Table from data in 'sortsrc.list'
Filename | Subroutine | Description
--- | --- | ---
abundances.c | AbundancesPrt | print all abundances, both gas phase and grains
abundances.c | AbundancesSet | sets initial abundances after parameters are entered by reading input
abundances.c | AbundancesTable | interpolate on table of points to do 'element table' command,
abundances.c | PrtElem | print chemical composition at start of calculation
abund_starburst.c | abund_starburst | generate abundance set from Fred Hamann's starburst evolution grid
age_check.c | AgeCheck | check various timescales after calculation complete to confirm time steady OK
assert_results.c | InitAssertResults | this must be called first, done at startup of ParseCommands
assert_results.c | lgCheckAsserts | checks asserts, last thing cloudy calls, returns TRUE if all are ok, FALSE if problems
assert_results.c | ParseAssertResults | - parse input stream
atmdat_2photon.c | atmdat_2phot_rate | hydrogen two photon emission, including induced emission
atmdat_2photon.c | atmdat_2phot_shapefunction | two photon emission function for hydrogen
atmdat_3body.c | atmdat_3body | derive three-body recombination coefficients
atmdat_3body.c | da | interpolate on three body recombination by Steve Cota
atmdat_char_tran.c | ChargTranEval | fill in the HCharExcIonOf and Rec arrays with Kingdon's fitted CT with H
atmdat_char_tran.c | ChargTranPun | punch charge transfer coef
atmdat_char_tran.c | ChargTranSumHeat | sum net heating due to charge transfer, called in HeatSum
atmdat_char_tran.c | HCTIon | H charge transfer ionization
atmdat_char_tran.c | HCTRecom | H charge transfer recombination
atmdat_char_tran.c | MakeHCTData | holds data for charge tranfer fits
atmdat_coll_ion.c | atmdat_coll_ion | D Verner's routine to compute collisional ionization rate coefficients
atmdat_dielrec_fe.c | atmdat_dielrec_fe | Dielectronic recombination rates for Fe from Arnaud & Raymond 1992
atmdat_dielsupres.c | atmdat_DielSupres | derive scale factors for suppression of Burgess dielectronic recombination
atmdat_HS_caseb.c | atmdat_HS_caseB | - interpolate on line emissivities from Storey & Hummer tables for hydrogen
atmdat_h_photocs_fit.c | atmdat_hpfit | state specific photoionization cross sections for model hydrogen atom for any level up through NHYDRO_MAX_LEVEL defined 401L in cddefines.h
atmdat_H_phot_cs.c | atmdat_H_phot_cs | -0 hydrogen cross sections
atmdat_h_rad_rec.c | atmdat_H_rad_rec | calculates state-specific recombination rates for hydrogen and hydrogen-like ions
atmdat_ligbar.c | ligbar | obtain collision strength for any Li-sequence line
atmdat_lines_setup.c | lines_setup | convert level 1 and level 2 line parameters and pointers into internal form used by code, line data were read in by atmdat_readin
atmdat_outer_shell.c | atmdat_outer_shell | determine outer shell, and statistical weights of that and higher ion, for any ion written by Dima Verner
atmdat_phfit.c | atmdat_phfit | derive photoionization cross sectoins for first 30 elements
atmdat_rad_rec.c | atmdat_rad_rec | calculates rates of radiative recombination for all ions
atmdat_readin.c | atmdat_readin | read in some data files, but only if this is very first call, called by Cloudy
atmdat_rec_lines.c | atmdat_rec_lines | effective recombination coefficients for lines of C, N, O, by D. Verner /
atom_fe2ovr.c | atoms_fe2ovr | compute FeII overlap with Lya
atom_fe2ovr.c | fe2par | evaluate FeII partition function
atom_fe2ovr.c | Fe2_ovr_DataInit | storing energy levels for Fred's FeII ground
atom_feii.c | AssertFeIIDep | called by assert feii depart coef command
atom_feii.c | FeIIAccel | called by rt_line_driving to compute radiative acceleration due to FeII lines
atom_feii.c | FeIIAddLines | save accumulated FeII intensities called by lineset4
atom_feii.c | FeIIBandsCreate | returns number of feii bands
atom_feii.c | FeIICollRatesBoltzmann | evaluate collision strenths, both interpolating on r-mat and creating g-bar find Boltzmann factors, evaluate collisional rate coefficients
atom_feii.c | FeIIContCreate | create FeII continuum bins to add lines into ncell cells between wavelengths lambda low and high, returns number of cells used
atom_feii.c | FeIICreate | read in needed data from file convert form of feii data, as read in from file within routine FeIICreate into physical form. called by atmdat_readin
atom_feii.c | FeIIIntenZero | zero out intensity of FeII atom
atom_feii.c | FeIILevelPops | main feii routine, called by CoolIron to evaluate iron cooling
atom_feii.c | FeIILyaPump | find rate of Lya excitation of the FeII atom
atom_feii.c | FeIIOvrLap | handle overlapping FeII lines
atom_feii.c | FeIIPoint | called by ContCreatePointers to create pointers for lines in large FeII atom
atom_feii.c | FeIIPrint | print feii information
atom_feii.c | FeIIPrint | print output from large feii atom, called by prtzone
atom_feii.c | FeIIPun1Depart | send the departure coef for physical level nPUN to unit ioPUN
atom_feii.c | FeIIPunchLevels | punch feii levels and energies
atom_feii.c | FeIIPunchLines | punch feii lines at end of calculation, if punch verner set, called by dopunch
atom_feii.c | FeIIPunchLineStuff | include FeII lines in punched optical depths, etc, called from PunchLineStuff
atom_feii.c | FeIIPunData | punch line data
atom_feii.c | FeIIPunDepart | punch some departure coef for large atom, set with punch feii departure command
atom_feii.c | FeIIPunPop | - punch level populations
atom_feii.c | FeIIReset | reset some variables, called by zero
atom_feii.c | FeIIRTMake | called by RT_line_all, does large FeII atom radiative transfer
atom_feii.c | FeIISumBand | sum up large FeII emission over certain bands, called in lineset4
atom_feii.c | FeIITauInc | called once per zone in RT_tau_inc to increment large FeII atom line optical depths
atom_feii.c | FeIIZero | initialize some variables, called by zero one time before commands parsed
atom_feii.c | FeII_Colden | maintain H2 column densities within X
atom_feii.c | FeII_LineZero | zero out storage for large FeII atom, called by tauout
atom_feii.c | FeII_OTS | do ots rates for FeII, called by RT_OTS
atom_feii.c | FeII_RTOut | do outward rates for FeII, called by RT_diffuse
atom_feii.c | FeII_RT_tau_reset | reset optical depths for large FeII atom, called by update after each iteration
atom_feii.c | ParseAtomFeII | parse the atom FeII command
atom_hyperfine.c | H21cm | computes rate for H 21 cm from upper to lower excitation by atomic hydrogen
atom_hyperfine.c | H21cm_electron | compute H 21 cm rate from upper to lower excitation by electrons - call by CoolEvaluate
atom_hyperfine.c | H21cm_H_atom | - evalutate H atom spin changing collision rate, called by CoolEvaluate
atom_hyperfine.c | h21_t_ge_20 | compute rate for H 21 cm from upper to lower excitation by atomic hydrogen
atom_hyperfine.c | h21_t_lt_20 | compute rate for H 21 cm from upper to lower excitation by atomic hydrogen
atom_hyperfine.c | HyperfineCreat | establish space for hf arrays, reads atomic data from hyperfine.dat
atom_hyperfine.c | HyperfineCS | - returns collision strengths for hyperfine struc transitions
atom_level2.c | atom_level2 | do level population and cooling for two level atom, side effects: set elements of EmLine struc cooling via CoolAdd( chLab, (long)t->WLAng , t->cool); cooling derivative
atom_level3.c | atom_level3 | compute three level atom, 10, 21, and 20 are line
atom_leveln.c | atom_levelN | compute an arbitrary N level atom
atom_oi.c | atom_oi | drive the solution of OI level populations, Ly-beta pumping
atom_oi.c | oi_level_pops | get OI level population with Ly-beta pumping
atom_pop2.c | atom_pop2 | do level population for simple two level atom, no radiative transfer
atom_pop3.c | atom_pop3 | solve 3-level atom without radiative transfer, returns pops of level 2 and 3
