You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardexpand all lines: README.md
+47-61
Original file line number
Diff line number
Diff line change
@@ -2,98 +2,84 @@
2
2
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.
3
3
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).
4
4
5
-
The project has been compiled and run only on Windows.
5
+
The project has been compiled and run only on `Windows x64`.
4. Choose `x86-Release` type from the top icon bar
52
-
5. In Build menu, build all the project
53
-
6. then from Build menu, Install the project
54
-
55
41
## Usage: Run the metric computations
56
42
To compute correctly the metrics, it is required that all input CIF files contain the primitive unit cell.
57
-
Running the executable 'voronoilatticedistances.exe' without parameters, it outputs the usage as follows:
43
+
Running the executable `voronoilatticedistances.exe` without parameters, it outputs the usage as follows:
58
44
59
45
Required options:
60
46
61
-
- -inputdir [Input Folder with CIF files]
62
-
- -outputdir [Output Folder to write metric results]
47
+
- `-inputdir` [Input Folder with CIF files]
48
+
- `-outputdir` [Output Folder to write metric results]
63
49
64
50
Output options (at least 1 required):
65
51
66
-
- -vol Outputs .csv file with Voronoi Cell volume
67
-
- -vtp Outputs .vtp files with Voronoi Cell of a Lattice (Paraview format file)
68
-
- -csv Outputs .csv files with Lattice and Voronoi Cell points
69
-
- -off Outputs .off files with Voronoi Cell vertices and faces
70
-
- -ds Outputs .csv file with Scale Invariant Distance matrix (n x n) between all n crystal lattices
71
-
- -dh Outputs .csv file with Extended Hausdorff Distance matrix (n x n) between all n crystal lattices
52
+
- `-vol` Outputs .csv file with Voronoi Cell volume
53
+
- `-vtp` Outputs .vtp files with Voronoi Cell of a Lattice (Paraview format file)
54
+
- `-csv` Outputs .csv files with Lattice and Voronoi Cell points
55
+
- `-off` Outputs .off files with Voronoi Cell vertices and faces
56
+
- `-ds` Outputs .csv file with Scale Invariant Distance matrix (n x n) between all n crystal lattices
57
+
- `-dh` Outputs .csv file with Extended Hausdorff Distance matrix (n x n) between all n crystal lattices
72
58
73
59
Optional commands:
74
60
75
-
- -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)
76
-
- -threads [integer t (default t=1)] Rotation samples are divided among t threads
61
+
- `-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)
62
+
- `-threads` [integer t (default t=1)] Rotation samples are divided among t threads
77
63
78
-
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.
64
+
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.
79
65
80
66
Required options:
81
67
82
-
- -inputdir [Input Folder with Voronoi Cell OFF files]
83
-
- -outputdir [Output Folder to write metric results]
68
+
- `-inputdir` [Input Folder with Voronoi Cell OFF files]
69
+
- `-outputdir` [Output Folder to write metric results]
84
70
85
71
Output options (at least 1 required):
86
72
87
-
- -ds Outputs .csv file with Scale Invariant Distance matrix (n x n) between all n crystal structures
88
-
- -dh Outputs .csv file with Extended Hausdorff Distance matrix (n x n) between all n crystal structures
73
+
- `-ds` Outputs .csv file with Scale Invariant Distance matrix (n x n) between all n crystal structures
74
+
- `-dh` Outputs .csv file with Extended Hausdorff Distance matrix (n x n) between all n crystal structures
89
75
90
76
Optional commands:
91
77
92
-
- -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)
93
-
- -threads [integer t (default t=1)] Rotation samples are divided among t threads
78
+
- `-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)
79
+
- `-threads` [integer t (default t=1)] Rotation samples are divided among t threads
94
80
95
81
## Example of Voronoi Domains
96
-
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.
82
+
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.
97
83
98
84
<p float="left">
99
85
<img src="images/epsilon.JPG" width="200" />
@@ -108,7 +94,7 @@ There are following the Voronoi domains of 5 real crystal lattices from the T2 d
108
94
109
95
110
96
## Dendrogram and Heatmap
111
-
The dendrogram and the heatmap of the Voronoi-based metrics can be generated with the following script. The input csv file is generated by the options -dh or -ds of the previous executables.
97
+
The dendrogram and the heatmap of the Voronoi-based metrics can be generated with the following script. The input csv file is generated by the options `-dh` or `-ds` of the previous executables.
0 commit comments