I made a mistake - didn't mean to do this.

.gitignore

@@ -0,0 +1,3 @@
+/bicrystal/outfile
+
+/bicrystal/workspace

README.md

@@ -1,69 +1,49 @@
 # BiCrystal
-``BiCrystal`` is a Python program that builds commensurate and incommensurate crystal structures of layered materials. The current version reads CIF files and writes the new structure to a QUANTUM ESPRESSO input file. The program also provides additional information such as the bond distance between atoms, lattice vectors in Bohr and Angstrom, and a simple 3D plot of each layer.
+``BiCrystal`` is a **Python 3** program that builds incommensurate crystal structures of layered materials. The current version reads CIF files and writes the new structure to a QUANTUM ESPRESSO input file. The program also provides additional information such as the bond distance between atoms, lattice vectors in Bohr and Angstrom, and a simple 3D plot of each layer.
 
 Contents
 ==========
 **Overview** \
 **Download** \
 **Packages** \
 **Files** \
-**Installation** \
 **Usage** \
 **Examples** \
 **Summary Table** \
 **References** \
 **License** 
 
 # Overview
-Building unit cells of arbitrary size is often an inevitable task when studying the physical and mechanical properties of layered materials such as graphene, hexagonal Boron Nitride, transition metal dichalcogenides. Although most visualzation software such as Xcrysden, VESTA or Avogadro provide very powerful tools for analysing and manipulating periodic crystal structures, constructing large unit cells in bilayers with one of the layers perturbed can be very daunting. ``BiCrystal`` provides a convinient and easy way of creating new crystal structures of arbitrary size from CIF files.
+Building unit cells of arbitrary size is often an inevitable task when studying the physical and mechanical properties of layered materials such as graphene, hexagonal Boron Nitride, transition metal dichalcogenides. Although most visualzation software such as Xcrysden, VESTA or Avogadro provide very powerful tools for analysing and manipulating periodic crystal structures, constructing large unit cells in bilayers with one of the layers perturbed can be very daunting. ``BiCrystal`` provides a convenient and easy way of creating new crystal structures of arbitrary size from CIF files.
 
-# Download
+# Download and Installation
 The latest version of ``BiCrystal`` can be found on github:
 
 https://github.com/tilaskabengele/BiCrystal
 
-**Contact**: Tilas Kabengele [email protected]
 
-# Packages
-`BiCrystal` is a python-based program that uses Scipy and Shapely libraries. Additionally, the Crystal package, which is not part of the standard Python packages, should be installed. i.e Install via pip or conda:
-
-     pip install crystals
-or
+**Contact**: Tilas Kabengele at [email protected] or [email protected]
 
-    conda install -c conda-forge crystals
-and
+# Packages
+We recommend running BiCrystal in python 3.8.x, where it has been thoroughly tested. Aditionally, we recommend installing BiCrystal and all its dependencies via poetry using the .lock and .toml files provided. These files contain all the dependencies of BiCrsytal with the appropriate versions used. You can learn more about poetry from the official website: https://python-poetry.org/. For more information on crystals and shapely, visit: https://pypi.org/project/crystals/ and https://pypi.org/project/Shapely/ respectively.
 
-    pip install shapely
-
-For more information on crystals and shapely, visit: https://pypi.org/project/crystals/ and https://pypi.org/project/Shapely/ respectively.
-
- # Files
+After you have installed poetry on your machine, cd into the source folder of the cloned repository and run 
 
+     poetry install
+
+This will create a virtual environment for BiCrystal. To activate the virtual environment and use BiCrystal, run
+
+     poetry shell
+
+# BiCrystal files
 **bicrystal** - Bash script which runs the python program \
 **cifs/** - Directory with sample cif files \
 **examples/** - Directory with 33 examples of QUANTUM ESPRESSO input files generated by BiCrystal \
 **periodic_table.csv** - Periodic table of elements \
-**program.py** - Python program to be called from bicrystal script
-
-# Installation
-After downloading the files from the github repository to the directory of your choice (_recommended: /usr/bin/_), make `bicrystal` and `program.py` into executables:
-
-    chmod u+x bicrystal program.py
-
-Next, add this directory to your $PATH variable. In Bash, adding the following lines to your `.bashrc file`:
-
-    vi ~/.bashrc
+**program.py** - Python program to be called from bicrystal script \
+**pyproject.toml** - Poetry file which contains summarized list of packages used \
+**poetry.lock* - Poetry file which contains detailed description of all packages used and their dependancies
 
-Add:
-
-    export PATH="$/path/to/your/directory/with/bicrysal/:$PATH"
-    export PYTHONPATH="${PYTHONPATH}:/path/to/your/directory/with/bicrysal/"
-
-Save, close then source your `.bashrc` file to activate the changes:
-
-    source ~/.bashrc
-
-Restart your terminal window to start using `bicrystal`.
 