atom_pop5.c | atom_pop5 | do five level atom population and cooling
atom_seq_beryllium.c | AtomSeqBeryllium | compute level populations and emissivity for Be-sequence ions
atom_seq_boron.c | AtomSeqBoron | compute cooling from 5-level boron sequence model atom
cddrive.c | cdCautions | print out all cautions after calculation, on arbitrary io unit
cddrive.c | cdClosePunchFiles | closes all the punch files that have been used
cddrive.c | cdColm | get the column density for a constituent
cddrive.c | cdDate | - puts date of code into string
cddrive.c | cdDLine | get the predicted emergent line intensity, also index for line in stack
cddrive.c | cdDrive | main routine to call cloudy under all circumstances)
cddrive.c | cdDrive | main routine to call cloudy under all circumstances)
cddrive.c | cdEms | obtain the local emissivity for a line, for the last computed zone
cddrive.c | cdEms_ip | obtain the local emissivity for a line with known index
cddrive.c | cdErrors | produce summary of all warnings, cautions, etc, on arbitrary io unit
cddrive.c | cdExecTime | any routine can call this, find the time [s] since cdInit was called ) prints all input commands into file
cddrive.c | cdGetCooling_last | routine to query results and return cooling of last zone
cddrive.c | cdGetDepth_depth | get depth structure from previous iteration
cddrive.c | cdGetHeating_last | routine to query results and return heating of last zone
cddrive.c | cdGetnZone | gets number of zones
cddrive.c | cdGetPressure_last | routine to query results and return pressure of last zone
cddrive.c | cdGetTemp_last | routine to query results and return temperature of last zone
cddrive.c | cdIonFrac | get ionization fractions for a constituent
cddrive.c | cdLine | get the predicted line intensity, also index for line in stack
cddrive.c | cdLineListPunch | create a file with a list of all emission lines punched, and their index within the emission line stack
cddrive.c | cdLine_ip | get the predicted line intensity, using index for line in stack
cddrive.c | cdNoExec | call this routine to tell code not to actually execute
cddrive.c | cdNotes | print stack of notes about current calculation
cddrive.c | cdNwcns | get the number of cautions and warnings, to tell if calculation is ok
cddrive.c | cdOutp | redirect output to arbitrary Fortran unit number
cddrive.c | cdPrtWL | print line wavelengths in Angstroms in the standard format - just a wrapper
cddrive.c | cdRead | routine to read in command lines when cloudy used as subroutine
cddrive.c | cdReasonGeo | wrte why the model stopped and type of geometry on io file
cddrive.c | cdSurprises | print out all surprises on arbitrary unit number
cddrive.c | cdTalk | tells the code whether to print results or be silent
cddrive.c | cdTemp | get mean electron temperature for any element
cddrive.c | cdTimescales | returns thermal, recombination, and H2 foramtion timescales
cddrive.c | cdVersion | produces string that gives version number of the code
cddrive.c | cdWarnings | write all warnings entered into comment stack
cddrive.c | debugLine | provides a debugging hook into the main line array
cdgetlinelist.c | cdGetLineList | routine to read in master list of emission line wavelengths and ids, for generating loc grids, someday add cdGetNLRLineList
cdinit.c | cdEXIT | exit handler to terminate calculation, called at end of calculation
cdinit.c | cdInit | routine to initialize variables, called at start of calculation
cdspec.c | cdSPEC | returns the spectrum needed for Keith Arnaud's XSPEC
cdspec.c | Spec_cont | called by cdSPEC to generate actual spectrum
cloudy.c | BadStart | announce that things are so bad the calculation cannot even start
cloudy.c | cloudy | the main routine, this IS Cloudy, ret 0 normal exit, 1 error exit, called by maincl when used as standalone program
cont_createmesh.c | ChckFill | perform sanity check confirming that the energy array has been properly filled
cont_createmesh.c | ContCreateMesh | calls fill to set up continuum energy mesh if first call, otherwise reset to original mesh
cont_createmesh.c | fill | define the continuum energy grid over a specified range
cont_createmesh.c | read_continuum_mesh | read the continuum definition from the file continuum_mesh.dat
cont_createmesh.c | rfield_opac_malloc | MALLOC space for opacity arrays
cont_createpointers.c | ContBandsCreate | - read set of continuum bands to enter total emission into line stack
cont_createpointers.c | ContCreatePointers | set up pointers for lines and continua called by cloudy after input read in and continuum mesh has been set
cont_createpointers.c | fiddle | adjust energy bounds of certain cells so that match ionization edges exactly
cont_createpointers.c | ipShells | assign continuum energy pointers to shells for all atoms, called by ContCreatePointers
cont_createpointers.c | LimitSh | sets upper energy limit to subshell integrations
cont_ffun.c | ffun | evaluate total flux for sum of all continuum sources
cont_ffun.c | ffun1 | derive flux at a specific energy, for one continuum
cont_ffun.c | ReadSB99 | called to work the table starburst command
cont_ffun.c | ReadTable | called by TABLE READ to read in continuum from PUNCH TRANSMITTED CONTINUUM
cont_gammas.c | GammaBn | evaluate photoionization rate for single shell with induced recomb
cont_gammas.c | GammaBnPL | evaluate photoionization rate for single shell with induced recomb
cont_gammas.c | GammaK | evaluate photoionization rate for single shell
cont_gammas.c | GammaPL | evaluate photoionization rate for power law photo cross section
cont_gammas.c | GammaPrt | special version of gamma function to print strong contributors
cont_gammas.c | GammaPrtRate | print photo rates for all shells of a ion and element
cont_gammas.c | GammaPrtShells | for the element nelem and ion, print total photo rate, subshells, and call GamaPrt for important subshells
cont_ipoint.c | ipContEnergy | generate unique pointer to energy within continuum array continuum energy in Rydbergs
cont_ipoint.c | ipFineCont | returns array index within fine energy mesh
cont_ipoint.c | ipLineEnergy | generate unique pointer to line energy within energy mesh line energy in Rydbergs
cont_ipoint.c | ipoint | returns pointer to any energy within energy mesh
cont_negative.c | ContNegative | sanity check for negative continuum intensities
cont_pump.c | ContPump | local continuum pumping rate radiative transfer for all lines
cont_pump.c | con_pump_op | routine used to get continuum pumping of lines used in ContPump in call to qg32
cont_pump.c | vfun | approximate form of Voit function
cont_setintensity.c | conorm | normalize continuum to proper intensity
cont_setintensity.c | ContSetIntensity | derive intensity of incident continuum
cont_setintensity.c | extin | do extinction of incident continuum as set by extinguish command
cont_setintensity.c | pintr | integrates L for any continuum between two limits, used for normalization
cont_setintensity.c | ptrcer | show continuum pointers in real time following drive pointers command
cont_setintensity.c | qintr | integrates Q for any continuum between two limits, used for normalization
cont_setintensity.c | sumcon | sums L and Q for net incident continuum
conv_base.c | ConvBase | main routine to drive ionization solution for all species, find total opacity called by ConvIoniz
conv_base.c | lgConverg | check whether ionization of element nelem has converged
conv_eden_ioniz.c | ConvEdenIoniz | called by ConvTempIonz, calls ConvIoniz solving for eden
conv_eden_ioniz.c | lgConvEden | returns true if electron density is converged
conv_fail.c | ConvFail | handle conergece failure
conv_init_solution.c | ConvInitSolution | drive search for initial temperature, for illuminated face
conv_ioniz.c | ConvIoniz | called by ConvEdenIonz, it calls ConvBase until converged
