AutoXRD

GSAS-II Installation

For Intel Mac, follow the guide from GSAS-II website:

• https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/InstallMac
• https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/MacSingleStepInstallerFigs (with screen shot)

Installation on Intel Mac

• This process worked for installing on Intel Mac Ventura 13.4.1
• Run g2="https://subversion.xray.aps.anl.gov/admin_pyGSAS/downloads/gsas2full-Latest-MacOSX-x86_64.sh" curl "$g2" > /tmp/g2.sh; bash /tmp/g2.sh -b -p ~/g2full in your terminal and install in default location. Leave the proxy blank.
• Create a new environment with python 3.10, and install numpy, scipy, wxpython, matplotlib, pandas:

  conda create --name myenv python=3.10
  conda activate myenv
  conda install numpy scipy matplotlib pandas
  pip install wxpython
  

• Run import sys, os sys.path.insert(0, "/Users/your_username/g2full/GSASII") import GSASIIscriptable as G2sc
• It should import successfully

Testing RangeDetermine.ipynb

• Make you set the system path to include the GSAS installation. Otherwise you won't be able to access it:

  import sys
  sys.path.append('/Users/suhasmahesh/g2full/GSASII')
  

• You will also have to install a bunch of libraries for it to work:
  • pip install numpyro jax jaxlib
• You may also have to delete EFtables = calcControls['EFtables'] from GSASIIstrMath.py
• You may also have to add the GSAS installation to the system path in gsas.py:

  gsas_bin = os.path.join(sys.base_prefix, "/Users/suhasmahesh/g2full/GSASII/bindist")
  gsas_path = os.path.join(sys.base_prefix, "/Users/suhasmahesh/g2full/GSASII")
  ``
  

Note

• .gpx is the GSAS-II project file, we import this GSAS project to our script
• .yaml is the anaconda environment file; it has the python packages needed to run the script
• b2 folder contains the necessary functions in .py scripts
• TrialRangeData folder contains the csv files of simulated data to be run in the 1_Inference.ipynb notebook
• Bkg substraction / Peak fitting: https://github.com/fang-ren/Discover_MG_CoVZr/tree/master/scripts/XRD_processing