updated documentation

define.h

@@ -194,10 +194,10 @@ struct Line{
 	long long int *iiLimitsC0_h, *iiLimitsC0_d;	//limits for Line blocks, min
 	long long int *iiLimitsC1_h, *iiLimitsC1_d;	//limits for Line blocks, max
 
-	long long int *iiLimitsAT_m, *iiLimitsAT_d;	//limits for all blocks, mapped memory
-	long long int *iiLimitsALT_m, *iiLimitsALT_d;	//limits for all blocks, mapped memory
-	long long int *iiLimitsART_m, *iiLimitsART_d;	//limits for all blocks, mapped memory
-	long long int *iiLimitsBT_m, *iiLimitsBT_d;	//limits for all blocks, mapped memory
-	long long int *iiLimitsCT_m, *iiLimitsCT_d;	//limits for all blocks, mapped memory
+	unsigned long long int *iiLimitsAT_m, *iiLimitsAT_d;	//limits for all blocks, mapped memory
+	unsigned long long int *iiLimitsALT_m, *iiLimitsALT_d;	//limits for all blocks, mapped memory
+	unsigned long long int *iiLimitsART_m, *iiLimitsART_d;	//limits for all blocks, mapped memory
+	unsigned long long int *iiLimitsBT_m, *iiLimitsBT_d;	//limits for all blocks, mapped memory
+	unsigned long long int *iiLimitsCT_m, *iiLimitsCT_d;	//limits for all blocks, mapped memory
 
 };

docs/helios_k/bins.rst

@@ -11,7 +11,7 @@ from small to large, and mapped to a new parameter y, rangin from 0 to 1.
 When the opcity function has empty parts inside or is not ranging to the full
 bin width, then the sorted opacity function is zero (or kmin, if used) on the
 lower part.
-| relevant parameters for this example:
+| Relevant parameters for this example:
 
  - doResampling = 0
  - doStoreFullK = 1
@@ -30,7 +30,7 @@ lower part.
 
 
 Using a binsfile
-================
+----------------
 
 When a ``binsFile`` name is given in the ``param.dat`` file, then this
 file is used to generate the boundaries of the bins. The bins do not have
@@ -52,7 +52,7 @@ An example of a ``binsFile`` is given below, and the result is shown in :numref:
    25000
    30000
 
-| relevant parameters for this example:
+| Relevant parameters for this example:
 
  - doResampling = 0
  - doStoreFullK = 1
@@ -69,7 +69,7 @@ An example of a ``binsFile`` is given below, and the result is shown in :numref:
 
 
 The output edges option
-=======================
+-----------------------
 
 Instead of writing the -per bin sorted- opacity function with the full resolution in
 wavenumbers, it is possible to print only averaged positions within the bins. 
@@ -84,6 +84,7 @@ An example of a ``outputedgesFile`` is given below, and the result is shown in
 the averaged points can appear to have too high values. 
 
 ::
+
    edges.dat
    ---------
    0.0
@@ -92,7 +93,7 @@ the averaged points can appear to have too high values.
    0.78
    1.0
 
-| relevant parameters for this example:
+| Relevant parameters for this example:
 
  - doResampling = 0
  - doStoreFullK = 1

docs/helios_k/compilation.rst

@@ -1,9 +1,12 @@
 Requirements
 ============
 
-| The opacity calculation from HELIOS-K is running on GPUs and require a Nvidia GPU with compute capability of 2.0 or higher. It and can run on Nvidia Tesla, GeForce and Quadro GPUs.
-| The code needs the CUDA toolkit to be installed. This can be downloaded from https://developer.nvidia.com/cuda-downloads.
-| Helper code for downloading the files and preprocessing are written in C++ and Python3. They require the following libraries:
+| The opacity calculation from HELIOS-K is running on GPUs and require a Nvidia GPUi
+ with compute capability of 3.0 or higher. It can run on Nvidia Tesla, GeForce and Quadro GPUs.
+| The code needs the CUDA toolkit to be installed. This can be downloaded from
+ https://developer.nvidia.com/cuda-downloads.
+| Helper code for downloading the files and preprocessing are written in C++ and Python3.
+ They require the following libraries:
 
 - exomol.py and exomol2.py
 
@@ -49,7 +52,7 @@ Requirements
  - argparse
 
 
-Note, when using a computing clusteri, all these libraries can be installed locally in the home directory  with: 
+Note, when using a computing cluster, all these libraries can be installed locally in the home directory  with: 
 
 ::
 

docs/helios_k/heliosk.rst

@@ -19,7 +19,7 @@ followed by optional console arguments, which are listed later.
 
