main.cpp

#include <iostream>
#include <casmutils/xtal/structure.hpp>
#include <casmutils/xtal/structure_tools.hpp>
#include <CLI/CLI.hpp>
#include <vector>

Eigen::Matrix3d read_matrix(const std::filesystem::path& input_path)
{
    std::ifstream mat_stream(input_path);

    Eigen::Matrix3d mat;
    for(int i=0; i<3; ++i)
    {
        for(int j=0; j<3; ++j)
        {
            mat_stream>>mat(i,j);
        }
    }

    mat_stream.close();
    return mat;
}

int main(int argc, char* argv[])
{
    namespace cu=casmutils;

    // Parse CLI
    CLI::App app;

    // Path to input structure
    cu::fs::path input_struc_path;
    cu::fs::path input_mat_path;
    cu::fs::path output_struc_path;

    app.add_option("-s,--structure",input_struc_path,"Path to input structure (vasp format).")->required()->check(CLI::ExistingFile);
    app.add_option("-m,--matrix",input_mat_path,"Path to file containing 3x3 transformation matrix.")->required()->check(CLI::ExistingFile);
    app.add_option("-o,--output",output_struc_path,"Path to write transformed structure to.")->required();

    CLI11_PARSE(app, argc, argv);

    // Read a structre
    auto input_struc=cu::xtal::Structure::from_poscar(input_struc_path);

    // Read a transformation matrix (col or rows?)
    Eigen::Matrix3d transform_mat=read_matrix(input_mat_path);

    // Apply transformation to lattice
    auto final_struc=cu::xtal::apply_deformation(input_struc, transform_mat);

    // Output transformed structure
    cu::xtal::write_poscar(final_struc,output_struc_path);

    return 0;
}