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====== xml_from_xdds ======
Macros for the creation of xml files from within a TOPAS .inp file. xml_from_xdds will create an xml file with a separate entry for each xdd within the .inp file, and a separate entry for each str within each xdd. Rietveld statistics, lattice parameters, weight percents and the fit data are all stored.
The xml files are a structured format which can be easily used to read the refinement results into other software, such as Python. I recommend using [[http://code.activestate.com/recipes/573463-converting-xml-to-dictionary-and-back/|this code]] to get the xml file into a Python dictionary for further manipulation. This is particularly valuable when working with large datasets, such as variable temperature data collections or analysing maps of diffraction data.
macro xml_create(file) { out file Out_String("") }
macro xml_add(file,name,value) {
out file append
Out_String("\n\t<") Out_String(name) Out(value,">%e") Out_String("")
}
macro xml_close(file) { out file append Out_String("\n") }
macro xml_from_xdds(file,append_to_file) {
#m_ifarg append_to_file 1
out file append
#m_else
out file
Out_String("")
#m_endif
Out(Get(r_wp), "\n\t%V")
Out(Get(r_exp), "\n\t%V")
Out(Get(gof), "\n\t%V")
for xdds { Out_String("\n\t")
Out(Get(r_wp), "\n\t\t%V")
Out(Get(r_exp), "\n\t\t%V")
Out(Get(gof), "\n\t\t%V")
Out(Get(mixture_density_g_on_cm3), "\n\t\t%4.8f") Out_String("")
for strs { Out_String("\n\t\t")
Out(Get(phase_name), "\n\t\t\t%s")
Out(Get(r_bragg), "\n\t\t\t%V")
Out_String("\n\t\t\t")
Out(Get(sp_grp_char), "\n\t\t\t\t%s")
Out(Get(a), "\n\t\t\t\t%V")
Out(Get(b), "\n\t\t\t\t%V")
Out(Get(c), "\n\t\t\t\t%V")
Out(Get(al), "\n\t\t\t\t%V")
Out(Get(be), "\n\t\t\t\t%V")
Out(Get(ga), "\n\t\t\t\t%V")
Out(Get(cell_volume), "\n\t\t\t\t%V")
Out(1.6605402 Get(cell_mass) / Get(cell_volume), "\n\t\t\t\t%4.8f") Out_String("")
Out_String("\n\t\t\t")
Out(Get(weight_percent), "\n\t\t\t%V")
Out(Get(scale) Get(all_scale_pks), "\n\t\t\t%e") Out_String("")
Out(Get(numerical_area), "\n\t\t\t%V")
Out_String("\n\t\t") }
Out_String("\n\t\t")
xdd_out file append load out_record out_fmt out_eqn
{
"\n\t\t\t%0.6f" = X;
"%0.6f" = Yobs;
"%0.6f" = Ycalc;
"%0.6f" = Yobs-Ycalc;
}
out file append
Out_String("\n\t\t")
Out_String("\n\t") }
#m_ifarg append_to_file 1
#m_else
Out_String("\n")
#m_endif
}
macro xml_from_xdds(file) { xml_from_xdds(file,0) }
**Example usage 1 - Create a file using the default values stored by xml_from_xdds**
Simply add the following towards the end of your .inp file.
xml_from_xdds("myfilename.xml")
**Example usage 2 - Adding your own values to the xml file, then using xml_from_xdds to append to the same file**
The use of xml_from_xdds writes out the standard data you want want from a refinement, but doesn't allow for the easy addition of other parameters. This example shows how to create an xml file which includes other values you may need to store.
- Create an empty xml file using xml_create.
- Adds a number of fixed values and parameters to the file using xml_add. The value will be added into the xml file as a node with the name given as the second parameter.
- Appends standard details of the xdds using xml_from_xdds. The '1' signifies that this is appending into the file, rather than creating a new file.
- Closes the end of the xml description using xml_close.
xml_create("myfilename.xml")
xml_add("myfilename.xml","myvalue1",1.0)
xml_add("myfilename.xml","myvalue2",2.0)
xml_add("myfilename.xml","myvalue3",aTopasPrmName)
xml_from_xdds("myfilename.xml",1)
xml_close("myfilename.xml")