 # Usage
 BiCrystal is an interactive program that instructs the user every step of the way. To start BiCrystal, in the terminal type:
@@ -75,13 +55,11 @@ The first thing you will be required to do is input your cif file, e.g. graphite
     ***Input cif file***
     graphite.cif
 
-Next, enter input parameters m and n, and rotation angle in degrees (_zero if you want both layers unperturbed_).
-Parameter m and n correspond to the scale of the lattice vectors along the x and y directions, respectively. As an example, let's take m = 2, n = 1 and rotation angle 21.79 degrees.
+Next, input scaling parameters m and n, which correspond to the scale of the lattice vectors along the x and y directions, respectively. As an example, let's take m = 2, n = 1. Bicrystal caculates the relative rotation angle for the given m and n. In this case, the rotation angle will be 21.79 degrees.
 
     ***Rotation parameters***
     Enter m 2
     Enter n 1
-    Enter rotation_angle 0
 
 After that, you will be required to pick a zeroeth atom from the top and bottom layer. If we were picking the atoms by hand using a visualization software such as Xcrysden, this would be the atom we start from when creating the new cell vectors. 
 
@@ -107,10 +85,13 @@ After that, you will be required to pick a zeroeth atom from the top and bottom
 
  ![cc28](https://user-images.githubusercontent.com/62076249/87927879-48795500-ca5a-11ea-98c1-b2949bb672e3.PNG)
 
- Finally, you can save your output as a QUANTUM ESPRESSO file and visualize with Xcrysden for a more sophisticated look.
+ Finally, you can save your output as a QUANTUM ESPRESSO file and visualize with VESTA or Xcrysden for a more sophisticated look.
 
      ********************* SUMMARY REPORT ***********************
-
+
+    Rotation angle (deg) =  19.107
+    Relative Rotation (deg) =  21.787
+
     Top atoms(rotated) =  14
     Bottom atoms  =  14
 
@@ -121,9 +102,8 @@ After that, you will be required to pick a zeroeth atom from the top and bottom
 
     Would you like to write Espresso file?[Y/n]
 
-   # Examples
-
-   Let's say we saved our output in the example given above as graphite28.scf.in, we can visualize this with Xcrysden.
+# Examples
+Let's say we saved our output in the example given above as graphite28.scf.in, we can visualize this with Xcrysden.
 
        xcrysden --pwi graphite28.scf.in
 
@@ -134,17 +114,17 @@ Looking from the top view, we can see that for this rotation, a Moire pattern wa
 The **examples/** folder has over 30 examples of Moire patterns graphite, Molebdenum Disulfide and blue Phosphorene generated from `bicrystal`. Below are some examples.
 
 # Graphite 364-atom unit cell
-The unit cell of graphite with 364 atoms can be generated by using parameters: m = 6, n = 5, and rotation angle of 6.01 degrees. Shown below is the top view.
+The unit cell of graphite with 364 atoms can be generated by using parameters: m = 6, n = 5. Shown below is the top view.
 
 ![cc364](https://user-images.githubusercontent.com/62076249/87933970-98f5b000-ca64-11ea-906b-15a1036989a1.PNG)
 
 # Blue phosphorene 172-atom unit cell
-The unit cell of blue phosphorene with 172 atoms can be generated by using parameters: m = 6, n = 1, and rotation angle of 44.82 degrees. Shown below is the top view.
+The unit cell of blue phosphorene with 172 atoms can be generated by using parameters: m = 6, n = 1. Shown below is the top view.
 
 ![bluep172](https://user-images.githubusercontent.com/62076249/87934152-e245ff80-ca64-11ea-8f36-b69b5799e3fa.PNG)
 
 # Molybdenun Disulfide 546-atom unit cell
-The unit cell of MoS<sub>2</sub> with 546 atoms atoms can be generated by using parameters: m = 6, n = 5, and rotation angle of 6.01 degrees. Shown below is the top view.
+The unit cell of MoS<sub>2</sub> with 546 atoms atoms can be generated by using parameters: m = 6, n = 5. Shown below is the top view.
 
 ![mos546](https://user-images.githubusercontent.com/62076249/87934312-2fc26c80-ca65-11ea-97a2-c9cdb3068a9d.PNG)
 
@@ -153,7 +133,7 @@ All the examples in the examples folder can be summarized in the table below:
 
 ![example_table](https://user-images.githubusercontent.com/62076249/87934662-dc045300-ca65-11ea-8f54-818b7183d6e1.PNG)
 
- # References
+# References
  For a detailed analysis of Moire patterns and angles:
 
  **Density functional calculations on the intricacies of Moiré patterns on graphite**, J. M. Campanera, G. Savini, I. Suarez-Martinez, and M. I. Heggie, _Phys. Rev. B 75, 235449 – Published 28 June 2007_
@@ -164,7 +144,7 @@ All the examples in the examples folder can be summarized in the table below:
 
  For further reading and related projects, visit **Johnson Group wiki**: http://schooner.chem.dal.ca/wiki/Johnson_Group_Wiki 
 
- # License
+# License
  Copyright (c) 2020 Tilas Kabengele, Johnson Chemistry Group, Dalhousie University.
 
