void cdNoExec ( )

cdNoExec This provides option to have the code prepare the initial conditions for a model, but not actually try to compute the model. I use this when setting up a large grid so that I can quickly run through the full grid as a check that the commands are entered properly and the parameters I am going to vary do so properly. The command is then commented out when the grid is properly set up.

References DEBUG_ENTRY, t_noexec::lgNoExec, and noexec.

void cdNotes ( FILE * )

produces list of Notes

References t_warnings::chNoteln, DEBUG_ENTRY, fprintf(), and warnings.

Referenced by PrtComment().

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void cdNwcns	(	long int *	NumberWarnings,
		long int *	NumberCautions,
		long int *	NumberNotes,
		long int *	NumberSurprises,
		long int *	NumberTempFailures,
		long int *	NumberPresFailures,
		long int *	NumberIonFailures,
		long int *	NumberNeFailures
	)

cdNwcns This command returns the number of warnings, cautions, notes, surprises, assorted types of failures found the last computed model

Parameters

*NumberWarnings	the number of warnings
*NumberCautions	the number of cautions
*NumberNotes	the number of notes
*NumberSurprises	the number of surprises
*NumberTempFailures	the number of temperature convergence failures
*NumberPresFailures	the number of pressure convergence failures
*NumberIonFailures	the number of ionization convergence failures
*NumberNeFailures	the number of electron density convergence failures

References t_warnings::chBangln, t_warnings::chCaunln, t_warnings::chNoteln, t_warnings::chWarnln, conv, DEBUG_ENTRY, t_conv::nIonFail, t_conv::nNeFail, t_conv::nPreFail, t_conv::nTeFail, and warnings.

Referenced by cdErrors(), and cdMain().

long int cdnZone ( )

cdnZone returns number of zones

References nzone.

void cdOutput	(	const string &	filename = `""`,
		const char *	mode = `"w"`
	)

cdOutput This tells the code where to send output. The arguments are as for the stdio.h fopen call, but the resulting file pointer is checked for validity. All further log output will go to this file. If filename = "", output is switched to stdout (and mode is ignored). If this routine is not called then all output will go to stdout, the standard c output

References t_save::chOutputFile, DEBUG_ENTRY, ioQQQ, NULL, open_data(), and save.

Referenced by cdMain(), and cdPrepareExit().

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void cdOutput	(	const string &	filename,
		FILE *	fp
	)

References t_save::chOutputFile, DEBUG_ENTRY, ioQQQ, NULL, and save.

void cdPressure_depth	(	double	TotalPressure[],
		double	GasPressure[],
		double	RadiationPressure[]
	)

cdPressure_depth This returns the pressure and its constituents for the last iteration. space was allocated in the calling routine for the vectors - before calling this, cdnZone should have been called to get the number of zones, then space allocated for the arrays

Parameters

TotalPressure[]	total pressure, all forms
GasPressure[]	gas pressure
RadiationPressure[]	radiation pressure

References DEBUG_ENTRY, t_struc::GasPressure, nzone, t_struc::pres_radiation_lines_curr, t_struc::pressure, and struc.

void cdPressure_last	(	double *	TotalPressure,
		double *	GasPressure,
		double *	RadiationPressure
	)

cdPressure_last

This returns the pressure and its constituents for the last computed zone.

Parameters

*TotalPressure	total pressure, all forms
*GasPressure	gas pressure
*RadiationPressure	radiation pressure

References DEBUG_ENTRY, t_pressure::pres_radiation_lines_curr, t_pressure::PresGasCurr, pressure, and t_pressure::PresTotlCurr.

void cdPrintCommands ( FILE * )

cdPrintCommands( FILE *) This routine prints all input commands into file whose handle is the argument

Parameters

*ioOUT [out] output file handle

References t_input::crd, fprintf(), and input.

Referenced by ShowMe().

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int cdRead ( const string & )

cdRead This sends commands to the code. The normal set of commands described in Part I of Hazy must be entered as a C-style or C++-style string. These strings are then fed to Cloudy with this command. The function returns the number of commands that can still be entered before the command stack is full. The code will stop if you try to continue giving it commands after the command has returned zero. This return value is the opposite of the standard - a non-zero return is normal

References AS_SILENT_TRY, cdEXIT, CardInfo::chCardSav, t_save::chOutputFile, t_input::crd, t_input::curInclLevel, DEBUG_ENTRY, EXIT_FAILURE, exp10(), fprintf(), Parser::getNumberDefault(), grid, Parser::hasCommand(), input, ioQQQ, lgcdInitCalled, t_grid::lgGrid, t_prt::lgIncludeBlends, t_input::lgInitPresent, lgIsCommentSeq(), t_optimize::lgNoVary, t_optimize::lgOptimr, t_prt::lgPrintTime, t_input::lgSetNoBuffering, t_trace::lgTrace, t_optimize::lgVaryOn, t_grid::nGridCommands, Parser::nMatch(), NULL, open_data(), optimize, ParseInit(), prt, rfield, save, Parser::setline(), t_mesh::setResolutionScaleFactor(), StripComment(), trace, and trimTrailingWhiteSpace().

Referenced by cdMain(), and ParseInitFile().

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void cdReasonGeo ( FILE * )

This prints the reason why the model stopped, and the model geometry, on the io file pointed to by the file handle

References t_warnings::chRgcln, DEBUG_ENTRY, fprintf(), and warnings.

