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1. Figure 4 4 Coupling the PDR code and DustEM 4 7 H formation and excitation H formation mechanisms are defined in the chemistry file By default chemistry files are con figures to form H by the Langmuir Hinshelwood LH and Eley Rideal ER mechanisms The efficiency of these two processes depends on several energy thresholds which themselves depend on dust composition It is also possible to fix H formation rate to a constant value or depending on the gas temperature in the chemistry file Physisorbed species on grains are noted as H a chemisorbed specie is indicated with symbols as H LH and ER mechanisms Our implementation of LH and ER mechanisms is described in Le Bourlot et al 2011 LH mechanism relies on two parameters the binding energy and diffusion barrier of H atoms on grains The first one is provided in the chemistry file and the latter one is hard coded The desorption energy threshold EVAPO h grain h 1 00E 00 0 00 658 00 118 Constant formation rate For comparison purpose it is possible to use a constant H formation rate e e Ry 310717 cm s For this e Remove all adsorbed and chemisorbed species in the chemistry file e Remove all reactions with adsorbed species e Add a single reaction at the begining of the reaction list OLDST h h h2 3 00E 17 0 50 1 00E2 0 wG The adopted scaling is 22 4 PARAMETERS OF THE PDR CODE where the coefficient are read in the2. PXDR_STR_DATA 90 and recompiling the code Density temperature profile files should have the pf1 extension and be placed in the data Astrodata directory The name of this file has to be associated to the fprofil parameter in pxdr6 in Format of a pf1 file e First line number of points in the profile First value should be for optical depth 0 e Following lines on three columns visual extinction Ay temperature in K proton density i 3 in cm The computation is done up to the maximal visual extinction provided as input parameter So to use the full profile maximal visual extinction in the input parameter file should be set accordingly to the profile To use the output of a previous run to build a pf1 file we provide the PREP_PFL tool Run PREP_PFL from the src directory and provide the name of an existing oo bar bin file The file oo bar pf1 will be created in out foo bar It can be used directly in data Astrodata Symmetrical model With user defined density temperature profile it is possible to force the profile to be symmetrical To do so use a negative values 1 for ifisob in pxdr6 in 4 PARAMETERS OF THE PDR CODE 17 Typical values for proton volume density ny 50 200cm in diffuse clouds and 104 106 em for dense PDRs or dark clouds Note that isobaric models are usually longer to run and may be less numerically stable de pending on physical conditions They may a
3. temperature of the gas or grains heating and cooling rates by individual process compute line intensities for different observation angles produce an excitation diagram compute column densities wrap the plan parallel results on a spherical geometry analyze locally the chemical processes The PDR code can be used for many problems For interpretation of observations its main limits are the stationary hypotheses and the plane parallel geometry Post processing permits to wrap results on 1D spherical models but assumes that the incident radiation field is uniform around the sphere So it not possible to model a spherical cloud close to a star which is a 2D problem The PDR code can also be used as a theoretical tool to study the effects of various physical and chemical processes in the interstellar medium Several articles describe the physics in the PDR code e Le Petit et al ApJ 2006 Main presentation of the PDR code e Goicoechea and Le Bourlot A amp A 2007 UV radiative transfer e Gonzalez Garcia at al A amp A 2008 Radiative transfer taking into account non local effects e Le Petit et al A amp A 2009 Moment equations applied to Ho and HD formation on grains e Le Bourlot et al A amp A 2011 H formation on grains by Langmuir Hinshelwood and Eley Rideal mechanisms 1Up to now it has been mainly used to study the physics and chemistry of interstellar clouds For some other specific conditions the user ma
4. 1 10E 10 1 10E 10 In the example line containing TRANS is just a comment line placed between gas tempera tures values and collision data We recommend to store de excitation rates in data files and to compute inside the code excitation rates 5 Au dul T exp AE T Note that computation of level populations can be unstable if detailed balance is not checked B 2 Add a new special species The PDR code computes abundances of all species in the chemistry file and the excitation of a few of them These latest species must be declared as special species and an index must be associated to them These indexes are for example i oh i hcop i_ohp They are declared in PXDR CHEM DATA f90 and filled in PXDR_READCHIM 90 One of the first step to add level excitation computation of a new species is to add such an index Second step is to add new species in the list of special species This is done adding them in file data spectre flag This file contains 5 columns e Flag 0 or 1 Used to activate 1 or not 0 computation of levels populations during a run e Name of species as it appears in chemistry file e Maximum number of levels to take into account To save computing time the PDR code can decrease the number of levels to take into account A 1 means we let the code to start from all levels in the database e Minimum number of levels to take into account in computation The code decrease the number of le
5. LECTUR CHOFRO Figure B 1 List of files to modify to add computation of excitation and line intensities of new species B 1 1 Levels files Level files must be named level_xx dat in which xx is the name of the species as it appears in the chemistry file These files are stored in data Levels Examples level co dat level o dat level cox dat We illustrate levels file format on the example of CO Levels files must start with some lines containing general informations on the levels These informations are read and used by the code to create metadata that describe each level e2ecoekeves Tag No more used in the code Line has to be filled with something 6335 Number of levels in the data file K Unit of levels energies in the data file This must be Kelvin 2 Number of quantum numbers to define a level fv Name of the first quantum level J Name of the second quantum level Two comments lines follow n g E K V J data read without format Following lines are levels data Each level is characterized by an index a degeneracy an en ergy in Kelvin and quantum numbers Levels must be sorted by increasing energies Quantum numbers are not used in any operations They are used to identify levels The way to write these data lines must follow this format e Index degeneracy energy levels must be written in the first 45 columns They must be separated by spaces We recommend to set the first lev
