Version 15 June 2007 compiled: 11-11-2009 - Hamburger Sternwarte

Messages of the day:
PHOENIX
Version 15
June 2007
compiled: 11-11-2009
Peter H. Hauschildt
Hamburger Sternwarte
Gojenbergsweg 112
21029 Hamburg, Germany
yeti@hs.uni-hamburg.de
Edward Baron
Department of Physics and Astronomy
University of Oklahoma, Norman, OK 73019-0225
baron@phyast.nhn.ou.ede
November 11, 2009
******************************************************************
* "real programmers don’t use pascal!" (E. Post, 1982) *
* and *
* "scientific progress goes ’boink’?!" (Watterson, 1991) *
******************************************************************
1

Abstract
This (very brief) manual is intended to serve as a guideline for users of PHOENIX. The description
is very short and preliminary, however, even a short manual seems to be better than no manual at
all. Warning: This manual is partly outdated, version 14 includes many more features than described
here. I basically have not enough time to update the manual continuously. The earliest versions of
this code were named SNIRIS but beginning with SNIRIS version 3.0α the code has been renamed to
PHOENIX. The main reasons are the large number of changes to the old code, so that PHOENIX has
“risen from the ashes” of SNIRIS. The first part of this manuscript gives a description of the purpose
of the code and the equations and numerical methods used in PHOENIX, whereas the second part
gives details about the input and output files and the control variables used by PHOENIX.
1 Introduction
Version 13 of PHOENIX includes
1. many NLTE species (too many to list, e.g., all CHIANTI or APED data can be included as NLTE
species),
2. molecular NLTE (currently for CO, water and TiO planned),
3. up to 110 chemical elements (all 83 with known solar abundances)
4. updated equations of state with more molecules and dust formation,
5. dust settling,
6. more molecular band and line opacities,
7. exponential density profile,
8. a much improved user interface (by using namelist input),
9. the capability to compute wind models for O stars and novae,
10. parameterized clouds (for very cool objects),
Later versions of this report will contain also information about the internal structure of PHOENIX
(subroutines/functions, calling sequences and code parameters/variables).
1.1 Purpose of PHOENIX
PHOENIX was designed as an extremely general stellar atmosphere code 1 . Its first first application
was the computation of the radiation emergent from a rapidly expanding supernova or nova envelope
during the first weeks and months after explosion. PHOENIX is also used to construct LTE and NLTE
model atmospheres for dwarf and giant stars all across the HRD, brown dwarfs, extrasolar planets
(including irradiation), hot winds from CVs in outburst, AGN disks (with Herbert Störzer), and a lot
of other things.
1.2 Physical assumptions
• spherical symmetry,
• steady state, i.e., ∂/∂t ≡ 0,
• homologous expansion, i.e., v(r) = v0(r/R0) for supernova models or constant mass-loss rate for
nova models,
• expansion velocity v0, typically v0 ≈ 10 4 km s −1 for supernovae and v0 ≈ 10 3 km s −1 for novae,
• power law density, i.e., ρ(r) = ρ0 (r/R0) −nρ , or exponential density profile
ρ(r) = ρ0 exp (ve/v0(r − R0)), or hydrostatic equilibrium,
• energy conservation, especially radiative equilibrium, in the Lagrangian frame,
1 The true purpose of the code is, of course, to be written and modified. Yes, it is self-sufficient!
2

• deviations from “local thermodynamic equilibrium”, i.e., the Saha-Boltzmann equation for the
atomic level populations, are allowed for important species as, e.g., H, He, Li, CNO, S, Si, Mg,
Ca, Ti, Co, Fe, for a total of more than 3700 NLTE level and more than 37000 primary NLTE
lines,
• local thermodynamic equilibrium for another ca. 40 elements and their ions.
• local chemical equilibrium for up to ≈ 229 molecules and some of their ions.
1.3 Most important model parameters
• exponent nρ of the density law, typically nρ ≈ 10 . . . 20 for supernovae and nρ ≈ 3 for novae;
• gravity (for stellar models)
• outer pressure Pout or outer density ρout;
• radius R0 at an optical depth of unity, i.e. rout has to be determined so that
� rout
R0
κ dr = 1;
• total radiative luminosity L0 or, equivalent, the “effective temperature” Teff;
• abundances ɛi for all considered elements,
• for NLTE calculations: number of levels of each model atom;
• for line calculations: number of lines to be included;
1.4 Numerical methods
• 1-D Newton or Brent’s method with respect to the electron pressure for the solution of the
coupled (generalized) Saha-Boltzmann equations for all elements (no molecules),
• Multi-D Newton method for the solution of the coupled (generalized) Saha-Boltzmann and
molecular dissociation equations for the ’big’ EOS,
• operator splitting/approximate Λ-operator iteration (OS/ALI) method for the solution of the
special relativistic radiative transfer equation for all wavelength points,
• rate operator formalism for multi-level direct NLTE,
• multi-D Newton-Raphson method (DOME), hybrid or modified Unsöld-Lucy method (OS/ALI)
for the solution of the energy conservation equation in the Lagrangian frame,
• Bulirsch-Stoer method for the solution of auxiliary ordinary differential equations, e.g., for the
energy equation dL/dr = f(r) and for the computation of the radial grid according to
dr/dτ = −1/κ,
• Shooting method for the computation of the outer radius Rout.
1.5 Model equations
• The time independent, special relativistic equation of radiative transfer, with the assumptions:
– spherical symmetry,
– time independence (∂/∂t ≡ 0),
Spherically symmetric, special relativistic equation of radiative transfer
– partial integro-differential equation,
– telegrapher’s equation: boundary value problem in r and initial value problem in λ as long
as the velocities are monotonically increasing.
The equation of radiative transfer
3

with
and
e ∂I ∂ ∂
+ (fI) + g (λI) + hI = η − χI
∂r ∂µ ∂λ
e(r, µ) = γ(µ + β)
f(r, µ) = γ(1 − µ 2 �
1 + βµ
) − γ
r
2 (µ + β) ∂β
�
∂r
� 2 β(1 − µ )
g(r, µ) = γ
+ γ
r
2 µ(µ + β) ∂β
�
�
∂r
2 β(1 − µ )
h(r, µ) = γ
+ γ
r
2 (1 + µ 2 + 2βµ) ∂β
�
∂r
– I(r, µ, λ): specific intensity scaled by r 2 ,
– r: radial coordinate,
– µ: cosine of the direction angle, µ = cos φ
– v: velocity, β = v/c, γ 2 = 1/(1 − β 2 ),
– χ(r, λ): extinction coefficient, χ = κ + σe + κlϕ(λ)
– η(r, λ): emissivity.
Example for η(r, λ) (thermal, electron scattering and line sources):
η = κBλ(T ) + σeJ + κlϕ(λ)
� ∞
0
ϕ(λ)J(λ) dλ
The form of η for line and NLTE calculation is more complicated but in principle similar.
Therefore, the radiative transfer equation is a partial integro-differential equation, which
describes a boundary value problem in r (the on the shell incident intensities are known) and
initial value problem in ν (only for the case of monotonic velocity fields).
• The equation of radiative equilibrium in the Lagrangian frame,
� ∞
0
χ(B − S) dν = 0,
where J = 1/2 � 1
I dµ is the mean intensity and B Planck’s function. This equation has to be
−1
fulfilled for all radial grid points in order to ensure energy conservation. The main physical
problem embedded in eq. ?? is the global coupling of the mean intensity with all r points
through the equation of radiative transfer and the interaction with the local quantity B.
• The Saha-Boltzmann equation: in thermodynamic equilibrium at temperature T and electron
pressure Pe, the atoms are distributed over their bound levels according to the Boltzmann
statistics. The number Nr,s of atoms in excitation state r of ionization state s (s = 0 for neutral
atoms) compared to the total number Ns of atoms in ionization state s is accordingly:
Nr,s
Ns
= gre −χr/kT
Qs(T, Pe)
where k is Boltzmann’s constant, Qs the partition function and χr the excitation potential
relative to the ground-state configuration of s. Between two ionization states, the Saha equation
has to be used:
Ns+1
Ns
= (2πm)3/2 (kT ) 5/2
h 3 Pe
4
2Qs+1e −χs,s+1/kT
Qs

with χs,s+1 =| χs − χs+1 |, the energy difference between the ionization states s and s + 1. These
equations have to be solved with respect to the constraints of particle (total and for each
element) and charge conservation:
Ntot = �
and
r,s,i
ɛiNtot = �
Ne = �
r,s
r,s�=0,i
Nr,s,i
Nr,s,i
Nr,s,i,
where ɛi denotes the abundance of the element i and Ntot and Ne denote the total and the
electron number densities, respectively. It can be shown, that this equations are equivalent to a
single non-linear equation for the electron density Ne.
• The rate equations for the species considered in NLTE:
�
ji
nj
n ∗ i
(Rij + Cij)
In eq. ??, bi denotes the departure coefficient of level i of the model atom, i.e. bi = ni/n∗ i , where
n∗ i denotes the LTE population of the level i computed from the actual number densities of the
ground state of the next ionization stage of the element and the electron density. (ni/nj) ∗
denotes the Saha-Boltzmann factor between the levels i and j, or the continuum stage κ. The
collisional rates Cij are given by Cij = ΩijNe and Ωij is a constant tabulated for each level of the
model atom. The radiative rates for the lines are given by
Rij = Bij ¯ Jij
Rji = Aji + Bji ¯ Jij
¯Jij =
� ∞
0
φij(λ)J(λ) dλ
Here Aji, Bji and Bij denote the Einstein coefficients for the transition i → j and φij(λ) is the
normalized line profile function for this transition. The radiative rates for the bound-free
transitions are given by
Riκ
= 4π
� ∞
� � hc
∗ � nκ 4π ∞
Rκi = ni hc 0 σiκλ
�
2
2hc
λ5 ⎫
⎬
⎭
0 σiκλJ(λ) dλ
�
+ J(λ) exp � − hc
�
kλT dλ
Here σiκ = σiκ(λ) denotes the photo ionization cross-section from level i to the continuum state
κ.
• Solution of the rate equations using an Operator Splitting method:
– define a “rate operator” in analogy to the Λ-operator:
Rij = [Rij][n]
5

