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> const & pos) { + static void insert(ionic::species const & sp, vector3> 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 const & pos) { + static void insert_fractional(ionic::species const & sp, vector3 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/input/species.hpp b/src/ionic/species.hpp similarity index 84% rename from src/input/species.hpp rename to src/ionic/species.hpp index 0b4c38be..17349260 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 // @@ -16,7 +16,7 @@ #include namespace inq { -namespace input { +namespace ionic { class species : public pseudo::element { @@ -90,12 +90,6 @@ class species : public pseudo::element { auto filter_pseudo() const { return filter_.value_or(true); } - - template - friend OStream & operator<<(OStream & out, species const & self){ - out << self.symbol(); - return out; - } }; @@ -103,8 +97,8 @@ 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 @@ -115,7 +109,7 @@ 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 +117,7 @@ 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 +126,7 @@ 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 +134,7 @@ 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 +142,7 @@ 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 2c0a567c..ff5896e0 100644 --- a/src/ionic/species_set.hpp +++ b/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 +#include namespace inq { namespace ionic { class species_set { - using container_type = std::unordered_map; + using container_type = std::unordered_map; 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 5726083c..8c257200 100644 --- a/src/parse/cif.hpp +++ b/src/parse/cif.hpp @@ -14,7 +14,7 @@ #include #include -#include +#include #include #include @@ -24,7 +24,7 @@ namespace parse { class cif { std::vector> lattice_vectors_; - std::vector atoms_; + std::vector atoms_; std::vector> 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 1bcc93b9..7f94c89c 100644 --- a/src/parse/poscar.hpp +++ b/src/parse/poscar.hpp @@ -19,7 +19,7 @@ #include #include -#include