6. field is x times the ISRF with x between 100 and 109 for PDRs We recommend when possible to use a specific stellar spectrum which is perpendicular to the slab to illuminate the cloud instead of multiplying by strong factors the ISRF which is isotropic Nevertheless in an exploratory phase and to avoid editing a spectrum file you may use high values of x which state equation to adopt Models with constant density are easier to analyze than constant pressure models To in terpret observations the activation of thermal balance is mandatory but may be switched off to study some specific processes in well defined temperature conditions You can also choose to adopt a specific density profile that as far as possible should be based on observations Then more specific parameters such as the grains properties size distribution quantity mini mum and maximum radii are set in pxar6 in and the chemical species and elementary abundances are set in the chemistry file Note that lines intensities available in the outputs of the PDR code depends on the configura tion file spectre flag 4 1 Geometry amp Incident radiation field Parameters F_ISRF radm radp srcpp d_sour 12 4 PARAMETERS OF THE PDR CODE The cloud may be irradiated from one side pseudo semi infinite cloud or from both sides To get an infinite slab set the radiation field intensity to 0 on the back side of the cloud The size of the slab is cont
7. illuminating the cloud star dat Spectral types used by the code to produce black bodies illuminating the cloud line of sight dat Dustextinction coefficients for specific lines of sight Table 3 1 List of input files 3 2 Output files Several output files are produced by the PDR code They share a common name set in pxdr6 in followed by a specific extension see table 3 2 The most important file is the bin file which contains the results of the model Other files contains various log or some An iteration number is usually appended to the bin extension e g bin15 Thus convergence is checked by comparing the results of the last two iterations or specific numerical problems can be analyzed by following a variable from iteration to iteration During normal usage of the code only the last file need be kept 10 3 INPUT AND OUTPUT FILES specific radiative quantities bin files are read with the post processing program PREP This must be done from the src directory where PDR was run and with PREP compiled with the same compiler File Description Page def Log file bin Results of a model Binary file to be read by the post processing program PREP uv Total attenuation through the cloud SEE Full map of the energy density u erg cm as a function of position Ay and wavelength A A Binary file to be read with the program read rf flin Incident radiation field Iesc Specific intensity 7 at
8. in the spectrum lux erg cm 2 s 1 nm 1 sr 1 0 0 0 0 26 7754 820 921 5083 97 8428 85 1For historic reasons this file uses nm and not A Conversion is done in the code 16 4 PARAMETERS OF THE PDR CODE 4 2 Equation of state temperature and density profiles Parameters densh ieqth tgas ifisob fprofil presse Temperature and density profiles can be controlled or computed in different ways The code can deal with e isothermal models e constant proton density models e isobaric models e user defined density and temperature profiles Thanks to the user defined profiles it is possible to model clumpy or fractal media 4 2 1 Density and temperature profiles The PDR code accepts different equations of state to control the temperature and proton den sity profiles Equation of state is controlled by the ifisob and the fprofil parameters ifisob Description 0 Constant density model ny is fixed to the value provided by the densh param eter in pxdr6 in 1 A specific density temperature profile provided in an ASCII file by the user is adopted In this case if thermal balance is solved temperature in the file is not used but a column has to be present 2 Isobaric model gas pressure P n x T is constant With thermal balance computation activated fall of temperature in the core will produce a rise of the density 3 Analytical temperature profile This requires editing routine FDENS in
9. initialization Photo reactions cross sections data are located in the directory data Sections It is quite simple to add new ones 4 5 Cosmic rays ionization rate and secondary photons flux Parameters fmrc Cosmic rays ionization rate is controlled by fmrc expressed in 10 17 Hy ionization per second The actual ionization rate by cosmic rays in the model is determined by this parameter and by some rates in the chemistry file By default the chemistry file gives h crp h electr 4 60E 01 00 00 1 h2 crp h h electr 4 00E 02 00 00 t h2 crp h2 electr 9 60E 01 00 00 1 Values in the first numerical column are multiplied by mrc As we see the total ionization rate by cosmic rays per H molecule is nearly twice the one of atomic hydrogen Branching rations for the H ionization comes from private communication by Alex Dalgarno 4 6 Grains properties and physics Parameters los_ext rrr cdunit gratio alpgr rgrmin rgrmax q_pah F_dustem Grains properties are involved in three important physical aspects e They determine the extinction curve used in the UV radiative transfer e They catalyze Hz formation and some other chemical reactions e They contribute to thermal balance through photo electric effect and collisions with the gas This last process can contribute either to heating or cooling of the gas depending on the difference of temperature between the gas and grains The current file lists all species for
10. is computed 3 Code how to use collision rates 4 Code how to excite species at its formation not explained in detail here 5 Add temporary arrays to store cooling rates and relative populations at each iteration 6 Modify the extraction program PREP to have access to cooling rate by new species The code uses some generic structures to store and manipulate species properties as molec ular structure spectroscopy level populations and lines emissivities A consequence is that once atomic and molecular data files are provided to the code it can nearly automatically com pute level excitation and lines intensities The main exception is collision rates that require a bit of coding to be used in the code Fig B 1 presents locations of the various files that must be modified The first requirement to add level excitation of new species is that these species be present in the chemical network In the explanations below we assume this requirement is fulfilled B 1 Atomic and molecular data files One has to prepare 1 afile with the list of levels 2 afile with radiative transitions properties and 3 several files for collision rates one per collision partner 36 B ADD EXCITATION OF NEW SPECIES PXDR PXDR PXDA Levels Lines Collisions spectre flag INITIAL COLSPE BILTHERM A N N N N Levels Lines data Collisions data files fies data files PXDR PXDR PXDR READCHIM STR DATA OUTPUT PXDR PREP PREP CHEM DATA
11. the case that some well known truth happens not to be true in a specific case It will show in this reaction list 5 6 Extract radiation field energy density A map of the full energy density u is saved in a specific binary file if the flag F_W_RF_ALB is set to 1 in pxdr6 in This file must be read with a specific tool found in src OTHER_ PROG e The full version of the PDR code saves 3 quantities as a function of Ay and A uj in erg cm Am the radiative energy density w Z the full albedo of the dust gas mixture note that strong Kdust Kgas 0 absorption by the gas leads to a lower albedo for fixed dust composition Kgas the contribution to absorption by the gas which includes both continuum processes e g C ionization and line processes e g H lines self shielding e PDR light only provides u since absorption by the gas has been removed from this simplified version The code read_rf_alb_abs 90 resp read_rf 90 must be compiled using any fortran compiler It runs so fast that no special care is needed to optimize it Then copy the resulting executable to the subdirectory where the rf_alb resp x rf file is located The code asks for the name of the binary file Then 4 resp 3 options are possible e 1 provide a specific A Then a 4 columns resp 2 columns output file is cre ated containing the full range of wavelength at that specific Ay Name of the file rf_out_Av_xxxx