conv_itercheck.c | ConvIterCheck | check whether model has converged or whether more iterations are needed - implements the iter to converg comnd
conv_pres_temp_eden_ioniz.c | ConvFail | handle conergece failure
conv_pres_temp_eden_ioniz.c | ConvPresTempEdenIoniz | solve for current pressure, calls PressureChange, ConvTempEdenIonize, called by cloudy
conv_temp_eden_ioniz.c | ConvTempEdenIoniz | determine temperature, called by ConPresTempEdenIoniz, calls ConvEdenIoniz to get electron density and ionization
conv_temp_eden_ioniz.c | CoolHeatError | evaluate ionization, and difference in heating and cooling, for temperature temp
conv_temp_eden_ioniz.c | lgConvTemp | returns true if heating-cooling is converged
conv_temp_eden_ioniz.c | MakeDeriv | derive numerical derivative of heating minus cooling
conv_temp_eden_ioniz.c | PutHetCol | save heating, cooling, and temperature in stack for numerical derivatives
cool_alum.c | CoolAlum | compute aluminum cooling
cool_argo.c | CoolArgo | compute argon cooling
cool_calc.c | CoolCalc | compute calcium cooling
cool_carb.c | CoolCarb | evaluate total cooling due to carbon
cool_chlo.c | CoolChlo | compute chlorine cooling
cool_chro.c | CoolChro | compute chromium cooling
cool_coba.c | CoolCoba | compute cobalt cooling
cool_dima.c | ColStrGBar | generate g-bar collision strengths for level 2 line2
cool_dima.c | CoolDima | compute cooling due to level 2 lines
cool_etc.c | CoolAdd | add coolants to the cooling stack, called in evaluation of cooling function
cool_etc.c | CoolSum | total cooling from all entries into cooling stack
cool_etc.c | CoolZero | set cooling and heating stack to zero
cool_eval.c | CoolEvaluate | main routine to call others, to evaluate total cooling
cool_fluo.c | CoolFluo | evaluate total cooling due to fluorine
cool_iron.c | CoolIron | compute iron cooling
cool_iron.c | Fe11Lev5 | compute populations and cooling due to 5 level Fe 11 ion
cool_iron.c | Fe13Lev5 | compute populations and cooling due to 5 level Fe 13 ion
cool_iron.c | fe14cs | compute collision strengths for forbidden transitions
cool_iron.c | Fe2_cooling | compute cooling due to FeII emission
cool_iron.c | Fe3Lev14 | compute populations and cooling due to 14 level Fe III ion
cool_iron.c | Fe4Lev12 | compute populations and cooling due to 12 level Fe IV ion
cool_iron.c | Fe7Lev8 | compute populations and cooling due to 8 level Fe VII ion
cool_iron.c | Fe_10_11_13_cs | evaluate collision stength for Fe
cool_magn.c | CoolMagn | compute magnesium cooling
cool_mang.c | CoolMang | compute manganese cooling
cool_neon.c | CoolNeon | evaluate total cooling due to neon
cool_nick.c | CoolNick | compute nickel cooling
cool_nitr.c | CoolNitr | evaluate total cooling due to nitrogen
cool_oxyg.c | CoolOxyg | evaluate total cooling due to oxygen
cool_phos.c | CoolPhos | compute phosphorus cooling
cool_pota.c | CoolPota | compute potassium cooling
cool_pr.c | coolpr | stores coolants before block printed, when printing cooling agents
cool_punch.c | CoolPunch | punch coolants
cool_scan.c | CoolScan | compute scandium cooling
cool_sili.c | CoolSili | compute silicon cooling
cool_sodi.c | CoolSodi | compute sodium cooling
cool_sulf.c | CoolSulf | compute sulphur cooling
cool_sulf.c | S2cs | compute [CoolHeavy] collision strengths compute collision strengths for [SII] transitions w/in S II ground term. From >>refer s2 cs Ramsbottom, C.A., Bell, K.L., Stafford, R.P. 1996, At. Data Nucl. Data Tables, 63, 57
cool_tita.c | CoolTita | compute titanium cooling
cool_vana.c | CoolVana | compute vanadium cooling
cool_zinc.c | CoolZinc | compute zinc cooling
dynamics.c | DynaCreateArrays | allocate some space needed to save the dynamics structure variables, called from DynaCreateArrays
dynamics.c | DynaEndIter | called at end of iteration when advection is turned on
dynamics.c | DynaEndZone | called at end of zone calculation when advection is turned on
dynamics.c | DynaIonize | called from ionize to evaluate advective terms for current conditions
dynamics.c | DynaPresChngFactor | called from PressureChange to evaluate new density needed for current conditions and wind solution, returns ratio of new to old density
dynamics.c | DynaPrtZone | - called to print zone results
dynamics.c | DynaPunch | punch output for dynamics solutions
dynamics.c | DynaPunch | punch info related to advection
dynamics.c | DynaStartZone | called at start of zone calculation when advection is turned on
dynamics.c | DynaZero | zero some dynamics variables, called from zero.c
fabden.c | fabden | called by dlaw command, returns density for any density law
grains.c | grain | main routine to converge grains thermal solution
grains_qheat.c | GrainMakeDiffuse | main routine for generating the grain diffuse emission, called by RT_diffuse
heat_punch.c | HeatPunch | punch contributors to local heating, with punch heat command, called by punch_do
heat_sum.c | HeatSum | evaluate heating and secondary ionization for current conditions
heat_sum.c | HeatZero | is called by ConvBase
helike.c | AGN_He1_CS | routine to punch table needed for AGN3 - collision strengths of HeI
helike.c | ContinuumLowering | - limit max prin. quan. no. due to continuum lowering processes
helike.c | defect | - calculate quantum defect.
helike.c | HeCreate | create he-like series, called by ContCreatePointers
helike.c | he_assign | - assigns quantum numbers and indices to iso.quant_desig and QuantumNumbers2Index, respectively
helike.c | he_energy | - calculates energy of a given level.
helike.c | printstuff | - in helike.h, printflag determines what will be printed.
helike.c | prt_He_like_DeparCoef | routine to print departure coefficients for he-like species
helike.c | prt_He_like_Pops | routine to print level populations for he-like species
helike_cs.c | AtomCSInterp | do the atom
helike_cs.c | CS_l_mixing_PS64 | - find rate for l-mixing collisions by protons, for neutrals
helike_cs.c | HeCollid | evaluate collisional rates
helike_cs.c | HeCSInterp | interpolate on He1 collision strengths
helike_cs.c | IonCSInterp | do the ions
helike_einsta.c | AngerJ | - used by scqdri
helike_einsta.c | DoFSMixing | - applies a fine structure mixing approximation to A's. To be replaced by method that treats the entire rate matrix.
helike_einsta.c | ForbiddenAuls | calculates transition probabilities for forbidden transitions.
helike_einsta.c | he_1trans | compute Aul for given line
helike_einsta.c | Jint | - used by scqdri
helike_einsta.c | ritoa | - converts the square of the radial integral for a transition (calculated by scqdri) to the transition probability, Aul.
helike_einsta.c | scqdri | - stands for Semi-Classical Quantum Defect Radial Integral
helike_level.c | HeLikeError | fills uncertainty arrays
helike_level.c | HeLikeLevel | level populations
helike_recom.c | cross_section | - calculates the photoionization cross_section for a given level and photon energy
helike_recom.c | HelikeCheckRecomb | - called by SanityCheck to confirm that recombination coef are ok, return value is relative error between new calculation of recom, and interp value
helike_recom.c | HeRecom | - do recomb coef for He, called by HeLike
helike_recom.c | He_cross_section | returns cross section (cm^-2), given EgammaRyd, the photon energy in Ryd, ipLevel, the index of the level, 0 is ground, 3 within 2 3P, nelem is charge, equal to 1 for Helium this is a wrapper for cross_section
helike_recom.c | He_RRCoef_Te | evaluated radiative recombination coef at some temperature
helike_recom.c | radrecomb | - calculates radiative recombination coefficients.
helike_recom.c | Recomb_Seaton59 | - find recombination for given n,using Seaton 59 approximation. The following three are needed by Recomb_Seaton59: ExponentialInt X1Int X2Int
helike_recom.c | RecomInt | - Integral in milne relation. Called by qg32.
