Develop

docs/conf.py

@@ -29,7 +29,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.4.198"
+release = "0.6.20"
 
 
 # -- General configuration ---------------------------------------------------

docs/usage/atmosphere.md

@@ -18,36 +18,34 @@ parameters, which is usually the same as that of the sme structure,
 but can be different, if for example the atmosphere is embedded, i.e.
 fixed, or has not been calculated yet.
 
-The atmopshere object has the following fields
+The atmopshere object has the following fields:
 
-- **`teff`**: Effective Temperature in Kelvin  
-- **`logg`**: Surface Gravity in log(cgs)  
-- **`monh`**: Metallicity relative to the individual abundances  
-- **`abund`**: The individual abundances (see [abund](#abund))  
-- **`vsini`**: Projected Rotational velocity in km/s  
-- **`vmic`**: Microturbulence velocity in km/s  
-- **`vmac`**: Macroturbulence velocity in km/s  
-- **`vturb`**: Turbulent velocity in km/s  
-- **`lonh`**: Mixing length   
-- **`source`**: Filename of the atmosphere grid  
-- **`depth`**:  
-  The depth scale to use for calculations.  
-  Either RHOX or TAU  
-- **`interp`**:  
-  The depth scale to use for interpolation.  
-  Either RHOX or TAU  
-- **`geom`**:  
-  The geometry of the atmosphere. Either Plane  
-  Parallel `'PP'` or Spherical `'SPH'`  
-- **`method`**:  
-  The method to use for interpolation. Either `'grid'`  
-  for a model grid or `'embedded'` if only a single  
-  atmosphere is given.  
-- **`rhox`**: 'Column density' depth scale  
-- **`tau`**: 'Optical depth' depth scale  
-- **`temp`**: Temperature profile  
-- **`xna`**: Number density of atoms, ions, and molecules in each depth  
-- **`xne`**: Number density of electrons in each depth  
+|Field name|Description|Allowed values or [Unit]|
+|:---:|:---:|:---:|
+|`teff`|Effective Temperature|[K]|
+|`logg`|Surface Gravity|[log(cgs)]|
+|`monh`|Metallicity||
+|`abund`|The individual abundances (see [abund](#abund))||
+|`vsini`|Projected Rotational velocity|[km/s]|
+|`vmic`|Microturbulence velocity|[km/s]|
+|`vmac`|Macroturbulence velocity|[km/s]|
+|`source`|Filename of the atmosphere grid|see [lfs](lfs.md)|
+|`depth`|The depth scale to use for calculations.|`RHOX` or `TAU`|
+|`interp`|The depth scale to use for interpolation.|`RHOX` or `TAU`|
+|`geom`|The geometry of the atmosphere.|Plane Parallel `'PP'` or Spherical `'SPH'`|
+|`method`|The method to use for interpolation|`'grid'` for a model grid or `'embedded'` if only a single atmosphere is given|
+|`rhox`|Mass column at each tabulated depth in the atmosphere|[$\mathrm{g~cm^{-2}}$]|
+|`tau`|Continuum optical depth at each tabulated depth in the atmosphere||
+|`temp`|Temperature at each tabulated depth in the atmosphere|[K]|
+|`xna`|Atomic number density (including atomic components of molecules) at each tabulated depth in the atmosphere.|[$\mathrm{cm^{-3}}$]|
+|`xne`|Electron number density at each tabulated depth in the atmosphere|[$\mathrm{cm^{-3}}$]|
+|`rho`|Mass density at each tabulated depth in the atmosphere.|[$\mathrm{g~cm^{-3}}$]|
+|`height`|Height above or below `radius` at each tabulated depth in a spherical atmosphere.|[cm]|
+|`radius`|Stellar radius corresponding to `height` of zero in a spherical atmosphere|[cm]|
+|`vturb`|Turbulent velocity used to generate the atmosphere|[km/s]|
+|`lonh`|Ratio of mixing length to pressure scale height (`/H) used to generate the atmosphere.||
+|`wlstd`|Wavelength for continuum optical depth scale.|Å, Default value: 5000Å|
+|`opflag`|Flags that indicate whether to enable various opacity packages during the radiative transfer calculation||
 
 ## Grid atmospheres 
 

docs/usage/fordev.md

@@ -137,6 +137,15 @@ This variable determines how the cscale and vrad being assigned, and can be spec
 If you create your own NLTE departure coefficient grid following the current public grid to a `DirectAccess` file and you use the `nlte.DirectAccess.wrtie` function, note that the `wrtie` and `read` code changes the shape of b-grid, tau and rhox. 
 Some extra test is needed to clear the situation. 
 