– define an “approximate rate operator” [R∗ ij ] and write the iteration scheme in the form:
�
ji
Rij = [R ∗ ij][nnew] + � [Rij] − [R ∗ ij] � [nold]
⎧
⎨�
[R
⎩
ji
∗ �
i
� ∗ �
nj [R ∗ ji][nnew]
nj,old
n ∗ i
+ �
nj,new ([∆Rji][nold] + Cji)
ji
[R ∗ ij][nnew]
⎧
⎨�
([∆Rij][nold] + Cij)
⎩
ji
∗ ⎫
�
⎬
([∆Rij][nold] + Cij)
i
⎭
� ∗ �
nj ([∆Rji][nold] + Cji) = 0.
nj,new
2 Some literature references
n ∗ i
Description of certain aspects of the code can be found in the literature list later in this paper.
3 PHOENIX program files and utilities
This section describes the files and modules of PHOENIX and the utilities which make the code usage
easier.
3.1 Program files and subdirectories
• phoenix.f: This is the main program PHOENIX.
• machine.*.f: modules with several small subroutines to make the conversion between
different machines easier and to collect the machine dependent program parts, e.g., CPU time
and date routines, file name conventions, contained in one module. Currently available for AIX,
HPUX, SGI, CRAY, AXP, and, of course, LINUX, Mac OS X & FreeBSD (with the NAG F90
compiler) systems. The parallel version (using MPI) is in production available on all these
platforms. There is no current or planned support for any version of Microsoft Windows type
systems 2
• input.f: module managing the namelist based I/O of input parameters
2 In fact, they would have to be added over my dead body!
6
⎫
⎬
⎭

• linecom.f: module with data structure and methods for the line opacity routines
• casscom.f: module with data structure and methods for the NLTE routines
• S3R2T/: The OS/ALI radiative transfer module, including the OS/ALI and Unsöld-Lucy
temperature correction methods. This module can be used together with matpack.f stand
alone for RT calculations.
NLTE/: This directory contains the atomic models for the NLTE species and the other model
atom related subroutines. Some service and debug routines are also included in this module.
• Cassandra/: This directory contains the OS/ALI multi-level NLTE method. It uses the results
of the OS/ALI RT and the atomic models provided in NLTE/. Completely rewritten for PHOENIX
version 13.
• Sybil/: This directory contains the OS/ALI multi-level NLTE method for molecules. It uses the
results of the OS/ALI RT. It started as a clone of Cassandra. It also includes the model molecule
routines (unlike Cassandra/, which needs NLTE/). Note, the main routine gets called
Cassandra/.
• FPPRESS/: The EOS modules. Contains both EOS solvers (IONS and PPRESS) as well as service
routines used by the EOS. It can be used stand alone.
• KAPCAL/: The continuum opacity routines. Contains the b-f cross-section routines and the
molecular band opacity routines. It can be used stand alone.
• MISC/: This module contains a number of smaller sub-modules, e.g., utility functions for use in
PHOENIX, numerical integration subroutines and BLOCK DATA with ionization potentials.
• LTELINES/: This directory contains the routines to handle the line lists, i.e., the atomic
(Kurucz) and molecular (Kurucz, Jørgensen, Miller & Tennyson, Goorvitch, Schwenke &
Partridge, HITRAN92) lists. It includes the routines for line selection (both old and new blocked
algorithms), line opacity calculations (including damping constants, inline Voigt profiles etc).
• FUZZ/: Treatment of the secondary NLTE lines, requires the Cassandra NLTE method.
• matpack.f: Module with matrix algebra subroutines used throughout PHOENIX.
• blasuse.f: Contains the BLAS routines PHOENIX or its modules use.
• linpack.f: Contains a large fraction of the LINPACK routines used by PHOENIX or its modules.
Obsolete, use the netlib provided LAPACK and ATLAS libraries instead.
• csppress.f: driver program to compute EOS tables.
• *.inc: include files that are used throughout PHOENIX, e.g., to specify parameter values, define
physical constants etc.
In addition, a few modules with development versions of new routines may be present.
3.2 Utilities
• mk *: Shell scripts that can directly compile PHOENIX from scratch on a number of systems.
• build: A perl program that detects the system type and creates the correct Makefiles for the
system on which it is invoked (or for the architecture that was given as argument to build).
• Makefile.in: These are the template Makefiles (present in most subdirectories) that are the
used by build to create the system specific Makefiles.
• Compiler.options: Master compiler options file for all system that PHOENIX supports. build
uses it to create the system specific options.make that is used by all Makefiles.
• *.pl: Perl programs that are used internally during the compilation phase of PHOENIX
(2*.pl) or that are used to apply global changed to all routines (e.g., to semi-automatically add
new NLTE species).
7

• mktar: shell script that creates a single gziped tar files with all files necessary to compile
PHOENIX.
3.3 PHOENIX files
3.3.1 logical units
It follows a description of the different input and output logical units and the corresponding files used
by PHOENIX.
• Unit 1: Input file. As Unit 2, but for molecular lines. This file should be connected to the
binary molecular line list. The current version of this list contains around 30 million molecular
lines for a number of sources.
• Unit 2: Input file. This file is only used, if EZL=.TRUE.. If used, this file should be connected to
the binary coded line list. This list contains approximately 42,000,000 lines taken from a line list
provided by R. L. Kurucz (1993, private communication) which has been transformed to make it
more compact and to improve the computational performance. The list consists of atomic data
needed to compute the absorption and emission from spectral lines of about 60 different species.
If EZL=.TRUE., but the file connected to unit 2 is empty, PHOENIX will ignore it and perform a
continuum computation without a warning. This file is read once in each model iteration.
• Unit 3 and 33: scratch file, used to “swap” currently unused blocks of the atomic lines out of
core.
• Unit 4: Input files. This unit is used by a number of different routines to read, e.g., the atomic
data needed to compute partition functions of a number of species or opacity data (tables, cross
sections etc). These files are needed to run PHOENIX and are described later. If the file is
missing, PHOENIX will crash after about 1–2 seconds CPU time.
• Unit 5: Input file. This file contains the control parameters of the run. This is a namelist
based description of the model that you like to run. Must be named fort.5 for the input
routine to locate it.
• Unit 6: Output file. All printer output, e.g., results, Lagrange frame spectra etc. is printed on
this unit. The file should have at least a LRECL of 133 for IBM mainframe systems.
• Unit 7: Output file. This file is only used, if ITER=0 in the unit 5 input file. If ITER=0, then the
Euler (or observer’s) frame spectrum is punched in the format: wavelength (in ˚A), log 10(Flux),
log 10(Planck function) and log 10(Flux(τstd(2))). On IBM mainframe systems the LRECL should be
80. For static models this file always contains the spectrum. The Flux is given as Fλ in cgs units
(erg/s/cm 2 /cm). There are additional columns in the file that are only of interest to PHOENIX
experts (e.g., line ID’s are collected here).
Unit 9: Output file. This file is used to communicate with Holger Beck’s chemistry code. The
first line gives the relevant model parameters. The Lagrange frame spectrum is punched in the
format: wavelength (in ˚A), log 10(mean intensity), log 10(Eddington flux) and
log 10(Planck function(λ, Teff)). On IBM mainframe systems the LRECL should be 80.
• Units 10,11: binary files with the partial pressure table and header. These files are read only
if the EOS table mode is selected in PHOENIX but they are unconditionally openend with
STATUS=’OLD’. The tables are created with csppress.
• Unit 17: Input file. File containing a “dump” in PHOENIX-internal format. Used only if JOB=5.
Use this file for communication with other codes or for the input of arbitrary density structures
to PHOENIX.
• Unit 18: Input file. This file contains the data computed in previous runs of PHOENIX. It holds
the parameters, temperature structure etc. in ASCII form and is read only if JOB = 1 in the unit
5 input file, otherwise it is ignored. Warning: This file contains case-sensitive data! PHOENIX
scans this file for certain keywords using the index function. Make sure that the case of the
letters in this file match the case of the compiled version of PHOENIX, otherwise the results will
8

e wrong!
• Unit 19: Output files. It contains the results of the iteration process for all iterations
performed by PHOENIX in the format used in the Unit 18 input file.
• Unit 20: Output file. This file contains the same information as the Unit 19 file, but only for
the last finished iteration of PHOENIX. It can directly be copied to the unit 18 file.
• Unit 21: Output file. If LINOUT is set to 2 in the control file, PHOENIX will print the list of lines
considered in the calculation onto this file as formatted test (detail in subroutine GRELCM of file
misc.f). Presently, only the LTE lines read from unit 2 are used, however, one of the next
versions will include the NLTE lines too.
• Unit 22: Output file. A “level 0 dump” of the results is printed here, in the same format as unit
17. It saves only the results of the last iteration.
• Unit 30: Input file. This unit will be used to read “fuzz.bin,” the binary list of NLTE
background lines. It is used (and opened) only if NLTE is switched on.
• Unit 31: scratch file, used to “swap” currently unused blocks of the NLTE background lines out
of core.
• Unit 32 and 35: scratch file, used to “swap” currently unused blocks of the molecular lines
out of core.
• Unit 36 and 37: scratch file, used to “swap” currently unused blocks of the molecular NLTE
lines out of core.
• Unit 33 and 3: scratch file, used to “swap” currently unused blocks of the atomic lines out of
core.
• Units 40-53: scratch files for the NLTE bock algorithm.
• Unit 66: Output file. Internal information and warnings are printed on this unit. The file is
mainly used for debugging purposes. For production runs, it can be connected to /dev/null on
UNIX systems or can be set to DUMMY on IBM mainframe machines (or equivalent for other
operating systems).
• Unit 67: scratch file, for debugging only
• Unit 71: Output file. Used to communicate with Herbert Störzer’s 3D radiative transfer code
(for AGN models).
• Unit 77: Output file. Used to write Sobolev optical depths for line IDs in SN mode.
• Unit 99: Output file. This file gives the iteration history for the “Cassandra” multi-level
non-LTE method. The columns give the iteration number, the maximum relative change of the
electron density, the maximum and average relative changes of the generalized departure
coefficients and the maximum and average relative changes of the population densities of the
non-LTE levels.
4 The Input to PHOENIX
This file contains the program control parameters for PHOENIX. We give here only a short description
of the most important variables. The description uses the name of the variables as defined for the
mkinput utility. The names used in PHOENIX may be slightly different.
4.1 Global job control parameters
• phxvers: version number of PHOENIX for which mkinput will generate the Unit 5 input file.
Currently allowed values are 3 to 8. This variable is no longer needed.
• comment: A CHARACTER variable. The value of this variable will be printed as a reminder for
the user.
• command: CHARACTER array with commands that are interpreted by mkinput. See the source
code of mkinput for details of the commands that are allowed.
9

