Merge branch 'rename_ions_to_ionic' into 'master'

Rename the ions:: namespace to ionic::

See merge request npneq/inq!1097

src/basis/spherical_grid.hpp

@@ -22,7 +22,7 @@
 #include <gpu/atomic.hpp>
 #include <gpu/run.hpp>
 #include <gpu/reduce.hpp>
-#include <ions/periodic_replicas.hpp>
+#include <ionic/periodic_replicas.hpp>
 #include <basis/containing_cube.hpp>
 #include <basis/real_space.hpp>
 #include <cassert>
@@ -59,7 +59,7 @@ namespace basis {
 		void initialize(const basis & parent_grid, const vector3<double> & center_point, const double radius){
 			CALI_CXX_MARK_SCOPE("spherical_grid::initialize");
 
-			ions::periodic_replicas const rep(parent_grid.cell(), center_point, parent_grid.diagonal_length());
+			ionic::periodic_replicas const rep(parent_grid.cell(), center_point, parent_grid.diagonal_length());
 
 			vector3<int> local_sizes = parent_grid.local_sizes();
 

src/bomd/propagate.hpp

@@ -9,7 +9,7 @@
 // file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
 #include <ground_state/calculate.hpp>
-#include <ions/propagator.hpp>
+#include <ionic/propagator.hpp>
 #include <options/real_time.hpp>
 #include <real_time/viewables.hpp>
 #include <systems/electrons.hpp>
@@ -21,7 +21,7 @@
 namespace inq {
 namespace bomd {
 
-template <typename ProcessFunction, typename IonSubPropagator = ions::propagator::molecular_dynamics>
+template <typename ProcessFunction, typename IonSubPropagator = ionic::propagator::molecular_dynamics>
 void propagate(systems::ions & ions, systems::electrons & electrons,  ProcessFunction func, const options::theory & inter, const options::real_time & opts, IonSubPropagator const& ion_propagator = {}){
 		CALI_CXX_MARK_FUNCTION;
 

src/ground_state/calculator.hpp

@@ -31,7 +31,6 @@
 #include <mixers/broyden.hpp>
 #include <eigensolvers/steepest_descent.hpp>
 #include <math/complex.hpp>
-#include <ions/interaction.hpp>
 #include <observables/dipole.hpp>
 #include <observables/magnetization.hpp>
 #include <options/ground_state.hpp>
@@ -136,7 +135,7 @@ class calculator {
 		sc_.update_ionic_fields(electrons.states_comm(), ions_, electrons.atomic_pot());
 		sc_.update_hamiltonian(ham_, res.energy, electrons.spin_density());
 
-		res.energy.ion(inq::ions::interaction_energy(ions_.cell(), ions_, electrons.atomic_pot()));
+		res.energy.ion(ionic::interaction_energy(ions_.cell(), ions_, electrons.atomic_pot()));
 
 		double old_exe = ham_.exchange().update(electrons);
 		double exe_diff = fabs(old_exe);

src/hamiltonian/exchange_operator.hpp

@@ -42,7 +42,7 @@ namespace hamiltonian {
 
   public:
 
-		exchange_operator(systems::cell const & cell, ions::brillouin const & bzone, double const exchange_coefficient, bool const use_ace):
+		exchange_operator(systems::cell const & cell, ionic::brillouin const & bzone, double const exchange_coefficient, bool const use_ace):
 			exchange_coefficient_(exchange_coefficient),
 			use_ace_(use_ace),
 			sing_(cell, bzone){

src/hamiltonian/forces.hpp

@@ -59,7 +59,7 @@ gpu::array<vector3<double>, 1> calculate_forces(const systems::ions & ions, syst
 		electrons.full_comm().all_reduce_n(raw_pointer_cast(forces_non_local.data_elements()), forces_non_local.size(), std::plus<>{});
 	}
 
-	auto ionic_forces = inq::ions::interaction_forces(ions.cell(), ions, electrons.atomic_pot());
+	auto ionic_forces = ionic::interaction_forces(ions.cell(), ions, electrons.atomic_pot());
 
 	gpu::array<vector3<double>, 1> forces_local(ions.size(), {0.0, 0.0, 0.0});
 

src/hamiltonian/ks_hamiltonian.hpp

@@ -76,7 +76,7 @@ class ks_hamiltonian {
 
 	////////////////////////////////////////////////////////////////////////////////////////////
 
-	ks_hamiltonian(const basis::real_space & basis, ions::brillouin const & bzone, states::ks_states const & states, atomic_potential const & pot, systems::ions const & ions,
+	ks_hamiltonian(const basis::real_space & basis, ionic::brillouin const & bzone, states::ks_states const & states, atomic_potential const & pot, systems::ions const & ions,
 								 const double exchange_coefficient, bool use_ace = false):
 		exchange_(basis.cell(), bzone, exchange_coefficient, use_ace),
 		scalar_potential_(basis, states.num_density_components()),
@@ -269,7 +269,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG){
 
   states::orbital_set<basis::real_space, complex> phi(rs, st.num_states(), 1, vector3<double, covariant>{0.0, 0.0, 0.0}, 0, cart_comm);
 