 
 HELIOS-K Input parameters
-=========================
+-------------------------
 
 The input parameters can be specified in the ``param.dat`` file. The
 used parameters are listed here, the order can not be changed.
@@ -58,14 +58,22 @@ used parameters are listed here, the order can not be changed.
 -  doResampling:
 
    - 0: no resampling is done.
-   - 1: all the sorted opacity functions per bin are resampled with a Chebyshev polynomial, and the coefficients from all bins are written to the file ``Out_<name>_cbin.dat``.
-   - 2: all the sorted opacity functions per bin are resampled with a Chebyshev polynomial, and the coefficients from each bin are written to a sepparate file ``Out_<name>_cbin<bin_number>.dat``.
+   - 1: all the sorted opacity functions per bin are resampled with a Chebyshev
+     polynomial, and the coefficients from all bins are written to the file ``Out_<name>_cbin.dat``.
+   - 2: all the sorted opacity functions per bin are resampled with a Chebyshev
+
+ polynomial, and the coefficients from each bin are written to a sepparate file
+ ``Out_<name>_cbin<bin_number>.dat``.
 
 
 -  nC: Number of Chebyshev coefficients use for the resampling.
--  doTransmission:
-   - 1: the transmission function per bin is computed for various numbers of m, and written to the file ``Out_<name>_tr.dat``.
+-  doTransmission: Compute the transmission function tau for a set of column masses m.
+
    - 0: no transmission function is calculated.
+   - 1: the transmission function per bin is calculated,
+     and all bins are written to the file ``Out_<name>_tr.dat``.
+   - 2: the transmission function per bin is calculated,
+     and each bin is written to a sepparate file ``Out_<name>_tr<bin_number>.dat``.
 
 -  nTr: nummber of points used for the transmission function.
 -  dTr: spacing of the points used for the transmission function in exp
@@ -83,9 +91,12 @@ used parameters are listed here, the order can not be changed.
 - pathToK: path and filename to read in an opacity function. When left blank, then no file is read in.
 
 -  doStoreSK:
+
    - 0: the resampled opacity function is not written to a file.
-   - 1: all bins from the resampled opacity function are written to the same file ``Out_<name>_bin.dat``.
-   - 2: all bins from the resampled opacity function are written to a sepparate file   with names ``Out_<name>_bin<bin_number>.dat``.
+   - 1: all bins from the resampled opacity function are written to the same
+     file ``Out_<name>_bin.dat``.
+   - 2: all bins from the resampled opacity function are written to a sepparate
+     file   with names ``Out_<name>_bin<bin_number>.dat``.
 
 -  nbins: number of bins
 -  binsfile: A '-' ignores this option, otherwise this option specifies
@@ -128,7 +139,7 @@ used parameters are listed here, the order can not be changed.
 
 
 Console Arguments
-=================
+-----------------
 
 Instead of using the parameter file, some arguments can also be set
 by console arguments. The console arguments have the highest priority
@@ -166,10 +177,10 @@ where ``<c>``\ is a string, ``<double>`` a floating point number, and
 
 
 Code parameters
-===============
+---------------
 
 The file define.h contains the physical parameters and some code
-parameters. After changing some entry, the code needs to be recompiled.
+parameters. After changing some entry here, the code needs to be recompiled.
 The code parameters are:
 
 -  def_TOL: Tolerance parameter in the Voigt function. See Algorithm 916

docs/helios_k/hitemp.rst

@@ -43,3 +43,4 @@ Step 4, data path
 Include the path of the directory, which contains the obtained binary
 files, the ``*.txt`` partition function files and the ``*.param`` file to
 the HELIOS-K ``param.dat`` file under ``pathToData``.
+

docs/helios_k/mean.rst

@@ -0,0 +1,73 @@
+Planck and Rosseland Means
+==========================
+
+.. _mean:
+
+With the ``doMean`` option in the ``param.dat`` file, the Plank and Rosseland means, 
+:math:`\kappa_P` and :math:`\kappa_R` respectively: 
+
+.. math::
+   :label: eq_a
+
+   \kappa_P = \frac{\int_0^\infty \kappa  B_{\nu}(T) d\nu}{\int_0^\infty B_{\nu}(T)  d\nu},
+
+and
+
+.. math::
+   :label: eq_b
+
+   \kappa_R = \left(  \frac{\int_0^\infty \kappa^{-1} \frac{\partial B_{\nu}(T)}{\partial T} d\nu}  {\int_0^\infty  \frac{\partial B_{\nu}(T)}{\partial T} d\nu} \right)^{-1} 
+
+can be calculated, where the infinity integral is truncated to the specified wavenumber limits, and :math:`d\nu` is 
+equal to ``dnu`` set in the ``param.dat`` file.
+
+Note that the denominators in :math:`\kappa_P` and :math:`\kappa_R` can be computed analytically as
+
+.. math::
+   :label: eq_0
+
+   \int_0^\infty B_{\nu}(T) d\nu = \frac{\sigma  T^4} {\pi}
+
+and
+
+.. math::
+   :label: eq_1
+
+   \int_0^\infty  \frac{\partial(B_{\nu}(T))}{ \partial (T)}  d\nu = \frac{4  \sigma  T^3} {\pi}.
+
+Therefor, it is usefull to compare those analytic results to the numerical integration
+
+.. math::
+   :label: eq_2
+
+   \int_0^\infty B_{\nu}(T) d\nu = \sum_i  B_{\nu}(T) dnu
+
+and 
+
+.. math::
+   :label: eq_3
+
+   \int_0^\infty  \frac{\partial(B_{\nu}(T))}{ \partial (T)}  d\nu =  \sum_i  \frac{\partial(B_{\nu}(T))}{ \partial (T)}  dnu
+
+
+
+The results of the Planck and Resseland means are stored in the file ``Out<name>_mean.dat``, together with 
+the analytic and numerical expressions :eq:`eq_0` to :eq:`eq_3`. If the numerical expressions deviate strongly
+from the analytical expression, then it is a hint that the wavenumber resolution is not set fine enough.
+
+
+An example of the Planck and Rosseland means is shown in :numref:`figmean`.
+
+
+| Relevant parameters for this example:
+
+ - doStoreFullK = 1
+ - doMean = 1
+
+
+.. figure:: ../plots/p007/plot001.png  
+   :name: figmean
+
+   Planck and Rosseland means
+
+