Referenced by PrtComment().

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void cdSetExecTime ( )

normally called by cdInit, this routine sets initial variables for times

References before, cdClock(), and lgCalled.

Referenced by cdInit().

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void cdSurprises ( FILE * )

produces list of surprises

References broke, t_warnings::chBangln, DEBUG_ENTRY, fprintf(), Singleton< FixitList >::Inst(), t_broke::lgPrintFixits, FixitList::list, and warnings.

Referenced by PrtComment().

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void cdTalk ( bool )

cdTalk tells the code whether or not to produce any of its normal output, If the argument is true (or if it is not called at all) it produces output, produces no output if it is false

References called, cpu, DEBUG_ENTRY, t_cpu::i(), t_cpu_i::lgMPI_talk(), t_called::lgTalk, and t_called::lgTalkForcedOff.

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int cdTemp	(	const char *	chLabel,
		long int	IonStage,
		double *	TeMean,
		const char *	chWeight
	)

Todo:: 2 this should have a last argument like cdIonFrac for whether or not weighting is wrt electron density

References caps(), t_elementnames::chElementNameShort, DEBUG_ENTRY, elementnames, TransitionProxy::Emis(), TransitionList::Emis(), exp10(), fprintf(), HFLines, ioQQQ, ipH1s, ipH2p, ipH_LIKE, ipHYDROGEN, iso_sp, LIMELM, mean, t_mean::MeanIon(), set_weighting(), SMALLFLOAT, EmissionProxy::TauCon(), t_mean::TempEdenMean, t_mean::TempH_21cmSpinMean, t_mean::TempHarMean, t_mean::TempIonMean, t_mean::TempMean, t_iso_sp::trans(), and trimTrailingWhiteSpace().

Referenced by DynaPunchTimeDep(), lgCheckMonitors(), optimize_func(), PrtFinal(), save_average(), save_DT(), test_cdTemp_molecules(), and timestep_next().

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int cdTemp	(	const string &	chLabel,
		double *	TeMean,
		const char *	chWeight
	)

cdTemp

* This routine finds the mean electron temperature for any ionization stage 
* It returns 0 if it could find the species, 1 if it could not find the species.
* The first argument is a string that gives the species in chemical notation,
* or a special label.
* This second argument will be returned as result.
* Last parameter is either "VOLUME" or "RADIUS" to give weighting.
*
* The special labels are the following:
* - "21CM" will return the temperature wrt the atomic hydrogen density.
* - "SPIN" will return the excitation temperature of the 21cm hyperfine states.
* - "OPTI" will return the temperature from the ratio of the 21cm and Lya
*    optical depths, see AGN3, Section 5.5.
* - "H2" will return the temperature weighted wrt the H2 density.
* - "TENE" will return the temperature weighted wrt the electron density.
* - "" will return a simple mean of the kinetic temperature.
*

Parameters

chLabel[in]	String for species or special label.
TeMean[out]	Temperature result.
chWeight[in]	String for weighting the average; must be "VOLUME" or "RADIUS".

Returns: 0 for success, 1 for failure.

References caps(), DEBUG_ENTRY, elem_symbol_to_index(), TransitionProxy::Emis(), TransitionList::Emis(), exp10(), fprintf(), HFLines, ioQQQ, ipH1s, ipH2p, ipH_LIKE, ipHYDROGEN, isAtomicIonValid(), isMolecule(), iso_sp, isSpecies(), LIMELM, mean, t_mean::MeanIon(), t_mean::MeanMoleculeTemp(), parse_chemical(), set_weighting(), SMALLFLOAT, EmissionProxy::TauCon(), t_mean::TempEdenMean, t_mean::TempH_21cmSpinMean, t_mean::TempHarMean, t_mean::TempMean, t_iso_sp::trans(), and trimTrailingWhiteSpace().

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double cdTemp_last ( )

cdTemp_last returns the temperature of the last zone on last iteration

References phycon, and t_phycon::te.

void cdTimescales	(	double *	TTherm,
		double *	THRecom,
		double *	TH2
	)

cdTimescales returns the longest thermal, recombination, and H2 formation timescales that occurred in the previous model

Parameters

*TTherm	the thermal cooling timescale
*THRecom	the hydrogen recombination timescale
*TH2	the H2 formation timescale

References DEBUG_ENTRY, MAX2, t_timesc::time_H2_Dest_longest, t_timesc::time_H2_Form_longest, t_timesc::time_Hrecom_long, t_timesc::time_therm_long, and timesc.

void cdVersion ( char chString[] )

cdVersion The argument is a string with at least 8 characters that will receive a null terminated string with the version number of the code.

References Singleton< t_version >::Inst().

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void cdWarnings ( FILE * )

These routines produce lists of warnings, cautions, notes, surprises These are the routines that are called by cdErrors. Normally cdErrors and not these routines would be called by the user.

References t_warnings::chWarnln, DEBUG_ENTRY, fprintf(), and warnings.

Referenced by cdErrors(), optimize_func(), PrtComment(), SaveLineIntensity(), SaveResults(), and ShowMe().

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long debugLine ( realnum wavelength )

debugLine provides a debugging hook into the main line array loops over whole array and finds every line that matches length, the wavelength, the argument to the function put breakpoint inside if test return value is number of matches, also prints all matches

Parameters