Improve docs a bit

Author: Marco M. Mosca

FindGemmi.cmake

@@ -18,7 +18,7 @@
 *]]
 IF(NOT DEFINED ENV{GEMMI_ROOT})
 	message(STATUS "Using local package for Gemmi library...")
-	set(PACKAGE_DIR_GEMMI "${CMAKE_CURRENT_SOURCE_DIR}/External/Gemmi")	
+	set(PACKAGE_DIR_GEMMI "${CMAKE_CURRENT_SOURCE_DIR}/External/gemmi-0.3.3")	
 ELSE()
 	message(STATUS "Using system environmental variable package for Gemmi library...")
 	set(PACKAGE_DIR_GEMMI "$ENV{GEMMI_ROOT}")

README.md

@@ -1,6 +1,5 @@
 # Voronoi-based Lattice Distances
-The repository contains the code of Voronoi-based Lattice Distances which encodes crystal lattices to Voronoi Domains and runs Voronoi-based metrics to compare them. 
-The code is written in C++ and CMake. More details on the used metrics can be found in our paper published in the Crystal Research & Technology Journal: [Voronoi-Based Similarity Distances between Arbitrary Crystal Lattices](https://onlinelibrary.wiley.com/doi/10.1002/crat.201900197).
+Voronoi-based Lattice Distances encodes crystal lattices to Voronoi Domains and runs Voronoi-based metrics to compare them. More details on the used metrics can be found in our paper published in the Crystal Research & Technology Journal: [Voronoi-Based Similarity Distances between Arbitrary Crystal Lattices](https://onlinelibrary.wiley.com/doi/10.1002/crat.201900197).
 
 The project has been compiled and run only on `Windows x64`.
 
@@ -16,7 +15,9 @@ The project has been compiled and run only on `Windows x64`.
     - `CMake C++ Tools for Windows`
     - `Git for Windows`
 
-2. The software and shared libraries below must be installed by the user through Windows installers:
+2. Download the repository
+
+3. The software below must be installed through Windows installers:
     - [CGAL-4.14.3-Setup.exe](https://github.com/CGAL/cgal/releases/tag/releases%2FCGAL-4.14.3) 
 
       Note: Install it in `VoronoiLatticeDistances\External\CGAL-4.14.3` folder and choose `64bit` binaries.
@@ -27,20 +28,36 @@ The project has been compiled and run only on `Windows x64`.
 
 3. Add the following environmental variables as User:
     - `VS_DIR`: Path to Visual Studio with all folders (e.g. `Microsoft Visual Studio\2022\Community`)
-    
-4. Download the repository
 
-5. Run the following in a `Command Prompt` (no PowerShell) to build and install it:
+5. Run the following in a `Command Prompt` (no PowerShell) to install it:
     ```
       "%VS_DIR%\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
       cd VoronoiLatticeDistances/windows-setup
       dotnet build
       dotnet run
     ```
+6. Restart the command prompt and run the executables: `voronoilatticedistances.exe` or `voronoilatticedistances_off.exe`.
 
-## Usage: Run the metric computations
-To compute correctly the metrics, it is required that all input CIF files contain the primitive unit cell.
-Running the executable `voronoilatticedistances.exe` without parameters, it outputs the usage as follows: 
+## Usage
+To compute correctly the metrics, it is required that all input `CIF` files contain the primitive unit cell.
+Run the executable without parameters for the usage. There are following some examples.
+### Produce Voronoi-based metrics from CIF files on 5 threads
+```
+  .\voronoilatticedistances.exe -inputdir "path\to\cif_folder" -outputdir "path\to\output_dir" -ds -dh -threads 5
+```
+### Generate OFF files of Voronoi Domains and their volumes
+```
+  .\voronoilatticedistances.exe -inputdir "path\to\cif_folder" -outputdir "path\to\output_dir" -off -vol
+```
+### Generate Voronoi Domains for 3D visualization
+File `.vtp` can be visualized with [Paraview software](https://www.paraview.org/).
+```
+  .\voronoilatticedistances.exe -inputdir "path\to\cif_folder" -outputdir "path\to\output_dir" -vtp
+```
+### Produce Voronoi-based metrics from OFF files
+```
+  .\voronoilatticedistances_off.exe -inputdir "path\to\off_folder" -outputdir "path\to\output_dir" -ds -dh 
+```
 
