Merge pull request #455 from toxa81/develop

[api] fix for intent in/out

VERSION

@@ -1 +1 @@
-6.4.2
+6.4.3

doc/doxygen.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME = "SIRIUS"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER = "6.4.2"
+PROJECT_NUMBER = "6.4.3"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

src/generated.f90

@@ -2754,54 +2754,54 @@ subroutine sirius_option_get_length_aux(section,length)&
 call sirius_option_get_length_aux(section,length)
 end subroutine sirius_option_get_length
 
-!> @brief return the name and a type of an option from its index
-!> @param [in] section name of the section
-!> @param [out] elem_ index of the option
-!> @param [out] key_name name of the option
-!> @param [out] type type of the option (real, integer, boolean, string)
-subroutine sirius_option_get_name_and_type(section,elem_,key_name,type)
+!> @brief Return the name and a type of an option from its index.
+!> @param [in] section Name of the section.
+!> @param [in] elem Index of the option.
+!> @param [out] key_name Name of the option.
+!> @param [out] type Type of the option (real, integer, boolean, string).
+subroutine sirius_option_get_name_and_type(section,elem,key_name,type)
 implicit none
 character(C_CHAR), dimension(*), intent(in) :: section
-integer(C_INT), intent(out) :: elem_
+integer(C_INT), intent(in) :: elem
 character(C_CHAR), dimension(*), intent(out) :: key_name
 integer(C_INT), intent(out) :: type
 interface
-subroutine sirius_option_get_name_and_type_aux(section,elem_,key_name,type)&
+subroutine sirius_option_get_name_and_type_aux(section,elem,key_name,type)&
 &bind(C, name="sirius_option_get_name_and_type")
 use, intrinsic :: ISO_C_BINDING
 character(C_CHAR), dimension(*), intent(in) :: section
-integer(C_INT), intent(out) :: elem_
+integer(C_INT), intent(in) :: elem
 character(C_CHAR), dimension(*), intent(out) :: key_name
 integer(C_INT), intent(out) :: type
 end subroutine
 end interface
 
-call sirius_option_get_name_and_type_aux(section,elem_,key_name,type)
+call sirius_option_get_name_and_type_aux(section,elem,key_name,type)
 end subroutine sirius_option_get_name_and_type
 
 !> @brief return the description and usage of a given option
 !> @param [in] section name of the section
 !> @param [in] name name of the option
-!> @param [out] desc_ description of the option
-!> @param [out] usage_ how to use the option
-subroutine sirius_option_get_description_usage(section,name,desc_,usage_)
+!> @param [out] desc description of the option
+!> @param [out] usage how to use the option
+subroutine sirius_option_get_description_usage(section,name,desc,usage)
 implicit none
 character(C_CHAR), dimension(*), intent(in) :: section
 character(C_CHAR), dimension(*), intent(in) :: name
-character(C_CHAR), dimension(*), intent(out) :: desc_
-character(C_CHAR), dimension(*), intent(out) :: usage_
+character(C_CHAR), dimension(*), intent(out) :: desc
+character(C_CHAR), dimension(*), intent(out) :: usage
 interface
-subroutine sirius_option_get_description_usage_aux(section,name,desc_,usage_)&
+subroutine sirius_option_get_description_usage_aux(section,name,desc,usage)&
 &bind(C, name="sirius_option_get_description_usage")
 use, intrinsic :: ISO_C_BINDING
 character(C_CHAR), dimension(*), intent(in) :: section
 character(C_CHAR), dimension(*), intent(in) :: name
-character(C_CHAR), dimension(*), intent(out) :: desc_
-character(C_CHAR), dimension(*), intent(out) :: usage_
+character(C_CHAR), dimension(*), intent(out) :: desc
+character(C_CHAR), dimension(*), intent(out) :: usage
 end subroutine
 end interface
 
-call sirius_option_get_description_usage_aux(section,name,desc_,usage_)
+call sirius_option_get_description_usage_aux(section,name,desc,usage)
 end subroutine sirius_option_get_description_usage
 
 !> @brief return the default value of the option

src/input.hpp

@@ -22,6 +22,7 @@
  * \brief Contains input parameters structures.
  *
  * \todo Some of the parameters belong to SCF ground state mini-app. Mini-app should parse this values itself.
+ * \todo parse atomic coordinates and magnetic field separtely, not as 6D vector.
  */
 
 #ifndef __INPUT_HPP__
@@ -47,25 +48,25 @@ namespace sirius {
  [a3_x, a3_y, a3_z]
  ],
 