-	auto bzone = ions::brillouin(ions, input::kpoints::gamma());
+	auto bzone = ionic::brillouin(ions, input::kpoints::gamma());
 
 	hamiltonian::ks_hamiltonian<double> ham(rs, bzone, st, pot, ions, 0.0);
 

src/hamiltonian/projector.hpp

@@ -13,7 +13,6 @@
 
 #include <gpu/array.hpp>
 #include <math/vector3.hpp>
-#include <ions/periodic_replicas.hpp>
 #include <basis/double_grid.hpp>
 #include <basis/real_space.hpp>
 #include <basis/spherical_grid.hpp>

src/hamiltonian/projector_all.hpp

@@ -11,7 +11,6 @@
 
 #include <gpu/array.hpp>
 #include <math/vector3.hpp>
-#include <ions/periodic_replicas.hpp>
 #include <basis/real_space.hpp>
 #include <basis/spherical_grid.hpp>
 #include <hamiltonian/atomic_potential.hpp>

src/hamiltonian/projector_fourier.hpp

@@ -16,7 +16,6 @@
 
 #include <gpu/array.hpp>
 #include <math/vector3.hpp>
-#include <ions/periodic_replicas.hpp>
 #include <basis/real_space.hpp>
 #include <basis/spherical_grid.hpp>
 #include <operations/transform.hpp>

src/hamiltonian/singularity_correction.hpp

@@ -9,7 +9,7 @@
 // License, v. 2.0. If a copy of the MPL was not distributed with this
 // file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
-#include <ions/brillouin.hpp>
+#include <ionic/brillouin.hpp>
 
 namespace inq {
 namespace hamiltonian {
@@ -44,7 +44,7 @@ class singularity_correction {
     return 4*M_PI*M_PI/val;
   }
 
-  singularity_correction(systems::cell const & cell, ions::brillouin const & bzone):
+  singularity_correction(systems::cell const & cell, ionic::brillouin const & bzone):
     fk_(bzone.size()),
     nkpoints_(bzone.size()),
     cell_volume_(cell.volume())
@@ -127,7 +127,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG){
 		auto ions = systems::ions(systems::cell::lattice({aa, 0.0_b, 0.0_b}, {0.0_b, aa, 0.0_b}, {0.0_b, 0.0_b, aa}));
     auto const & cell = ions.cell();
 
-    auto bzone = ions::brillouin(ions, input::kpoints::grid({2, 2, 2}));
+    auto bzone = ionic::brillouin(ions, input::kpoints::grid({2, 2, 2}));
 
     CHECK(hamiltonian::singularity_correction::auxiliary(cell, 2.0*M_PI*vector3<double, covariant>{0.0, -0.5, 0.0}) == 25.9081_a);
     CHECK(hamiltonian::singularity_correction::auxiliary(cell, 2.0*M_PI*vector3<double, covariant>{8.3333333333333332E-003, 7.4999999999999997E-002, 0.26666666666666666}) == 42.650855183181122_a);

src/interface/kpoints.hpp

@@ -10,7 +10,7 @@
 // file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
 #include <input/environment.hpp>
-#include <ions/brillouin.hpp>
+#include <ionic/brillouin.hpp>
 
 namespace inq {
 namespace interface {
@@ -102,7 +102,7 @@ These are the options available:
 	}
 
   static void status() {
-		auto bz = ions::brillouin::load(".inq/default_brillouin");
+		auto bz = ionic::brillouin::load(".inq/default_brillouin");
 		if(input::environment::global().comm().root()) std::cout << bz;
 	}
 
@@ -111,30 +111,30 @@ These are the options available:
 	}
 
   static void gamma() {
-		auto bz = ions::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
+		auto bz = ionic::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
 		bz.save(input::environment::global().comm(), ".inq/default_brillouin");
 	}
 
   static void grid(int nx, int ny, int nz) {
-		auto bz = ions::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::grid({nx, ny, nz}));
+		auto bz = ionic::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::grid({nx, ny, nz}));
 		bz.save(input::environment::global().comm(), ".inq/default_brillouin");
 	}
 
   static void shifted_grid(int nx, int ny, int nz) {
-		auto bz = ions::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::grid({nx, ny, nz}, true));
+		auto bz = ionic::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::grid({nx, ny, nz}, true));
 		bz.save(input::environment::global().comm(), ".inq/default_brillouin");
 	}
 
   static void insert(double const & kx, double const & ky, double const & kz, double const & weight) {
-    auto bz = ions::brillouin{};
-    try { bz = ions::brillouin::load(".inq/default_brillouin"); }
+    auto bz = ionic::brillouin{};
+    try { bz = ionic::brillouin::load(".inq/default_brillouin"); }
     catch(...){  }
     bz.insert({kx, ky, kz}, weight);
 		bz.save(input::environment::global().comm(), ".inq/default_brillouin");
   }
 
   static void clear() {
-    auto bz = ions::brillouin{};
+    auto bz = ionic::brillouin{};
     bz.save(input::environment::global().comm(), ".inq/default_brillouin");
   }
 

src/interface/run.hpp

@@ -67,9 +67,9 @@ These are the options available:
 	static void ground_state() {
 		auto ions = systems::ions::load(".inq/default_ions");
 