highen.c | highen | do high energy radiation field - gas interaction, Compton scattering, etc
hydrobranch.c | HydroBranch | compute branching ratios for Jason Ferguson's model hydrogen atom
hydrocollid.c | C6cs123 | line collision rates for lower levels of hydrogenic carbon, n=1,2,3
hydrocollid.c | Ca20cs123 | line collision rates for lower levels of hydrogenic calcium, n=1,2,3
hydrocollid.c | Fe26cs123 | line collision rates for lower levels of hydrogenic iron, n=1,2,3
hydrocollid.c | H1cs123 | hydrogen collision data levels involving 1s,2s,2p,3.
hydrocollid.c | HCSAR_interp | interpolate on collision strengths
hydrocollid.c | He2cs123 | line collision strengths for lower levels of helium ion, n=1,2,3, by K Korista
hydrocollid.c | Hydcs123 | Hydrogenic de-excitation collision rates n=1,2,3
hydrocollid.c | HydroCollid | evaluate collision rate for model hydrogen atom
hydrocollid.c | Ne10cs123 | line collision rates for lower levels of hydrogenic neon, n=1,2,3
hydroeinsta.c | HydroEinstA | calculates Einstein A's from osillator strengths
hydrogenic.c | Hydrogenic | main routine to call HydroLevel and determine model hydrogen atom level balance
hydrogenic.c | HydroRenorm | - renormalize H so that it agrees with the chemistry
hydrolevel.c | HydroLevel | calls HydroLevelPop or HydroT2Low to solve for ionization balance and level populations of model hydrogen atom
hydrolevel.c | PrtHydroTrace1 | print trace info for hydrogen-like species
hydrolevelpop.c | HydroLevelPop | solve for ionization balance level populations of model hydrogen atom
hydrooscilstr.c | HydroOscilStr | computes hydrogenic oscillator strengths, used in the function hdexct.
hydroreccool.c | HydroRecCool | hydrogen recombination cooling, called by iso_cool
hydrorecom.c | HydroRecom | photoionization, recombination, radiative rates for model hydrogen atom
hydrot2low.c | HydroT2Low | called to do hydrogenic level populations when temp too low for matrix, forces total of level populations to add up to iso.xIonSimple[ipH_LIKE][nelem], so results of this routine will always agree with that value
hydro_bauman.c | In this version, quantites that would normal cause a 64-bit floating point processor
hydro_bauman.c | ( or is it precision ). We use LOG_10 for convenience.
hydro_bauman.c | hv | calculates photon energy in ergs for n -> n' transitions for H and H-like ions
hydro_bauman.c | H_Einstein_A_lin | calculates Einstein A for any nlz
hydro_bauman.c | H_photo_cs_lin | returns hydrogenic photoionization cross section in cm-2
hydro_bauman.c | other | version begins to fail. The trade-off is, of course, lower accuracy
hydro_bauman.c | This | allows us to use an upper principle quantum number `n' greater than which the
hydro_bauman.c | to | either underflow or overflow are evaluated using logs instead of floating point math.
hydro_vs_rates.c | Hion_colldeexc_cs | collision strength for collisional de-excitation for any levels of hydrogenic Z
hydro_vs_rates.c | Hion_coll_ioniz_ratecoef | calculate hydrogenic ionization rates for ions with all n, and Z
hydro_vs_rates.c | hydro_vs_deexcit | compute collision strength for collisional deexcitation for hydrogen atom, from >>refer H1 collision Vriens, L., & Smeets, A.H.M. 1980, Phys Rev A 22, 940 hydro_vs_ioniz generate hydrogenic collisional ionization rate coefficients for quantum number n
hypho.c | hypho | - create hydrogenic photoionization cross sections
input_init.c | input_init | initial input_readarray array for storing line images at start of calculation line image is up and low case
ion_alumi.c | IonAlumi | ionization balance for aluminum
ion_argon.c | IonArgon | compute ionization balance of argon
ion_beryl.c | IonBeryl | ionization balance for beryllium
ion_boron.c | IonBoron | ionization balance for boron
ion_calci.c | IonCalci | perform ionization balance for calcium
ion_carbo.c | IonCarbo | compute ionization balance for carbon
ion_chlor.c | IonChlor | ionization balance for chlorine
ion_chrom.c | IonChrom | do ionization balance for chromium
ion_cobal.c | IonCobal | do ionization balance for cobalt
ion_collis.c | ion_collis | fill in collisional ionization rates, and resulting cooling
ion_coppe.c | IonCoppe | do ionization balance for copper The testing can be commented out
ion_DR_Badnell.c | init < 0 or init >302 or final < 0 or final > 302
ion_DR_Badnell.c | '-1': the transition is not defined
ion_DR_Badnell.c | '-2': initial <= final
ion_DR_Badnell.c | '99': unknown invalid entries
ion_DR_Badnell.c | It returns
ion_fluor.c | IonFluor | compute ionization balance for fluorine
ion_helium.c | IonHelium | solve ionization balance for helium
ion_iron.c | IonIron | ionization balance for iron
ion_lithi.c | IonLithi | compute ionization balance for lithium
ion_magne.c | IonMagne | ionization balance for magnesium
ion_manga.c | IonManga | derive ionization balance for manganese
ion_neon.c | IonNeon | ionization balance for neon
ion_nicke.c | IonNicke | ionization balance for nickel
ion_nitro.c | IonNitro | ionization balance for nitrogen
ion_oxyge.c | IonOxyge | derive ionization balance for oxygen
ion_phosi.c | IonPhosi | derive ionization balance for phosphorus
ion_photo.c | ion_photo | fill array PhotoRate with photoionization rates for heavy elements
ion_potas.c | IonPotas | compute ionization equilibrium for Potassium
ion_recomb.c | ion_recomb | generate recombination coefficients for any species
ion_recomb.c | ion_recombAGN | generate recombination coefficients for AGN table
ion_recomb.c | lint | -e817 pclint generates tons of bogus nelem < 0 warnings
ion_scand.c | IonScand | do ionization balance for scandium
ion_silic.c | IonSilic | determine ionization balance of Silicon
ion_sodiu.c | IonSodiu | ionization balance for sodium
ion_solver.c | ion_solver | solve the bi-diagonal matrix for ionization balance
ion_sulph.c | IonSulph | compute ionization balance for sulphur
ion_titan.c | IonTitan | determine ionization balance for titanium
ion_trim.c | ion_trim | raise or lower most extreme stages of ionization considered, called by ConvBase - ion limits were originally set by
ion_vanad.c | IonVanad | do ionization balance for vanadium
ion_zero.c | ion_zero | zero out heating save arrays
ion_zinc.c | IonZinc | ionization balance for zinc
iso_cool.c | iso_cool | compute net cooling due to hydrogenc atom species, ground state photoionization of hydrogenic species done in sumheat
iso_create.c | iso_create | create data for hydrogen and helium, 1 per coreload, called by ContCreatePointers in turn called after commands parsed
iso_create.c | iso_zero | zero data for hydrogen and helium
iso_ionize_recombine.c | ChargeTransferUpdate | update rate of ct ionization and recombination for H atoms
iso_ionize_recombine.c | iso_ionize_recombine | find state specific creation and destruction rates for iso sequences
iso_photo.c | iso_photo | do photoionization rates for element nelem on the ipISO isoelectronic sequence
iter_end_chk.c | iter_end_check | after each zone by Cloudy, determines whether model is complete
iter_startend.c | IterRestart | restart iteration
iter_startend.c | IterStart | set and save values of many variables at start of iteration
lines_service.c | abscf | convert gf into absorption coefficient
lines_service.c | chIonLbl | use information in line array to generate a null terminated ion label in "Fe 2"
lines_service.c | chLineLbl | use information in line transfer arrays to generate a line label
lines_service.c | DumpLine | print various information about an emission line vector, used in debugging, print to std out, ioQQQ
lines_service.c | eina | convert a gf into an Einstein A
lines_service.c | emit_frac | returns fraction of populations the produce emission
lines_service.c | EmLineJunk | set all elements of EmLine struc to dangerous values
lines_service.c | EmLineZero | set all elements of EmLine struc to zero
lines_service.c | FndLineHt | search through line heat arrays to find the strongest heat source
lines_service.c | gbar0 | compute g-bar gaunt factor for neutrals
lines_service.c | gbar1 | compute g-bar collision strength using Mewe approximations
lines_service.c | GetGF | convert Einstein A into oscillator strength
lines_service.c | HLineTransOpacSetdefine | current transition probabilities and opacities for H lines
lines_service.c | lgTauGood | returns true is we have not overrun optical depth scale
lines_service.c | linadd | enter lines into the line storage array, called once per zone
lines_service.c | lindst | add local line intensity to line luminosity stack
lines_service.c | LineConvRate2CS | convert down coll rate back into electron cs in case other parts of code need this for reference
lines_service.c | MakeCS | compute collision strength by g-bar approximations
lines_service.c | OccupationNumberLine | - derive the photon occupation number at line center for any line
lines_service.c | outline | - adds line photons to reflin and outlin
lines_service.c | PntForLine | generate pointer for forbidden line
lines_service.c | PutCS | enter a collision strength into an individual line vector
lines_service.c | PutExtra | enter and 'extra' intensity source for some line
lines_service.c | PutLine | enter local line intensity into the intensity stack for eventual printout
lines_service.c | RefIndex | calculates the index of refraction of air using the line energy in wavenumbers, used to convert vacuum wavelengths to air wavelengths.