12. which some information exists However most of them have not yet been checked and should be used with caution 20 4 PARAMETERS OF THE PDR CODE 4 6 1 Line of sight extinction curve and Ry parameter Grains of the ISM absorb the UV radiation field by simple absorption scattering or by photo electric effect The optical depth due to dust at a wavelength A is 1 E A V Ay Ry E B V 2 5 log o e TA 1 The Meudon PDR code uses Fitzpatrick and Massa 1990 formalism to parametrize the ex tinction curve Several lines of sight are already introduced in the code and can be found in the line o sight dat file in the data Astrodata directory New lines of sight can be introduced adding Fitzpatrick and Massa parameters in this file Typical value Galaxy which correspond to the mean extinction curve in the Galaxy Parameter Ry should be modified accordingly to the choice of the line of sight extinction curve Typical value 3 1 for diffuse medium of our Galaxy In dense PDRs where grains are assumed to be bigger than in the diffuse medium Ry may be up to 5 5 as for the Orion Bar 4 6 2 Gas to dust ratio The quantity of gas with respect to the quantity of dust on the line of sight is defined by the parameter Gas to dust ratio which correspond to N H 2 x N H3 ep E B V Typical value From Copernicus observations a typical value in the diffuse ISM is 5 8 10 cm mag Bohlin et al 1974 FUSE observat
13. Meudon PDR code Quick introduction Franck Le petit amp Jacques Le Bourlot Spring 2014 Contents 3 1 3 2 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 Overview Installation Input and output files Input files cc ah 4 0 de amp Aue AD xu beam nam RR BA So ne get a A awd Output Tiles 4s 22 24 a a A th RR Nt ee ee ee re Parameters of the PDR code Geometry amp Incident radiation field Equation of state temperature and density profiles Number of global iterations Photo reactions amp UV radiative transfer Cosmic rays ionization rate and secondary photons flux Grains properties and physics H formation and excitation Elementary abundances and metallicity Chemistty 2 2 2 nuu ee aye Sew ee Pru R 4 10 Lines intensities and levels excitation 5 1 5 2 5 3 5 4 5 5 5 6 B 1 B 2 B 3 B 4 B 5 B 6 Analyze results aca Ari une DRE La RSS Se RM eh eat Clo d StrUctUre re a a Re arae qax du d dy aA Lines intensities and properties Spherical clouds ru 22 RR REGES ee GE Ghemistry analysis e acd drame OE eee chubby vod Boece d a OE are aile Extract radiation field energy density Chemistry file Add excitation of new sp
14. cloud edge erg cm s7 ster Table 3 2 List of output files 2 Development are under way to use a much more flexible file format within the framework of the Virtual Observatory However this will not be addressed in this document 11 Chapter 4 Parameters of the PDR code Most of the input parameters defining the properties of the cloud computed have to be provided in the pxdr6 in file located in the data directory Some other files may have to be modified as explained below The Meudon PDR code is not difficult to use It is far more difficult to understand the results because of the non linearity and coupling of the various physical processes A good way to begin to use the code is to run the code with the default pxdr6 in and to play with the results Itis a low excitation cloud so the physical and chemical processes that can take place are more limited than in a dense and bright PDR Once ready to run a real model the user should ask to himself e which geometry to choose A 1 side or 2 sides model and with which size In most real cases 2 sides models are a good choice Even to study a bright PDR it is better to simulate 2 sides clouds with a large enough size using a strong radiation field on one side and the standard ISRF on the other what kind of incident radiation field to use The question is important for the study of PDRs It is common to read in the literature that the intensity of the radiation
15. creation of fractal density profiles 1On many platform it is sufficient to specify LIBS1 llapack 1blas since this libraries are standard de velopment tools You may need first to remove the most agressive optimization option to get a running code Start with only 02 Once the code run smoothly add more optimization options This results in a huge gain in running time You may need to refer to your compiler user manual or the web 2 INSTALLATION Chapter 3 Input and output files 3 1 Input files Input parameters to control a run are provided in several files located in the data directory The two most important ones are the pxdr6 in file and a chemistry file identified by the extension chi Other files can be modified for specific reasons as to introduce a specific density temperature profile or to define a user spectral profile Input parameters files are presented in table 3 1 File Description Page pxdr6 in Input parameters file to control properties of the cloud x chi Chemistry file Provides the list of species the elementary abundances the chemical reactions spectre flag File providing the list of species for which detailed balance is computed and lines intensities pfl Optional specific temperature and density profiles photodest flag List of species for which photo reaction rates are computed by direct integration of cross sections F x txt Optional file providing a specific stellar spectrum
16. cription As noted by Mathieu Kopp during his PhD thesis different expressions of Draine s ISRF can be found in the literature We use the expression by Sternberg and Dalgarno 1985 because of its good precision Draine s ISRF is only provided up to 2000 A Nevertheless in the latest versions of the PDR code we use it up to 10 000 A Above 2000 A the Near UV Visible Near I R component provided by Mathis et al dominates the extrapolation of Draine s ISRF The fact that this expression is provided by Draine only up to 2000 A is the main reason why we recommend to use Mathis expression of the ISRF 1 6 3600 107 1 0237 10 4 0812 10 A lt 200 a m 38 T 2 Comparison of the expressions of the ISRF To compare the energy received by the cloud with the various expressions of the ISRF we integrate the energy density u from 912A almost the Lyman limit to 2400A above which Ha is no more photo dissociated by UV photons 4 PARAMETERS OF THE PDR CODE 15 J ux dA Ratio relative to Ratio relative to erg cm Habing Draine Habing 5 89 10 1 1 0 42 Draine 1 04 10 P 1 76 1 Mathis 7 01 10714 1 2 0 68 4 1 2 Stellar spectrum It is possible to add a stellar spectrum to illuminate the cloud Even if a star is added it is possible to have the ISRF In this case the recommended scaling factor is 1 to simulate that interstellar isotropic incident radiation field is always present To add a stellar sp
