aurostd_xparser.h

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// ***************************************************************************
// *                                                                         *
// *           Aflow STEFANO CURTAROLO - Duke University 2003-2024           *
// *                                                                         *
// ***************************************************************************
 
#ifndef _AUROSTD_XPARSER_H_
#define _AUROSTD_XPARSER_H_
 
#include <filesystem>
#include <fstream>
#include <iostream>
#include <map>
#include <memory>
#include <string>
#include <utility>
#include <vector>
 
#include "aurostd.h"
#include "aurostd_xmatrix.h"
#include "aurostd_xvector.h"
 
// compound specification is how a compound is specified
// composition (Mn2Pt3) is ORTHOGONAL to pseudopotential string (Mn_pvPt)
// for instance, H1.25 can be a pseudopotential and NOT a composition
enum elements_string_type {
  composition_string,
  pp_string,
};
 
// CO20190712 - see VASP_PseudoPotential_CleanName_InPlace() in aflow_ivasp.cpp
const std::string CAPITAL_LETTERS_PP_LIST =
    "_GW2"    // CO20190712 - potpaw_LDA/potpaw_LDA.20100505/Li_AE_GW2
    ",_GW"    // CO20190712 - potpaw_PBE/potpaw_PBE.20100506/As_GW
    ",_ZORA"  // CO20190712 - potpaw_PBE/potpaw_PBE.20100506/Pt_ZORA
    ",_LDApU" // CO20190712 - potpaw_LDA/potpaw_LDA.20100505/Zn_sv_LDApU
    ",_AE"    // CO20190712 - potpaw_LDA/potpaw_LDA.20100505/Li_AE_GW2
    ",_NC2"   // CO20190712 - potpaw_LDA/potpaw_LDA.20100505/As_NC2
    ",_200eV"
    "";
 
namespace aurostd {
  void VASP_PseudoPotential_CleanName_InPlace(std::string& species, bool capital_letters_only = false, bool remove_floats = true); // CO20190712  //CO20210623 - added remove_floats
  void elementsFromCompositionString(const std::string& input);  // CO20190712
  template <class utype> void elementsFromCompositionString(const std::string& input, std::vector<std::string>& velements, std::vector<utype>& vcomposition); // CO20190712
  void elementsFromPPString(const std::string& input, std::vector<std::string>& velements, bool keep_pp = false); // CO20190712
  // returns UNSORTED vector<string> from string
  std::vector<std::string> getElements(const std::string& input); // CO20190712
  std::vector<std::string> getElements(const std::string& input, elements_string_type e_str_type, bool clean = true, bool sort_elements = false, bool keep_pp = false, std::ostream& oss = std::cout);
  template <class utype>
  std::vector<std::string> getElements(const std::string& input, std::vector<utype>& vcomposition, bool clean = true, bool sort_elements = false, bool keep_pp = false, std::ostream& oss = std::cout);
  std::vector<std::string> getElements(const std::string& input, elements_string_type e_str_type, std::ofstream& FileMESSAGE, bool clean = true, bool sort_elements = false, bool keep_pp = false, std::ostream& oss = std::cout);
  template <class utype>
  std::vector<std::string> getElements(const std::string& input, std::vector<utype>& vcomposition, elements_string_type e_str_type, bool clean = true, bool sort_elements = false, bool keep_pp = false, std::ostream& oss = std::cout);
  template <class utype>
  std::vector<std::string> getElements(
      const std::string& input, std::vector<utype>& vcomposition, elements_string_type e_str_type, std::ofstream& FileMESSAGE, bool clean = true, bool sort_elements = false, bool keep_pp = false, std::ostream& oss = std::cout);
} // namespace aurostd
 