lines_service.c | TexcLine | derive excitation temperature of line from contents of line array
lines_service.c | totlin | sum total intensity of cooling, recombination, or intensity lines
lines_service.c | WavlenErrorGet | - find difference between two wavelengths
magnetic.c | Magnetic_evaluate | evaluate some parameters to do with magnetic field
magnetic.c | Magnetic_init | initialize magnetic field parameters
magnetic.c | Magnetic_reinit | - reinitialized magnetic field at start of new iteration
magnetic.c | ParseMagnet | parse magnetic field command
maincl.c | main | program that reads input and calls cloudy to compute a single model, or try to optimize an observed model. Routine returns 0 if model is ok, and 1 if problems occurred.
map.c | map_do | produce map of heating-cooling space for specified zone, called as result of map command
math_complex.c | cmabs | dp complex absolute value
math_complex.c | cmadd | retn the sum of two dp complex nos.
math_complex.c | cmdiv | retn the quotient of two dp complex nos.
math_complex.c | cmexp | dp complex exponential
math_complex.c | cmmul | retn the product of two dp complex nos.
math_complex.c | cmneg | dp complex unary minus operation
math_complex.c | cmsub | retn the difference of two dp complex nos.
math_complex.c | ftocm | convert floats to dp complex
mean.c | aver | compute average of various quantities over the computed geometry called by startenditer to initialize, radinc to increment, and prtfinal for final results
mean.c | MeanInc | increment mean ionization fractions and temperatures over computed structure, in radius_increment
mean.c | MeanIonRadius | do radius mean ionization fractions or temperature over radius for any element
mean.c | MeanIonVolume | do volume mean ionization fractions or temperature over volume for any element
mean.c | MeanZero | zero mean of ionization fractions array
molcol.c | molcol | generate and print molecular column densities
mole_co_atom.c | cdCO_colden | return column density in H2, negative -1 if cannot find state, header is cddrive
mole_co_atom.c | CO_PopsEmisCool | evaluate rotation levels populations, emission, and cooling
mole_co_drive.c | CO_drive | - public routine, calls CO_solve to converge molecules
mole_co_drive.c | lgMolecAver | average old and new molecular equilibrium balance from CO_solve
mole_co_ele_recomb.c | CO_ele_recomb() contains all heavy element reactions with electrons
mole_co_etc.c | CO_Init | called from cdInit to initialized co routines
mole_co_etc.c | CO_update_chem_rates | update rate coefficients, only temp part - in mole_co_etc.c
mole_co_gas_grain.c | CO_gasgrain | defines matrix elements for gas-grain chemistry of heavy element molecules
mole_co_hyd_he.c | CO_step | fills in matrix for heavy elements molecular routines
mole_co_monox.c | CO_step | fills in matrix for heavy elements molecular routines
mole_co_photo.c | CO_photo | fills in matrix elements for heavy element photon and cosmic ray processes
mole_co_rates.c | CO_rates | calculates all the rates for coupled reactions in the heavy element network.
mole_co_solve.c | CO_step | fills in matrix for heavy elements molecular routines
mole_co_step.c | CO_step | fills in matrix for heavy elements molecular routines
mole_h2.c | cdH2_colden | return column density in H2, negative -1 if cannot find state, header is cddrive
mole_h2.c | H2_Accel | radiative acceleration due to H2
mole_h2.c | H2_Colden | maintain H2 column densities within X
mole_h2.c | H2_collid_rates | - set H2 collision rates
mole_h2.c | H2_ContPoint | set the ipCont struc element for the H2 molecule, called by ContCreatePointers
mole_h2.c | H2_cooling | evaluate cooling and heating due to H2 molecule
mole_h2.c | H2_DR | choose next zone thickness based on H2 big molecule
mole_h2.c | H2_InterEnergy | internal energy of H2 called in PresTotCurrent
mole_h2.c | H2_itrzn | - average number of H2 pop evaluations per zone
mole_h2.c | H2_LevelPops | do level H2_populations for H2, called by Hydrogenic
mole_h2.c | H2_Level_low_matrix | evaluate CO rotation cooling
mole_h2.c | H2_LineZero | initialize optical depths in H2, called from RT_tau_init
mole_h2.c | H2_RadPress | rad pre due to h2 lines called in PresTotCurrent
mole_h2.c | H2_RTMake | do RT for H2 - called from RT_line_all
mole_h2.c | H2_RT_diffuse | do emission from H2 - called from RT_diffuse
mole_h2.c | H2_RT_tau_inc | increment optical depth for the H2 molecule, called from RT_tau_inc
mole_h2.c | H2_RT_tau_reset | the large H2 molecule, called from RT_tau_reset
mole_h2.c | H2_X_coll_rate_evaluate | find collisional rates within X
mole_h2.c | turn | this flag on to do minimal debug print of pops
mole_h2_create.c | H2_Create | create variables for the H2 molecule, called by ContCreatePointers after continuum mesh has been set up
mole_h2_etc.c | H2_gs_rates | evaluate rates between ground and star states of H2 for use in chemistry
mole_h2_etc.c | H2_init | - called to initialize things from cdInit
mole_h2_etc.c | H2_Solomon_rate | find rates between H2s and H2g and other levels, for eventual use in the chemistry
mole_h2_etc.c | H2_Zero | zero out vars in the large H2 molecule, called from zero before any commands are parsed
mole_h2_etc.c | H2_zero_pops_too_low | - zero out some H2 variables if we decide not to compute the full sim, called by H2_LevelPops
mole_h2_etc.c | mole_H2_LTE | sets Boltzmann factors and LTE unit population of large H2 molecular
mole_h2_form.c | mole_H2_form | find state specific rates grains and H- form H2
mole_h2_io.c | cdH2_Line returns 1 if we found the line, or FALSE==0 if we did not find the line because ohoto-para transition or upper level has lower energy than lower level
mole_h2_io.c | chMolBranch | returns a char with the spectroscopic branch of a transition
mole_h2_io.c | H2_LinesAdd | add in explicit lines from the large H2 molecule, called by lines_molecules
mole_h2_io.c | H2_ParsePunch | parse the punch h2 command
mole_h2_io.c | H2_ParsePunch | parse the punch h2 command
mole_h2_io.c | H2_Prt_column_density | print H2 info into zone results, called from prtzone for each printed zone
mole_h2_io.c | H2_Prt_line_tau | print line optical depths, called from premet in response to print line optical depths command
mole_h2_io.c | H2_Prt_Zone | print H2 info into zone results, called from prtzone for each printed zone
mole_h2_io.c | H2_PunchDo | punch some properties of the large H2 molecule
mole_h2_io.c | H2_PunchLineStuff | include H2 lines in punched optical depths, etc, called from PunchLineStuff
mole_h2_io.c | H2_Punch_line_data | punch line data for H2 molecule
mole_h2_io.c | H2_ReadCollRates | read collision rates
mole_h2_io.c | H2_ReadDissprob | read dissociation probabilities and kinetic energies for all electronic levels
mole_h2_io.c | H2_ReadEnergies | read energies for all electronic levels
mole_h2_io.c | H2_ReadTransprob | read transition probabilities
mole_h2_io.c | H2_Read_hminus_distribution | read distribution function for H2 population following formation from H minus
mole_h_drive.c | hmole | determine populations of hydrogen molecules
mole_h_drive.c | hmole_init | - initialize some hmole vars
mole_h_drive.c | hmole_old | determine populations of hydrogen molecules
mole_h_drive.c | hmole_reactions | update hmole reactions
mole_h_step.c | >> chng 02 nov 7 rjrw, Mole Moreliano: changes to linearized iterative form
mole_h_step.c | about | generating the in and out vectors from a text string, e.g. "H +
mole_h_step.c | and | next to switch on the prints in the matrix assembly which apply to
mole_h_step.c | from | Robin Williams:
mole_h_step.c | H | => H2" ;-), but you'd have to verify uniqueness).