17. cture of PDR regions rely on a detailed treatment of the UV radiative transfer and its interaction with the gas and grains The radiation field is absorbed in lines of atoms and molecules as well as in the continuum by dust Rates of photo reactions depends directly on the UV radiation field The Meudon PDR code can solve the UV radiative transfer by two methods 18 4 PARAMETERS OF THE PDR CODE e FGK approximation in this method described in Federman Glassgold and Kwan 1979 line self shielding of Hz is done approximatively using an escape probability scheme and there is no line overlap neither for lines of the same species nor between lines of different species e Exact method What we call the exact method is described in Goicoechea amp Le Bourlot 2008 Overlapping of H H and CO UV absorption lines is taken into account At each position in the cloud specific intensity with lines absorptions is known not available in PDR light The exact method is CPU time consuming but depending on the object of the study it may be mandatory to use it It is the case for models of diffuse clouds in which the computation of the H H transition require a detailed treatment of shielding processes To study complex chem istry in dark clouds this method is not required The FGK approximation may not compute a accurate position of the H H transition but this will not affect what happens in the shielded parts of the cloud Parameter itrfer is
18. d with read_rf e 0 Save only partial informations on radiation field The binary database of the cloud state is post processed using PREP This is a text driven tool that proved robust over the years despite its old age PDR and PREP must be used from the same directory and must be compiled A with the same compiler with a single call to make PREP may create various files in the out foo bar directory To prevent loss of data it can only create new files and it will crash if trying to overwrite an existing file This may seem annoying but years of experience have shown that it is really a mandatory precaution If you need to re create a file first remove it by hand The first question asked by PREP is wether you want to save a copy of all interactions during the current session This produces a small text file named prepin in src that can subsequently be used to produce exactly the same output from another run You may rename this file typically to prep out and reuse it by redirecting to the input of PREP S gt PREP lt prepin 26 5 ANALYZE RESULTS Usually you just have to change the name of the binary and output files on lines 2 and 3 to be done Experienced users may venture to modify other parameters The Q A procedure follows a tree structure Most answer are integer numbers and possible answers are explicitly specified at the end of the question The main exceptions are species name that must be provi
19. ded in lowercase Which variable is x 1 tau 2 Av 3 NH 4 N H2 Select next variable kind end Abundance 2 Column density 3 Emissivity Heating Cooling N x variable is number 2 Else T density ions Pseudo Spherical cloud Experimental Re Gas Temperature Dust Temperatures ND 5 2 Cloud structure One should always check the cloud structure first Before going to any comparison with obser vations We suggest using systematically the following output e Gas temperature e lonization degree e Local abundances of H H2 Ct C CO Thus a minimal standard prep out file would be src 2 more prep std out 0 P 5e4 R 1e2 N bini5 P 5e4 R 1e2 N outi15 B comment HO HO HO UT HU N 5 ANALYZE RESULTS 27 h2 0 0 c 0 c 0 co 0 1 0 Note that for species for which detailed balance is solved you are proposed to output level pop ulations Here the answer was consistently No For H you may also output the Ortho Para ratio 5 3 Lines intensities and properties Integrated line intensities are written in a separate file When selecting main option 3 Emis Sivity you have to chose 1 Line intensities then give an output file name foo bar emi will usually do Then you are asked if you want the full line profiles Well you don t These are very useful to understand subtle physical effects but for optically thick lines at least they bear little resembla
20. diation field x 100 this leads to a higher visible radiation field too Conversely setting radm to a vanishingly small value say 10 does not suppress the high energy part of the visible component that extends down to 912 Strong values of x usually reflect the presence of stars in the neighborhood The best solution is then to keep radm and radp to 1 and to add a stellar spectrum The chemistry file must be chosen depending on the selected ISRF Fits to the rates of photo reactions depend on the shape of the ISRF Several A chemistry files are provided corresponding to Mathis or Draine s radiation fields 14 4 PARAMETERS OF THE PDR CODE 1e 06 T T T T ISRF Mathis FUV Mathis UV Vis IR 1e 07 Dust ees 1 CMB Mathis et al 1983 10 kpc 1e 08 1e 09 1e 10 erg cm s Ang str 1e 11 E 1e 12 abit 1e 13 f 1000 10000 100000 1e 06 1e 07 1e 08 Angstroms Figure 4 3 ISRF in the Meudon PDR code Mathis prescription The expression of the far UV radiation field based on Mathis et al 1983 and Black 1994 and fitted by Jacques Le Bourlot is lt 8000 I A tanh 4 07 10 x 4 5991 1 0 x 107 192 x 17259 In this expression the wavelength is in Angstroms and the specific intensity 7 in erg cm s ster The intensity of this component can be scaled by the radm and radp parameters in the input data file Draine s pres
21. e declared allocated and initialized in 40 B ADD EXCITATION OF NEW SPECIES PXDR_STR_DATA 90 filled in PXDR_BILTHERM 90 and used in PXDR_INITIAL 90 It is quite simple to add new species with a copy paste of what is done for OH B 6 Access data with PREP program Species indexes have to be stored and read respectively in PXDR_OUTPUT 90 and PREP_LECTURE Levels populations line emissivities and lines intensities will be automatically stored in the raw output file In the PREP program level populations line intensities and emissivities will be automatically accessible If one wish to have access to specific cooling rates due to new species one should add access to it on the example of OH in PREP CHOFRO 90 Here again a simple copy paste should be enough
22. ecies Atomic and molecular data files Add a new special species Use collision xtates an ues Era A a A ee ae Excitation at formations 2 22 4 2 24 a aera gus af Ha TEmporary arrays a 2 dec AI ea Uu das ee Access data with PREP program 11 11 16 17 17 19 19 21 22 22 22 25 25 26 27 28 30 31 33 CONTENTS Chapter 1 Overview This note is a quick guide explaining how to use the PDR code It does not describe the detailed physics in the code This is done in several articles References are provided below This is work in progress many items are still empty It is written for the full fetched PDR code All options do not exist in the trimmed version PDR light The Meudon PDR code simulates a stationary plane parallel slab of gas and dust illuminated by an external radiation field coming from one or both sides of the slab the two intensities can be different mb 4 2 LH ER Pen 3 005 y 1 0x10 Abundance X protons density Gas Temperature K PTT TEN 0 4 Molecular 0 001 0 01 0 1 1 10 100 Ww gt c region Ay mag H D cr CO T Ha HD C e oe At each position in the cloud the code solves e the continuum radiative transfer from the UV to radio wavelengths taking into account absorption in the continuum by dust and gas and in discrete transitions of H H2 and
