From a44ea2b51cb76b4a406d52f997a12e69d6a82618 Mon Sep 17 00:00:00 2001
From: Xavier Andrade <xavier@tddft.org>
Date: Mon, 1 Jul 2024 21:16:44 -0700
Subject: [PATCH 1/3] Moved input/species.hpp to ionic/species.hpp

---
 src/{input => ionic}/species.hpp | 8 ++++----
 src/ionic/species_set.hpp        | 2 +-
 src/parse/cif.hpp                | 2 +-
 src/parse/poscar.hpp             | 2 +-
 src/parse/xyz.hpp                | 2 +-
 src/systems/ions.hpp             | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)
 rename src/{input => ionic}/species.hpp (96%)

diff --git a/src/input/species.hpp b/src/ionic/species.hpp
similarity index 96%
rename from src/input/species.hpp
rename to src/ionic/species.hpp
index 0b4c38be..3addfa63 100644
--- a/src/input/species.hpp
+++ b/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
 //
@@ -103,8 +103,8 @@ class species : public pseudo::element {
 }
 #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>
 
diff --git a/src/ionic/species_set.hpp b/src/ionic/species_set.hpp
index 2c0a567c..99d89757 100644
--- a/src/ionic/species_set.hpp
+++ b/src/ionic/species_set.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 <input/species.hpp>
+#include <ionic/species.hpp>
 
 namespace inq {
 namespace ionic {
diff --git a/src/parse/cif.hpp b/src/parse/cif.hpp
index 5726083c..f44fb419 100644
--- a/src/parse/cif.hpp
+++ b/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>
 
diff --git a/src/parse/poscar.hpp b/src/parse/poscar.hpp
index 1bcc93b9..9f68f808 100644
--- a/src/parse/poscar.hpp
+++ b/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>
 
diff --git a/src/parse/xyz.hpp b/src/parse/xyz.hpp
index ad396623..6de98bf4 100644
--- a/src/parse/xyz.hpp
+++ b/src/parse/xyz.hpp
@@ -15,7 +15,7 @@
 #include <math/vector3.hpp>
 
 #include <pseudopod/element.hpp>
-#include <input/species.hpp>
+#include <ionic/species.hpp>
 #include <magnitude/length.hpp>
 
 namespace inq {
diff --git a/src/systems/ions.hpp b/src/systems/ions.hpp
index f4cf510b..4596248e 100644
--- a/src/systems/ions.hpp
+++ b/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>

From 726cd62c57137d4c7283dee1655d2f8a4587d140 Mon Sep 17 00:00:00 2001
From: Xavier Andrade <xavier@tddft.org>
Date: Mon, 1 Jul 2024 21:22:44 -0700
Subject: [PATCH 2/3] Moved species to the ionic namespace.

---
 src/hamiltonian/atomic_potential.hpp |  4 ++--
 src/interface/ions.hpp               |  4 ++--
 src/ionic/species.hpp                | 12 ++++++------
 src/ionic/species_set.hpp            |  4 ++--
 src/parse/cif.hpp                    |  2 +-
 src/parse/poscar.hpp                 |  8 ++++----
 src/parse/xyz.hpp                    |  2 +-
 src/systems/ions.hpp                 | 14 +++++++-------
 tests/bo.cpp                         |  2 +-
 tests/hydrogen_local.cpp             |  2 +-
 tests/pseudos.cpp                    |  4 ++--
 11 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/src/hamiltonian/atomic_potential.hpp b/src/hamiltonian/atomic_potential.hpp
index aa247817..9f17a56c 100644
--- a/src/hamiltonian/atomic_potential.hpp
+++ b/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;
 
diff --git a/src/interface/ions.hpp b/src/interface/ions.hpp
index cb921944..2ca4c104 100644
--- a/src/interface/ions.hpp
+++ b/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");
diff --git a/src/ionic/species.hpp b/src/ionic/species.hpp
index 3addfa63..ed5e65ea 100644
--- a/src/ionic/species.hpp
+++ b/src/ionic/species.hpp
@@ -16,7 +16,7 @@
 #include <optional>
 
 namespace inq {
-namespace input {
+namespace ionic {
 
 class species : public pseudo::element {
 
@@ -115,7 +115,7 @@ 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());
@@ -123,7 +123,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
 	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());
@@ -132,7 +132,7 @@ 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);
@@ -140,7 +140,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 	
 	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);
@@ -148,7 +148,7 @@ TEST_CASE(INQ_TEST_FILE, INQ_TEST_TAG) {
 
 	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());
diff --git a/src/ionic/species_set.hpp b/src/ionic/species_set.hpp
index 99d89757..ff5896e0 100644
--- a/src/ionic/species_set.hpp
+++ b/src/ionic/species_set.hpp
@@ -16,7 +16,7 @@ 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);
 	}
 
diff --git a/src/parse/cif.hpp b/src/parse/cif.hpp
index f44fb419..8c257200 100644
--- a/src/parse/cif.hpp
+++ b/src/parse/cif.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){
diff --git a/src/parse/poscar.hpp b/src/parse/poscar.hpp
index 9f68f808..7f94c89c 100644
--- a/src/parse/poscar.hpp
+++ b/src/parse/poscar.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);					
 				}
diff --git a/src/parse/xyz.hpp b/src/parse/xyz.hpp
index 6de98bf4..7ad53f8b 100644
--- a/src/parse/xyz.hpp
+++ b/src/parse/xyz.hpp
@@ -23,7 +23,7 @@ namespace parse {
 
 class xyz {
 
-	std::vector<input::species> atoms_;
+	std::vector<ionic::species> atoms_;
 	std::vector<vector3<double>> positions_;
 
 	public:
diff --git a/src/systems/ions.hpp b/src/systems/ions.hpp
index 4596248e..de406265 100644
--- a/src/systems/ions.hpp
+++ b/src/systems/ions.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);
diff --git a/tests/bo.cpp b/tests/bo.cpp
index 1c4d2631..79823ea7 100644
--- a/tests/bo.cpp
+++ b/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);
diff --git a/tests/hydrogen_local.cpp b/tests/hydrogen_local.cpp
index 5cedfe66..c623eb9c 100644
--- a/tests/hydrogen_local.cpp
+++ b/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});
diff --git a/tests/pseudos.cpp b/tests/pseudos.cpp
index 432d68e6..5c500706 100644
--- a/tests/pseudos.cpp
+++ 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));
 		

From 83bce901c164dbfddf282e912e93d0a8cb4b80d8 Mon Sep 17 00:00:00 2001
From: Xavier Andrade <xavier@tddft.org>
Date: Mon, 1 Jul 2024 21:25:40 -0700
Subject: [PATCH 3/3] Remove operator << for species that is not used.

---
 src/ionic/species.hpp | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/src/ionic/species.hpp b/src/ionic/species.hpp
index ed5e65ea..17349260 100644
--- a/src/ionic/species.hpp
+++ b/src/ionic/species.hpp
@@ -90,12 +90,6 @@ 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;
-	}
 	
 };