 BiCrystal is a free program: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

_config.yml

@@ -1 +1 @@
-theme: jekyll-theme-minimal
+theme: jekyll-theme-dinky

bicrystal/bicrystal

@@ -1,50 +1,49 @@
 #!/bin/bash
 
+# Remove unnecessary files
 rm -f number_of_atoms unitcell body outfile heading heading_nat atoms sorted_atoms k_points
 
-t1=$(whereis program.py | awk '{print $2}')
-t2=$(whereis program.py | awk '{print $2}' | sed -r 's/.{10}$//')
-echo $t2 > workspace
-python $t1 2>&1 | tee outfile
-rm -f workspace
-
-echo "Would you like to write Espresso file?[Y/n]"
+# Execute python script for bicrystal
+python program.py 2>&1 | tee outfile
 
+# Post-process the results and prepare output file
+echo -e "\nWould you like to write an Espresso file? [Y/n]"
 read reply
 
-if [[ "$reply" == "y" ]]
-	 then
-		echo "Save as:"
-		read filename
-elif [[ "$reply" == "Y" ]]
-	then
-		echo "Save as"
-		read filename
-elif [[ "$reply" == "n" ]]
-         then
-                exit
-elif [[ "$reply" == "N" ]]
-        then
-                exit
-else 
-	echo "Invalid"
-	echo "Stop"
-	exit
+if [[ "$reply" == "y" || "$reply" == "Y" ]]; then
+  echo "Save as:"
+  read -r filename
+elif [[ "$reply" == "n" || "$reply" == "N" ]]; then
+  echo -e "\n\n\nGoodbye!\n\n***\n\n"
+  rm -f outfile
+  exit
+else
+  echo "Invalid input. Stop."
+  rm -f outfile
+  exit
 fi
-tail -n -4 outfile | head -n 1 > number_of_atoms
-uc=$(sed -n '/CELL_PARAMETERS/,+3p' outfile | column -t | tail -n 3 | sed -e "s/^/     /")
+
+# Extract relevant data from the output file
+number_of_atoms=$(grep -m 1 -A 1 "Total atoms" outfile | tail -n 1 | awk '{print $NF}')
+uc=$(sed -n '/CELL_PARAMETERS/,+3p' outfile)
 echo "$uc" > unitcell
 sed -n '/control/,/ATOMIC_POSITIONS/p' outfile > heading
-sed "s/= atoms/$(cat number_of_atoms)/g" heading > heading_nat
+sed "s/nat[[:space:]]*=[[:space:]]*atoms/nat = $number_of_atoms/" heading > heading_nat
 sed -n '/ATOMIC_POSITIONS/,/K_POINTS/p' outfile | tail -n +2 | head -n -2 > atoms
-sort -k 4n atoms > sorted_atoms
+sort -k 4n -o sorted_atoms atoms
 echo >> sorted_atoms
 sed -n '/K_POINTS/,+1p' outfile > k_points
 echo >> k_points
-sed -n '/CELL_PARAMETERS/,+0p' outfile > cell_par
-cat heading_nat sorted_atoms k_points cell_par unitcell > $filename
+sed -n '/CELL_PARAMETERS/,-1p' outfile | tail -n 3  > cell_par
+
+# Combine the extracted data into the final output file
+cat heading_nat sorted_atoms k_points cell_par unitcell > "$filename"
+
+# Replace the number of atoms in the output file
+sed -i "s/nat = atoms/nat = $number_of_atoms/" "$filename"
 
+# Remove unnecessary files
 rm -f number_of_atoms cell_par unitcell body outfile heading heading_nat atoms sorted_atoms k_points
 
-rm -f outfile
+echo -e "\n\n\nGoodbye!\n\n***\n\n"
 

bicrystal/cifs/mos2.cif

@@ -0,0 +1,37 @@
+# generated using pymatgen
+data_MoS2
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   3.19223791
+_cell_length_b   3.19223791
+_cell_length_c   13.37829400
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   MoS2
+_chemical_formula_sum   'Mo2 S4'
+_cell_volume   118.06518982
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Mo4+  4.0
+  S2-  -2.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Mo4+  Mo0  1  0.66666667  0.33333333  0.25000000  1
+  Mo4+  Mo1  1  0.33333333  0.66666667  0.75000000  1
+  S2-  S2  1  0.66666667  0.33333333  0.63308200  1
+  S2-  S3  1  0.33333333  0.66666667  0.36691800  1
+  S2-  S4  1  0.66666667  0.33333333  0.86691800  1
+  S2-  S5  1  0.33333333  0.66666667  0.13308200  1