-		auto bz = ions::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
+		auto bz = ionic::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
 
-		try { bz = ions::brillouin::load(".inq/default_brillouin"); }
+		try { bz = ionic::brillouin::load(".inq/default_brillouin"); }
 		catch(...) {
 			bz.save(input::environment::global().comm(), ".inq/default_brillouin");
 		}
@@ -88,9 +88,9 @@ These are the options available:
 	static void real_time() {
 		auto ions = systems::ions::load(".inq/default_ions");
 
-		auto bz = ions::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
+		auto bz = ionic::brillouin(systems::ions::load(".inq/default_ions"), input::kpoints::gamma());
 
-		try { bz = ions::brillouin::load(".inq/default_brillouin"); }
+		try { bz = ionic::brillouin::load(".inq/default_brillouin"); }
 		catch(...) {
 			bz.save(input::environment::global().comm(), ".inq/default_brillouin");
 		}

src/ions/brillouin.hpp → src/ionic/brillouin.hpp

@@ -13,7 +13,7 @@
 #include <systems/ions.hpp>
 
 namespace inq {
-namespace ions {
+namespace ionic {
 
 class brillouin {
 
@@ -169,8 +169,8 @@ class brillouin {
 }
 #endif
 
-#ifdef INQ_IONS_BRILLOUIN_UNIT_TEST
-#undef INQ_IONS_BRILLOUIN_UNIT_TEST
+#ifdef INQ_IONIC_BRILLOUIN_UNIT_TEST
+#undef INQ_IONIC_BRILLOUIN_UNIT_TEST
 
 #include <catch2/catch_all.hpp>
 
@@ -192,7 +192,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		ions.insert_fractional("C", {0.0 , 0.0 , 0.0 });
 		ions.insert_fractional("C", {0.25, 0.25, 0.25});
 
-		auto bz1 = ions::brillouin(ions, input::kpoints::gamma());
+		auto bz1 = ionic::brillouin(ions, input::kpoints::gamma());
 
 		CHECK(bz1.size() == 1);
 		CHECK(bz1.kpoint(0)[0] == 0.0_a);
@@ -212,7 +212,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		bz1.clear();
 		CHECK(bz1.size() == 0);
 
-		auto bz2 = ions::brillouin(ions, input::kpoints::grid({1, 2, 3}));
+		auto bz2 = ionic::brillouin(ions, input::kpoints::grid({1, 2, 3}));
 
 		CHECK(bz2.size() == 6);
 
@@ -240,7 +240,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		CHECK(bz2.kpoint(5)[1]/(2*M_PI) == -0.5_a);
 		CHECK(bz2.kpoint(5)[2]/(2*M_PI) == -0.3333333333_a);
 
-		auto bz3 = ions::brillouin(ions, input::kpoints::grid({2, 2, 2}, true));
+		auto bz3 = ionic::brillouin(ions, input::kpoints::grid({2, 2, 2}, true));
 
 		CHECK(bz3.size() == 8);
 
@@ -277,7 +277,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		CHECK(bz3.kpoint(7)[2]/(2*M_PI) == -0.25_a);
 
 		bz3.save(comm, "save_brillouin_3");
-		auto read_bz3 = ions::brillouin::load("save_brillouin_3");
+		auto read_bz3 = ionic::brillouin::load("save_brillouin_3");
 
 		CHECK(read_bz3.size() == 8);
 
@@ -319,7 +319,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		kpts.insert({0.1, 0.2,  0.3}, 2.0);
 		kpts.insert({1.0, -0.01, 0.0}, 0.0);
 
-		auto bz4 = ions::brillouin(ions, kpts);
+		auto bz4 = ionic::brillouin(ions, kpts);
 
 		CHECK(bz4.size() == 3);
 
@@ -340,7 +340,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 		CHECK(bz4.kpoint_weight(2) ==  0.0_a);
 
 		bz4.save(comm, "save_brillouin_4");
-		auto read_bz4 = ions::brillouin::load("save_brillouin_4");
+		auto read_bz4 = ionic::brillouin::load("save_brillouin_4");
 
 		CHECK(read_bz4.size() == 3);