Merge branch 'move_species_to_ionic' into 'master'

Move species to ionic

See merge request npneq/inq!1099

src/hamiltonian/atomic_potential.hpp

@@ -100,7 +100,7 @@ namespace hamiltonian {
 			return nel;
 		}
 
-		auto & pseudo_for_element(input::species const & el) const {
+		auto & pseudo_for_element(ionic::species const & el) const {
 			return pseudopotential_list_.at(el.symbol());
 		}
 
@@ -332,7 +332,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG){
 	using namespace inq::magnitude;
 	using namespace Catch::literals;
 	using Catch::Approx;
-	using input::species;
+	using ionic::species;
 
 	double const gcut = 0.785;
 

src/interface/ions.hpp

@@ -141,13 +141,13 @@ These are the uses for the command:
 		status();
 	}
 
-	static void insert(input::species const & sp, vector3<quantity<magnitude::length>> const & pos) {
+	static void insert(ionic::species const & sp, vector3<quantity<magnitude::length>> const & pos) {
 		auto ions = systems::ions::load(".inq/default_ions");
 		ions.insert(sp, pos);
 		ions.save(input::environment::global().comm(), ".inq/default_ions");
 	}
 
-	static void insert_fractional(input::species const & sp, vector3<double, contravariant> const & pos) {
+	static void insert_fractional(ionic::species const & sp, vector3<double, contravariant> const & pos) {
 		auto ions = systems::ions::load(".inq/default_ions");
 		ions.insert_fractional(sp, pos);
 		ions.save(input::environment::global().comm(), ".inq/default_ions");

src/input/species.hpp → src/ionic/species.hpp

@@ -1,7 +1,7 @@
 /* -*- indent-tabs-mode: t -*- */
 
-#ifndef INPUT__SPECIES
-#define INPUT__SPECIES
+#ifndef IONIC__SPECIES
+#define IONIC__SPECIES
 
 // Copyright (C) 2019-2023 Lawrence Livermore National Security, LLC., Xavier Andrade, Alfredo A. Correa
 //
@@ -16,7 +16,7 @@
 #include <optional>
 
 namespace inq {
-namespace input {
+namespace ionic {
 
 class species : public pseudo::element {
 
@@ -90,21 +90,15 @@ class species : public pseudo::element {
 	auto filter_pseudo() const {
 		return filter_.value_or(true);
 	}
-
-	template<class OStream>
-	friend OStream & operator<<(OStream & out, species const & self){
-		out << self.symbol();
-		return out;
-	}
 
 };
 
 }
 }
 #endif
 
-#ifdef INQ_INPUT_SPECIES_UNIT_TEST
-#undef INQ_INPUT_SPECIES_UNIT_TEST
+#ifdef INQ_IONIC_SPECIES_UNIT_TEST
+#undef INQ_IONIC_SPECIES_UNIT_TEST
 
 #include <catch2/catch_all.hpp>
 
@@ -115,15 +109,15 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
 	SECTION("Constructor"){
 
-		auto s = input::species("Xe");
+		auto s = ionic::species("Xe");
 
 		CHECK(s.atomic_number() == 54);
 		CHECK(not s.has_file());
 	}
 
 	SECTION("Constructor with options"){
 
-		auto s = input::species("Xe").mass(20);
+		auto s = ionic::species("Xe").mass(20);
 
 		CHECK(s.atomic_number() == 54);
 		CHECK(not s.has_file());
@@ -132,23 +126,23 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
 	SECTION("Option mass"){
 
-		auto s = input::species("U").mass(235);
+		auto s = ionic::species("U").mass(235);
 
 		CHECK(s.symbol() == "U");
 		CHECK(s.mass() == 428378.7975_a);
 	}
 
 	SECTION("Option symbol"){
 
-		auto s = input::species("U").symbol("U235").mass(235);
+		auto s = ionic::species("U").symbol("U235").mass(235);
 
 		CHECK(s.symbol() == "U235");
 		CHECK(s.mass() == 428378.7975_a);
 	}
 
 	SECTION("Option pseudopotential"){
 
-		auto s = input::species("He").pseudo("hola");
+		auto s = ionic::species("He").pseudo("hola");
 
 		CHECK(s.symbol() == "He");
 		CHECK(s.has_file());

src/ionic/species_set.hpp

@@ -9,14 +9,14 @@
 // 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 <input/species.hpp>
+#include <ionic/species.hpp>
 
 namespace inq {
 namespace ionic {
 
 class species_set {
 
-	using container_type = 	std::unordered_map<std::string, input::species>;
+	using container_type = 	std::unordered_map<std::string, ionic::species>;
 
 	container_type list_;
 
