D How to calculate a NLTE model with TMAP

D.1 Basics

First a short explanation of the directory structure:

user=${LOGNAME}

For our script, we use the following definitions / shell variables:

setenv AA /home/<user>/adaten

setenv BI /home/<user>/bimod

setenv FF /home/<user>/fgrids

setenv JO /home/<user>/jobs

setenv MO /home/<user>/models

D.2 Creation of atomic data files with ATOMS2

• Change into the directory /home/<user>/jobs/atoms2 and copy the template job file to <name>.job. It needs a file <name> with the atomic data in /home/<user>/adaten. The name <name> can be chosen to contain all the elements used in the model (e.g. H+He)
• You need to edit both files, test_atmos_lte.job and test_atoms.job (e.g. with emacs). The first one is for LTE2, the second one for PRO2.
• After editing, execute the job files and create output files for both jobs with
  

  <name>_atoms.job

  > <name>_atoms.out and

  <name>_atoms_lte.job

  > <name>_atoms_lte.out .

• Check both output files (with emacs) for error messages.
• The jobs create ASCII files, e.g. /home/<user>/adaten/<name>.atoms2.
  

D.3 Creation of a frequency grid with SETF2

• edit both files <name>_lte_setf2 and <name>_setf2 in /home/<user>/jobs/setf2.
  Adjust the temperature and make sure that it refers to <name>_lte.atoms2
• run both jobs and create output files with

  <name>_setf2

  > <name>_setf2.out and

  <name>_lte_setf2

  > <name>_lte_setf2.out .

• it writes the files <name>_<temperature>_lte.setf2 and <name>_<temperature>.setf2
  to /home/<user>/fgrids
  

D.4 Adaption of the Parameter files

• extract the parameters from the <name>_atoms.out file with
  grep para <name>_atoms.out and from the output file <name>_setf2.out of the frequency grid
• if you want to save the parameters you can write them in a file with
  grep para <name>_atoms.out > object.out
• the parameter files for PRO2 can be found in /home/<user>/PARAMETER/pro2
• copy the existing parameter files to PARA_<name>.INC, PARA1_<name>.INC,
  PARA3_<name>.INC and adjust them by using the parameters from
  <name>_atoms.out
  NOTICE: the values in the parameter files should never be 0!
• compile with ssh aithp3 load pro2 <name> [x64/p64] (use x64 for 64 bit machines, p64 for penryn-processor (our quad core) 64 bit machines),
  the executable is copied to /home/<user>/bimod/pro2_<name>.Linux_[x64]
  

D.5 Calculation of a start model with LTE2

• edit <name>_lte.job with emacs. Adjust the temperature, log g, and the abundances of the elements used (as normalized number fraction) and check if the used files have the right name
• input files: <name>_lte.atoms2, <name>_temperature_lte.setf2
• start the job and write it into an output file with
  nice +19 <name>_lte.job > <name>_lte.out
• the lte model is written to /home/<user>/model/<name>/lte. The file is called
  temperature_logg_numberfraction element a_numberfraction element b,
  e.g. 0100000_7.00_1.000_0.000
  

D.6 Calculation of a NLTE model with PRO2

• edit the <name>_nlte.job in emacs. Adjust the temperature, log g and the
  abundances of the used elements and check if the used files have the right name
• input files: <name>.atoms2, <name>_temperature.setf2 and the LTE2 model as input model
• start the job with nice +19 <name>_nlte.job > <name>_nlte.out
• the output model is written to /home/<user>/model/<name>/
  

D.7 Strategy to calculate a NLTE model with PRO2

Some models calculate without any problem using the LTE2 start model and an atomic data files that contains all lines. This can be tested first. In case that this approach fails, try to follow these steps

D.8 Example: A model with hydrogen and helium

T = 100000 K, log g = 7 and number fractions H = 0.9 and He = 0.1
Basic H and He model atoms are provided by TMAD ( http://astro.uni-_tuebingen.de/~TMAD). These are combined then in ${AA}/H+He.

D.8.1 ATOMS2

• Copy the job file in /home/<user>/jobs/atoms2 to H+He.job. It needs a file H+He with the atomic data in /home/<user>/adaten. Edit both files the test_atmos.job and the test_atoms_lte.job (with emacs). Make sure you use the atomic data file H+He.
• After editing, execute the job file and create an output file for both jobs and check the output files for error messages.
  

D.8.2 SETF2

• Edit both files H+He_lte_setf2 and H+He_setf2 in /home/<user>/jobs/setf2. Set the temperature on 100000K and make sure that it refers to H+He_lte.atoms2.

  ---

  Table 7: Example for a setf2.job in the case of LTE and NLTE model atmosphere calculations LTE model NLTE model #!/bin/sh #!/bin/sh set +x;. ${HOME}/.jobstart set +x;. ${HOME}/.jobstart # # TT=0100000 TT=0100000 # # type='_lte' type=' ' # # cp ${AA}/H+He${type}.atoms2 ATOMS cp ${AA}/H+He${type}.atoms2 ATOMS # # ${BI}/setf2${sys} << % ${BI}/setf2${sys} << % $TT $TT PRINT CHECK PRINT CHECK 1.30E+16 1.30E+16 -1 -1 10 10 10 10 % % # # if test -s FGRID if test -s FGRID then then cp FGRID ${FF}/H+He_${TT}${type}.setf2 cp FGRID ${FF}/H+He_${TT}${type}.setf2 else else echo 'no FGRID created' echo 'no FGRID created' fi fi # # set +x; ${HOME}/.jobend ${TMPDIR} set +x; ${HOME}/.jobend ${TMPDIR}

  ---

• Run both jobs and create output files for them. The files H+He_100000(_lte).setf2 and are written to /home/<user>/fgrids.