23. ectrum 1 provide the distance between the star and the cloud in the variable d_sour The star can be located on the observer side or on the back side of the cloud e d sour lt 0 the star is on the observer side of the cloud e d sour gt 0 the star is on the back side of the cloud e d_sour 0 no stellar spectrum is added 2 provide a stellar spectrum with the srcpp parameter You can choose either to select a spectral type in this case the code will add a black body or to provide the name an ASCII file containing a specific spectrum Kurucz spectrum for example The list of recognized spectral types can be found in data Astrodata star dat To provide a specific stellar spectrum build an ASCII file containing the flux as a function of wavelength This file has to be placed in the data Astrodata directory The name of this file should begin with F_ and has to be indicated in the srcpp parameter in pxdr6 in Format ofar file is e first line radius of the star in solar radius second line effective temperature in K third line number of points in the spectrum fourth line comment then the spectrum in two columns with on the first one the wavelength in nm and on the second one the specific intensity in erg cm s nm ster Example 2 26 10500 1170 dnm F 90 50 91 50 92 50 93 50 Star radius in solar radius O Effective temperature K Number of points in wavelength
24. el at OK e Quantum numbers must be written after the 45th column They must be separated by spaces They are read as strings Example 0 000000 0 0 5 532146 0 1 16 596225 0 2 33 191816 0 3 55 318285 0 4 Ci WN EF won ower B ADD EXCITATION OF NEW SPECIES 37 B 1 2 Lines files Lines files must be named line_xx dat with xx the species name as it appears in the chemistry file These files are stored in the data Lines directory Again we use CO as an example First two lines are informations about the data file 43664 Number of lines in the data file K Energy unit of transitions It must be Kelvin Two comment lines must then be present n nu nl E K Aij s 1 quant vu Ju vl Jl info Description data The file continues with the data These data contains in several columns n Index of the transition nu Index of the upper level in the corresponding levels file nl Index of the lower level in the corresponding levels file E K Energy of the transition in Kelvin Aij s 1 De excitation Einstein coefficient in s71 quantum numbers List of quantum levels defining the transition no more used Description Various informations to characterize transitions A data line must not be longer than 200 characters The most important part is the five first columns Indexes nu and n1 have to be the indexes of upper and lower levels as defined in the corresponding levels data file Quantum numbers part
25. gt v 0 J 4 576 268 GHz 6 v 0 J 6 gt v 0 J 5 691 473 GHz 28 5 ANALYZE RESULTS 7 v 0 J 7 gt v 0 J 6 806 652 GHz 8 v 0 J 8 gt v 0 J 7 921 800 GHz 9 v 0 J 9 gt v 0 J 8 1036 912 GHz 10 v 0 J 10 gt v 0 J 9 1151 985 GHz Transition 0 end Give the identification number of the lines you are interested in and finish with 0 You are back to the species choice menu In the output file you ll find one line per transition mu 1 000000E 00 lev up lev down Freq MHz Wave l micron I int erg s 1 cm 2 ster I int K km s co v 0 J 1 gt v 0 J 0 115 27 2600 8260 1 80069E 07 1 14725E 02 v 0 J 2 gt v 0 J 1 230 54 1300 4130 1 36539E 06 1 08739E 02 For each transition we recall first the wavelength then the frequency Thus you may check the line is really what you think it is Then you get the intensities first in physical units erg cm s ster then in observer units K kms 5 4 Spherical clouds The Meudon PDR code is a plane parallel model This can be a bit restrictive to interpret observations of edge on PDRs or objects with spherical geometries A new features of the post processor code PREP is to wrap the structure to simulate a spherical cloud This as sumes that the radiation field illuminating the sphere is uniform It is not possible to simulate a spherical cloud near a star this is a 2D problem To use this fac
26. hem This is both a source of potential numerical instabilities and a heavy burden in terms of computing time Thus the user should select only those species relevant to the problem at hand This is done by setting a flag in the first column of the file spectre flag located in the data directory e 1 Compute detailed balance e 0 Do not compute 4 PARAMETERS OF THE PDR CODE 23 A full description of this file together with a detailed description of how one may introduce a new species is given in Appendix B 24 4 PARAMETERS OF THE PDR CODE 25 Chapter 5 Analyze results 5 1 Result files The full results of a computation are stored in a subdirectory in out The name of the subdi rectory is the character chain given as a first parameter in pxdr6 in That chain is also used as a radix for most file names Thus results of model foo_bar at the end of iteration number 20 are found in file out foo_bar foo_bar bin20 The only exception to this rule is radiation field related quantities Since they can be huge all iterations are not saved and they are stored in supplementary files The number of binary files saved is controlled by the flag F_W_ALL_BIN e 1 Keep all binary files useful for debugging purpose e 0 Keep every tenth file plus last two enough for ordinary use Writing the full radiation field at all positions and wavelength is controlled by flag F_W_RF_ALB e 1 Write full radiation field binary file to be rea
27. ility run a model with the same radiation field on both sides of the cloud then with the PREP post processor ask for line intensities in spherical conditions You will have to provide the position of the line of sight 5 ANALYZE RESULTS Observation line of sight SN x NC em Ra Figure 5 1 wrapping a plane parallel model in a spherical model 29 30 5 ANALYZE RESULTS 5 5 Chemistry analysis The CHEM_ANALYSER tool is used to check for formation and destruction reactions of any species anywhere in the cloud It is run from the src directory The input file is the same binary file as for PREP The code first asks if you want the evolution of reaction rates with Ay That part is experimental so answer 0 No Then you must chose a position within the cloud by giving the index from the relevant Ay Usually you know it in advance from examination of the model results see previous sections If not it is a trial and error process where you must accept a value of Ay to validate it Chemistry Analysis at a fixed Av Give Av position index max value iopt 284 End analysis 1 150 Point 150 Av 1 3883252147247764 T 72 798804174257199 Keep that point 1 yes 0 no Give threshold Higher gt more reactions All gt 0 100 H2 para 0 93734616374331203 h2 ortho 6 2653836256687356E 002 The code reminds you of the value of 4y and of the local temperature useful
28. ions of diffuse clouds confirmed this result Rachford et al 2002 ApJ 577 221 4 6 3 DustEM detailed computation of grains I R emission Use of DustEM is not available with PDR light DustEM is a code developed at Institut d Astrophysique in Orsay devoted to the study of the properties of interstellar grains It assumes a distribution of grains different components and sizes and for a given incident radiation field computes the temperature distribution and charge distribution of each component then the emissivity of the grain population A version of Dust EM is provided with the PDR code It is located in the dustem directory and has to be compiled separately The PDR code computes grains temperature following Hollenbach et al prescription The emission is then computed It is possible to replace all this part of the code by a call to DustEM In this case at each position the UV radiation field computed by PDR is sent to DustEM which sends back the local properties of the dust absorption scattering coefficient and local emissivity This permits to get PAHs lines emission and to get a precise I R radiation field that are taken into account in the pumping of some molecules as H20 The use DustEM is controlled by the flag F_dustem not included in PDR light e F dustem 0 DustEM is not used e F dustem 1 DustEM is activated 4 PARAMETERS OF THE PDR CODE 21 Position IR grains emission