 Required options: 
 
@@ -61,23 +78,6 @@ Optional commands:
 - `-intervals`	[integer n (default n=2)]	It affects the number of rotation samples to be considered for metric computations (total number of rotations: 4*pi^2*n^3) 
 - `-threads`		[integer t (default t=1)]	Rotation samples are divided among t threads
 
-If users want to divide the voronoi cell computation from the metric computation, they can run `voronoilatticedistances_off.exe` to compute only the metrics from OFF files.
-
-Required options:
-
-- `-inputdir`		[Input Folder with Voronoi Cell OFF files]
-- `-outputdir`	[Output Folder to write metric results]
-
-Output options (at least 1 required):
-
-- `-ds`	Outputs .csv file with Scale Invariant Distance matrix (n x n) between all n crystal structures
-- `-dh`	Outputs .csv file with Extended Hausdorff Distance matrix (n x n) between all n crystal structures
-
-Optional commands:
-
-- `-intervals`	[integer n (default n=2)]	It affects the number of rotation samples to be considered for metric computations (number of rotations: 4*pi^2*n^3)
-- `-threads`		[integer t (default t=1)]	Rotation samples are divided among t threads
-
 ## Example of Voronoi Domains
 There are following the Voronoi domains of 5 real crystal lattices from the `T2 dataset` used in our experiments: T2-epsilon, T2-delta, T2-beta, T2-gamma and T2-alpha. Plus, the voronoi domains of the standard cubic, body-centred cubic and face-centred cubic lattices.
 

windows-setup/Setup.fs

@@ -52,7 +52,9 @@ let configure (src_dir:string) (variables: string array) =
         "-L";
         "-G"; "Visual Studio 17 2022";
         sprintf @"-DCMAKE_INSTALL_PREFIX=%s" (Path.Combine(src_dir, "install"));
-        @"-DCMAKE_C_COMPILER=cl"; 
+        @"-DCMAKE_C_COMPILER=cl";
+        @"-DBUILD_EXAMPLES=OFF";
+        @"-DBUILD_TESTING=OFF";
     |]
     |> Array.append variables
     |> start_process "cmake"
@@ -77,7 +79,6 @@ let main args =
     let ext_dir = Path.GetFullPath(@"..\External")
     assert Directory.Exists(ext_dir)
     let boost_dir = Path.Combine(ext_dir, @"boost_1_69_0")
-    // Set by Windows installer
     let cgal_dir = Path.Combine(ext_dir, @"CGAL-4.14.3")
 
     assert Directory.Exists(ext_dir)
@@ -110,8 +111,6 @@ let main args =
         unzip ext_dir path_to_file
         File.Delete(path_to_file)
 
-    Directory.Move(Path.Combine(ext_dir,"gemmi-0.3.3"), Path.Combine(ext_dir,"Gemmi"))
-
     let function_object_h = Path.Combine(cgal_dir, "include/CGAL/Cartesian/function_objects.h")
     assert File.Exists(function_object_h)
     let function_object_lines = 
@@ -122,7 +121,7 @@ let main args =
     File.Delete(function_object_h)
     File.WriteAllLines(function_object_h, function_object_lines)
 
-    let small_hpp = Path.Combine(ext_dir, "Gemmi/include/gemmi/small.hpp")
+    let small_hpp = Path.Combine(ext_dir, "gemmi-0.3.3/include/gemmi/small.hpp")
     assert File.Exists(small_hpp)
     let new_lines = [| 
         @"  if (len > 1) {";
@@ -146,7 +145,7 @@ let main args =
         Path.Combine(cgal_dir, @"auxiliary\gmp\lib");
         Path.Combine(vtk_dir, @"bin");
         Path.Combine(boost_dir, @"lib64-msvc-14.1");
-        Path.Combine(libxml2_dir, @"bin"); 
+        Path.Combine(libxml2_dir, @"bin");
         Path.Combine(zlib_dir, @"bin"); |] do
         assert Directory.Exists(path_value)
         let mutable path = Environment.GetEnvironmentVariable("Path", EnvironmentVariableTarget.User);