Add voronotalt headers and begin class

src/analysis.cpp

@@ -26,6 +26,8 @@
 #include <range/v3/numeric/accumulate.hpp>
 #include <range/v3/view/zip.hpp>
 
+#include "voronotalt/voronotalt.h" // assuming that the "voronotalt" directory is in the include path
+
 #include <iomanip>
 #include <iostream>
 #include <memory>
@@ -2712,4 +2714,8 @@ void SavePenaltyEnergy::_sample() {
     }
 }
 
+void Voronota::_sample() {
+    voronotalt::RadicalTessellation::Result result;
+}
+
 } // namespace Faunus::analysis

src/analysis.h

@@ -262,7 +262,7 @@ class ElectricPotential : public Analysis {
     unsigned int calculations_per_sample_event = 1;
     std::string file_prefix; //!< Output filename prefix for potential histogram and correlation
     struct Target {
-        Point position;                                               //!< Target position
+        Point position;                                                //!< Target position
         Average<double> mean_potential;                               //!< mean potential at position
         std::unique_ptr<SparseHistogram<double>> potential_histogram; //!< Histogram of observed potentials
     };
@@ -1086,6 +1086,38 @@ class SavePenaltyEnergy : public Analysis {
     SavePenaltyEnergy(const json& j, const Space& spc, const Energy::Hamiltonian& pot);
 };
 
+class Voronota : public Analysis {
+  private:
+    using average_type = Average<double>;
+    struct Ball {
+        double x;
+        double y;
+        double z;
+        double r;
+    };
+    struct Averages {
+        average_type area;
+        average_type area_squared;
+    };                     //!< Placeholder class for average properties
+    Averages average_data; //!< Stores all averages for the selected molecule
+
+    std::unique_ptr<std::ostream> output_stream; //!< output stream
+
+    double probe_radius; //!< radius of the probe sphere
+    int slices_per_atom; //!< number of slices of each sphere in SASA calculation
+
+    std::string filename;                         //!< output file name
+
+    virtual void _to_json(json& j) const override;
+    virtual void _from_json(const json& input) override;
+    virtual void _to_disk() override;
+    virtual void _sample() override;
+
+  public:
+    Voronota(const json& j, const Space& spc);
+    Voronota(double probe_radius, const Space& spc);
+};
+
 } // namespace analysis
 
 } // namespace Faunus

src/voronotalt/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2023 Kliment Olechnovic
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.