// HE20220314 BEGIN X3DWriter
namespace aurostd {
  class x3DWriter {
  private:
    enum class object_types { MATERIAL, SPHERE, FACET, OPEN_CYLINDER };
    void copy(const x3DWriter& x3w);

    struct storage_object {
      object_types type;
      std::shared_ptr<void> obj;
    };
    std::vector<storage_object> objects; 

    struct Sphere {
      xvector<double> center;
      double radius;
      std::string material;
    };

    struct ConvexFacets {
      std::vector<xvector<double>> vertexes;
      std::vector<std::vector<uint>> facets;
      std::string material;
    };

    struct OpenCylinder {
      xvector<double> base;
      xvector<double> apex;
      xvector<double> center;
      double radius;
      std::string material;
      double height;
      double phi; // rotation around 1 0 0
      double theta; // rotation around 0 0 1
    };

    struct Material {
      std::string name;
      xvector<double> color;
      double ambient;
      double opacity;
      double specular;
      double diffuse;
      Material() : ambient(0.6), opacity(1.0), specular(0.05), diffuse(0.4) {};
    };
 
    double max_distance = 0.0; 
    double tachyon_zoom = 2.0; 
    const double tachyon_camera_angle = 45.0; 
    xvector<double> tachyon_camera_position; 
    std::vector<std::pair<xvector<double>, xvector<double>>> tachyon_lattice_views; 
    void tachyon_calculate_camera();
    static std::string x3d_material(const std::shared_ptr<x3DWriter::Material>& material);
 