@@ -30,7 +30,7 @@ class species_set {
 		return list_;
 	}
 
-	auto insert(input::species const & sp) {
+	auto insert(ionic::species const & sp) {
 		list_.insert_or_assign(sp.symbol(), sp);
 	}
 

src/parse/cif.hpp

@@ -14,7 +14,7 @@
 #include <gemmi/symmetry.hpp>
 #include <vector>
 
-#include <input/species.hpp>
+#include <ionic/species.hpp>
 #include <magnitude/length.hpp>
 #include <math/vector3.hpp>
 
@@ -24,7 +24,7 @@ namespace parse {
 class cif {
 
 	std::vector<vector3<double>> lattice_vectors_;
-	std::vector<input::species> atoms_;
+	std::vector<ionic::species> atoms_;
 	std::vector<vector3<double, contravariant>> positions_;
 
   static auto to_double(std::string const * strptr, std::string const & cif_file_name){

src/parse/poscar.hpp

@@ -19,7 +19,7 @@
 #include <math/vector3.hpp>
 
 #include <pseudopod/element.hpp>
-#include <input/species.hpp>
+#include <ionic/species.hpp>
 #include <magnitude/length.hpp>
 #include <magnitude/time.hpp>
 
@@ -29,7 +29,7 @@ namespace parse {
 class poscar {
 
 	std::vector<vector3<double>> lattice_vectors_;
-	std::vector<input::species> atoms_;
+	std::vector<ionic::species> atoms_;
 	std::vector<vector3<double>> positions_;
 	std::vector<vector3<double>> velocities_;
 
@@ -81,7 +81,7 @@ class poscar {
 			iss >> species_name;
 			if(iss.eof()) break;
 			species.push_back(species_name);
-			input::species sp(species.back());
+			ionic::species sp(species.back());
 			if(not sp.valid()) throw std::runtime_error("Cannot read the species from POSCAR file \'" + poscar_file_name +
 																									"\'. Make sure your file contains the optional \'Species names\' line (see\n https://www.vasp.at/wiki/index.php/POSCAR for details).");
 		}
@@ -104,7 +104,7 @@ class poscar {
 				for(int iatom = 0; iatom < species_num[ispecies]; iatom++){
 					vector3<double> pos;
 					poscar_file >> pos;
-					atoms_.emplace_back(input::species(species[ispecies]));
+					atoms_.emplace_back(ionic::species(species[ispecies]));
 					positions_.emplace_back(scaling_factor*in_atomic_units(1.0_A*pos));
 					std::getline(poscar_file, tail);
 				}
@@ -117,7 +117,7 @@ class poscar {
 				for(int iatom = 0; iatom < species_num[ispecies]; iatom++){
 					vector3<double, contravariant> pos;
 					poscar_file >> pos;
-					atoms_.emplace_back(input::species(species[ispecies]));
+					atoms_.emplace_back(ionic::species(species[ispecies]));
 					positions_.emplace_back(cell.metric().to_cartesian(pos));
 					std::getline(poscar_file, tail);					
 				}

src/parse/xyz.hpp

@@ -15,15 +15,15 @@
 #include <math/vector3.hpp>
 
 #include <pseudopod/element.hpp>
-#include <input/species.hpp>
+#include <ionic/species.hpp>
 #include <magnitude/length.hpp>
 
 namespace inq {
 namespace parse {
 
 class xyz {
 
-	std::vector<input::species> atoms_;
+	std::vector<ionic::species> atoms_;
 	std::vector<vector3<double>> positions_;
 
 	public:

src/systems/ions.hpp

@@ -14,7 +14,7 @@
 #include <spglib.h>
 
 #include <systems/cell.hpp>
-#include <input/species.hpp>
+#include <ionic/species.hpp>
 #include <ionic/species_set.hpp>
 #include <gpu/array.hpp>
 #include <parse/cif.hpp>
@@ -42,7 +42,7 @@ class ions {
 	ionic::species_set species_list_;
 
 	template <typename PositionType>
-	void add_atom(input::species const & element, PositionType const & position, vector3<double> const & vel = vector3<double>(0.0, 0.0, 0.0)){
+	void add_atom(ionic::species const & element, PositionType const & position, vector3<double> const & vel = vector3<double>(0.0, 0.0, 0.0)){
 		atoms_.push_back(element.symbol());
 		positions_.push_back(in_atomic_units(position));
 		velocities_.push_back(vel);
@@ -220,11 +220,11 @@ class ions {
 		return cell_;
 	}
 
-	void insert(input::species const & sp, vector3<quantity<magnitude::length>> const & pos){
+	void insert(ionic::species const & sp, vector3<quantity<magnitude::length>> const & pos){
 		add_atom(sp, pos);
 	}
 
