This guide assumes that the software has been correctly installed and its command line programs PDFgetX3, PDFgetN3 and PDFgetS3 can be executed by typing pdfgetx3, pdfgetn3, or pdfgets3 in a shell window. Please, refer to the installation section if this is not working yet.
The pdfgetx3 program is a command-line application, therefore all the input files and run-parameters are supplied either as command-line arguments or through a configuration file. In general, the pdfgetx3 is executed from a command shell as
pdfgetx3 [options] input1 input2 ... inputN
inputN stands for an input powder diffraction data. The
inputN file is a simple two-column text file, where the first
column corresponds to either the 2Θ diffraction angle, or a
momentum transfer, Q, in inverse nanometer or inverse ångström units.
The second column contains the corresponding X-ray intensities. The
input file may start with a header containing comments or metadata
related to the measurement. PDFgetX3 will ignore any text leading to a
long two-column section. The example input files in this manual were
created with the
FIT2D program using
its “chi” output format, thus we will also refer to them as “chi-files”.
A typical content of a “chi” file looks as folows:
Pt_bulk-00055.tif: 2-theta Scan 2-Theta Angle (Degrees) 1465 2.0003892E-02 0.0000000E+00 6.0011677E-02 0.0000000E+00 1.0001946E-01 0.0000000E+00 1.4002724E-01 0.0000000E+00 1.8003502E-01 0.0000000E+00 ...
The command-line options are arguments that start with a dash “-” and
are used to specify run-parameters or modify the program behavior. The
options can be specified in a short form that consists of a dash and
a single character, or in a long, more descriptive format starting with
a doubled dash
--. Options may require values. For short options,
the value may be joined to the option string, for example
-w0.142774, while for the long options it has to be separated
with an equal sign, e.g.,
all the PDF calculation parameters can be passed as command line
options, it is often more convenient to set them in a configuration
file. When run parameter is present both in a configuration file and
as command-line option, the command-line value takes precedence. The
command-line options are all described in the Options and parameters section of
this manual. A brief summary of options can be also displayed by
The best way of getting familiar with PDFgetX3 is to process
the example diffraction data described in the Tutorial.
In general, the first step is to create a commented configuration file
The configuration file can have any name, but it is preferable
to use either
for these files are automatically loaded by PDFgetX3. All
other configuration files must be passed explicitly to the program
-c, --config option.
Open the pdfgetx3.cfg file in a text editor. The lines that
start with a hash mark
# are comments and are not used. The lines
starting with a right brace
[ denote sections in the configuration
file. The active lines are all formatted as
“NAME=VALUE”. Although PDFgetX3 has many options, in general only a few
of them are critical for the PDF calculation:
dataformat– specifies the input data format
wavelength– radiation wavelength in Å required for the “twotheta” format.
composition– chemical composition of the sample
qmaxinst– upper Q boundary for a meaningful measurement intensities.
qmax– Q-cutoff for the Fourier transformation that yields the PDF.
Save the updated configuration file and run pdfgetx3 on the input data
pdfgetx3 --verbose=info -t gr FILENAME.chi
--verbose=info option makes pdfgetx3
more information about its operation. This helps to verify
if the configuration file is indeed loaded and if the parameter
values are assigned as intended. The PDFgetX3 will not write
any output files unless told so. The
-t gr option
tells the program to save the final G(r) curve as a
FILENAME.gr file in the working directory.
The saved .gr file contains a header with all the calculation parameters and the input file name. The .gr file can be therefore also used as a configuration file in order to redo the same calculation
pdfgetx3 -c FILENAME.gr --plot=fq,gr
Note this command does not include any .chi file and this will as
a result process the previously used input
--plot=fq,gr option tells PDFgetX3 to
display 2 plots for the reduced structure function F(Q) and the
final PDF G(r). The
--plot option also implies an
therefore the program does not exit, but starts an
interactive IPython session. To exit the interactive mode,
exit() and press Enter.
The pdfgetx3 and pdfgetn3 programs operate in a very similar fashion
apart from being set to assume X-ray and neutron data respectively.
The type of the scattering data can be also specified using the
--mode option. Running
pdfgetn3 is nearly identical
pdfgetx3 --mode=neutron. The only difference between
these commands is that pdfgetx3 checks for configuration files
pdfgetn3 looks for
The pdfgets3 program is virtually the same as its counterparts for x-ray
(pdfgetx3) and neutron (pdfgetn3) diffraction data. The only difference
is that instead of referencing the well documented x-ray or neutron
scattering form factor data, a user-defined form factor data is used
for getting the PDF from a small-angle scattering (SAS) data. This
behavior is enabled by specifying
mode = sas in the configuration
file or in the command line tool. The pdfgets3 program by default
searches for a configuration named
.pdfgets3.cfg in order, when no configuration file is specified.
Please refer to the tutorial section for a step-by-step processing of the example data files and for demonstration of the capabilities in PDFgetX3, PDFgetN3 and PDFgetS3.