    const float turbo_cmap[256][3] = {
        {0.18995, 0.07176, 0.23217},
        {0.19483, 0.08339, 0.26149},
        {0.19956, 0.09498, 0.29024},
        {0.20415, 0.10652, 0.31844},
        {0.20860, 0.11802, 0.34607},
        {0.21291, 0.12947, 0.37314},
        {0.21708, 0.14087, 0.39964},
        {0.22111, 0.15223, 0.42558},
        {0.22500, 0.16354, 0.45096},
        {0.22875, 0.17481, 0.47578},
        {0.23236, 0.18603, 0.50004},
        {0.23582, 0.19720, 0.52373},
        {0.23915, 0.20833, 0.54686},
        {0.24234, 0.21941, 0.56942},
        {0.24539, 0.23044, 0.59142},
        {0.24830, 0.24143, 0.61286},
        {0.25107, 0.25237, 0.63374},
        {0.25369, 0.26327, 0.65406},
        {0.25618, 0.27412, 0.67381},
        {0.25853, 0.28492, 0.69300},
        {0.26074, 0.29568, 0.71162},
        {0.26280, 0.30639, 0.72968},
        {0.26473, 0.31706, 0.74718},
        {0.26652, 0.32768, 0.76412},
        {0.26816, 0.33825, 0.78050},
        {0.26967, 0.34878, 0.79631},
        {0.27103, 0.35926, 0.81156},
        {0.27226, 0.36970, 0.82624},
        {0.27334, 0.38008, 0.84037},
        {0.27429, 0.39043, 0.85393},
        {0.27509, 0.40072, 0.86692},
        {0.27576, 0.41097, 0.87936},
        {0.27628, 0.42118, 0.89123},
        {0.27667, 0.43134, 0.90254},
        {0.27691, 0.44145, 0.91328},
        {0.27701, 0.45152, 0.92347},
        {0.27698, 0.46153, 0.93309},
        {0.27680, 0.47151, 0.94214},
        {0.27648, 0.48144, 0.95064},
        {0.27603, 0.49132, 0.95857},
        {0.27543, 0.50115, 0.96594},
        {0.27469, 0.51094, 0.97275},
        {0.27381, 0.52069, 0.97899},
        {0.27273, 0.53040, 0.98461},
        {0.27106, 0.54015, 0.98930},
        {0.26878, 0.54995, 0.99303},
        {0.26592, 0.55979, 0.99583},
        {0.26252, 0.56967, 0.99773},
        {0.25862, 0.57958, 0.99876},
        {0.25425, 0.58950, 0.99896},
        {0.24946, 0.59943, 0.99835},
        {0.24427, 0.60937, 0.99697},
        {0.23874, 0.61931, 0.99485},
        {0.23288, 0.62923, 0.99202},
        {0.22676, 0.63913, 0.98851},
        {0.22039, 0.64901, 0.98436},
        {0.21382, 0.65886, 0.97959},
        {0.20708, 0.66866, 0.97423},
        {0.20021, 0.67842, 0.96833},
        {0.19326, 0.68812, 0.96190},
        {0.18625, 0.69775, 0.95498},
        {0.17923, 0.70732, 0.94761},
        {0.17223, 0.71680, 0.93981},
        {0.16529, 0.72620, 0.93161},
        {0.15844, 0.73551, 0.92305},
        {0.15173, 0.74472, 0.91416},
        {0.14519, 0.75381, 0.90496},
        {0.13886, 0.76279, 0.89550},
        {0.13278, 0.77165, 0.88580},
        {0.12698, 0.78037, 0.87590},
        {0.12151, 0.78896, 0.86581},
        {0.11639, 0.79740, 0.85559},
        {0.11167, 0.80569, 0.84525},
        {0.10738, 0.81381, 0.83484},
        {0.10357, 0.82177, 0.82437},
        {0.10026, 0.82955, 0.81389},
        {0.09750, 0.83714, 0.80342},
        {0.09532, 0.84455, 0.79299},
        {0.09377, 0.85175, 0.78264},
        {0.09287, 0.85875, 0.77240},
        {0.09267, 0.86554, 0.76230},
        {0.09320, 0.87211, 0.75237},
        {0.09451, 0.87844, 0.74265},
        {0.09662, 0.88454, 0.73316},
        {0.09958, 0.89040, 0.72393},
        {0.10342, 0.89600, 0.71500},
        {0.10815, 0.90142, 0.70599},
        {0.11374, 0.90673, 0.69651},
        {0.12014, 0.91193, 0.68660},
        {0.12733, 0.91701, 0.67627},
        {0.13526, 0.92197, 0.66556},
        {0.14391, 0.92680, 0.65448},
        {0.15323, 0.93151, 0.64308},
        {0.16319, 0.93609, 0.63137},
        {0.17377, 0.94053, 0.61938},
        {0.18491, 0.94484, 0.60713},
        {0.19659, 0.94901, 0.59466},
        {0.20877, 0.95304, 0.58199},
        {0.22142, 0.95692, 0.56914},
        {0.23449, 0.96065, 0.55614},
        {0.24797, 0.96423, 0.54303},
        {0.26180, 0.96765, 0.52981},
        {0.27597, 0.97092, 0.51653},
        {0.29042, 0.97403, 0.50321},
        {0.30513, 0.97697, 0.48987},
        {0.32006, 0.97974, 0.47654},
        {0.33517, 0.98234, 0.46325},
        {0.35043, 0.98477, 0.45002},
        {0.36581, 0.98702, 0.43688},
        {0.38127, 0.98909, 0.42386},
        {0.39678, 0.99098, 0.41098},
        {0.41229, 0.99268, 0.39826},
        {0.42778, 0.99419, 0.38575},
        {0.44321, 0.99551, 0.37345},
        {0.45854, 0.99663, 0.36140},
        {0.47375, 0.99755, 0.34963},
        {0.48879, 0.99828, 0.33816},
        {0.50362, 0.99879, 0.32701},
        {0.51822, 0.99910, 0.31622},
        {0.53255, 0.99919, 0.30581},
        {0.54658, 0.99907, 0.29581},
        {0.56026, 0.99873, 0.28623},
        {0.57357, 0.99817, 0.27712},
        {0.58646, 0.99739, 0.26849},
        {0.59891, 0.99638, 0.26038},
        {0.61088, 0.99514, 0.25280},
        {0.62233, 0.99366, 0.24579},
        {0.63323, 0.99195, 0.23937},
