move initializers for structs from header file to implementation, add constructors
This commit is contained in:
Axel Kohlmeyer
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@ -11,7 +11,6 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef COMMAND_CLASS
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// clang-format off
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CommandStyle(fitpod,FitPOD);
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@ -33,14 +32,17 @@ public:
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private:
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struct datastruct {
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std::string file_format = "extxyz";
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std::string file_extension = "xyz";
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datastruct();
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void copydatainfo(datastruct &data) const;
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std::string file_format;
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std::string file_extension;
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std::string data_path;
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std::vector<std::string> data_files; // sorted file names
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std::vector<std::string> group_names; // sorted group names
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std::vector<std::string> filenames;
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std::string filenametag = "pod";
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std::string group_weight_type = "global";
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std::string filenametag;
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std::string group_weight_type;
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std::vector<int> num_atom;
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std::vector<int> num_atom_cumsum;
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@ -52,86 +54,65 @@ private:
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int num_atom_max;
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int num_config_sum;
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double *lattice=nullptr;
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double *energy=nullptr;
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double *stress=nullptr;
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double *position=nullptr;
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double *force=nullptr;
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int *atomtype=nullptr;
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double *lattice;
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double *energy;
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double *stress;
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double *position;
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double *force;
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int *atomtype;
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// Group weights will have same size as energy.
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double *we=nullptr;
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double *wf=nullptr;
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double *we;
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double *wf;
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int training = 1;
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int normalizeenergy = 1;
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int training_analysis = 1;
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int test_analysis = 1;
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int training_calculation = 0;
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int test_calculation = 0;
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int randomize = 1;
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int precision = 8;
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double fraction = 1.0;
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int training;
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int normalizeenergy;
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int training_analysis;
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int test_analysis;
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int training_calculation;
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int test_calculation;
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int randomize;
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int precision;
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double fraction;
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std::unordered_map<std::string, double> we_map;
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std::unordered_map<std::string, double> wf_map;
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double fitting_weights[12] = {100.0, 1.0, 0.0, 1, 1, 0, 0, 1, 1, 1, 1, 1e-10};
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void copydatainfo(datastruct &data) const
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{
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data.data_path = data_path;
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data.file_format = file_format;
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data.file_extension = file_extension;
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data.data_files = data_files;
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data.filenametag = filenametag;
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data.filenames = filenames;
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data.training_analysis = training_analysis;
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data.test_analysis = test_analysis;
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data.training_calculation = training_calculation;
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data.test_calculation = test_calculation;
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data.fraction = fraction;
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data.randomize = randomize;
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data.precision = precision;
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data.training = training;
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data.normalizeenergy = normalizeenergy;
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for (int i = 0; i < 12; i++)
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data.fitting_weights[i] = fitting_weights[i];
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data.we_map = we_map;
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data.wf_map = wf_map;
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}
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double fitting_weights[12];
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};
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struct neighborstruct {
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int *alist=nullptr;
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int *pairnum=nullptr;
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int *pairnum_cumsum=nullptr;
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int *pairlist=nullptr;
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double *y=nullptr;
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neighborstruct();
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//int natom;
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//int nalist;
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int natom_max = 0;
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int sze = 0;
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int sza = 0;
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int szy = 0;
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int szp = 0;
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int *alist;
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int *pairnum;
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int *pairnum_cumsum;
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int *pairlist;
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double *y;
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int natom_max;
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int sze;
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int sza;
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int szy;
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int szp;
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};
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struct descriptorstruct {
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double *bd=nullptr; // base descriptors
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double *pd=nullptr; // multi-environment descriptors (probabilities)
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double *gd=nullptr; // global descriptors
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double *gdd=nullptr; // derivatives of global descriptors and peratom descriptors
