clease - npm Package Compare versions

Comparing version 1.0.5 to 1.0.6

clease.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: clease
-Version: 1.0.5
+Version: 1.0.6
 Summary: CLuster Expansion in Atomistic Simulation Environment
@@ -5,0 +5,0 @@ Home-page: https://gitlab.com/computationalmaterials/clease/

clease.egg-info/requires.txt

@@ -16,21 +16,21 @@ ase>=3.22
 [all]
-pytest-mock
+clang-format>=14.0.3
+ipython
+sphinx_rtd_theme
+cython
+black>=22.1.0
 pre-commit
 pytest
-pytest-cov
-twine
+pytest-mock
+mock
+pyclean>=2.0.0
+pytest-benchmark[histogram]>=3.4.1
 tox>=4
+build
+pip
 sphinx
-pyclean>=2.0.0
-black>=22.1.0
-build
-clang-format>=14.0.3
-sphinx_rtd_theme
-pytest-benchmark[histogram]>=3.4.1
-ipython
+clease-gui
 pylint
-mock
-cython
-clease-gui
-pip
+twine
+pytest-cov
 
@@ -37,0 +37,0 @@ [dev]

clease/_version.txt

@@ -1,1 +0,1 @@
-1.0.5
+1.0.6

clease/montecarlo/montecarlo.py

@@ -81,2 +81,5 @@ """Monte Carlo method for ase."""
         self.current_energy = self.evaluator.get_energy()
+        self.current_energy += sum(
+            bias.calculate_from_scratch(self.atoms) for bias in self.bias_potentials
+        )
         logger.debug("Updating current energy to %s", self.current_energy)
@@ -83,0 +86,0 @@ self.evaluator.reset()

clease/regression/regression.py

@@ -6,2 +6,3 @@ """Collection of classess to perform regression."""
 from sklearn.linear_model import Lasso as skLasso
+from scipy.linalg import lstsq
 from clease.data_normalizer import DataNormalizer
@@ -45,12 +46,4 @@
         self._ensure_weight_matrix_consistency(y)
+        return lstsq(X, y)[0]  # Only fetch the solution
 
-        # We use SVD to carry out the fit
-        U, D, V_h = np.linalg.svd(X, full_matrices=False)
-        V = V_h.T
-        diag_item = np.zeros_like(D)
-        mask = np.abs(D) > self.tol
-        diag_item[mask] = 1.0 / D[mask]
-        coeff = V.dot(np.diag(diag_item)).dot(U.T).dot(y)
-        return coeff
-
     def precision_matrix(self, X: np.ndarray) -> np.ndarray:
@@ -57,0 +50,0 @@ D, V_h = np.linalg.svd(X, full_matrices=False)[1:]  # U is unused

cxx/include/basis_function.hpp

@@ -38,3 +38,2 @@ #ifndef BASIS_FUNCTION_H
    private:
-    const Symbols *symb_ptr{nullptr};
     std::vector<double> bfs;
@@ -41,0 +40,0 @@ unsigned int num_bfs{0};

cxx/include/ce_updater.hpp

@@ -7,2 +7,3 @@ #ifndef CE_UPDATER_H
 #include <map>
+#include <memory>
 #include <set>
@@ -24,14 +25,5 @@ #include <string>
 
-// Read values from name_list
-// name_list[symm_group][cluster_size] = vector of string variables of all the cluster names
-typedef std::vector<std::vector<std::vector<std::string>>> name_list;
-
-// Read values form cluster_list
-// cluster_list[symm_group][cluster_size][indx] = vector of indices belonging to the cluster #indx.
-typedef std::vector<std::vector<std::vector<std::vector<std::vector<int>>>>> cluster_list;
 typedef std::vector<std::map<std::string, double>> bf_list;
 typedef std::array<SymbolChange, 2> swap_move;
-typedef std::unordered_map<std::string, Cluster> cluster_dict;
 
-// typedef std::unordered_map<std::string,double> cf;
 typedef NamedArray cf;
@@ -75,5 +67,2 @@
 
-    /** New copy. NOTE: the pointer has to be deleted */
-    CEUpdater *copy() const;
-
     /** Initialize the object (cluster_info should contain duplication factors) */
@@ -198,5 +187,4 @@ void init(PyObject *py_atoms, PyObject *settings, PyObject *corrFunc, PyObject *eci,
 
-    // std::vector<std::string> symbols;
-    Symbols *symbols_with_id{nullptr};
-    // std::vector<cluster_dict> clusters;
+    std::unique_ptr<Symbols> symbols_with_id{nullptr};
+
     ClusterList clusters;
@@ -207,8 +195,7 @@ std::vector<int> trans_symm_group;
 
-    // bf_list basis_functions;
-    BasisFunction *basis_functions{nullptr};
+    std::unique_ptr<BasisFunction> basis_functions{nullptr};
 
     Status_t status{Status_t::NOT_INITIALIZED};
-    // Matrix<int> trans_matrix;
     RowSparseStructMatrix trans_matrix;
+
     std::map<std::string, int> ctype_lookup;
@@ -220,3 +207,3 @@ NamedArray eci;
     bool assume_no_self_interactions{false};
-    CFHistoryTracker *history{nullptr};
+    std::unique_ptr<CFHistoryTracker> history{nullptr};
     PyObject *atoms{nullptr};
@@ -223,0 +210,0 @@ std::vector<std::string> singlets;

cxx/include/symbols_with_numbers.hpp

@@ -8,2 +8,3 @@ #ifndef SYMBOLS_H
 
+typedef unsigned short int symb_id_t;
 typedef std::vector<std::string> vec_str_t;
@@ -19,3 +20,3 @@ typedef std::set<std::string> set_str_t;
     /** Return the symbol ID of the atom at site indx */
-    inline unsigned int id(unsigned int indx) const {
+    inline symb_id_t id(unsigned int indx) const {
         return symb_ids[indx];
@@ -59,4 +60,3 @@ };
    private:
-    // unsigned int *symb_ids{nullptr};
-    std::vector<unsigned int> symb_ids;
+    std::vector<symb_id_t> symb_ids;
     vec_str_t symbols;
@@ -63,0 +63,0 @@ dict_uint_t symb_id_translation;

cxx/src/basis_function.cpp

@@ -11,7 +11,7 @@ #include "basis_function.hpp"
 