• job: INTEGER variable indicating the main task of the job; 0: start a new model with a plane
parallel grey temperature stratification and LTE occupation numbers for all species; 1: use data
read from unit 18 to continue an previous calculation; 5: read a “dump” file from unit 17 and use
the density stratification for the computation. This is used for (a) using arbitrary density
profiles and (b) for reading in structures produced by other codes. The utility rdvis converts
Lisa Ensman’s VISPHOT files into PHOENIX dump-files. Some more values will be accepted by
PHOENIX, but they are obsolete and will be removed in a later version.
• aufg: an alias for job
• doid: LOGICAL flag, .FALSE. for normal operation of PHOENIX. If set to .TRUE., the spectrum
file will include line identification based on the optical depth of the lines (with a considerable
increase on CPU time for the run). Currently, the line ID feature works only for static models.
See the separate (in development) chapter for a detailed description of the line ID output file.
• allow interpol: .TRUE. allows the restart file reader to interpolate in the number of layers.
Default is .FALSE., i.e., a mismatch in the number of layers between PHOENIX and the restart
data causes an error.
• iter: INTEGER variable, gives the maximum number of model iterations to perform. The value
0 for this variable instructs PHOENIX to perform one iteration and compute an observer’s frame
spectrum, which will be punched on the logical unit 7.
• ngrrad: Number of radiative iterations. Starting with iteration number ngrrad+1, one
intermediate and subsequent fully convective iterations will be performed. Useful only for
Dwarf and Giant models. Setting ngrrad=0 will start with a convective iteration. Note that
mkinput will set this input parameter to iter+1 for SN and Nova models.
• convec opacity flag: INTEGER variable. It chooses the opacity that will be used for the
convection calculations. 0: the same opacity as for the τstd grid will be used, 1 to 4 select the
different mean opacities that are available (see fcthyd in misc.f for further details).
• tau conv min: REAL variable. Minimum optical depth at which the convection will be
considered. Usually set to zero (everywhere). Can be used to accelerate convergence in models
with bad initial guesses of the outer temperature structure (mostly giants)
• mixlng: ratio of mixing length to scale height parameter.
• ntc: number of species to used to calculate the adiabatic gradient. Default set by mkinput.
• codcnv: list of codes of the adiabatic gradient species. Default set by mkinput.
• ieos: indicates the EOS to be used. 0 selects the big EOS of France Allard, including molecules,
1 selects the much faster EOS including only atoms and positive ions. Partial pressure tables in
the format used by PPRESS are used for IEOS=2.
• idirect: allows control of ppress startup estimates: 0: no direct mode, i.e., table interpolation
(for ieos=2); 1: direct mode using usual ppress.f startups; 2: direct mode using EOS tables as
startup.
• use zusu old: set to .TRUE. to use the old atomic partition function routines. The default is
.FALSE., i.e., using the new partition function routines for atoms and ions. The new Q routines
are required to use the new additional chemical elements in the EOS.
• use qas: set to .FALSE. to ignore the asymptotic parts of the partition functions for atoms and
ions. This works only with the new Q routines (use zusu old=.FALSE.) and only for LTE
species.
• dchi factor: REAL variable used to control ionization potential reduction. dchi is multiplied
by dchi factor. set to 0.d0 to turn ionization limit lowering off, set to 1.d0 to use standard
values.
• no dchi for neg ions: LOGICAL flag for ionization potential lowering for negative ions.
.TRUE.: will use dchi for negative ions, .FALSE.: will not use ionization potential reduction for
negative ions.
• hminus meth: Sets which H − opacities to use: 0: John (1988) data, uses implicit Saha factor, 1:
original data, use H − pressure for b-f. Results are (in strict LTE) nearly the same.
10

• newcia: set which CIA version to use: .TRUE.: new CIA data, .FALSE.: old CIA data
• shomate: Set to .TRUE. to use the SHOMATE data for the EOS.
• sch2: Set to .TRUE. to use the SC Q(H2) rather than the old one.
• fastmode: 1: selects the faster, smaller EOS (IONS) for the integration of the hydro static
equation (after that the EOS chosen with IEOS will be used to recompute EOS at the grid
points) for test purposes, 0: use the same EOS for the whole run (can be very slow if IEOS=0).
• inlte: INTEGER variable; 0: LTE calculation, 1: NLTE calculation for the selected species.
• imolnlte: INTEGER variable; 0: molecular LTE calculation, 1: molecular NLTE calculation for
the selected species see sec. (??).
• ezl: LOGICAL variable. If EZL=.TRUE. line blanketing of the LTE lines will be included in the
calculation, otherwise only NLTE lines will be included.
• ezlmol: LOGICAL variable. If .TRUE. line blanketing of the LTE molecular lines will be
included in the calculation, otherwise only molecular bands will be included.
• laus: INTEGER variable. Setting laus to a value greater than 0 will result in an increasing
output on unit 6 for debugging purposes and additional information output, e.g., partial
pressures of all species.
• hydstop: INTEGER variable. Default: 0, normal operations, 1: stop after hydrostatic integration
and EOS output, 2: stop after wind integration
• use rkqc: LOGICAL variable. .FALSE. (default) uses Burlirsch-Stoer method for hydro
integration, .TRUE. uses Runge-Kutta.
• opac out: wavelength dependent opacity output flag. 0: no output, 1: ASCII output (huge!), 2:
binary output (not much smaller!).
• blkalg: .TRUE. selects the blocked line blanketing algorithm. This parameter is obsolete
because the old non-block algorithm has been disabled in the source code. Setting this
parameter to .FALSE. will cause an error exit.
4.2 Parameters for the parallel mode
• nworkers: INTEGER variable, number of worker nodes per wavelength cluster (?, see).
• nwlnodes: INTEGER variable, number of wavelength clusters (?, see). If ≤ 0, the total number of
available MPI tasks will be used.
The product nwlnodes * nworkers must be equal to the total number of processors or nodes
allocated to the PHOENIX run. If this is not the case, PHOENIX will complain and stop.
• nsynch: INTEGER variable, number of wavelength points to calculate before a barrier call
synchronizes all worker nodes within a wavelength cluster. Normally set to a large number to
disable this feature. Very convenient when an MPI implementation has some bugs.
• n rt: INTEGER variable, number of worker nodes per wavelength cluster that will work on the
radiative transfer solution at each wavelength point.
• j pipeline: LOGICAL variable, .TRUE. to use the J-pipeline between wavelength clusters.
Normally .FALSE..
• n nlte opac: INTEGER variable, number of worker nodes per wavelength cluster that will work
on the NLTE opacity calculation at each wavelength point. Note that this number must be the
same as n nlte rates.
• n nlte rates: INTEGER variable, number of worker nodes per wavelength cluster that will
work on the NLTE rate calculation at each wavelength point. Note that this number must be the
same as n nlte opac.
• n nlte grp: INTEGER variable, number of distinct NLTE groups that should be automatically
distributed onto a single cluster.
• n lin atm v: INTEGER variable, number of worker nodes per wavelength cluster that will work
on the LTE background atomic lines with Voigt profiles.
11

• n lin atm g: INTEGER variable, number of worker nodes per wavelength cluster that will work
on the LTE background atomic lines with Gauss profiles.
• n lin mol v: INTEGER variable, number of worker nodes per wavelength cluster that will work
on the LTE background molecular lines with Voigt profiles.
• n lin mol g: INTEGER variable, number of worker nodes per wavelength cluster that will work
on the LTE background molecular lines with Gauss profiles.
• n selec atm: INTEGER variable, number of nodes that will work on the line selection for the
LTE background atomic lines. Can be set to some large number so that all nodes will work on
the line selection.
• n selec mol: INTEGER variable, number of nodes that will work on the line selection for the
LTE background molecular lines. Can be set to some large number so that all nodes will work
on the line selection.
• n selec fuzz: INTEGER variable, number of nodes that will work on the line selection for the
NLTE secondary lines. Can be set to some large number so that all nodes will work on the line
selection.
4.3 Code parameters affecting memory usage
These parameters will have an effect only if PHOENIX was compiled in module-mode.
• linmax: INTEGER variable, blocksize for the atomic Voigt and Gauss line blocks. Should be
around 20,000.
• linmaxm: INTEGER variable, blocksize for the molecular Voigt and Gauss line blocks. Should be
around 20,000.
• linmaxf: INTEGER variable, blocksize for the secondary NLTE Voigt and Gauss line blocks.
Should be around 50,000.
• ncache atm v: INTEGER variable, number of atomic Voigt line cache blocks, normally around
3–5.
• ncache atm g: INTEGER variable, number of atomic Gauss line cache blocks, normally around
3.
• ncache mol v: INTEGER variable, number of molecular Voigt line cache blocks, normally
around 3–5.
• ncache mol g: INTEGER variable, number of molecular Gauss line cache blocks, normally
around 3.
• ncache fuzz: INTEGER variable, number of secondary NLTE line cache blocks, normally
around 3.
• lin blksize div:INTEGER variable, used to reduce the blocksize of the LTE line IO by this
factor. It must divide the stored blocksize so that
mod(store block size,lin blksize div)=0. This is used to reduce the cache sizes for
faster parallel performance.
4.4 Outline of the Wind Model Package
Update: (jpa, 13/dec/02)
See Aufdenberg et al. (2002) ApJ 570, 344 for another description of wind module.
Wind models (model = 7) for hot and cool stars use
1. a “β” velocity law (ivelcalc = 0) of the form: v(r) = v∞(1 − R∗/r) β or
v(r) = v0(1 − r0/r) windbeta in terms of input parameters.
2. OR a linear velocity law (ivelcalc = 2) of the form: v(r) = vmax(r − R∗)/(Rmax − R∗) or
v(r) = v0(r − r0)/(rmaxw − r0) in terms of input parameters.
12