        {0.64362, 0.98999, 0.23356},
        {0.65394, 0.98775, 0.22835},
        {0.66428, 0.98524, 0.22370},
        {0.67462, 0.98246, 0.21960},
        {0.68494, 0.97941, 0.21602},
        {0.69525, 0.97610, 0.21294},
        {0.70553, 0.97255, 0.21032},
        {0.71577, 0.96875, 0.20815},
        {0.72596, 0.96470, 0.20640},
        {0.73610, 0.96043, 0.20504},
        {0.74617, 0.95593, 0.20406},
        {0.75617, 0.95121, 0.20343},
        {0.76608, 0.94627, 0.20311},
        {0.77591, 0.94113, 0.20310},
        {0.78563, 0.93579, 0.20336},
        {0.79524, 0.93025, 0.20386},
        {0.80473, 0.92452, 0.20459},
        {0.81410, 0.91861, 0.20552},
        {0.82333, 0.91253, 0.20663},
        {0.83241, 0.90627, 0.20788},
        {0.84133, 0.89986, 0.20926},
        {0.85010, 0.89328, 0.21074},
        {0.85868, 0.88655, 0.21230},
        {0.86709, 0.87968, 0.21391},
        {0.87530, 0.87267, 0.21555},
        {0.88331, 0.86553, 0.21719},
        {0.89112, 0.85826, 0.21880},
        {0.89870, 0.85087, 0.22038},
        {0.90605, 0.84337, 0.22188},
        {0.91317, 0.83576, 0.22328},
        {0.92004, 0.82806, 0.22456},
        {0.92666, 0.82025, 0.22570},
        {0.93301, 0.81236, 0.22667},
        {0.93909, 0.80439, 0.22744},
        {0.94489, 0.79634, 0.22800},
        {0.95039, 0.78823, 0.22831},
        {0.95560, 0.78005, 0.22836},
        {0.96049, 0.77181, 0.22811},
        {0.96507, 0.76352, 0.22754},
        {0.96931, 0.75519, 0.22663},
        {0.97323, 0.74682, 0.22536},
        {0.97679, 0.73842, 0.22369},
        {0.98000, 0.73000, 0.22161},
        {0.98289, 0.72140, 0.21918},
        {0.98549, 0.71250, 0.21650},
        {0.98781, 0.70330, 0.21358},
        {0.98986, 0.69382, 0.21043},
        {0.99163, 0.68408, 0.20706},
        {0.99314, 0.67408, 0.20348},
        {0.99438, 0.66386, 0.19971},
        {0.99535, 0.65341, 0.19577},
        {0.99607, 0.64277, 0.19165},
        {0.99654, 0.63193, 0.18738},
        {0.99675, 0.62093, 0.18297},
        {0.99672, 0.60977, 0.17842},
        {0.99644, 0.59846, 0.17376},
        {0.99593, 0.58703, 0.16899},
        {0.99517, 0.57549, 0.16412},
        {0.99419, 0.56386, 0.15918},
        {0.99297, 0.55214, 0.15417},
        {0.99153, 0.54036, 0.14910},
        {0.98987, 0.52854, 0.14398},
        {0.98799, 0.51667, 0.13883},
        {0.98590, 0.50479, 0.13367},
        {0.98360, 0.49291, 0.12849},
        {0.98108, 0.48104, 0.12332},
        {0.97837, 0.46920, 0.11817},
        {0.97545, 0.45740, 0.11305},
        {0.97234, 0.44565, 0.10797},
        {0.96904, 0.43399, 0.10294},
        {0.96555, 0.42241, 0.09798},
        {0.96187, 0.41093, 0.09310},
        {0.95801, 0.39958, 0.08831},
        {0.95398, 0.38836, 0.08362},
        {0.94977, 0.37729, 0.07905},
        {0.94538, 0.36638, 0.07461},
        {0.94084, 0.35566, 0.07031},
        {0.93612, 0.34513, 0.06616},
        {0.93125, 0.33482, 0.06218},
        {0.92623, 0.32473, 0.05837},
        {0.92105, 0.31489, 0.05475},
        {0.91572, 0.30530, 0.05134},
        {0.91024, 0.29599, 0.04814},
        {0.90463, 0.28696, 0.04516},
        {0.89888, 0.27824, 0.04243},
        {0.89298, 0.26981, 0.03993},
        {0.88691, 0.26152, 0.03753},
        {0.88066, 0.25334, 0.03521},
        {0.87422, 0.24526, 0.03297},
        {0.86760, 0.23730, 0.03082},
        {0.86079, 0.22945, 0.02875},
        {0.85380, 0.22170, 0.02677},
        {0.84662, 0.21407, 0.02487},
        {0.83926, 0.20654, 0.02305},
        {0.83172, 0.19912, 0.02131},
        {0.82399, 0.19182, 0.01966},
        {0.81608, 0.18462, 0.01809},
        {0.80799, 0.17753, 0.01660},
        {0.79971, 0.17055, 0.01520},
        {0.79125, 0.16368, 0.01387},
        {0.78260, 0.15693, 0.01264},
        {0.77377, 0.15028, 0.01148},
        {0.76476, 0.14374, 0.01041},
        {0.75556, 0.13731, 0.00942},
        {0.74617, 0.13098, 0.00851},
        {0.73661, 0.12477, 0.00769},
        {0.72686, 0.11867, 0.00695},
        {0.71692, 0.11268, 0.00629},
        {0.70680, 0.10680, 0.00571},
        {0.69650, 0.10102, 0.00522},
        {0.68602, 0.09536, 0.00481},
        {0.67535, 0.08980, 0.00449},
        {0.66449, 0.08436, 0.00424},
        {0.65345, 0.07902, 0.00408},
        {0.64223, 0.07380, 0.00401},
        {0.63082, 0.06868, 0.00401},
        {0.61923, 0.06367, 0.00410},
        {0.60746, 0.05878, 0.00427},
        {0.59550, 0.05399, 0.00453},
        {0.58336, 0.04931, 0.00486},
        {0.57103, 0.04474, 0.00529},
        {0.55852, 0.04028, 0.00579},
        {0.54583, 0.03593, 0.00638},
        {0.53295, 0.03169, 0.00705},
        {0.51989, 0.02756, 0.00780},
        {0.50664, 0.02354, 0.00863},
        {0.49321, 0.01963, 0.00955},
        {0.47960, 0.01583, 0.01055}
    }; 
 