docs/helios_k/output.rst

@@ -1,20 +1,20 @@
 Output Files
 ============
 
-Different Output files are written, depending to the values in the
+Different Output files are written, depending on the values in the
 ``param.dat`` file
 
 .. _info_<name>.dat:
 
 ``Info_<name>.dat``
-===================
+-------------------
 
 Contains all used parameters, and timing information
 
 .. _out_<name>.dat:
 
 ``Out_<name>.dat``
-==================
+------------------
 
 It contains nu and K(nu), where nu are the wavenumbers and K(nu) is the
 full opacity function. When the ``PFile`` option is used, then the files
@@ -23,7 +23,7 @@ contain also the values of T and P.
 .. _out_<name>_bin.dat:
 
 ``Out_<name>_bin.dat``
-======================
+----------------------
 
 It contains the values of y and K(y) per bin. y goes from 0 to 1. K(y)
 is the per bin sorted opacity function. The bins are separated by two
@@ -45,7 +45,7 @@ files with names ``Out_<name>_bin< bin index>.dat`` .
 .. _out_<name>_cbin.dat:
 
 ``Out_<name>_cbin.dat``
-=======================
+-----------------------
 
 It contains the Chebyshev coefficients of the per bins sorted natural
 logarithm of the opacity functions in the format
@@ -103,7 +103,7 @@ sorted opacity function from the Chebyshev coefficients:
 .. _out_<name>_tr.dat:
 
 ``Out_<name>_tr.dat``
-=====================
+---------------------
 
 It contains m and T. m is the column mass, m_i = exp((i - nTr/2) \* dTr)
 T is the Transmission function Int_0^1 exp(-K(y)m) dy When the PFile is
@@ -114,7 +114,7 @@ files with names ``Out_<name>_tr< bin index>.dat``
 .. _out_<name>_mean.dat:
 
 ``Out_<name>_mean.dat``
-=======================
+-----------------------
 
 | When the argument doMean is set to one, this file contains the Planck
   and Rosseland means. They are computed over the entire range in

docs/helios_k/param.rst

@@ -20,12 +20,13 @@ The next section explains the structure of these files and shows how to generate
 
 
 The ``<species_name>.param`` file
-=================================
+---------------------------------
 
 Each molecular or atomic species, which will be processed by HELIOS-K,
 needs a ``<species_name>.param`` file, which contains all necessary
 information about the line list database and other parameters.
-This files can be generated automatically by the tools in HELIOS-K. However, when using a different database, they must be created manually.
+This files can be generated automatically by the tools in HELIOS-K. However, when using
+a different database, they must be created manually.
 
 
 Example

docs/helios_k/resampling.rst

@@ -14,7 +14,7 @@ files.
 An example of a resampled bin is shown in :numref:`figresample`.
 
 
-| relevant parameters for this example:
+| Relevant parameters for this example:
 
  - doResampling = 1
  - nC = 20

docs/helios_k/transmission.rst

@@ -0,0 +1,41 @@
+The transmission function
+=========================
+
+.. _transmission:
+
+With the ``doTransmission`` option in the ``param.dat`` file, the transmissions function
+:math:`\tau` 
+
+.. math::
+
+   \tau = \int_0^\infty e^{-\kappa \tilde{m}} d\nu = \int_0^1 e^{-\kappa \tilde{m}} dy
+
+can be calculated for a set of column masses :math:`\tilde{m}`, where :math:`\tilde{m}`
+is set according to:
+
+.. math::
+
+    \tilde{m}_i = e^{((i - nTr/2) \cdot dTr)}.
+
+The parameters ``nTr`` and ``dTr`` can be set in the ``param.dat`` file.
+The transmission function is stored in the file ``Out<name>_tr.dat``,
+
+
+An example of the transmission function for fife bins is shown in :numref:`figtransmission`.
+
+
+| Relevant parameters for this example:
+
+ - doStoreFullK = 1
+ - doTransmission = 2
+ - nbins = 5
+ - nTr = 1000
+ - dTr = 0.05
+
+
+.. figure:: ../plots/p006/plot001.png  
+   :name: figtransmission
+
+   Transmission function 
+
+