3. OR a velocity law for a red giant (ivelcalc = 3) of the form: v(r) = vmaxc1(r/R) m for r/R < 3.75
and v(r) = vmax(1 − e −c2(r/R−c3) ) for r/R > 3.75 for the cool component of EG And (see Vogel
1991, A&A, 249,173)
4. Here, r0 is the “photospheric” radius which is located at the base of the wind. The maximum
radius of the wind model is specified by rmaxw. In both the beta and linear velocity law cases,
the density structure,in the dynamic (v(r) > 0) layers, is calculated from the continuity
equation, ρ(r) = ˙ M/4πr 2 v(r). The mass-loss rate, ˙ M, is specified by the input parameter dmdt in
units of solar masses per year.
5. The velocity field may be further characterized by either a constant or depth dependent
turbulence. A constant, depth-independent turbulence is specified via the parameter vturb or
xi (see also xinlte). A depth-dependent turbulence (vturb2 in the code) is parameterized via
vturbmaxfrac (default = 0). If model = 7, the vturb2 array read from unit 18 is overwritten.
vturb2(r) = vturbmaxfrac · v∞ if v(r) > vturbmaxfrac · v∞,
vturb2(r) = v(r) if v(r) ≤ vturbmaxfrac · v∞,
vturb2(r) = xi if v(r) = 0.
6. The radial grid for wind models is setup to finely grid the velocity field in the region of large
acceleration, near the base of the wind, and more coarsely sample the velocity field in the
outermost layers, near the terminal velocity (v0). Radial grid options (irgrid = 0 or 1, 1 is
default) include a hyperbolic cosine distribution (irgrid = 0) and an exponential distribution
(irgrid = 1), parameterized by cosh fac and steff fac respectively.
7. For an optically thin wind, the structure of the hydrostatic region (below iswlayer) is
computed on a fixed optical depth grid where dr/dτ is evaluated to compute the radius at each
layer. The maximum optical depth in the hydrostatic zones is specified by tmaxlg. The density
is calculated from the equation of state under the condition of hydrostatic equilibrium.
8. Mass-loss rates greater than ˙ M ∼ 10 −4 M⊙ yr −1 may result in an optically thick wind with no
hydrostatic base. In this case, it will likely be required to adjust steff fac or steff fac,
iswlayer, and tmaxlg to achieve a reasonable radial grid for the density and velocity
structure. Optically thick models are currently defined as structures in which the optical depth
at the supposed dynamic/static boundary (ie. iswlayer) is greater than the maximum optical
depth, tmaxlg. Very high mass-loss rates are tricky, so try large values of dmdt at your own
risk! (optically thick wind models are still largely experimental)
9. Wind models (model = 7) where the velocity field is calculated (ivelcalc = 1) from the run of
radiative acceleration with depth is still in the development stage. Use ivelcalc = 1 at your
own risk!!
10. Wind models were initially developed for hot and luminous stars (Teff > 9000 K and gravities
log(g)

turbulent velocity (see above). Default = 0. (From de Koter, Hubeny,& Heap (1994) ApJ, 435, 71.)
• ivelcalc: Velocity law type. 0: standard β law wind models 1: self-consistent velocity
calculation (under development) 2: linear velocity law
• windbeta: The exponent β in the velocity law in the case ivelcalc = 0. Typically β � 1.0 for
O- and early B-type stars, up to 3.0 for late B- and A-type supergiants.
• tmaxlg: Gives the maximum optical depth of the hydrostatic zone. The grid (in this zone) will be
logarithmically spaced between the optical depth at the base of the wind (not known in advance)
and τlayer = 10 tmaxlg . This parameter is not ignored if job=1, so make you sure you use the right
value! tmaxlg = 2 for most wind models, tmaxlg = 2 to 3 for optically thick wind models.
4.4.2 Self-consistent Velocity Field (ivelcalc = 1) Parameters
These models must restarted (job = 1) from an existing ivelcalc = 0 model in order to supply
radiative acceleration structure required for the velocity field calculation. Both ˙ M and v(r) will be
computed in this mode.
• model: For all wind models, model=7.
• ivelcalc: For these models ivelcalc = 1.
• teff: Effective temperature [in K].
• logg: gives log(g) at the radius r0.
• r0: The reference radius [in cm], used in the wind velocity law. In addition, r0 sets the
luminosity of the model via L = 4πR2 0σT 4 eff , and is the radius at which logg is specified.
• rmaxw: The outer radius [in cm] of the wind model, typically 200R0.
In this self-consistent wind convergence scheme the temperature correction iterations and
velocity field computation iterations are interleaved following each solution of the radiative
transfer equation. The next four parameters allow control of the order and spacing of these
iterations.
• ivelcntmx: Maximum number of velocity iterations for a fixed temperature structure (default
3).
• itempcntmx: Maximum number of temperature correction iterations for a fixed velocity
structure (default 3).
• ivelcount: start velocity iterations at this number (default 0, do velocity iterations first)
• itempcount: start temp. corr. iterations at this number (default 1, do temp. corr. iterations
second).
4.4.3 Additional Optional Wind Parameters
These parameters, which specify the grid of the radial points, apply to all wind models.
• iswlayer: Model layer for switch from dynamic to static structure (default is 30). Dynamic
region from (1,...,iswlayer) and static region from (iswlayer+1,...,layer). If the total
number of layers in PHOENIX is different from 50, you’ll want to change this.
• irgrid: The type of radius grid construction, 0: use cosh fac, 1:use steff fac (default)
• inewrgrid: For a restarted model (job = 1), 0: use radii from restart file (unit 18) (default), 1:
construct new radial grid from parameters rmaxw, rtau1, and irgrid in the input file, but
continue to use the temperature structure from restart file (unit 18).
• steff fac: Radial points distributed using a exponential scheme from (Steffan et al.1997,
A&AS, 126, 39.) of which steff fac is a scale factor (default 1.5). Adjusting this value may be
useful for redistributing radial points in some cases (e.g. high-mass loss, low velocity). The grid
is very sensitive to this parameter, adjust in units of 0.1.
• cosh fac: Radial points distributed using a hyperbolic cosine of which cosh fac is a scale
factor. Useful for redistributing radial points (default is 15), values 10-15 seem to work well.
14

• itaugrid: The type of tau-grid construction, 0: original scheme (default), 1: new adaptive
scheme.
• velminp: The percentage of terminal or max velocity V0 which will be the minimum velocity in
the hydrodynamic layers (default is 0.0002 or 0.2 %). This sets the velocity of the lowest radial
grid point in the wind. Useful to getting a good density match between the dynamic and static
layers in tough cases.
4.5 Dust Clouds and Gravitational Settling parameters
Over the years since the first inclusion of dust opacities in phoenix the code was subjected to several
cloud models, each involving a set of input parameters, some of which are no longer supported. We
list those models and their parameters and indicate which methods can still be used below.
4.5.1 General Dust Opacity Parameters
These parameters concern only the use of the opacity cross-sections themselves and are required with
any of the method described below.
• igrains: (icond in phoenix.f) flag for use with grains: 0: grains are ignored, 1: grains are
considered in the EOS but ignored in the opacity, 2: grains are consistently included in the EOS
and the opacity, 3: as before, but the grains are ignored in the calculation of the PHOENIX
standard optical depth grid.
• dust porosity: value f of the assumed dust grain porosity to be applied as a multiplication
factor to a grain’s mass density (grain rho new = (1.d0-f)* grain rho). This is done in
KAPCAL/gnsize.f and KAPCAL/kapdust.f for the two main cloud methods. Must be ≤ f < 1.
Default is no porosity i.e. 0.d0.
• usedust: DOUBLE array with dust opacity multipliers for each individual dust ’species’ that
have supported opacities. Default depend on the original setup. Setting an element of this array
to zero remove that species’ opacity completely. Used to adjust dust opacities.
• cloud covering factor: sets the cloud covering fraction, from 0.d0 to 1.d0 in the spectrum
only (vcapdustcloud). Possibility to use a different fraction for each layer and species of dust
particle for which we have an opacity profile (clouds matix), however not turned on in phoenix.f
though. Default is 1.d0.
• use clouds: switch to choose from cloud methods: ≤ 0: equilibrium model, > 0: settling model.
4.5.2 Rainout Model:
Produce 100% grain settling i.e. all grains sedimented out and corresponding refractory metal
depletion. The fraction “xout” (0 for no settling, 1 for maximum settling) can be changed the rainout.f
routine directly (in KAPCAL/rainout.f). The rainout option is available in csppress.f for EOS
calculations as in phoenix.f for direct mode model calculations.
• rainout: Set to .TRUE. to use the RAINOUT EOS.
This option is independent of other cloud models and of variables like use clouds or settleos. Rainout
should be used with standard EOS parameters like ieos and idirect and with at least igrains=1.
4.5.3 Equilibrium Cloud Model:
When use clouds ≤ 0 this cloud model is chosen, where number densities of grains as provided by the
EOS with igrains > 1 are used in csgrain0 with a log-normal distribution of grain sizes defined in
gnsize.f as called from input.f is used. This type of cloud models generate dust opacities all through
15