  public:
    xvector<double> scene_center; 
    double join_threshold = 1E-5; 
    double tachyon_camera_theta = 0.0; 
    double tachyon_camera_phi = 0.0; 
    int tachyon_lattice_views_idx = -1; 
    bool tachyon_camera_orthographic = false;
    //@brief available animation formats
    enum class animation_format { GIF, WEBM, MP4 };
    animation_format ani_type = animation_format::GIF; 
    std::vector<std::pair<std::string, std::string>> meta; 
    x3DWriter();
    x3DWriter(const x3DWriter& x3w);
    ~x3DWriter();
    x3DWriter& operator=(const x3DWriter& x3w);
    void clear();
 
    void prepareSceneLattice(const xmatrix<double>& lattice);
    void addMaterial(const std::string& name, const xvector<double>& color);
    void addMaterial(const Material& newMaterial);
    std::vector<std::string> addColorSpreadMaterial(uint count);
    template <class Container> std::map<std::string, std::string> addNamedColorSpreadMaterial(const Container& names);
 
    void addSphere(const xvector<double>& center, double radius, const std::string& material = "bm_black");
    void addSpheres(const std::vector<xvector<double>>& center, double radius, const std::string& material = "bm_black");
    void addOpenCylinder(const xvector<double>& base, const xvector<double>& apex, double radius, const std::string& material = "bm_grey");
    void addConvexFacets(const std::vector<xvector<double>>& vertexes, const std::vector<std::vector<uint>>& facets, const std::string& material = "bm_grey_glass", const xvector<double>& shift = {0, 0, 0});
    void addConvexFacets(const std::vector<xvector<double>>& vertexes, const std::vector<std::vector<uint>>& facets, const xvector<double>& shift);
    void addLatticeBox(const xmatrix<double>& lattice, double radius, const std::string& material = "bm_black", bool axis = false);
 
    void joinFacets(std::vector<xvector<double>>& vertexes, std::vector<std::vector<uint>>& facets, const std::vector<xvector<double>>& new_vertexes, const std::vector<std::vector<uint>>& new_facets) const;
 
    void animate(float duration, const std::filesystem::path& out_folder, uint fps = 30, bool lr = true);
 
    std::string toHTML();
    std::string toX3D(bool include_xml = true, bool replace_material = false);
    std::string toTachyon();
  };
} // namespace aurostd
// HE20220314 END X3DWriter
 
namespace aurostd {
  std::vector<std::string> extractJsonKeysAflow(const std::string& json);
  std::string extractJsonValueAflow(const std::string& json, std::string key);
  std::vector<std::string> extractJsonVectorAflow(const std::string& json, std::string key); // SD20220504
  std::vector<std::vector<std::string>> extractJsonMatrixAflow(const std::string& json, std::string key); // SD20220504
} // namespace aurostd
 
#endif // _AUROSTD_XPARSER_H_
 
// ***************************************************************************
// *                                                                         *
// *           Aflow STEFANO CURTAROLO - Duke University 2003-2024           *
// *                                                                         *
// ***************************************************************************