D.8.3 Parameter files

• Extract the parameters from the H+He_atoms.out file with
  grep para H+He_atoms.out and from the output file H+He_setf2.out of the
  frequency grid If you want to save the parameters you can write them in a file with
  grep para H+He_atoms.out > object.out
• the parameter files for PRO2 can be found in /home/<user>/PARAMETER/pro2
• copy the existing parameter files to PARA_H+He.INC, PARA1_H+He.INC, PARA3_H+He.INC and adjust them by using the parameters from H+He_atoms.out and H+He_setf2.out.
  NOTICE: the values in the parameter files should be never 0!
• compile with ssh aithp3 load pro2 H+He [x64/p64] (use x64 for 64 bit machines, p64 for penryn-processor (our quad core) 64 bit machines). The executable /home/<user>/bimod/pro2_H+He.Linux_[x64] is created
  

D.8.4 LTE2

• Edit H+He_lte.job with emacs. Set T=100000K, logg=7 and H=0.9 and He=0.1. The input files are H+He_lte.atoms2 and H+He_100000_lte.setf2.
• Start the job (an example is given below) and write its output into a file.
  nice +19 H+He_lte.job > H+He_lte.out The lte model is written to /home/<user>/model/H+He/lte. The file is called
  0100000_7.00_0.900_0.100.
  

D.8.5 PRO2

• Edit the H+He_nlte.job in emacs. Adjust the temperature, log gand the abundances of the used elements as before and check if the used files have the right name. The Input files are H+He.atoms2, H+He_100000.setf2 and the model from LTE2 is the input model.
• Start the job (an example is given in table below) with
  nice +19 H+He_nlte.job > H+He_nlte.out
• The output model is written to /home/<user>/model/H+He/.

D.9 Naming the TMAP models

In the framework of the Virtual Observatory, TMAP models and SEDs that are calculated from them have to follow a general rule. The models’ names have to start with Teff (TTTTTTT) and logg (G.GG), followed by the element abundances in mass fractions. An example is

0100000_7.00_H:__9.0000E-01_HE:_1.0000E-01 .

This is suitable for a small number of elements, where the level name stays relatively short. Thus, the general form for a model name is then

TTTTTTT_G.GG_ABUND_<nnn> ,

where nnn is a three digit integer code. ABUND_nnn corresponds to a file with the same name (located e.g. in the model directory). It has the form

H9.0000E-01<source ...>
HE3.0000E-05<source ...>
C4.0000E-06<source ...>
N2.0000E-06<source ...>
O1.0000E-05<source ...>
NE2.0000E-03<source ...>
SI8.0000E-06<source ...>
FE1.0000E-03<source ...>
NI2.0000E-05<source ...>

Please use one line per element, starting with the TMAP element code. The abundances are in mass fraction. The entry for the source of the abundances is optional and format free. Avoid to use any string that will be erroneously identified as an element code by a UNIX grep command!

In the TMAP jobs, the following has to be inserted to set some shell variables (${moddir} is the model directory, ${abund_old} and ${abund_new} may be used for different abundances).

#
abund_old="ABUND_001"
abund_new="ABUND_001"
#
#
# abundances in mass fraction (see files)
#
# old abundances
oldabund=${moddir}/${abund_old}
#
Hold=`grep "H" ${oldabund} | awk '{ print $2 }'`
HEold=`grep "HE" ${oldabund} | awk '{ print $2 }'`
Cold=`grep "C" ${oldabund} | awk '{ print $2 }'`
Nold=`grep "N" ${oldabund} | awk '{ print $2 }'`
Oold=`grep "O" ${oldabund} | awk '{ print $2 }'`
NEold=`grep "NE" ${oldabund} | awk '{ print $2 }'`
SIold=`grep "SI" ${oldabund} | awk '{ print $2 }'`
FEold=`grep "FE" ${oldabund} | awk '{ print $2 }'`
NIold=`grep "NI" ${oldabund} | awk '{ print $2 }'`
#
#
# new abundances
newabund=${moddir}/${abund_new}
#
Hnew=`grep "H" ${newabund} | awk '{ print $2 }'`
HEnew=`grep "HE" ${newabund} | awk '{ print $2 }'`
Cnew=`grep "C" ${newabund} | awk '{ print $2 }'`
Nnew=`grep "N" ${newabund} | awk '{ print $2 }'`
Onew=`grep "O" ${newabund} | awk '{ print $2 }'`
NEnew=`grep "NE" ${newabund} | awk '{ print $2 }'`
SInew=`grep "SI" ${newabund} | awk '{ print $2 }'`
FEnew=`grep "FE" ${newabund} | awk '{ print $2 }'`
NInew=`grep "NI" ${newabund} | awk '{ print $2 }'`
#

In the input files of e.g. PRO2 respective cards have to use the XXnew variables (XX is the element):

CHANGEABUNDANCEH${Hnew}MASS FRACTION
CHANGEABUNDANCEHE${HEnew}MASS FRACTION
CHANGEABUNDANCEC${Cnew}MASS FRACTION
CHANGEABUNDANCEN${Nnew}MASS FRACTION
CHANGEABUNDANCEO${Onew}MASS FRACTION
CHANGEABUNDANCENE${NEnew}MASS FRACTION
CHANGEABUNDANCESI${SInew}MASS FRACTION
CHANGEABUNDANCEFE${FEnew}MASS FRACTION
CHANGEABUNDANCENI${NInew}MASS FRACTION