+## SME
+
+### `Trasf` function
+
+1. `AutoIonization`
+2. Calculate Line center opacity using `LINEOPAC`.
+3. Calculate Line contribution limits using `OPMTRX`.
+    - Step 2 and 3 go through all the input lines
+
 ## IDLSME
 
 ### Installation

docs/usage/installation.md

@@ -13,6 +13,11 @@ Currently PySME is tested with Python verion 3.9-3.13.
 - For the "stable" version (recommended):
     - `pip install pysme-astro`
 
+```{warning}
+- PySME requires the pre-compled C++/Fortran SME library to run. Currently we deliver SME library with Linux and Mac version; for Windows users, we recommend to use WSL and hence the Linux version. 
+- The files (mainly atmosphere models and NLTE departure coefficnent grids) required by PySME will be saved inside `~/.sme/`. These files can be large thus if your home directory is small, we recommend to create a softlink for `~/.sme`.
+```
+
 ```{warning}
 PySME requires the pre-compled C++/Fortran SME library to run. Currently we deliver SME library with Linux and Mac version; for Windows users, we recommend to use WSL and hence the Linux version. 
 ```

src/pysme/atmosphere/marcsfile.py

@@ -227,7 +227,7 @@ def __init__(self, filename, calcRHOX=False):
         if self.geom.upper() == 'SPH':
             self.radius = data["radius"]
         self.depth = 'RHOX' if self.geom.upper() == 'SPH' else 'TAU'  # spherical models should depth calculate using RHOX
-        self.interp = 'TAU'  # not sure this is needed for embedded models
+        self.interp = 'RHOX'  # not sure this is needed for embedded models
         self.vturb = data["vturb"]
 
         self.abund = Abund(monh=data["monh"], pattern=data["abund_inclmonh"].to_numpy()[0]-data["monh"], type="H=12")

src/pysme/gui/plot_plotly.py

@@ -354,7 +354,7 @@ def create_plot(self, current_segment):
             if self.lines is not None and len(self.lines) != 0:
                 seg_annotations = []
                 xlimits = self.wave[seg][[0, -1]]
-                xlimits *= 1 - self.vrad[seg] / clight
+                xlimits = xlimits * (1 - self.vrad[seg] / clight)
                 lines = (self.lines.wlcent > xlimits[0]) & (
                     self.lines.wlcent < xlimits[1]
                 )

src/pysme/solve.py

@@ -600,8 +600,7 @@ def sanitize_parameter_names(self, sme, param_names):
             if sme.vrad_flag in ["fix", "none"]:
                 sme.vrad_flag = "whole"
                 logger.info(
-                    "Removed fit parameter 'vrad', instead set radial velocity flag to %s",
-                    sme.vrad_flag,
+                    f"Removed fit parameter 'vrad', instead set radial velocity flag to {sme.vrad_flag}"
                 )
 
         if "cont" in param_names:
@@ -734,9 +733,9 @@ def solve(self, sme, param_names=None, segments="all", bounds=None, step_sizes=N
             )
 
         # Setup LineList only once (Mingjie: not needed?)
-        dll = self.synthesizer.get_dll()
-        dll.SetLibraryPath()
-        _ = dll.InputLineList(sme.linelist)
+        # dll = self.synthesizer.get_dll()
+        # dll.SetLibraryPath()
+        # _ = dll.InputLineList(sme.linelist)
 
         # Do the heavy lifting
         if self.nparam > 0:
@@ -794,7 +793,7 @@ def solve(self, sme, param_names=None, segments="all", bounds=None, step_sizes=N
             # We could try to reuse the already calculated synthetic spectrum (if it already exists)
             # However it is much lower resolution then the newly synthethized one (usually)
             # Therefore the radial velocity wont be as good as when redoing the whole thing
-            sme = self.synthesizer.synthesize_spectrum(sme, segments)
+            sme = self.synthesizer.synthesize_spectrum(sme, segments, linelist_mode=linelist_mode)
         else:
             raise ValueError("No fit parameters given")