mole_h_step.c | hmirat | compute radiative association rate for H-
mole_h_step.c | hmole_step | do a step in chemical network
mole_h_step.c | kind | of naming scheme for the reactions may come in handy (I'd thought
mole_h_step.c | lint | -e778 const express eval to 0
mole_h_step.c | of | a pain grepping down to find the 47th reaction, so I guess some
mole_h_step.c | switch | printsol on to check which terms in the chemical matrix change,
mole_h_step.c | The | process for these kind of problems seems to be pretty uniform:
mole_h_step.c | the | species involved to find what reactions are involved. It's a bit
opacity_add1element.c | OpacityAdd1Element | enter total photo cross section for all subshells into opacity array
opacity_add1subshell.c | OpacityAdd1Subshell | add opacity due to single shell to main opacity array
opacity_add1subshell.c | OpacityAdd1SubshellInduc | add opacity of individual species, including stimulated emission
opacity_addtotal.c | OpacityAddTotal | derive total opacity for this position, called by ConvBase
opacity_createall.c | hmiopc | derive total H- H minus opacity
opacity_createall.c | OpacityCreate1Element | generate ionic subshell opacities by calling atmdat_phfit
opacity_createall.c | OpacityCreateAll | compute initial set of opacities for all species
opacity_createall.c | OpacityValenceRescale | routine to rescale non-OP valence shell cross sections
opacity_createall.c | Opacity_iso_photo_cs | returns photoionization cross section for isoelectronic sequences
opacity_createall.c | opacity_more_memory | allocate more memory for opacity stack
opacity_createall.c | rayleh | compute Rayleigh scattering cross section for Lya
opacity_createall.c | Yan_H2_CS | - cross sections for the photoionization of H2 NB NB NB NB NB NB NB NB NB NB NB NB NB NB everything set here must be written to the opacity store files
opacity_zero.c | OpacityZero | zero out opacity save arrays, save old opacity in OldOpacSave array
optimize_amoeba.c | optimize_amoeba | routine for optimizing model parameters
optimize_do.c | optimize_do | main driver for optimization runs
optimize_func.c | optimize_func | actual function called during evaluation of optimization run
optimize_phymir.c | optimize_phymir | Peter van Hoof's optimization routine
optimize_powell.c | optimize_powell | - spectrum minimization routine - logic closely based on routine in Press et al, but totally recoded to be redistributable
parse_absmag.c | ParseAbsMag | parse the absolute magnitude command
parse_abundances.c | ParseAbundances | parse and read in composition as set by abundances command
parse_age.c | ParseAge | parse parameters off the age command
parse_agn.c | ParseAgn | parse parameters for the AGN continuum shape command
parse_atomco.c | ParseAtomCO | parse information from the rotor command line
parse_atomh2.c | ParseAtomH2 | parse information from the atom command line
parse_atomhelike.c | ParseAtomHeLike | parse parameters off the helium command
parse_atomhlike.c | ParseAtomHLike | parse information from the atom h-like command line
parse_backgrd.c | ParseBackgrd | parse options for the BACKGROUND command - this actually enters two continua
parse_blackbody.c | ParseBlackbody | parse parameters off black body command
parse_CMB.c | ParseCMB | parse parameters from fireball command
parse_commands.c | ParseCommands | main command line parser, decode command, then call other routines to read
parse_compile.c | ParseCompile | compile werner or kurucz model atmospheres into cloudy format, originallly by K Volk, also compile opacity and grains
parse_constant.c | ParseConstant | parse parameters from the 'constant ...' command
parse_coronal.c | ParseCoronal | parse parameters off coronal equilibrium command
parse_cosmic_rays.c | ParseCosmicRays | parse the cosmic rays command
parse_crashdo.c | ParseCrashDo | any of several tests to check that the code can crash
parse_dlaw.c | ParseDLaw | parse parameters on the dlaw command
parse_dont.c | ParseDont | parse the dont command - do not do something
parse_drivecmnd.c | dgaunt | drive gaunt factor routines by letting user query values
parse_drivecmnd.c | DrvCaseBHS | allow user to query hydrogen A's, asks for up, low level, gives A, drive hyas
parse_drivecmnd.c | DrvHyas | allow user to query hydrogen A's, asks for up, low level, gives A, drive hyas
parse_drivecmnd.c | ParseDriveCmnd | parse the drive command - drive calls to various subs
parse_element.c | ParseElement | parse options on element command
parse_fluc.c | ParseFluc | parse the fluctuations command, which affects either density or abundances
parse_f_nu.c | ParseF_nu | parse intensity command parameters
parse_globule.c | ParseGlobule | parse parameters off the globule command
parse_grain.c | ParseGrain | parse parameters on grains command
parse_hden.c | ParseHDEN | parse the hden command
parse_init.c | ParseInit | bring an initialization file into input stream before parse
parse_interp.c | ParseInterp | parse parameters on interpolate command
parse_ionpar.c | ParseIonPar | parse the ionization parameter command
parse_map.c | ParseMap | parse map command to produce map of heating and cooling, map is produced by calling punt(" map")
parse_metal.c | ParseMetal | parse parameters on metal command
parse_norm.c | ParseNorm | parse parameters on the normalize command
parse_optimize.c | GetOptColDen | read observed column densities & errors for optimizer
parse_optimize.c | GetOptLineInt | parse observed line intensites for optimization routines
parse_optimize.c | GetOptTemp | read observed temperatures & errors for optimizer
parse_optimize.c | ParseOptimize | parse the optimize command line
parse_plot.c | ParsePlot | parse the plot command
parse_plot.c | ParsePlotRangeOption | parse range from plot command
parse_powerlawcontinuum.c | ParsePowerlawContinuum | parse the power law continuum command
parse_print.c | ParsePrint | parse the print command
parse_print.c | prt_constants | print physical constants
parse_punch.c | ChkUnits | check for keyword UNITS on line, then scan wavelength or energy units if present
parse_punch.c | ClosePunchFiles | close all punch files
parse_punch.c | ParsePunch | parse the punch command
parse_punch.c | PunchFilesInit | initialize punch file pointers, called from cdInit
parse_radius.c | ParseRadius | parse the radius command
parse_rangeoption.c | ParseRangeOption | parse the range option on the luminosity command
parse_ratio.c | ParseRatio | derive continuum luminosity of this continuum relative to previous
parse_set.c | ParseSet | scan parameters off SET command
parse_sphere.c | ParseSphere | parse parameters on sphere command
parse_stop.c | ParseStop | parse the stop command
parse_table.c | lines_table | envoked by table lines command, check if we can find all lines in a given list
parse_table.c | ParseTable | parse the table read command
parse_table.c | read_hm05 | read in the data files and interpolate the continuum to the correct redshift
parse_tlaw.c | ParseTLaw | parse parameters on the tlaw command to set temperature as function of depth, currently only does Bertoldi & Draine simple T law
parse_trace.c | ParseTrace | read in options off the trace command line
plot.c | plot | master routine to generate some sort of plot
pressure_change.c | lgConvPres | finds amount by which density should change to move towards pressure equilibrium returns true if pressure is converged
pressure_change.c | PressureChange | called by ConvPresTempEdenIoniz evaluate the current pressure, change needed to get it to converge, the global static variable pressure_change_factor aplies this correction factor to all gas constituents, sets conv.lgConvPres true if good pressure, false if pressure change capped
pressure_total.c | PresTotCurrent | determine the gas and line radiation pressures for current conditions, this sets values of pressure.PresTotlCurr, also calls tfidle
prt.c | prt_LineLabels | punch all labels and wavelengths for emission line array
prt.c | prt_wl | - print floating wavelength in Angstroms, in output format
prt.c | sprt_wl | write wavelength to string - must be kept parallel with prt_wl
prt_alltau.c | PrtAllTau | master routine controlling printout of optical depths at end of calculation