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double *A=nullptr; // least-square matrix for all descriptors
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double *b=nullptr; // least-square vector for all descriptors
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double *c=nullptr; // coefficents of descriptors
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int szd = 0;
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int nCoeffAll = 0; // number of global descriptors
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int nClusters = 0; // number of environment clusters
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descriptorstruct();
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double *bd; // base descriptors
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double *pd; // multi-environment descriptors (probabilities)
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double *gd; // global descriptors
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double *gdd; // derivatives of global descriptors and peratom descriptors
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double *A; // least-square matrix for all descriptors
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double *b; // least-square vector for all descriptors
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double *c; // coefficents of descriptors
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int szd;
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int nCoeffAll; // number of global descriptors
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int nClusters; // number of environment clusters
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};
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int save_descriptors = 0;
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int compute_descriptors = 0;
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int save_descriptors;
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int compute_descriptors;
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datastruct traindata;
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datastruct testdata;
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datastruct envdata;
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@ -159,9 +140,12 @@ private:
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void matrix33_inverse(double *invA, double *A1, double *A2, double *A3);
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double squareDistance(const double *a, const double *b, int DIMENSIONS);
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void assignPointsToClusters(double *points, double *centroids, int *assignments, int *clusterSizes, int NUM_POINTS, int NUM_CLUSTERS, int DIMENSION);
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void updateCentroids(double *points, double *centroids, int *assignments, int *clusterSizes, int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS);
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void KmeansClustering(double *points, double *centroids, int *assignments, int *clusterSizes, int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS, int MAX_ITER);
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void assignPointsToClusters(double *points, double *centroids, int *assignments,
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int *clusterSizes, int NUM_POINTS, int NUM_CLUSTERS, int DIMENSION);
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void updateCentroids(double *points, double *centroids, int *assignments, int *clusterSizes,
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int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS);
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void KmeansClustering(double *points, double *centroids, int *assignments, int *clusterSizes,
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int NUM_POINTS, int NUM_CLUSTERS, int DIMENSIONS, int MAX_ITER);
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void savedata2textfile(std::string filename, std::string text, double *A, int n, int m, int dim);
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void savematrix2binfile(std::string filename, double *A, int nrows, int ncols);
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@ -169,14 +153,20 @@ private:
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// functions for reading input files and fitting
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int read_data_file(double *fitting_weights, std::string &file_format, std::string &file_extension, std::string &env_path,
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std::string &test_path, std::string &training_path, std::string &filenametag, const std::string &data_file, std::string &group_weight_type,
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std::unordered_map<std::string, double> &we_map, std::unordered_map<std::string, double> &wf_map);
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void get_exyz_files(std::vector<std::string> &, std::vector<std::string> &, const std::string &, const std::string &);
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int read_data_file(double *fitting_weights, std::string &file_format, std::string &file_extension,
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std::string &env_path, std::string &test_path, std::string &training_path,
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std::string &filenametag, const std::string &data_file,
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std::string &group_weight_type,
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std::unordered_map<std::string, double> &we_map,
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std::unordered_map<std::string, double> &wf_map);
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void get_exyz_files(std::vector<std::string> &, std::vector<std::string> &, const std::string &,
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const std::string &);
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int get_number_atom_exyz(std::vector<int> &num_atom, int &num_atom_sum, std::string file);
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int get_number_atoms(std::vector<int>& num_atom, std::vector<int> &num_atom_sum, std::vector<int>& num_config, std::vector<std::string> training_files);
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void read_exyz_file(double *lattice, double *stress, double *energy, double *we, double *wf, double *pos, double *forces,
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int *atomtype, std::string file, std::vector<std::string> species, double we_group, double wf_group);
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int get_number_atoms(std::vector<int> &num_atom, std::vector<int> &num_atom_sum,
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std::vector<int> &num_config, std::vector<std::string> training_files);
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void read_exyz_file(double *lattice, double *stress, double *energy, double *we, double *wf,
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double *pos, double *forces, int *atomtype, std::string file,
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std::vector<std::string> species, double we_group, double wf_group);
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void get_data(datastruct &data, const std::vector<std::string> &species);
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std::vector<int> linspace(int start_in, int end_in, int num_in);
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std::vector<int> shuffle(int start_in, int end_in, int num_in);
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@ -188,7 +178,8 @@ private:
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int podneighborlist(int *neighlist, int *numneigh, double *r, double rcutsq, int nx, int N,
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int dim);
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int podfullneighborlist(double *y, int *alist, int *neighlist, int *numneigh, int *numneighsum,
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double *x, double *a1, double *a2, double *a3, double rcut, int *pbc, int nx);
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double *x, double *a1, double *a2, double *a3, double rcut, int *pbc,
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int nx);
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void estimate_memory_neighborstruct(const datastruct &data, int *pbc, double rcut, int nelements);
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void allocate_memory_neighborstruct();
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void allocate_memory_descriptorstruct(int nd);
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@ -204,8 +195,6 @@ private:
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double energyforce_calculation_fastpod(double *force, const datastruct &data, int ci);
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void energyforce_calculation(const datastruct &data);
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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