Instruction to generate mineral data web page

New Preview: https://mineralscloud.github.io/resources/mineralsdatabase/

Old Preview in https://www.jappoker.com/mineralsdatabase/Acimite.html

Install Ruby and jekyll: Jekyll Installation

1. Install Homebrew and then install ruby

# Install Homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install ruby via Homebrew

brew install ruby

Add the brew ruby path to your shell config:

echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.bash_profile

3. Install Jekyll: local install

gem install --user-install bundler jekyll

and then get your Ruby version using

ruby -v
ruby 2.7.1p83 (2020-03-31 revision a0c7c23c9c)

Then append your path file with the following, replacing the X.X with the first two digits of your Ruby version.

echo 'export PATH="$HOME/.gem/ruby/X.X.0/bin:$PATH"' >> ~/.bash_profile

To check that your gem paths point to your home directory run:

gem env

Install this webpage repository

1. git clone this repository

git clone https://github.com/jappoker/mineral_input_data.git

2. go to the folder and then run this in your terminal

bundle exec jekyll serve

then follow the given local address to see your web page!

Add/Edit the minerals

1. The mineral data is hosted in two folders:

   • _posts/: a markdown file for each mineral containing data and infomation

   • mineralsdata/: a folder for each mineral contaning images, input files, cif files

   each mineral, i.e. Aegirine, it has _posts/0001-01-01-Acimite.md and mineralsdata/Acimite/.

2. Markdown file for 0001-01-01-The_Mineral.md mineral in _posts/, e.g.

   In _posts/0001-01-01-Acimite.md, the header of this markdown includes:

   • ---
     layout: mineral
     title: "Acmite"
     date: 0001-01-01 00:00:00 -0400
     
     name: Acmite
     formula: NaFeSi<sub>2</sub>O<sub>6</sub>, Z=4
     space_group: "#15, C2/c"
     lattice_parameters:
         a: 9.6554
         b: 8.7952
         c: 5.2942
         α: 90
         β: 107.396
         γ: 90
         volume(Å<sup>3</sup>): 429.026
     
     ineqv_atom_position:
         -   atom: Na
             x: 0.00000
             y: 0.29880
             z: 0.25000
             site: 4e
     
         -   atom: Fe
             x: 0.00000
             y: 0.89900
             z: 0.25000
             site: 4e
             
             ...
             
             ...
             
      coordi_primitive:
         -   atom: Na
             x: 0.2988
             y: 0.2988
             z: 0.25
     
         -   atom: Na
             x: 0.2988
             y: 0.2988
             z: 0.25
             
          ...
          
          ...
          
      structure_img: /mineralsdata/Aegirine/Aegirine.png
     
     cif: |-
         long_cif_information_without_quotes
     
     structure_source: 
         name: Almandine
         url: http://rruff.geo.arizona.edu/AMS/download.php?id=08950.amc&down=amc
         database_code: _database_code_amcsd 0007689
     
     input: /mineralsdata/Aegirine/Aegirine_AMS_DATA.POSCAR.vasp
     --- 

     Do not need to fill all of them! If leave them empty they will now show on the web page.

   • The header is included between the

   • --- 
     layout: mineral
     title: "Acmite"
     date: 0001-01-01 00:00:00 -0400
     
     ....: ....
     --- 

     And everything belown the header will be parsed into normal markdown format.

3. Generate Markdown file using /pyscript/generate_from_cif.py Enter the /pyscript folder

   cd pyscript/
   

   modify the information in generate_from_cif.py which lines in the very bottom, for example:

   mineral_name = "Almandine"
   cifdata = read_cif("../mineralsdata/Almandine/Almandine AMS_DATA.cif")
   get_output(cifdata)

   then run it! A tmp.md will show up in this pyscript/ folder. Add & edit the stuff in the markdown file and copy & paste into _posts/0001-01-01-***.md!

4. Note that the numeric subscripts and etc in formula should be written in html syntax, i.e.

   Fe<sub>2</sub>O<sub>3<sub>
   Fe<sup>3+</sup>