prt_columns.c | PrtColumns | print column densities of all elements
prt_comment.c | badprt | print out coolants if energy not conserved
prt_comment.c | chkCaHeps | check whether CaII K and H epsilon overlap
prt_comment.c | outsum | sum outward continuum beams
prt_comment.c | PrtComment | analyze model, generating comments on its features
prt_comment.c | prt_smooth_predictions | check whether fluctuations in any predicted quantities occurred
prt_continuum.c | PrtContinuum | print information about continuum if requested with PRINT CONTINUUM command, called by PrtFinal
prt_final.c | gett2 | analyze computed structure to get structural t^2
prt_final.c | gett2o3 | analyze computed [OIII] spectrum to get t^2
prt_final.c | PrtFinal | create PrtFinal pages of printout, emission line intensities, etc
prt_final.c | StuffComment | routine to stuff comments into the stack of comments, def in lines.h
prt_header.c | PrtHeader | print program's header, including luminosities and ionization parameters
prt_linepres.c | PrtLinePres | print line radiation pressures for current conditions
prt_lines.c | Drive_cdLine | do the drive cdLine command
prt_lines.c | lines | main routine to put emission line intensities into line stack, calls lineset1, 2, 3, 4
prt_linesum.c | PrtLineSum | parse print line sum command to enter set of lines into sum
prt_lines_continuum.c | lines_continuum | put energetics, H, and He lines into line intensity stack
prt_lines_general.c | GetMaxhLine | find the strongest heating line
prt_lines_general.c | lines_general | put general information and energetics into line intensity stack
prt_lines_grains.c | lines_hydro | put H-iso seq into line intensity stack
prt_lines_helium.c | lines_helium | put energetics, H, and He lines into line intensity stack
prt_lines_helium.c | TempInterp | interpolates on a grid of values to produce predicted value at current Te.
prt_lines_hydro.c | lines_hydro | put H-iso seq into line intensity stack
prt_lines_lv1_k_zn.c | lines_lv1_k_zn | place lines of elements potatium and heavier into lines storage stack
prt_lines_lv1_li_ne.c | lines_lv1_li_ne | place lines of elements lithium through neon into lines storage stack n_ion for C, N, or O recombination lines from Dima's list, also zero's line in master stack so not entered second time in later dump of all rec lines
prt_lines_lv1_na_ar.c | lines_lv1_na_ar | place lines of elements sodium through argon into lines storage stack
prt_lines_molecules.c | lines_molecules | put energetics, H, and He lines into line intensity stack
prt_meanion.c | PrtMeanIon | print mean ionization fractions or temperatures for all elements
prt_met.c | prtmet | print all line optical depths at end of iteration
prt_zone.c | PrtZone | print out individual zone results
prt_zone.c | prt_H_like_DeparCoef | print out hydrogenic populations
prt_zone.c | prt_H_like_Pops | print out hydrogenic populations
punch_do.c | pun1Line | called by PunchLineStuff to produce output for one line
punch_do.c | punch | h emiss, for chapt 4, routine is below
punch_do.c | PunchDo | produce punch output during calculation, chTime is 'MIDL' during calculation, 'LAST' at the end
punch_do.c | PunchGaunts | called by punch gaunts command to output gaunt factors
punch_do.c | PunchLineStuff | punch optical depths or source functions for all transferred lines
punch_do.c | PunchNewContinuum | produce the 'punch new continuum' output
punch_do.c | PunchNewContinuum | produce the 'punch new continuum' output
punch_do.c | PunchSpecial | generate output for the punch special command
punch_do.c | PunLineIntensity | produce the 'punch lines intensity' output
punch_do.c | punResults | punch results from punch results command
punch_do.c | PunResults1Line | do single line of output for the punch results and punch line intensity commands
punch_do.c | PunResults1Line | do single line of output for the punch results and punch line intensity commands
punch_do.c | the | number of emission lines across one line of printout
punch_line.c | punch_line | parse punch lines command, or actually do the punch lines output
punch_line.c | Punch_Line_RT | parse the punch line rt command - read in a set of lines
punch_linedata.c | Punch1LineData | punch data for one line
punch_linedata.c | PunchLineData | punches selected line data for all lines transferred in code
punch_opacity.c | punch_opacity | punch total opacity in any element, punch opacity command
punch_special.c | PunchSpecial | generate output for the punch special command
radius_first.c | radius.drad
radius_first.c | radius.drad_x_fillfac
radius_first.c | radius_first | derive thickness of first zone, called after conditions in first zone are established, sets
radius_increment.c | pnegopc | punch negative opacities on io unit, iff 'set negopc' command was given
radius_increment.c | radius_increment | do work associated with geometry increments of this zone, called before RT_tau_inc
radius_next.c | ContRate | called by radius_next to find energy of maximum continuum-gas interaction
radius_next.c | GrainRateDr | called by radius_next to find grain heating rate dr
radius_next.c | radius_next | use adaptive logic to find next zone thickness
radius_next.c | TODO | 2 - this routine is very important since it sets the pace for the calculation, and directly affects the convergence of the code. Most of the logic is very old and messy. 1) make sure all test cases have punch dr 2) cat all these reasons together into one file and sort on the reason 3) discover what logic is the main pacesetter for the code 4) which are never triggered and so can be removed
rt_continuum_shield_fcn.c | conpmp | local continuum pumping rate radiative transfer for all lines
rt_continuum_shield_fcn.c | conpmp | local continuum pumping rate radiative transfer for all lines
rt_continuum_shield_fcn.c | rt_continuum_shield_fcn | computing continuum shielding due to single line
rt_continuum_shield_fcn.c | vfun | voit function helper routine
rt_diffuse.c | RT_diffuse | evaluate local diffuse emission for this zone, fill in ConEmitLocal array with diffuse emission, OTS rates for this zone were set in RT_OTS, called by Cloudy, this routine adds energy to the outward beam
rt_escprob.c | esca0k2 | derive Hummer's K2 escape probability for Doppler core only
rt_escprob.c | esc_CRDcore | escape probability for CRD with no wings
rt_escprob.c | esc_CRDwing | escape probability for CRD with wings
rt_escprob.c | esc_CRDwing_1side | fundamental escape probability radiative transfer routine, for complete redistribution
rt_escprob.c | esc_PRD | escape probability radiative transfer for incomplete redistribution
rt_escprob.c | esc_PRD_1side | fundamental escape probability radiative transfer routine for incomplete redistribution
rt_escprob.c | RTesc_lya | escape prob for hydrogen atom Lya, using Hummer and Kunasz results, called by hydropesc
rt_escprob.c | RT_DestProb | returns line destruction probability due to continuum opacity
rt_escprob.c | RT_LineWidth | determine half width of any line with known optical depths
rt_line_all.c | RT_line_all | do escape and destruction probs for all lines in code. Called with FALSE arg by ionize, to only redo destruction probabilites, and with TRUE by cloudy to do both escape and destruction
rt_line_driving.c | RT_line_driving | derive radiative acceleration due to line absorption of incident continuum
rt_line_one.c | RT_line_static | do line radiative transfer for static geometry, evaluates escape and destruction probability, called by HydroPEsc, RT_line_all
rt_line_one.c | RT_line_wind | do line radiative transfer for wind geometry
rt_line_one_tauinc.c | RT_line_one_tauinc | increment optical depths for all heavy element lines, zone by zone, mainly called by RT_tau_inc, but also by FeII
rt_line_one_tau_reset.c | RT_line_one_tau_reset | computes average of old and new optical depths for new scale at end of iter, called by update, also FeIILevelPops
rt_ots.c | RT_OTS | compute diffuse fields due to H, He atoms, ion, triplets, metal recombination, called by ConvBase
rt_ots.c | RT_OTS_AddCont | add local destruction of continuum to ots field
rt_ots.c | RT_OTS_AddLine | add local destruction of lines to ots field
