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--- xml_from_xdds [2019/06/18 16:01] – change of tabbing for relative_scale pac079
+++ xml_from_xdds [2022/11/03 15:08] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
+====== 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.
+<code topas>
+macro xml_create(file) { out file Out_String("<root>") }
+macro xml_add(file,name,value) {
+	out file append
+	Out_String("\n\t<") Out_String(name) Out(value,">%e") Out_String("</") Out_String(name) Out_String(">")
+}
+macro xml_close(file) { out file append Out_String("\n</root>") }
+macro xml_from_xdds(file,append_to_file) {
+	#m_ifarg append_to_file 1
+		out file append
+	#m_else
+		out file
+		Out_String("<root>")
+	#m_endif
+		Out(Get(r_wp), "\n\t<r_wp>%V</r_wp>")
+		Out(Get(r_exp), "\n\t<r_exp>%V</r_exp>")
+		Out(Get(gof), "\n\t<gof>%V</gof>")
+		for xdds { Out_String("\n\t<xdd>")
+			Out(Get(r_wp), "\n\t\t<r_wp>%V</r_wp>")
+			Out(Get(r_exp), "\n\t\t<r_exp>%V</r_exp>")
+			Out(Get(gof), "\n\t\t<gof>%V</gof>")
+			Out(Get(mixture_density_g_on_cm3), "\n\t\t<mixture_density>%4.8f") Out_String("</mixture_density>")
+			for strs { Out_String("\n\t\t<str>")
+				Out(Get(phase_name), "\n\t\t\t<phase_name>%s</phase_name>")
+				Out(Get(r_bragg), "\n\t\t\t<r_bragg>%V</r_bragg>")
+				Out_String("\n\t\t\t<unit_cell>")
+					Out(Get(sp_grp_char), "\n\t\t\t\t<space_group>%s</space_group>")
+					Out(Get(a), "\n\t\t\t\t<a>%V</a>")
+					Out(Get(b), "\n\t\t\t\t<b>%V</b>")
+					Out(Get(c), "\n\t\t\t\t<c>%V</c>")
+					Out(Get(al), "\n\t\t\t\t<al>%V</al>")
+					Out(Get(be), "\n\t\t\t\t<be>%V</be>")
+					Out(Get(ga), "\n\t\t\t\t<ga>%V</ga>")
+					Out(Get(cell_volume), "\n\t\t\t\t<volume>%V</volume>")
+					Out(1.6605402 Get(cell_mass) / Get(cell_volume), "\n\t\t\t\t<density>%4.8f") Out_String("</density>")
+				Out_String("\n\t\t\t</unit_cell>")
+				Out(Get(weight_percent), "\n\t\t\t<weight_percent>%V</weight_percent>")
+				Out(Get(scale) Get(all_scale_pks), "\n\t\t\t<relative_scale>%e") Out_String("</relative_scale>")
+				Out(Get(numerical_area), "\n\t\t\t<numerical_area>%V</numerical_area>")
+			Out_String("\n\t\t</str>") }
+			Out_String("\n\t\t<data>")
+				xdd_out file append load out_record out_fmt out_eqn
+				{
+	          "\n\t\t\t<X>%0.6f</X>" = X;
+	          "<Y>%0.6f</Y>"         = Yobs;
+	          "<Ycalc>%0.6f</Ycalc>" = Ycalc;
+	          "<Diff>%0.6f</Diff>"   = Yobs-Ycalc;
+				}
+			out file append
+			Out_String("\n\t\t</data>")
+		Out_String("\n\t</xdd>") }
+	#m_ifarg append_to_file 1
+	#m_else
+		Out_String("\n</root>")
+	#m_endif
+	}
+macro xml_from_xdds(file) { xml_from_xdds(file,0) }
+</code>
+**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.
+<code topas>
+xml_from_xdds("myfilename.xml")
+</code>
+**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.
+<code topas>
+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")
+</code>