29. is no more used in the code It is still present for convenience when reading lines files Note that each line is still properly characterized by quantum numbers but these ones are obtained by a matching of levels indexes between lines files and associated levels data files Finally the description is used to provide convenient informations about lines as wavelengths in other units than Kelvin This last part is read as a string Format for data is quite simple One just has to use spaces to separate columns For historical reasons the quantum numbers part starts with keyword quant and symbol is used as separators of quantum numbers Description part starts with keyword info Example 0 info 115 271 GHz 1 5 53200000 7 2040000E 08 quant 0 1 2 5 LOG 00 2 3 2 11 06400000 6 9110000E 07 quant 0 2 0 1 info 230 538 GHz 3 4 3 16 59600000 2 4960000E 06 quant 0 3 0 2 info 345 796 GHz 4 5 4 22 12600000 6 1270000E 06 quant 0 4 0 3 info 461 041 GHz 5 6 5 27 65600000 1 2210000E 05 quant 0 5 0 4 info 576 268 GHz B 1 3 Collision rates data One has to provide one collision rates file per collision partner These files are stored in data Collisions Browsing files in this directory one may notice that all of them do not follow the same rules Some of them contain parameters of fits of collision rates other ones contain collision rates Since the developer has to code how to read these files and how to manipulate the
30. lso be more difficult to interpret because of the variations of both density and temperature 4 2 2 Thermal balance and isothermal models Thermal balance is solved if the flag ieqth is set to 1 If 0 the temperature is fixed to the value provided by tgas This temperature is also used for initialization in all cases A good guess may help to speed up a bit the code a very bad guess may prevent numerical convergence If thermal bistability is physically possible this initial temperature can also control on which solution the system converges If a specific density temperature profile is provided see below these parameters are not used 4 3 Number of global iterations Parameter ifafm Because each point of the slab sees a radiation field coming from both sides even if there is no radiation field on the back side backscattering by dust induces a radiation field from the back side towards the observer side the code converges towards a solution after several iterations over the whole cloud Users have to define the number of global iterations he wishes the code do This is controlled by the ifafm parameter It is difficult to define the number of required iterations automatically because all quantities do not converge at the same time It would be pointless to wait for the convergence of a quantity that is not interesting for the user 4 4 Photo reactions amp UV radiative transfer Parameters itrfer jfgkh2 Models of the stru
31. nce to true observed lines This comes from the fact that there is absolutely no macroscopic velocity field in the code It leads to strong self absorption that may become unphysical while the integrated intensities are correct Thin lines are OK but there is nothing interesting in them So either way you do not need line profiles until later Answer 0 No Then you re asked for the line of sight direction This is with respect to the normal to the cloud and expressed in radian Use 0 0 You may try a larger angle but do not go beyond 3 read 1 Remember the cloud is infinite in the other two directions so going to an angle of 5 leads to an infinite line of sight and divergence of the intensities Yes This means that you can not simulate a pure edge on PDR This is a feature not a bug You are then provided with the list of species for which detailed balance has been solved and whose line intensity you may hence compute Let us chose CO The code will then provide a list of available lines starting usually from the longest wavelength Lines are identified by a number followed by a short description E g Which species end 1 CO 2 co co Emission lines of co List length Max 107 10 num v J gt y J 1 v 0 J 1 gt v 0 J 0 115 271 GHz 2 v 0 J 2 gt v 0 J 1 230 538 GHz 3 v 0 J 3 gt v 0 J 2 345 796 GHz 4 v 0 J 4 gt v 0 J 3 461 041 GHz 5 v 0 J 5
32. onization dissociation at the edge of the cloud and 8 a factor com puted for a specific radiation field Both are provided in the chemistry file In this expression the probability of photo reaction takes into account only the absorption of the radiation field by dust through the Ay parameter Moreover this coefficient has been evaluated for a specific dust composition that may differ from the one adopted in a given run 4 PARAMETERS OF THE PDR CODE 19 If the cross section is known then a better destruction rate is computed by direct integration over the local radiation field of the cross sections o by d Alim IA 1 Alim p af 525407 s f ox Aux dd Gy 912 a hc h Jou 2 To use this option one has to select in the photodest flag file located in data for which species photo reaction rates should be computed thus by setting a flag in the first column e 1 Integrate cross section e 0 Use approximate rate coefficient If the exact radiative transfer method is used the specific intensity at each wavelength and each position in the cloud takes into account H H and optionally CO absorption lines Then photo reaction rates will include the effect of shielding by lines This effect may become signif icant for the shielding of C by H There is no need to modify the chemistry file If the photo reaction is present in the chemistry file while the expression corresponding to Eq 4 1 is used then it will be skipped during
33. optionally CO and its isotopes Depending on the algorithm selected to treat these processes the code can take into account mutual shielding effects to compute accurately photo ionization and photo dissociation rates e the thermal balance This is done assuming heating rate equals cooling rate Heating mechanisms include the photoelectric effect on grains cosmic rays ionizations exother mal chemical reactions Main cooling processes rely on infrared to sub millimeter line emission To solve this the PDR code determines levels excitation of the most important species taking into account collisional and radiative processes This includes pumping by 1 OVERVIEW dust I R emission as well as atomic molecular emissions Photons escape probabilities are computed taking into account non local effects Some mechanisms can heat or cool the gas depending on the local physical conditions mostly Hz cascades and gas grains collisions the chemistry The chemical network takes into account several hundred species and thousands reactions The number of species and reactions can easily be modified In version 1 4 4 1 5 2 and PDR light surface reactions with Langmuir Hinshelwood and Eley Rideal mechanisms are implemented for Ha formation After a batch run the code produces several output files that contain the structure of the cloud Post processing with PREP program or PDRAnalyser can extract profiles such as abundances levels populations