from the base of the cloud to the uppermost atmospheric layers, hence overestimating the cloud
opacity contribution in the upper atmosphere. But these provide a limiting case to the effects of
grains on atmospheres. Other relevant parameters for this model are:
• gnsize: base size of the grains im µm. The grain sizes are distributed as
arad(n) = gnsize ∗ (1.d0/(1.0d0 − f)) ∗ (1.5 n−1 )
for n = 1 . . . 10 and where f is the dust porosity factor (see below).
• gnexp is the power of the power law for the dust size distribution function, arad(i) gnexp .
4.5.4 Rossow Gravitational Settling Cloud Model:
When use clouds > 0 this cloud model is chosen. Here a new computational step is introduced
between the hydrostatic and the radiative transfer, that solves a diffusion equation involving
microphysical timescales for the most important processus involved in determining the fraction of
grains produced by the EOS which would sediment out of the current layer. These are the
condensation, coagulation, sedimentation and mixing (assumed convective). In the radiative zone, the
mixing must be assumed. For this we use the fall-off of the convective velocity (usually exponential
from the top of the convection zone in hydro models), but a parameter (itmix) can be used to try other
assumptions. The Settling model can be computed with or without repercussion on the elemental
abundances (settleos). But when turned on, the repercussion causes stratified abundances and such a
model must therefore be compute in direct mode also for the hydrostatic so that these abundances
changes are taken into account on the structure as well. For this, use France’s EOS (ieos=0) and to
facilitate restart use the partial pressures (TOTN matrix) stored from a previous iteration/model on
the input .20 file. This can be done with the idirect switch (idirect=1). Finally, we also offer a variety
of scenarios for the initial abundances to deplete from (see istartsolar).
• itmix: switch to choose, in the radiative zone only, the shape of the mixing time scale profile as
a function of height in the atmosphere: 1: tmix shape is parabolic, 2: tmix shape is fixed to
alpha clouds, 3: tmix shape is fixed to dldhp/vconv out, where vconv out is the convective
velocity at the top of the innermost convection zone. Default is 1.
• alpha clouds: Value of the mixing time scale in sec used in the radiative zones unless itmix
(see above) specified otherwise. Default is 1.d5 sec.
• settleos: flag (.true./.false.) to turn on/off a readjustment of the elemental abundances due to
the gravitational settling of grains. When .true. a matrix SEHEU will store the resulting
stratified abundances. Careful! Default is .false.! In newer phoenix versions, settleos=true also
allows use of input .20 seheu abundances in the hydrostatic T-P structure solver.
• istartsolar: flag used in the Rossow cloud model to choose from various scenarios of the
thermal hystory of the gas. This is done by choosing amongst various original abundance mix:
istartsolar=0: use stored .20 abundances at first iteration and deplete from there at each layer
from iteration to iteration, 1: deplete the atmosphere progressively from bottom to top using
scaled solar abundances (zscal) in bottom-most layer (=nlayer), and, 2: use scaled solar
abundances throughout at first iteration and deplete from there at each layer from iteration to
iteration. Use 0 to account for thermal history of the gas from model to model (inconvenient and
unnecessary as abundances only change by gas cooling, use solely for test purposes), use 1 when
the atmosphere only cools over time (e.g. brown dwarf grids), use 2 to neglect any former
thermal history of the gas (results depend upon iteration route, leave it for test purposes).
Default is 1. This flag has NOTHING to do with the use of the input .20 seheu stratified
abundances in the hydrostatic. This will be done simply if settleos=true.
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4.5.5 Ad’hoc Gravitational Settling Cloud Model:
This method is the first we have developed to account for gravitational settling back in 1999. It is
crap! But apparently still available in the code (kapdust and vcapdustcloud, ie both in the hydrostatic
and on the spectrum) and can even be turned on along with the new settling model stuff, though not
for long if I can help it :-) The method is turned off when dust settl > 0 which is the case by default.
• alpha clouds: Sets the top of the clouds at alpha clouds times the pressure scale height at
the top of the innermost convection zone. Default is 1.0.
• dust settl: Fraction on the total mass density assumed to be sedimented out (same for all
layers). Default is 5.d-5.
• settl speed: Argument of exponential function in vcapdustcloud intended to “accelerate” the
settling. Default is 0.d0.
4.6 Input for using C.Hellings input data and/or chemistry
If C.Hellings data are used (helling.out = true), a file called helling.out will be generated,
which contains the molecules considered by C.H., their array index and a flag of usage. The file exists
for information purposes only.
• use helling: LOGICAL variable. The Kp’s in FPPRESS/discon.f will be calculated by
C.Helling’s data for selected molecules if set true. h use all and h use molec (see below) will
be ignored if set false.
• h use all: LOGICAL variable. If set true, every available molecule-Kp from C.H. will be used.
• h use molec: LOGICALarray. Only valid, if h use all is false. The array has as many entries
as C.H.’s number of molecules are available. If the appropriate entry is set true, the molecule
will be considered for C.H.’s Kp-calculation.
4.7 Radiative transfer parameters
• irtmth: INTEGER variable. This flag controls the radiative transfer method used in the
calculation. irtmth = 0 selects the DOME method and irtmth = 1 selects the OS/ALI method.
• lwdth: bandwidth of the acceleration operator for the operator splitting radiative transfer
method. 0 selects the diagonal operator (very slow), 1 the tri-diagonal operator (best overall
performance) and ¿1 sets the bandwidth directly (can give performance improvements on some
types of machines).
• didl discr meth: set S3R2T weight distribution for dI/dλ discretization. Must be in [0, 1], 0
gives S3R2T version 3 discretization, 1 the original version 2 discretization.
• nmue pp: INTEGER variable specifying the number of angular points per half-sphere if the
OS/ALI plane parallel radiative transfer is used. The points are distributed according to a
Gauss-quadrature formula.
• ncore: number of core intersecting characteristics. They are distributed linearly in (static) µ
from 1 to the last shell.
• nadd: number of additional characteristics. They are distributed linearly between shell indices
nvon and nbis. An error will occur if an additional characteristic lies exactly on top of a regular
characteristic.
• wldiscr: INTEGER flag specifying the type of the wavelength derivative discretization used in
the CMF RT. 0 uses the fully implicit 2 point formula, 1 the implicit 3-point discretization
(default).
• clambavg: INTEGER flag specifying the form of the implicit term of the wavelength derivative
discretization used in the CMF RT. 1 is the default and should be used for all models. 0 is a test
setting and should not be used for anything but testing.
17

• irfout: INTEGER variable specifying the unit number of the output of the full angular
dependent radiation field. If set to 0 (default), no output will be produced. For values greater
than zero, the angles are represented by the direction cosine, µ (mu). For values less than zero,
the angles are angular radii, � (1 − µ 2 ), useful for very extended atmospheres and winds.
[update: jpa, 13/dec/02]
• lay rf: INTEGER variable specifying the radial gridpoint number for which the angular
dependent radiation field might be printed, default is the outermost point (1).
• mkhint: LOGICAL parameter. The default value is false, and should only be set to true (which
must be done explicitly by the user) when using irradiation mode. When set to true, PHOENIX
will solve the radiative transfer equation twice per global iteration. The first solution is without
any incident flux, and the second is with the incident flux.
4.8 Specific model parameters
• teff: The effective temperature Teff [K]. Typically be in the range from about 6000 K to about
15000 K for supernova model calculations and about 10000 K to 40000 K for nova models.
• logg: gives log(g) for the stellar modes of PHOENIX. Note that logg is an alias for vfold.
• r0: The radius, where τstd is unity [cm]. This parameter fixes together with Teff the model
luminosity, L = 4πR 2 0σ Teff 4 . In the giant models, r0 gives the outer radius (and logg is the
gravity the outer radius).
• reff: used with new giant mode to define the radius of a giant model at tstd=1. In this mode,
R0 is considered a first estimate for the outer radius of the star.
• new giant mode: Used with modtyp=4, invokes the sliding scale height which is defines the
gravity, log(g), at (currently) tstd=1 for a radius called reff. Phoenix needs teff, logg, and r0 to
calculate a model, lsun and msun can be read in, see below. Note: teff must be one of the 3 input
parameters.
• v0: The expansion velocity in [ km s −1 ] (!). For modtyp = 1 (SN standard), v0 is assumed to be
the expansion velocity at τstd = 1, for modtyp = 2 (Novae) and modtyp = 3 (SN mode 2), v0 is
the maximum expansion velocity (v(r = rmax)). For supernova models, v0 should be
5000–20000 km s −1 , and for novae it should be around 2000 km s −1 . For nova models (modtyp =
2), PHOENIX accepts also values less than zero and treats them as the mass-loss rate in M⊙ yr −1 .
Warning: If the maximum velocity is greater than about 5 × 10 4 km s −1 and irtmth=0, the
current version of PHOENIX will crash because of a simplification in the DOME radiative
transfer code. The OS/ALI method, however, will work for higher velocities.
• model: Type of the model as an INTEGER variable (called modtyp in PHOENIX). 1 stands for
supernova models, 2 for nova models, 3 denotes SN models with v0 interpreted as the maximum
expansion velocity. Stellar atmosphere models are indicated by the code 4 for giants (spherical
RT, g varies with radius) and 5 for dwarf atmospheres (plane parallel, g constant). AGN models
are denoted by model=6, these models use a dump file to read in a structure (fixed Pg) and use
the static, plane-parallel radiative transfer. All other values result in an error message and an
emergency stop of the main program.
• dentyp: Type of the density profile. 1: pure power law density profile (n is the power law index),
2: exponential density profile (vfold and v0 give the exponential index, 3: arbitrary density
profile read from unit 17 is used (interpreted as constant ρ (model=1, job=5) or Pg (model=6,
job=5) according to model), 4: hydrostatic equation is solved to compute the density profile (for
model=4,5).
• vfold: The e-folding velocity if the exponential density law is used. vfold/v0 gives then the
power law density index at τstd = 1. Note that vfold and logg are aliases, so that vfold will
be log(g) in dwarf or giant models. Warning: If the exponential density profile is used and vfold
is set too large, the code will crash with negative radii!
• etaparm: parameter to multiply total instantaneous radiative decay energy by to use for target
18