-	void insert_fractional(input::species const & sp, vector3<double, contravariant> const & pos){
+	void insert_fractional(ionic::species const & sp, vector3<double, contravariant> const & pos){
 		add_atom(sp, cell_.metric().to_cartesian(pos));
 	}
 
@@ -345,7 +345,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
     CHECK(ions.size() == 1);
     CHECK(ions.species(0).atomic_number() == 54);
-    CHECK(ions.species(0) == input::species(54));
+    CHECK(ions.species(0) == ionic::species(54));
     CHECK(ions.species(0).charge() == -54.0_a);
     CHECK(ions.species(0).mass() == 239333.5935636_a);
     CHECK(ions.positions()[0][0] == 1000.0_a);
@@ -402,7 +402,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
     CHECK(ions.size() == 13);
     CHECK(ions.species(12).atomic_number() == 17);
-    CHECK(ions.species(12) == input::species(17));
+    CHECK(ions.species(12) == ionic::species(17));
     CHECK(ions.species(12).charge() == -17.0_a);
     CHECK(ions.species(12).mass() == 64614.105771_a);
     CHECK(ions.positions()[12][0] == -3.0_a);
@@ -448,7 +448,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
     CHECK(read_ions.velocities()[11][2] == 0.0_a);
 
     CHECK(read_ions.species(12).atomic_number() == 17);
-    CHECK(read_ions.species(12) == input::species(17));
+    CHECK(read_ions.species(12) == ionic::species(17));
     CHECK(read_ions.species(12).charge() == -17.0_a);
     CHECK(read_ions.species(12).mass() == 64614.105771_a);
     CHECK(read_ions.positions()[12][0] == -3.0_a);
@@ -506,7 +506,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
     CHECK(ions.size() == 13);
     CHECK(ions.species(12).atomic_number() == 17);
-    CHECK(ions.species(12) == input::species(17));
+    CHECK(ions.species(12) == ionic::species(17));
     CHECK(ions.species(12).charge() == -17.0_a);
     CHECK(ions.species(12).mass() == 64614.105771_a);
     CHECK(ions.positions()[12][0] == -3.0_a);

tests/bo.cpp

@@ -18,7 +18,7 @@ int main(int argc, char ** argv){
   //SINGLE ATOM SANITY CHECK
   {
     systems::ions ions(systems::cell::cubic(8.0_b).finite());
-    ions.insert(input::species("He").nofilter(), {0.0_b, 0.0_b, 0.0_b});
+    ions.insert(ionic::species("He").nofilter(), {0.0_b, 0.0_b, 0.0_b});
 
     systems::electrons electrons(ions, options::electrons{}.extra_states(3).cutoff(30.0_Ha));
     ground_state::initial_guess(ions, electrons);

tests/hydrogen_local.cpp

@@ -14,7 +14,7 @@ int main(int argc, char ** argv){
 
 	inq::utils::match energy_match(3.0e-5);
 
-	auto local_h = inq::input::species("H").symbol("Hloc").pseudo(inq::config::path::unit_tests_data() + "H.blyp-vbc.UPF");
+	auto local_h = inq::ionic::species("H").symbol("Hloc").pseudo(inq::config::path::unit_tests_data() + "H.blyp-vbc.UPF");
 
 	inq::systems::ions ions(inq::systems::cell::cubic(15.0_b).finite());
 	ions.insert(local_h, {150.0_b, -30.0_b, 0.0_b});

tests/pseudos.cpp

@@ -20,7 +20,7 @@ int main(int argc, char ** argv){
 	{
 		systems::ions ions(cell);
 
-		ions.insert(input::species("C").pseudo(inq::config::path::unit_tests_data() + "C_ONCV_PBE-1.2.xml"), {0.0_b, 0.0_b, 0.0_b});
+		ions.insert(ionic::species("C").pseudo(inq::config::path::unit_tests_data() + "C_ONCV_PBE-1.2.xml"), {0.0_b, 0.0_b, 0.0_b});
 
 		systems::electrons electrons(ions, options::electrons{}.cutoff(25.0_Ha).extra_states(4).temperature(300.0_K));
 
@@ -44,7 +44,7 @@ int main(int argc, char ** argv){
 	{
 		systems::ions ions(cell);
 
-		ions.insert(input::species("C"), {0.0_b, 0.0_b, 0.0_b});
+		ions.insert(ionic::species("C"), {0.0_b, 0.0_b, 0.0_b});
 
 		systems::electrons electrons(ions, options::electrons{}.pseudopotentials(pseudo::set::ccecp()).cutoff(25.0_Ha).extra_states(4).temperature(300.0_K));