34. order y a 5 A Do not forget to set itype to 0 last parameter on reaction definition 4 8 Elementary abundances and metallicity Elementary abundances are provided in the chemistry file The first part of a chemistry file contains the list of species whose abundances are computed The informations concerning each species are the name atomic composition initial abundances and formation enthalpy Elementary abundances are controlled thanks to the initial abundances Most species have an initial abundance of 0 Typical non zero values below are for Solar abundances accounting for depletion on grains All values are relative to ny Species Initial abundance H 0 8 Ha 0 1 He 0 1 O 3 191074 N 7 51075 ct 1 321074 gt 1 86 10 5 Sit 8 21077 Fe 1 5 1078 There is no metallicity parameter in the code All values must be adjusted individually in the chemistry file 4 9 Chemistry A few chemistry files are provided in data Chimie They have been compiled and revised to suit our needs over the years from standard data base UMIST OSU KIDA supplemented by recent publications or a few private communication Any result published using these files should both aknowledge the original work and this com pilation 4 10 Lines intensities and levels excitation The PDR code can solve detailed balance equations for a number of species 33 species as of 30 1V 2014 However it is rarely useful to compute all of t
35. re that excitation rates have to be computed thanks to de excitation rates The best way to do so is to duplicate and modify a pre coded subroutine as COLOR Once excitation and de excitation rates between levels 1evu and levl are known eqcol is filled with eqcol levu levu eqcol levu levu ratdo eqcol levu levl eqcol levu levl ratup eqcol levl levl eqcol levl levl ratup eqcol levl levu eqcol levl levu ratdo In the example above ratdo and ratup are respectively collisional excitation rates from upper to lower level and from lower to upper level In the matrix elements are stored as eqcol final level initial level Subroutines COLXX are called in the thermal balance part of the code file PXDR_BILTHERM 90 subroutine COLSPE One should add a call to the new subroutine following other species as examples B 4 Excitation at formation By default the PDR code assumes that molecules are formed in levels following a Boltzmann distribution at gas temperature Nevertheless energy liberated by some chemical reactions may contribute to the excitation It is possible to do so modifying the default Boltzmann distri bution This documentation will be completed on this point if asked by users B 5 Temporary arrays Two arrays are used to temporary store relative levels populations and cooling rates of species respectively xrexxx and refxxx These arrays ar
36. rolled by the Avmax parameter the total visual extinction For a constant density model the conversion to size in cm is given by Ny Cp Av x E NH NH Ry where Ny is the column density of protons in cm ny the volume density of protons in cm 3 Cp Nu V D B V B V parameters are Cp 5 8 10 cm and Ry 3 1 and Ry E Standard galactic observational values for these last two avmax gt avmax ONE Isotropjc RF pe LAr o KR Observer 7 Ww EN Borok RF radm radp radm radp 0 Observer side Back side Observer side Back side Figure 4 1 Two sides and one side models Two kinds of radiation fields that can be combined can illuminate each side of the cloud e an isotropic radiation field the interstellar standard radiation field ISRF It can be scaled by multiplicative factors radm and radp for respectively the observer side and the back side of the cloud These two parameters correspond to x or Go that can be found in the literature See Figure 4 1 e a beamed radiation field that simulate the radiation field of a star To add such a radiation field the user has to specify the distance in parsecs between the star and the cloud with the d_sour parameter and the shape of the spectrum with the srcpp parameter Depending on the sign of d_sour the star is located on the observer side or on the back side The stellar spectrum can be either a black body or a specific spectrum p
37. rovided by the user Thanks to these parameters it is possible to define several configurations Figure 4 2 presents a 2 sides model in which the cloud on the observer side is illuminated by a star The angle of observation of the PDR plays no role in the computation of the cloud structure It does only in the post processing part when lines intensities are computed A beamed radiation field penetrates deeper in the cloud than an isotropic one Except for specific tests isotropic radiation field should always be present Typical values To study the chemistry of dark clouds one may adopt a 1 side or 2 sides model with Ay 20 or more and may analyze results once the UV radiation field has been absorbed For diffuse clouds a typical value of Ay 0 5 with x 1 on both sides is a good starting point For dense and bright PDRs one can adopt a 2 sides models with a large Ay and with the observer side illuminated by a strong radiation field e g x gt 10 or better to keep x 1 and add a stellar spectrum The back side would then be illuminated by the ISRF radp 1 4 PARAMETERS OF THE PDR CODE 13 avmax 20 Isotropig RF gt gt Isotropic RF au Beamed RF be b Star in front of the PDR radm 1 radp 1 vA Observer side Back side d sour 0 4 pc Figure 4 2 Example of a 2 sides models on which both side of the cloud are illuminated by the ISRF The observer side of the cloud is also illumina
38. se data one can choose to provide collision rates both ways In this document we explain how to include files containing collision rates in cm s We will use collisions between OH and ortho H as example Contrary to levels and lines data files collision rates files can have any name Files headers must contain some specific informations 38 B ADD EXCITATION OF NEW SPECIES NUMBER OF ENERGY LEVELS 20 NUMBER OF COLL TRANS 190 NUMBER OF COLL TEMPS 6 COLL TEMPS 15 0 30 0 60 0 100 0 200 0 300 0 These lines indicate the number of energy levels for which collision rates are provided the number of collisional transitions and the number of gas temperature for which rates are pro vided A line provides values of these temperatures separated by spaces Collision rates are then provided one transition per line for each temperature Collision rates should be provided in cm s Before this three columns of integers provide an index for the transition and indexes of the upper and of the lower level of the transition using the same indexes as in the corresponding levels data files Example TRANS UP LOW DOWNCOLLRATES cm3 s 1 12 1 2 30E 10 2 80E 10 3 20E 10 3 30E 10 3 30E 10 3 30E 10 2 4 5 20E 11 5 90E 11 6 90E 11 7 80E 11 9 10E 11 9 60E 11 3 4 1 5 00E 11 5 20E 11 5 40E 11 5 50E 11 5 70E 11 6 00E 11 432 5 10E 11 5 50E 11 5 90E 11 6 40E 11 7 50E 11 8 20E 11 531 6 30E 11 7 00E 11 8 20E 11 9 30E 11
39. ted by a B 0 star located at 0 4 pc 4 1 1 Interstellar Standard Radiation Field ISRF The ISRF used in the Meudon PDR code goes from the far UV Lyman cut off at 912 to beyond H 21cm line It is the sum of 4 components Only the first one the far UV part is scaled by radm and or raap parameters e Far UV to Near UV The prescription for this component can be chosen between 2 expressions Mathis et al 1983 or Draine 1978 This is controlled by the F_ISRF flag in the pxdr6 in input parameter file We recommend to use Mathis expression for the ISRF since it takes into account more precisely the near UV to near IR components of the ISRF F_ISRF 1 Mathis ISRF F ISRF 2 Draine ISRF Near UV Visible Near IR Relatively cold stars are responsible for this part of the ISRF spectrum Our expression is an update of Mathis et al 1983 It is the combination of 3 black bodies at 6184 6123 and 2539 K Dust emission IR The I R component produced by dust has been estimated with the DustEM code The resulting specific intensity is the sum of the emission by PAHs very small grains and big grains Data are provided in the file data Astrodata IR field dustem dat Cosmic Microwave Background is a black body at the temperature of the CMB by default 2 73 K It can be modified in PXDR INITIAL f90 All components extend to the whole wavelength range to avoid discontinuities across bound aries In the case of strong ra