luminosity (used in makehydro)
• useetaparm: flag to determine whether to use etaparam
• uselumparm: flag to determine if the target luminosity is set using lumparm
• lumparm: value of the target luminosity (r 2 H)
• usemodellum: read the target luminiosity from the hydro model (used in makehydro)
• ihydrotype sets the type of input model 10, 11 are models that have just gone homologous and
are expanded to the target day after explosion (tsince). Model 20 is a light curve calculation
where the data is actually for the target date
• outer point fix: determines whether the bi of the outermost zone are set bi(1) = bi(2) where
1,2 refer to the layer number
• rhtohe: ratio of hydrogen to helium. Hydrogen as read in is “burned” to helium such that the
final NH/NHe = rhtohe
• use cmflux j set .TRUE.to use standard Eddington factor H/J in integrating the target
luminosity
• n: The exponent in the power law density as an INTEGER variable. It should be about 10 for
supernova models and about 3 for nova models.
• pout: The outer pressure on the model atmosphere [dyn cm −2 ]. The value should be small
enough to ensure that the material above the model atmosphere is optically thin at all
wavelengths. Usually this variable is set to 10 −4...−6 for supernova and to 10 −3...−4 for nova
models.
• aradfac: multiplicative factor for radiation pressure in hydrostatic equation, zero neglects
radiation pressure, 1 uses normal radiation pressure in the hydrostatic equation (as computed
in the previous model iteration).
• lwd: specifies the luminosity of an external radiation source illuminating the outside of the
model. The energy distribution of the source is assumed to be a Planck-function.
• twd: specifies the radiation temperature of the external source.
• d2: specifies the distance of the external source to the outermost gridpoint of the model.
• domue: specifies the index of the angle point that received the incoming radiation.
• redist: REAL variable. The incident flux at the surface will be multiplied by redist. redist
should normally be set to 1 or 0.5, but may be anything you like! redist = 0.5 would imply a
redistribution of the incident flux over the entire irradiated hemisphere. redist = 1.0 would
imply no redistribution.
4.9 Parameters describing the optical depth grid
• wltau: reference wavelength (in ˚A) of the optical depth grid. Typical value is 5000 ˚A, for cool
models 1.2 µ.
• extscl: LOGICAL variable, if .TRUE. the extinction χ = κ + σ will be used instead of κ in
eq. (1). This has influence on the optical depth scale grid. For relatively cool models
( Teff ≤ 10 4 K) extscl should be .true., but for hot models it could be better to use
extscl=.false. in order to obtain smooth convergence. WARNING: Although extscl is a
quite important parameter of the models, it is not saved in the continuation files. Be careful to
use the correct value of extscl if a continuation file is used!
• tminlg: see tmaxlg
• tmaxlg: Gives together with tminlg the standard optical depth scale. The grid will be
logarithmically spaced between τstd,2 = 10 −tminlg and τstd,layer = 10 tmaxlg . τstd,1 will always be
zero. The important point τstd = 1 will be inserted automatically. Both parameters will be
ignored, if job=1. The data given be tauskala will be used, if tminlg > tmaxlg.
• tauskala: The following array gives the standard optical depth scale used by PHOENIX if
job=0 and tminlg > tmaxlg, otherwise it will be ignored.
19

4.10 Parameters to handle opacity tables
• do opac table: set true for calculation of an opacity table over a grid with the temperature T
and Pgas or ρ as the second independent variable. opac out has to be 0.
• logt: flag specifying the temperature grid (0: log10, 1: linear, 2: linear in θ = 5040/T)
• modeos: set the second independent variable (0: Pgas, 1: rho)
• tstart: starting point of the temperature grid (logarithmic or linear value, depending on logt)
• tstop: last point of the temperature grid (logarithmic or linear value, depending on logt)
• tstep: increment for the temperature grid (logarithmic or linear value, depending on logt)
• pstart: starting point for the second variable (logarithmic value)
• pstop: last point of the second variable (logarithmic value)
• pstep: increment for the second variable (logarithmic value)
• tstart2, ..., tstart5, tstop2, ..., tstop5, tstep2, ..., tstep5: to define
multiple temperature grids.
The opacity table has a size of Σ = (tstop − tstart)/tstep ∗ (pstop − pstart)/pstep. In each iteration
one point of the table will be calculated for each layer. For calculation of a complete opacity table
N = Σ/layer iterations are necessary. An incomplete opacity table can be used for input to complete
the calculation by use of some more iterations. The opacity table is written to fort.19 and fort.20 as an
unformated and a formated table after all iterations are done. Use as many layers as possible to
minimize the number of iterations.
• use opac table: set true to read a rosseland mean opacity grid for the optical depth grid from
an opacity table. Copy the formatted opacity table to fort.48 before the start of the model
calculation. This opacity table should be calculated for the same parameters like in the model
which uses the table.
4.11 Standard wind model parameters
v(r) = v∞(1 − R∗/r) β
v(r) = V0(1 − R0/r) WINDBETA
• model: For standard wind models, model=7.
• r0: The radius [in cm], used in the standard wind velocity law, v(r) = v∞(1 − r0/r) β . In wind
models, r0 is the radius at which logg is specified. The parameter rmaxw sets the outer radius
of the wind model. This parameter fixes together with Teff the model luminosity,
L = 4πR 2 0σ Teff 4 .
• rmaxw: The outer radius of the wind model, typically 100r0.
• logg: gives log(g) at the radius r0.
• v0: The terminal velocity (v∞) of the wind in [ km s −1 ] (!).
• windbeta: The exponent β in the velocity law. Typically between 0.5 and 1.0.
• dmdt: The mass-loss rate in M⊙ yr −1 .
The density structure in the standard wind model is calculated assuming a constant mass lost rate,
ρ = M⊙ /4πr 2 v, where the radial grid is determined by integrating dr/dτ. A non standard tau grid is
used to give a fine tau spacing around the high acceleration region of the wind. Below the
“photospheric” radius, specified by R0 the density structure is determined from hydrostatic
equilibrium and the velocity is calculated such that mass loss rate is held constant.
4.12 Parameters for the temperature correction
• dotcor: LOGICAL parameter. If set to .true., the temperature correction procedure is
activated, otherwise no temperature correction is attempted (and PHOENIX will run about 20%
20

faster if the DOME radiative transfer method is used). dotcor=.false. is mainly used
together with iter=0 and irtmth=0 to compute high resolution observer’s frame spectra using
the DOME transfer code. The overhead of the temperature correction procedure for the OS/ALI
method is relatively small and can be neglected.
• tcor min: REAL variable. If the temperature corrections at all layers are all less than
tcor min, no more iterations will be preformed. The default value is 1K.
• idmin: INTEGER variable which gives the minimum damping factor for the temperature
iterations. The iterations will be damped with 2 −idmin in order to avoid over corrections and
oscillations. Usually this parameter should be between 1 and 2. If idmin < 0, −idmin gives the
maximum allowed temperature correction ∆T in % (this may help in difficult cases).
• ultcor: .TRUE., if the modified Unsöld-Lucy temperature correction method is selected (this
requires the OS/ALI radiative transfer), the default is .FALSE., selecting the Newton-hybrid
temperature correction.
• tsw: A technical parameter. At this standard optical depth, PHOENIX will switch from the
� κ(J − B) dλ condition to the “luminosity” condition. For an extinction optical depth scale, the
value of tsw should be around 1, for an absorption scale around 10 −2 . If the value is too small,
the temperature iteration will be strongly unstable in the outer parts of the atmosphere; if the
value is too large, large over-corrections of the temperature will occur. This variable is not used,
if dotcor (see below) is .false..
• tapp: A technical parameter. The temperature for τstd < τapp will be set constant. This
parameter is useful to speed up the temperature iteration for some models. Usually set to zero.
4.13 LTE atomic, ionic and molecular line parameters
• greli: lines selection threshold parameter. A LTE line will be included in the calculation, if
κlc/κcont ≥ greli for the reference layers, otherwise it is ignored. Here κlc denotes the
absorption coefficient at the line center and κcont the corresponding continuum absorption
coefficient. If greli = 0, all available lines will be included until the arrays for storing line data
are filled and the time consuming selection procedure is skipped. Not used, if EZL=.FALSE..
• gremlin: As greli but for molecular lines. Not used if ezlmol=.false..
• cas greli: As greli but for the NLTE lines from the Cassandra data structures. Not used if
inlte=0.
• skip select: LOGICAL variable, set to .TRUE. to skip molecular line selection after first
iteration when running in MPI parallel mode. Default is .FALSE.. Warning: if you use this
speed-up, make sure to select all important lines on the first run, e.g., by choosing extremely small
thresholds.
• grelvoigt: used only for iwhprof=2 and gives the threshold for lines with full Voigt profiles
(works like greli).
• gremvoigt: like grelvoigt but for the molecular lines
• nonunfm: set to .TRUE. to allow non uniform abundances in SN modes.
• binary compositions: Set to .TRUE. to read composition file in binary mode.
• nref: number of references points for the line selection procedure. Default is 3, if set to layer
the line selection procedure will be done automatically for all radial grid points.
• tauref: standard optical depth points used for the line selection procedure. Default set by
mkinput.
• sobid: .TRUE. to turn on Sobolev ID’s for SN models (used only for IDs, nothing else).
• nsobref: number of references points for Sobolev line ID procedure. Default is 4, if set to
layer the Sobolev line ID procedure will be done automatically for all radial grid points.
• tausobref: standard optical depth points used for the Sobolev line ID procedure. Default set
by mkinput.
21