rt_ots.c | RT_OTS_ChkSum | sanity check confirms summed continua reflect contents of individuals
rt_ots.c | RT_OTS_Update | sum flux, otscon, otslin, ConInterOut, outlin, to form SummeDif, SummedCon SummedOcc
rt_ots.c | RT_OTS_Zero | - zero out some vectors - this is only called when code initialized by ContSetIntensity
rt_radiative_acceleration.c | RT_radiative_acceleration | radiative acceleration due to incident continuum, calls rt_line_driving for lines
rt_recom_effic.c | RT_recom_effic | generate escape probability function for continua,
rt_stark.c | RT_stark | compute stark broadening escape probabilities using Puetter formalism
rt_tau_inc.c | RT_tau_inc | increment optical depths once per zone, called after radius_increment
rt_tau_init.c | RT_tau_init | set initial outward optical depths at start of first iteration, it is only called by cloudy one time per complete calculation, just after continuum set up and before start of convergence attempts. RT_tau_reset after first iteration, updates the optical depths, mirroring this routine but with the previous iteration's variables
rt_tau_reset.c | RT_tau_reset | after first iteration, updates the optical depths, mirroring this routine but with the previous iteration's variables
sanity_check.c | SanityCheck | check that various parts of the code still work, called by Cloudy after continuum and optical depth arrays are set up, but before initial temperature and ionization
service.c | AnuUnit | produce continuum energy in arbitrary units
service.c | BadMalloc | announce memory allocation failure - put breakpoint here to find where
service.c | BadOpen | general error handler for trying to open file, but failing
service.c | BadRead | general error handler for trying to read data, but failing
service.c | broken | set flag saying that the code is broken,
service.c | cap4 | convert first 4 char of input line chLab into chCAP all in caps, null termination
service.c | caps | convert input command line (through eol) to ALL CAPS
service.c | cdEXIT | the routine that should be called to exit cloudy
service.c | chIonLbl | use information in line array to generate a null terminated ion label in "Fe 2"
service.c | CodeReview | - placed next to code that needs to be checked
service.c | csphot | returns photoionization cross section from opacity stage using std pointers
service.c | dbg_printf | is a debug print routine that was provided by Peter Teuben, as a component from his NEMO package. It offers run-time specification of the level of debugging
service.c | dsexp | safe exponential function for doubles
service.c | e2 | second exponential integral
service.c | FFmtRead | scan input line for free format number
service.c | fixit | - say that code needs to be fixed
service.c | fudge | enter fudge factors, or some arbitrary number, with fudge command
service.c | GetElem | scans line image, finds element. returns atomic number j, on C scale
service.c | GetQuote | get any name between double quotes off command line return string as chLabel, is null terminated
service.c | insane | set flag saying that insanity has occurred
service.c | lgMatch | determine whether match to a keyword occurs on command line, return value is 0 if no match, and position of match within string if hit
service.c | MyAssert | a version of assert that fails gracefully
service.c | MyCalloc | wrapper for calloc(). Returns a good pointer or dies.
service.c | MyGaussRanGauss | a wrapper for RandGauss, see below
service.c | MyMalloc | wrapper for malloc(). Returns a good pointer or dies.
service.c | NoNumb | general error handler for no numbers on input line
service.c | qg32 | 32 point Gaussian quadrature, original fortran given to Gary F by Jim Lattimer
service.c | qip | compute pow(x,n) for positive integer n through repeated sqarings
service.c | RandGauss | normal random variate generator
service.c | sexp | safe exponential function
service.c | ShowMe | produce request to send information to GJF after a crash
service.c | spsort | netlib routine to sort array returning sorted indices this label is null terminated
service.c | TestCode | set flag saying that test code is in place
service.c | the | prototypes are in cddefines.h and so are automatically picked up by all routines
service.c | TotalInsanity | general error handler for something that cannot happen
stars_atlas.c | AtlasCompile | rebin Kurucz stellar models to match energy grid of code
stars_atlas.c | AtlasGetOne | get one of the Atlas model atmospheres, coded by K. Volk
stars_atlas.c | AtlasInterpolate | interpolate on atlas model atmospheres, by K Volk
stars_costar.c | CoStarCompile | rebin costar stellar atmospheres to match cloudy energy grid, called by the compile stars command
stars_costar.c | CoStarInterpolate | read in and interpolate on costar grid of windy O atmospheres
stars_kurucz79.c | kurucz79 | obtain interpolated Kurucz stellar atmosphere
stars_mihals.c | mihals | generate continuum from Mihalas stellar atmosphere
stars_rauch02.c | RauchCompile02 | rebin Rauch stellar models to match energy grid of code
stars_rauch02.c | RauchInitialize02 | K Volk's routine to compact the 66 Rauch atmospheres into a large ascii file.
stars_rauch02.c | RauchInterpolate02 | get one of the Rauch model atmospheres, original version by K. Volk
stars_rauch_old.c | RauchCompile | rebin Rauch stellar models to match energy grid of code
stars_rauch_old.c | RauchInitialize | K Volk's routine to compact the 66 Rauch atmospheres into a large ascii file.
stars_rauch_old.c | RauchInterpolate | get one of the Rauch model atmospheres, original version by K. Volk
stars_werner.c | WernerCompile | rebin Werner stellar atmospheres to match cloudy energy grid
stars_werner.c | WernerInterpolate | read in and interpolate on Werner grid of PN atmospheres, by K Volk
stars_werner.c | WernerInterpolate_one | get a single Werner PN atmosphere, by K Volk
tabden.c | tabden | interpolate on table of points for density with dlaw table command, by K Volk
tfidle.c | tauff | compute optical depth where cloud is thin to free-free and plasma freq
tfidle.c | tfidle | update some temperature dependent variables
tfidle.c | velset | set thermal velocities for all particles in gas
thirdparty.c | This | file contains routines (perhaps in modified form) written by third parties. Use and distribution of these works are determined by their respective copyrights.
thirdparty_bevington.c | linfit | do linear least squares fit to arrays
thirdparty_lapack.c | These | are wrappers for lapack linear algebra routines. There are two versions of the lapack routines - a fortran version that I converted to C with forc to use if nothing else is available (included in the Cloudy distribution), and an option to link into an external lapack library that may be optimized for your machine. By default the tralated C routines will be used. To use your machine's lapack library instead, define the macro LAPACK and link into your library. This is usually done with a command line switch "-DLAPACK" on the compiler command, and the linker option "-llapack"
vary_input.c | vary_input | sets input lines to feed into cloudy in optimization runs
warnings.c | bangin | called by routine comment to enter surprise into comment stack
warnings.c | caunin | called by comment to enter caution into comment stack
warnings.c | notein | enter a note about calculation into comment array
warnings.c | warnin | enter warnings at the end of the calculations into large stack
warnings.c | wcnint | initialize stack or warnings, cautions, notes
zero.c | rfield_optac_zero | zero out rfield arrays between certain limits
zero.c | zero | zero out or initialize variables, called by cdInit, but also by optimize_func during optimization, this is called before any commands are parsed, called one time per model, at very start
zerologic.c | Zerologic | set initial values for logical variables this is called before any commands are parsed
zone_startend.c | ZoneEnd | last routine called after all zone calculations, before iter_end_check, upon exit radiation field is for outer edge of current zone
zone_startend.c | ZoneStart | set variables that change with each zone, like radius, depth, upon exit flux will be flux at center of zone about to be computed