40. to compute analytical rate coefficients The threshold is the ratio of the larger to the smaller reaction rate that will be displayed In the given example a value of 100 means that only reactions that are at least 1 of the strongest one are displayed You may now enter a species of your choice e g Hi Which species fin 1 h3 Number of reactions 37 Chemistry of h3 Av 1 3883252147247764 T 72 798804174257199 K fabric 2 233850E 13 cm 3 s 1 destru 2 233827E 13 cm 3 s 1 abond 1 125436E 06 cm 3 Formation Processes of h3 63 52 4h2 h2 h h3 2 2338E 13 cm 3 s 1 1 9849E 07 s 1 100 00 Destruction of h3 4 h3 lectr h h h 1 4190E 13 cm 3 s 1 1 2608E 07 s 1 4 h3 lectr he AZ 7 6156E 14 cm 3 s 1 6 7668E 08 s 1 34 09 4 o h34 h2 oh 3 5242E 15 cm 3 s 1 3 1314E 09 s 1 Each reaction is preceded by its type parameter itype then the formation or destruction rate at the given position l e not the rate coefficient but the number of particle created or destroyed per unit volume and per unit time then the same divided by the abundance of the species under inquiry which gives a kind of characteristic time and finally the contribution of this reaction to the total formation or destruction of the molecule 1 58 oe oe oe oe 5 ANALYZE RESULTS 31 If any unusual behavior is detected it is very useful to check the chemistry this way It is often
41. used to select the method e itrfer 0 FGK approximation e itrfer 2 Exact method Line overlapping of H and Ha is taken into account In this case for H5 another parameter jfgkh2 has also to be set It is the value of the J level of H under which the exact method is used FGK approximation is used for all electronic transitions from a lower level equal to or above this rotational level e itrfer 3 Exact method Add lines of CO default 30 levels e itrfer 4 Exact method Add lines of CO default 30 levels e itrfer 5 Exact method Add lines of C180 default 30 levels and HD experimental Note that parameter itrfer is not available in PDR light Typical values H absorption lines are narrow above J 2 so a value of jfgkh2 of 3 is sufficient to take into account detailed shielding effects Most of the time higher values are only useful if the purpose of the model is to produce an absorption spectrum with H lines Output files provide the absorption spectrum through the slab of gas as well as the density of energy at each position as a function of the wavelength With FGK approximation these spectra do not contain H H5 and CO absorption lines whereas in the case of the exact radiative transfer they do Computation of photo reaction rates By default photo reaction rates are computed from rate constants in the chemistry file with the expression P Ay Po xe Av si 4 1 with Po the probability of i
42. vels below this threshold e Atomic mass of species B ADD EXCITATION OF NEW SPECIES 39 B 3 Use collision rates B 3 1 Read collision rates files Collision rates files are read during the initialization of the code in PXDR_INITIAL 90 To read new collision rates the simplest way is to copy paste a part of the code as OH collision rates reading and adapt it to new species This part of the code starts with IF i_oh 0 THEN In this example we see that one has to read the number of collision rates and the number of temperatures nttoh allocate an array for collision rates q_oh_ph2 and another one for temperatures tempcoh and store data in these arrays Arrays are allocated with the number of temperatures in the data file plus one This extra temperature is used for extrapolation Indexes of the collision rates array are for temperature upper level lower level B 3 2 Fill collisions matrix The next step is to use collision rates to compute level excitations This is done creating a subroutine usually called COLXX with xx the name of the species This subroutine has two arguments the gas temperature and the number of levels used for that species They are respectively called ttry and nused These subroutines are located in PXDR_COLSPE 90 The goal in this subroutine is to fill the eqcol 1 3 array To do so one has to combine collision rates of species xx with different partners at the proper temperature It is he
43. x dat where xxxxx is the requested Ay 2 provide a specific Then a 4 columns resp 2 columns output file is created contain ing the full range of positions at that specific A Name of the file r _out_WL_xxxxx dat where xxxxx is the requested 3 This produces a map at all Ay in a specific wavelength interval Amin and Amaz are requested first then an ASCII file is created suited to plot surfaces with e g gnuplot The radiation field may be scaled by its value at Amin which may be helpful to better see the line profiles Name of the file rf_out_2D dat 4 full PDR only out put the radiation field at a specific Ay in Dust EM input format This is useful to run Dust EM as a standalone code using results from the PDR code 32 5 ANALYZE RESULTS Appendix A Chemistry file 34 A CHEMISTRY FILE 35 Appendix B Add excitation of new species Adding computation of level excitation and line intensities for new species is not as straightfor ward than adding new species in the chemistry This requires a bit of coding and the prepara tion of several data files The most simple way to doit is to contact developers of the PDR code so that somebody will include these new species To do it yourself here are a few explanations The main steps are 1 Prepare atomic and molecular data files levels radiative transitions collision rates 2 Declare new species in the list of species for which detailed balance
44. y have to modify some parameters in the source code Chapter 2 Installation To install the PDR code you need e A fortran 90 compiler e LAPACK and BLAS libraries We suggest using gfortran which is available on all platform and is now fully optimized PDR is able to take advantage of its autoparallelization features Good version for Mac OS can be found at http hpc sourceforge net Once the code is downloaded edit the Makefile in the src directory to adapt the call to LA PACK and BLAS libraries Select a compiler and its options and modify compilation options to your needs Then run make This will produce three executables e PDR the PDR code e PREP the post processor code e CHEM_ANALYSER the Chemistry analyser post processor Other tools are provided as a version of Dust EM This code can be used synchronously with the PDR code to compute more precisely grains properties temperature emissivities than with the PDR code alone It has to be compiled separately Before doing so edit DM constants f90 and modify PATH_TO_PDR to the proper path on your computer A de tailed user guide is not yet available In src or src OTHER_PROG several small programs are provided e PREP_PFL tool to extract a profile file see Sect 4 2 1 from the output of a run e read rf tool to read binary radiation files rf produced by the PDR code e build FractalGrid A tool devoted to the
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