• iwhprof: INTEGER flag for the line profiles for the LTE atomic lines. 0: pure Gauss profiles; 1:
old Voigt profiles for all lines using computed damping constants (see France’s thesis for details);
2: use pre-computed (during line selection) damping constants for lines that are stronger than
GRELVOIGT, Gaussian profiles for the weaker lines, 3: like 2 but with improved vdW damping
constant computation.
• molprof: like iwhprof but for the molecular lines.
• c6corr: sets the correction factor for C6 in LTE and NLTE lines (also molecular lines). Default
is 10 1.8 , set to unity to disable correction (useful for the Sun etc!!)
• gamnatver: INTEGER flag specifying the way the natural radiative damping constants are
calculated for atomic lines: 0 uses internal approximation, 1 the values read from the line list
file.
• gam4ver: INTEGER flag specifying the way the quadratic Stark damping constants are
calculated for atomic lines: 0 uses internal approximation, 1 the values read from the line list
• gam6ver: INTEGER flag specifying the way the vdW damping constants are calculated for
atomic lines: 0 uses internal approximation, 1 the values read from the line list file.
• dlilam: Gives the wavelength range [ ˚A] around which PHOENIX will search for LTE-lines at
each Lagrangian wavelength point. The value should be considerably larger than the width of
the lines. If the value is too large, the execution time will increase; if it is too small, the results
may be not accurate enough. Ignored, if EZL=.FALSE..
• gausswin: Gives the wavelength range in Doppler widths which PHOENIX will search for Gauss
LTE-lines at each Lagrangian wavelength point. See dlilam for caveats.
• gremol: As greli but for the molecular bands. Note that gremol is the negative logarithm of
the threshold. Recommended value is 40.
• dmolam: As dlilam but for molecular bands.
• h2olin: INTEGER variable to control the use of either the Ludwig water opacity routines (0) or
the water linelist found in the unit 1 file. If ezlmol is .FALSE., h2olin will be set
automatically to 0, regardless of the input value. The default for this parameter is 0. Note: This
parameter is now superseded by uselin and should not be used.
• jh2o: INTEGER switch to select the Jørgensen water vapor opacity sampling table. 1: selects the
table, 0: selects Ludwig water opacity.
• tioeps: INTEGER switch to selectively switch off the Jørgensen TiO epsilon band. 0: use the
lines of the TiO epsilon band from Jørgensen, 1: use JOLA for the TiO epsilon band.
• new tio fel: LOGICAL switch to selectively change the J-TiO (Jørgensen TiO) fel values.
.TRUE.: use the new values, .FALSE.: use the values stored in the line list. This conversion is
done by bkdecode f90. This switch must be set to .TRUE. to make the next 3 switches active!
• ames TiO version: INTEGER selector to change the AMES-TiO fel values. Currently allowed
values are
1005: use setup of PHOENIX version 10.5 and earlier
1103: use setup of PHOENIX version 11.3 and earlier
1104: use setup of PHOENIX version 11.4 and later
This conversion is done by bkdecode f90 and requires new tio fel=.TRUE..
• VO version: INTEGER selector to change the VO fel values. Currently allowed values are
1005: use setup of PHOENIX version 10.5 and earlier
1103: use setup of PHOENIX version 11.3 and earlier
1104: use setup of PHOENIX version 11.4 and later
This conversion is done by bkdecode f90 and requires new tio fel=.TRUE..
• FeH version: INTEGER selector to change the FeH fel values. Currently allowed values are
1005: use setup of PHOENIX version 10.5 and earlier
1103: use setup of PHOENIX version 11.3 and earlier
1104: use setup of PHOENIX version 11.4 and later
This conversion is done by bkdecode f90 and requires new tio fel=.TRUE..
22

• uselin: INTEGER array with flags for line or band usage. For every molecular isotope (with
lines in the current list) the flag controls of these lines should be considered (uselin=1) or
neglected (uselin=0) in the model calculation. If corresponding JOLA bands exist for the
molecule, they will be automatically switched off if one of its isotopes is considered as lines (this
concerns currently TiO, CN, OH, H2O, MgH). Note that there are currently lines of the same
band systems of one molecule but from different sources (e.g., TiO+CN Kurucz and Jørgensen;
CO Kurucz and Jørgensen and Goorvitch and HITRAN92; H2O Miller+Tennyson and HITRAN92,
this list is incomplete) in the molecular line list. Warning: Currently no tests for inconsistencies
are done by PHOENIX!!
• usedust: DOUBLE array with dust opacity multipliers for each individual dust ’species’ that
have supported opacities. Default depend on the original setup. Setting an element of this array
to zero remove that species’ opacity completely. Used to adjust dust opacities.
• use clouds: 0: clouds are off (default), 1: clouds are on. If set to 1, mkinput will automatically
set settl speed=0.
• alpha clouds: Sets the top of the clouds at alpha clouds times the pressure scale height at
the top of the innermost convection zone. Default is 1.0.
• covering factor set the cloud covering factor, 0 to 1, DOUBLE
• gnsize: base size of the grains im µm. The grain sizes are distributed as
arad(n) = gnsize ∗ (1.d0/(1.0d0 − f)) ∗ (1.5 n−1 )
for n = 1 . . . 10 and where f is the dust porosity factor (see below).
• gnexp is the power of the power law for the dust size distribution function, arad(i) gnexp .
• dust porosity: dust porosity factor f (see above), must be 0 ≤ f < 1.
• vturb: micro turbulence (or statistical) velocity in [ km s −1 ]. Should be around v0/10 for
supernova and nova models. This parameter determines essentially the width of the lines.
• xi: alias for vturb.
• xilte: If positive, statistical velocity used for the LTE lines; if not set or negative, xi will be
used.
• ximolec: as xilte, but for the molecular lines.
• epslin: LTE line thermalization parameter. The LTE line opacity,χ l is divided into line
absorption κ l = epslin ∗ χ l and line scattering σ l = (1 − epslin) ∗ χ l .
• epsmoL: As epslin but for the molecular lines.
• linout: INTEGER variable. If this parameter is set to 1, all considered lines will be echoed on
logical unit 6, if set to 2 the printout will go to unit 21 (this may result in extremely large output
files!). Not used, if EZL=.FALSE..
• anf, ende, step, elmin, elmax: These parameters control the output level of the line
statistics. Not used, if EZL=.FALSE..
4.14 Non-thermal parameter
• tsince: time in days since explosion or creation of the decaying cobalt and nickel nuclei. Used
to compute the radioactive energy input and the number of non-thermal electrons generated.
Makes sense only in SN models.
• frnth0: fraction of the non-thermal electrons with respect to all free electrons. Can be chosen
arbitrarily, but should be connected to the Ni and Co abundances to ensure physical
self-consistence.
• xlumx: Luminosity of a radiation field impinging on the outer boundary of the star, in cgs units.
If set to 0, the outer boundary condition is the standard (zero incoming intensity) assumption.
Useful for all classes of models.
• tcirc: Blackbody radiation temperature for the impinging radiation field. At the moment, a
strict BB for the “circumstellar” radiation field is assumed. Can be changed rather arbitrarily by
23

adapting the code in the subroutine wavcon in misc.f. tcirc=0 will also disable the
impinging radiation field.
4.15 Eulerian and Lagrangian continuum wavelength grids
• intber: An array containing the interval boundaries for the wavelength grid used for the
observer’s frame by PHOENIX. The wavelengths are given in ˚A, a zero indicates the last point
used. The length of the array is fixed to 50, the last value should be 0 if not all entries are used.
• intdis: This array contains the step size between the corresponding intber points [ ˚A]. If the
step size is larger than the difference between the corresponding intber points, an error
message will be issued. If the total number of wavelength points is too large to fit into the
internal arrays on PHOENIX, a warning will be printed, and the maximum number of points will
be used. To increase this maximum number of points, increase maxobs in all subroutines of
PHOENIX and recompile. These computed Euler grid will only be used, if iter is zero, otherwise
it will be ignored.
• cmtber: analogous to intber, but for the Lagrangian frame
• cmtdis: analogous to intdis, but for the Lagrangian frame. The number of Lagrange frame
points will influence the CPU time used for one temperature iteration (linear).
• fmt vfld: string for format code for spectrum output to channel 7, used for models with a
velocity field. Note: the number and type of the arguments must be exactly like the default
setup or a runtime error will occur. This setting is useful if high resolution wavelength and flux
outputs are needed.
• fmt stat: string for format code for spectrum output to channel 7, used for static models. Note:
the number and type of the arguments must be exactly like the default setup or a runtime error
will occur. This setting is useful if high resolution wavelength and flux outputs are needed.
• fmt id: string for format code for spectrum output to channel 7, used for static models in ID
mode (see doid). Note: the number and type of the arguments must be exactly like the default
setup or a runtime error will occur. This setting is useful if high resolution wavelength and flux
outputs are needed.
• read wl grid: logical switch. Defaults to false. If set to true PHOENIX reads a wavelength grid
from an input file called wl.grid. This file can contain several “wavelength chunks”. The first
line of a chunk is the number of wavelength points for this chunk in integer format. Then follow
the wavelength points, one wavelength point per line, read in as double precision. Usually, there
is only one chunk. The wavelength points need not to be sorted. The grid will be ADDED to the
existing LAGRANGIAN frame grid.
4.16 NLTE parameters
The number of NLTE species has rapidly increased since the first version of the manual was written.
The new version of the NLTE routines use a generalized input scheme for the NLTE species
description, see below. One goal is the existing parameters here. The number of levels treated in
NLTE can be set for each ion individually. The naming convection for the parameters is nXX# where
XX is the chemical symbol (e.g., fe for iron) and # is the ionization stage (1 for the neutral element, 2
singly ionized stages etc.). For example, nsi4=50 specifies that 50 levels of Si IV are treated in
NLTE. The number given in the input file will be set to the maximum number of levels available if it
exceeds that value.
• chianti path: full pathname to CHIANTI data file root directory, this is used only if NLTE
species using CHIANTI data files are requested. The directory structure has to be a standard
CHIANTI 3.03 system.
• chianti4 path: same as chianti path, but for CHIANTI 4.02 data.
• aped path: same as chianti path, but for APED (ATOMDB) data.
24