-BasisFunction::BasisFunction(const bf_raw_t &raw_bf_data, const Symbols &symb_with_num)
-    : symb_ptr(&symb_with_num) {
-    // We do not store the raw_bf_data, so we need to extract as much as we need now.
+BasisFunction::BasisFunction(const bf_raw_t &raw_bf_data, const Symbols &symb_with_num) {
+    /* We do not store the raw_bf_data, so we need to extract as much as we need now.
+    Same with the symbols array */
     num_bfs = raw_bf_data.size();
-    num_bf_values = symb_ptr->num_unique_symbols();
+    num_bf_values = symb_with_num.num_unique_symbols();
 
@@ -24,3 +24,3 @@ this->bfs.clear();
         for (auto iter = raw_bf_data[dec_num].begin(); iter != raw_bf_data[dec_num].end(); ++iter) {
-            unsigned int indx = get_index(dec_num, symb_ptr->get_symbol_id(iter->first));
+            unsigned int indx = get_index(dec_num, symb_with_num.get_symbol_id(iter->first));
             /* Assign with bounds check, since this isn't performance critical,
@@ -45,3 +45,2 @@ as this construction is only done during initialization. */
 void BasisFunction::swap(const BasisFunction &other) {
-    this->symb_ptr = other.symb_ptr;
     this->num_bfs = other.num_bfs;
@@ -48,0 +47,0 @@ this->num_bf_values = other.num_bf_values;

cxx/src/with_numpy/ce_updater.cpp

@@ -19,11 +19,4 @@ #include "ce_updater.hpp"
 CEUpdater::CEUpdater(){};
-CEUpdater::~CEUpdater() {
-    delete history;
+CEUpdater::~CEUpdater(){};
 
-    delete symbols_with_id;
-    delete basis_functions;
-    symbols_with_id = nullptr;
-    basis_functions = nullptr;
-}
-
 void CEUpdater::init(PyObject *py_atoms, PyObject *settings, PyObject *corrFunc, PyObject *pyeci,
@@ -62,3 +55,3 @@ PyObject *cluster_list) {
     insert_in_set(symbols, unique_symbols);
-    symbols_with_id = new Symbols(symbols, unique_symbols);
+    symbols_with_id = std::make_unique<Symbols>(symbols, unique_symbols);
 
@@ -169,3 +162,3 @@ // Build read the translational sites
 
-    this->basis_functions = new BasisFunction(basis_func_raw, *symbols_with_id);
+    this->basis_functions = std::make_unique<BasisFunction>(basis_func_raw, *symbols_with_id);
 
@@ -197,3 +190,4 @@ #ifdef PRINT_DEBUG
     flattened_cf_names(flattened_cnames);
-    history = new CFHistoryTracker(eci.get_names());
+
+    history = std::make_unique<CFHistoryTracker>(eci.get_names());
     history->insert(corrFunc, nullptr);
@@ -613,22 +607,2 @@
 
-CEUpdater *CEUpdater::copy() const {
-    CEUpdater *obj = new CEUpdater();
-    obj->symbols_with_id = new Symbols(*symbols_with_id);
-    obj->clusters = clusters;
-    obj->trans_symm_group = trans_symm_group;
-    obj->trans_symm_group_count = trans_symm_group_count;
-    obj->normalisation_factor = normalisation_factor;
-    obj->basis_functions = new BasisFunction(*basis_functions);
-    obj->status = status;
-    obj->trans_matrix = trans_matrix;
-    obj->ctype_lookup = ctype_lookup;
-    obj->eci = eci;
-    obj->cname_with_dec = cname_with_dec;
-    obj->is_background_index = is_background_index;
-    obj->num_non_bkg_sites = num_non_bkg_sites;
-    obj->history = new CFHistoryTracker(*history);
-    obj->atoms = nullptr;  // Left as nullptr by intention
-    return obj;
-}
-
 void CEUpdater::set_symbols(const vector<string> &new_symbs) {
@@ -635,0 +609,0 @@ if (new_symbs.size() != symbols_with_id->size()) {

doc/source/releasenotes.rst

@@ -7,2 +7,8 @@ .. _releasenotes:
 
+1.0.6
+======
+* Now requires the ``c++14`` compiler flag.
+* Fixed updating current energy for metadynamics.
+  See `!590 <https://gitlab.com/computationalmaterials/clease/-/merge_requests/590>`_.
+
 1.0.5
@@ -9,0 +15,0 @@ ======

PKG-INFO

 Metadata-Version: 2.1
 Name: clease
-Version: 1.0.5
+Version: 1.0.6
 Summary: CLuster Expansion in Atomistic Simulation Environment
@@ -5,0 +5,0 @@ Home-page: https://gitlab.com/computationalmaterials/clease/

setup.py

@@ -66,3 +66,3 @@ import os
 src_files = get_source_files()
-extra_comp_args = ["-std=c++11"]
+extra_comp_args = ["-std=c++14"]
 extra_link_args = []
@@ -69,0 +69,0 @@ define_macros = []

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Worsened metrics

Total package byte prevSize

1622418

-0.09%

Lines of code

17005

-0.02%