Stable

README.md

@@ -1,5 +1,5 @@
 # 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 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
 ==========
@@ -20,12 +20,13 @@ Building unit cells of arbitrary size is often an inevitable task when studying
 # Download
 The latest version of ``BiCrystal`` can be found on github:
 
-https://github.com/tilaskabengele/BiCrystal
+https://github.com/tilaskabengele/BiCrystal/tree/stable
+
 
 **Contact**: Tilas Kabengele tilas.kabengele@dal.ca
 
 # 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:
+`BiCrystal` is a python-based program that uses Scipy and Shapely libraries. Additionally, the Crystal and shapely packages, which is not part of the standard Python packages, should be installed. i.e Install via pip or conda:
 
      pip install crystals
 or
@@ -38,7 +39,6 @@ and
 For more information on crystals and shapely, visit: https://pypi.org/project/crystals/ and https://pypi.org/project/Shapely/ respectively.
 
  # 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 \
@@ -48,7 +48,7 @@ For more information on crystals and shapely, visit: https://pypi.org/project/cr
 # 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
+    chmod r+x bicrystal program.py
 
 Next, add this directory to your $PATH variable. In Bash, adding the following lines to your `.bashrc file`:
 
@@ -75,13 +75,11 @@ 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. 
 
@@ -110,7 +108,10 @@ After that, you will be required to pick a zeroeth atom from the top and bottom
  Finally, you can save your output as a QUANTUM ESPRESSO file and visualize with 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
 
@@ -122,7 +123,6 @@ 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.
 
        xcrysden --pwi graphite28.scf.in
@@ -134,17 +134,17 @@ 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)
 

bicrystal/README.md

@@ -1,5 +1,5 @@
 # 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 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
 ==========
@@ -26,7 +26,7 @@ https://github.com/tilaskabengele/BiCrystal/
 **Contact**: Tilas Kabengele tilas.kabengele@dal.ca
 
 # 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:
+`BiCrystal` is a python-based program that uses Scipy and Shapely libraries. Additionally, the Crystal and shapely packages, which is not part of the standard Python packages, should be installed. i.e Install via pip or conda:
 
      pip install crystals
 or
@@ -39,7 +39,6 @@ and
 For more information on crystals and shapely, visit: https://pypi.org/project/crystals/ and https://pypi.org/project/Shapely/ respectively.
 
  # 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 \
@@ -49,7 +48,7 @@ For more information on crystals and shapely, visit: https://pypi.org/project/cr
 # 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
+    chmod r+x bicrystal program.py
 
 Next, add this directory to your $PATH variable. In Bash, adding the following lines to your `.bashrc file`:
 
@@ -76,13 +75,11 @@ 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. 
 
@@ -111,7 +108,10 @@ After that, you will be required to pick a zeroeth atom from the top and bottom
  Finally, you can save your output as a QUANTUM ESPRESSO file and visualize with 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
 
@@ -123,7 +123,6 @@ 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.
 
        xcrysden --pwi graphite28.scf.in
@@ -135,17 +134,17 @@ 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)