• phoenix path: full pathname to PHOENIX .atom files. Used only if NLTE species using
PHOENIX data files are requested. This path is also used to locate special line profiles (as they
depend on the atomic level data used).
• h1 internal: .TRUE. (default) to use the internally coded PHOENIX model atom for H I.
.FALSE. uses the external file data.
• he1 internal: .TRUE. (default) to use the internally coded PHOENIX model atom for He I.
.FALSE. uses the external file data.
• he2 internal: .TRUE. (default) to use the internally coded PHOENIX model atom for He II.
.FALSE. uses the external file data.
• ne1 internal: .TRUE. (default) to use the internally coded PHOENIX model atom for Ne I.
.FALSE. uses the external file data.
• nlte z list(???): nuclear charge for NLTE species number “???”, 1 for H, 2 for He etc.
• nlte ion stg list(???): Ionization state for species number “???’, e.h., 1 for I (neutral), 2 for
II (singly ionized) etc.
• nlte level number(???): Number of levels to be considered in the model atom for species
number “???”. Can be set to large number to request maximum available.
• nlte dataset(???): Code for NLTE dataset to use for species number “???”: 1 for PHOENIX
.atom file, 2 for CHIANTI version 3 dataset, 3 for CHIANTI version 4 dataset and 4 for APED
(ATOMDB) dataset. Other values are reserved and will be available later.
• nlte line mode: INTEGER flag selecting the formula to use for Cassandra NLTE lines.
Currently allowed values are 0: strict LTE formula, 1: standard Cassandra formula, 2: classic
formula. Default is ’1’. ’2’ is automatically selected in opacity table mode. ’0’ should be selected if
Cassandra is just used to compute detailed line profiles for cool stars.
• profile files(???): List of file names for special NLTE line profile files. The max. number of
files is set in input.f. The path to the files is given in phoenix path. The files must be
compatible with cas profile read and give all profiles for a given set of transitions that share
the same relative profile for a number of temperatures and perturbers.
• n wl 4 prfs: number of wavelength points per special NLTE line profile for normalization and
interpolation. Points are automatically distributed.
• use van reg: set to .TRUE. to allow the use of the Van Regemorter formula for collisional rates
if no other data are available. .FALSE. will resort to Allen’s old formula.
• pb h coll rates: set to .TRUE. to use new H I bound-bound collision rates from Przybilla &
Butler (2004) for levels n

• lamlor: real array giving the nlor wavelength points (in units of the Lorentz width) which are
inserted for NLTE lines at both sides of their profile.
• dvmax: size of the NLTE line search window for Voigt lines, measured in Doppler widths.
• dgmax: size of the NLTE line search window for Gauss lines, measured in Doppler widths.
• voigt cutoff: size of the NLTE line search window for Voigt lines, measured in ˚Angstroem.
• p coll chianti4: Set to .TRUE. to use the proton-proton collision data of the CHIANTI
version 4 database.
• p coll aped: Set to .TRUE. to use the proton-proton collision data of the APED (ATOMDB)
database.
• brems em chianti4: Set to .TRUE. to use the relativistic bremsstrahlung continuum data of
the CHIANTI version 4 database, calculated by the analytic fitting formula of Sutherland
[MNRAS 300, 321 (1998)] for the low temperatures and Itoh et. al [ApJS 128, 125 (2000)] for
temperatures T> 10 6 K.
• twoph chianti4: Set to .TRUE. to use the 2-photon continuum emission data of the CHIANTI
version 4 database. Data is available for the isoelectronic sequence of hydrogen and helium like
ions.
• fb el chianti4: Set to .TRUE. to use the free-bound emissivity data of the CHIANTI version
4 database. It is calculated by including more accurate ground photoionization cross sections
and, for excited levels, using the gaunt factors of Karzas & Latter [ApJS 6, 167 (1961)].
ATTENTION: THIS HAS NOT BEEN TESTED, YET!
4.17 Cassandra acceleration parameters
• iaccel: 0: no convergence acceleration method will be used, 1: use Ng (4th order) acceleration
in Cassandra, 2: use Orthomin acceleration of order inord in Cassandra.
• inord: order of the Orthomin acceleration, if selected. If set to too large a value it will be
automatically set to the maximum available order.
• iaccst: number of the iteration for which the acceleration will start. This variable counts the
internal OS/ALI iterations of Cassandra which will be done without using convergence
acceleration procedures. Beginning with iteration iaccst, the convergence acceleration will be
applied.
4.18 Molecular NLTE (Sybil) parameters
This part is only relevant, if imolnlte is not zero.
• ncosu: Number of CO levels to be calculated in NLTE.
The molecular NLTE calculation uses superlevels. The necessary superlevel information is read in
from three files for each molecule. As an example, the files for CO are explained. The names of the
files for the other molecules can be obtained by exchanging co with the molecule name.
• co.super: Contains the superlevel data information.
• co.actual: Contains the energies and the degeneracy (g) for the actual individual levels.
• co.grid: Contains the wavelength grid to properly sample the transitions between superlevels.
Furthermore, the molecular line list needs to be modified that the integer field for the natural
damping constant contains the number of the upper superlevel and the integer field for the vdW
damping constant contains the number of the lower superlevel.
The selection of a particular superlevel model is done by linking the appropriate files to co.super,
co.actual and co.grid and by using the appropriate molecular input file.
26

4.19 EOS parameters, e.g., abundances, molecules
• nelem: number of elements to consider in the EOS. If set to -1 or not given, all 39 elements will
be considered. The abundances will be updated according to the data given in nome, eheu, and
istg.
• nome: INTEGER array giving the code of an element to consider in the EOS and the opacity
calculation. Format is Z*100.
• eheu: array giving the logarithmic abundance by number of the corresponding element. Will be
re-normalized and re-scaled in PHOENIX.
• yscl: scaling factor for the helium abundance (by number).
• zscl: scaling factor for the metal abundances (by number).
• istg: number of ionization stages to consider for the corresponding element (positive ions).
• mol: flag for use with molecules: 0: molecules are ignored, 1: molecules are considered in the
EOS but ignored in the opacity, 2: molecules are consistently included in the EOS and the
opacity.
• igrains: flag for use with grains: 0: grains are ignored, 1: grains are considered in the EOS but
ignored in the opacity, 2: grains are consistently included in the EOS and the opacity, 3: as
before, but the grains are ignored in the calculation of the PHOENIX standard optical depth grid.
• nneg: number of negative ions to consider
• negion: codes of the negative ions to consider
• nmol: number of molecules to consider
• molcod: codes of the molecules to consider
4.20 Nonmonotonic coupling of wavelengths
The radiative transfer problem can be alternatively solved with a matrix formulation of the formal
solution. Then the radiative transfer is not solved wavelength by wavelength but instead for all
wavelengths at the same time.
This means a complification of the numerical approach as the opacity data for all wavelengths as well
as the ray data (interpolation coefficients, optical depth etc) must be known at the same time for all
wavelengths simultanouesly.
This is a resource demanding approach that has a great benefit, however. Without being an initial
value problem, arbitrary wavelength couplings may be added to the radiative transport problem.
These couplings include for instance:
• non monotonic velocity fields
• general relativistic wavelength couplings due to a graviational field
• arbitrary shock fronts
• any combination of the above
The only aspect of a normal PHOENIX run that is changed is the calculation of the radiative transfer
in S3R2T. The routines necessary to replace the transfer are found in the NMS3 directory (NMS3 =
NonMonotonicSphericalSymmetricSpecial. . . ) and in the according module found in nms3 module.f.
4.20.1 Namelist parameters affecting NMS3
• use nms3 : Logical switch. If set to .true. the radiative transfer will be solved via the NMS3
framework and S3R2T is omitted.
• nms3 solver : Integer switch. It determines the method for the formal solution.
27

nms3 solver method
0 standard band matrix solver
1 SuperLU solver (old)
2 rapido solver (Zurmühl)
3 simple...
4 SuperLU (new) default
5 SuperLU Dist (parallel)
6 Jacobi solver
7 Gauss-Seidel solver
8 7 with Ng acceleration
9 7 with improved starting conditions
10 9 with Ng acceleration
11 10 with additional Ng acceleration in the ALI
Default is SuperLU (new). In
large scale applications one of the GS routines with improved starting conditions should be
chosen.
• nms3 nonblocking IO : Logical switch. If set to .true. the NMS3 setup routines use a sheme
that is better suited for nonparallel filesystems. Set to .true. for the use on nathan or seneca.
Leave it alone on Hanni or NERSC.
• track allocs nms3 : Logical switch. If set to .true. allocation statements will be written to
fort.6.(May bloat the output.)
• spectrum output nms3 : Logical switch. If set to .true. a spectrum calculation is forced on
every ALI step. See also spectrum output mpi gr.
• spectrum output mpi gr : Logical switch. If set to .true. a spectrum will only be calculated
after the ALI is done. Note that spectrum output mpi gr and spectrum output nms3
cannot be true at the same time,PHOENIX will stop.
• nms3 s3r2t nlte compatibility : Logical switch. If set to .true. the parallel NMS3 NLTE
code will calculate ∂J
∂B exactly the same as the S3R2T version. This will in general be different
from the result of serial version that is recovered if set to .false.. (For debugging and
regression)
5 Sending UNIX signals to PHOENIX
PHOENIX currently catches two signals :
• SIGHUP (1): Finishes the current iteration and then stops.
• SIGTERM (15): Stops the current run immediately. But also closes all files and produces all
output up to the current point of calculation.
28

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