Merge pull request #2 from wcwitt/main

Make website release-ready

Author: wcwitt

.gitignore

@@ -2,3 +2,6 @@ build
 external/lbfgs/lbfgs_um
 pyrofess/__pycache__
 test/__pycache__
+website/source/user-guide/generated
+website/build
+.ipynb_checkpoints

CMakeLists.txt

@@ -65,10 +65,11 @@ target_include_directories(profess PUBLIC ${LIBXC_INCLUDE_DIR})
 target_link_directories(profess PUBLIC ${LIBXC_LIBRARY_DIR})
 target_link_libraries(profess PUBLIC xc)
 
-# pyrofess
-pybind11_add_module(pyrofess MODULE pyrofess/pyrofess.cpp)
-target_link_libraries(pyrofess PUBLIC profess)
+# profess-pybind
+pybind11_add_module(profess-pybind MODULE pyrofess/pyrofess.cpp)
+target_link_libraries(profess-pybind PUBLIC profess)
+set_target_properties(profess-pybind PROPERTIES OUTPUT_NAME profess)
 
-# pyrofess extras
+# profess-pybind extras
 pybind11_add_module(extras MODULE pyrofess/extras.cpp)
 target_link_libraries(extras PUBLIC profess)

external/ase

@@ -32,7 +32,7 @@ class Ions
     std::vector<std::function<double(double)>>
             ft_potential_derivatives();
 
-    Ions& add_ion_type_coulomb(double z);
+    Ions& add_ion_type_coulomb(double z, double cutoff=-1.0);
     Ions& add_ion_type_recpot(std::string filename);
     Ions& add_ion_type_harmonic_compactified(double w, double r1, double r2);
     Ions& add_ion_type_generic(

include/ions.hpp

@@ -13,15 +13,22 @@ namespace profess
 
 class System
 {
-public:
 
+public:
+    // public constructors (named constructor idiom)
+    static
+    System create(
+        std::array<std::array<double,3>,3> box_vectors,
+        double energy_cutoff,
+        std::array<std::string,2> units={"b","h"});
+    static
+    System create_from_grid_shape(
+        std::array<std::array<double,3>,3> box_vectors,
+        std::array<size_t,3> grid_shape,
+        std::string unit={"b"});
+private:
     System(std::array<size_t,3> grid_shape);
-
-    static std::array<size_t,3> get_shape(
-            std::array<std::array<double,3>,3> box_vectors,
-            double energy_cutoff,
-            std::array<std::string,2> units={"b","h"});
-
+public:
     // rule of five
     // copy construction/assignment disabled b/c class has unique ptrs
     ~System() = default;
@@ -47,7 +54,8 @@ class System
     System& add_coulomb_ions(
         double z,
         std::vector<std::array<double,3>> coords,
-        std::string unit={"b"});
+        std::string unit={"b"},
+        double cutoff=-1.0);
     System& add_harmonic_ions();
 
     std::vector<std::array<double,3>> ions_xyz_coords(std::string unit);
@@ -57,29 +65,31 @@ class System
     System& add_ion_electron_functional();
     System& add_luo_karasiev_trickey_functional(double a=1.3,
                                                 double tiny_den=1e-12);
-    System& add_libxc_functional(std::vector<int>);
-    System& add_kinetic_class_a_functional(
+    System& add_libxc_functional(std::vector<int> xc_func_ids);
+    System& add_generic_nonlocal_a_functional(
         double a,
         double b,
         std::function<double(double)> f,
         std::function<double(double)> fp,
-        double den0);
+        double den0=-1);
     System& add_perdew_burke_ernzerhof_functional();
     System& add_perdew_zunger_functional();
-    System& add_perrot_functional(double den0);
-    System& add_smargiassi_madden_functional(double den0);
+    System& add_perrot_functional(double den0=-1.0);
+    System& add_smargiassi_madden_functional(double den0=-1.0);
     System& add_thomas_fermi_functional();
     System& add_wang_govind_carter_functional(
-        double den0,
+        double den0=-1.0,
         double alpha=(5.0+std::sqrt(5.0))/6.0,
         double beta=(5.0-std::sqrt(5.0))/6.0,
         double gamma=2.7);
-    System& add_wang_govind_carter_1999_i_functional(double den0);
-    System& add_wang_teter_functional(double den0);
+    System& add_wang_govind_carter_1999_i_functional(double den0=-1.0);
+    System& add_wang_teter_functional(double den0=-1.0);
     System& add_weizsaecker_functional();
 
     System& remove_functional(std::string name);
 
+    System& add_ion_ion_interaction();
+
     // basic information about the system
     double energy(std::string unit={"h"});
     std::tuple<double, Double3D> energy_potential(bool compute_ion_ion=true);
@@ -89,9 +99,10 @@ class System
     double pressure(std::string unit={"h/b3"});
     double enthalpy(std::string unit={"h"});
     double energy_cutoff(std::string unit={"h"});
+    double total_ion_charge();
 
     // basic manipulations
-    System& distribute_electrons_uniformly(const double electrons);
+    System& add_electrons(double electrons=-1.0);
     System& move_ions(
             std::vector<std::array<double,3>> xyz_coords,
             std::string length_unit={"b"});
@@ -110,6 +121,10 @@ class System
         double energy_tol=1e-5,
         size_t window_size=3,
         size_t max_iter=100);
+
+private:
+
+    bool _ion_ion_interaction = false;
 };
 
 }

include/system.hpp

@@ -27,8 +27,8 @@ def init_optimizer(atoms, algorithm):
     return optimizer
 
 def minimize_forces(system, algorithm, fmax=1e-4, steps=100):
-    atoms = Atoms('H' + str(system.ions.count()),
-            positions=system.ions.xyz_coords(),
+    atoms = Atoms('H' + str(len(system.ions_xyz_coords())),
+            positions=system.ions_xyz_coords(),
             cell=system.box_vectors(),
             pbc=True)
     atoms.calc = Profess(system)
@@ -44,8 +44,8 @@ def minimize_stress(
         hydrostatic_strain=False,
         constant_volume=False,
         scalar_pressure=0.0):
-    atoms = Atoms('H' + str(system.ions.count()),
-            positions=system.ions.xyz_coords(),
+    atoms = Atoms('H' + str(len(system.ions_xyz_coords())),
+            positions=system.ions_xyz_coords(),
             cell=system.box_vectors(),
             pbc=True)
     atoms.calc = Profess(system)
@@ -67,7 +67,7 @@ def minimize_forces_stress(
         hydrostatic_strain=False,
         constant_volume=False,
         scalar_pressure=0.0):
-    atoms = Atoms('H' + str(system.ions.count()),
+    atoms = Atoms('H' + str(len(system.ions_xyz_coords())),
             positions=system.ions_xyz_coords(),
             cell=system.box_vectors(),
             pbc=True)
@@ -102,4 +102,4 @@ def optimize_geometry(init_system, box_vectors, xyz_coords, energy_cutoff):
             return system
         else:
             box_vectors = np.array(system.box.vectors()).T
-            xyz_coords = np.array(system.ions.xyz_coords())
+            xyz_coords = np.array(system.ions_xyz_coords())