- "lattice_vectors_scale" : scale,
+ "lattice_vectors_scale" : (float) scale,
 
- "atom_types" : [label_A, label_B, ...],
+ "atom_types" : ["label_A", "label_B", ...],
 
  "atom_files" : {
- label_A : file_A,
- label_B : file_B,
+ "label_A" : "file_A",
+ "label_B" : "file_B",
  ...
  },
 
  "atom_coordinate_units" : units,
 
  "atoms" : {
- label_A: [
+ "label_A": [
  coordinates_A_1,
  coordinates_A_2,
  ...
  ],
- label_B : [
+ "label_B" : [
  coordinates_B_1,
  coordinates_B_2,
  ...
@@ -187,6 +188,15 @@ struct Unit_cell_input
 };
 
 /// Parse mixer input section.
+/** The following part of the input file is parsed:
+ \code{.json}
+ "mixer" : {
+ "beta" : (float) beta,
+ "beta0" : beta0,
+ "linear_mix_rms_tol" : 
+ }
+ \endcode
+ */
 struct Mixer_input
 {
  /// Mixing paramter.

src/sirius_api.cpp

@@ -2625,118 +2625,127 @@ void sirius_update_atomic_potential(void* const* handler__)
 }
 
 
-/* @fortran begin function void sirius_option_get_length  return the number of options in a given section
- @fortran argument in required string section  name of the seciton
- @fortran argument out required int length   number of options contained in the section
+/* @fortran begin function void sirius_option_get_length return the number of options in a given section
+ @fortran argument in required string section name of the seciton
+ @fortran argument out required int length number of options contained in the section
  @fortran end */
 
-void sirius_option_get_length(char *section, int *length)
+void sirius_option_get_length(char const* section__, int *length__)
 {
- const json &parser = sirius::get_options_dictionary();
- // ugly as hell but fortran is a piece of ....
- for ( char *p = section; *p; p++) *p = tolower(*p);
+ auto const& parser = sirius::get_options_dictionary();
+
+ auto section = std::string(section__);
+ std::transform(section.begin(), section.end(), section.begin(), ::tolower);
 
- *length = parser[section].size();
+ *length__ = parser[section].size();
 }
 
-/* @fortran begin function void sirius_option_get_name_and_type  return the name and a type of an option from its index
- @fortran argument in required string section  name of the section
- @fortran argument out required int elem_   index of the option
- @fortran argument out required string key_name  name of the option
- @fortran argument out required int type  type of the option (real, integer, boolean, string)
+/* @fortran begin function void sirius_option_get_name_and_type Return the name and a type of an option from its index.
+ @fortran argument in required string section Name of the section.
+ @fortran argument in required int  elem Index of the option.
+ @fortran argument out required string key_name Name of the option.
+ @fortran argument out required int  type Type of the option (real, integer, boolean, string).
  @fortran end */
 
-void sirius_option_get_name_and_type(char *section, int *elem_, char *key_name, int *type)
+void sirius_option_get_name_and_type(char const* section__, int const* elem__, char* key_name__, int* type__)
 {
  const json &dict = sirius::get_options_dictionary();
 
- // ugly as hell but fortran is a piece of ....
- for ( char *p = section; *p; p++) *p = tolower(*p);
+ auto section = std::string(section__);
+ std::transform(section.begin(), section.end(), section.begin(), ::tolower);
 
  int elem = 0;
- *type = -1;
- for (auto& el : dict[section].items())
- {
- if (elem == *elem_) {
+ *type__ = -1;
+ for (auto& el : dict[section].items()) {
+ if (elem == *elem__) {
  if (!dict[section][el.key()].count("default_value")) {
  std::cout << "key : " << el.key() << "\n the default_value key is missing" << std::endl;
  exit(0);
  }
  if (dict[section][el.key()]["default_value"].is_array()) {
- *type = 10;
- if (dict[section][el.key()]["default_value"][0].is_number_integer())
- *type += 1;
- if (dict[section][el.key()]["default_value"][0].is_number_float())
- *type += 2;
- if (dict[section][el.key()]["default_value"][0].is_boolean())
- *type += 3;
- if (dict[section][el.key()]["default_value"][0].is_string())
- *type += 4;
+ *type__ = 10;
+ if (dict[section][el.key()]["default_value"][0].is_number_integer()) {
+ *type__ += 1;
+ }
+ if (dict[section][el.key()]["default_value"][0].is_number_float()) {
+ *type__ += 2;
+ }
+ if (dict[section][el.key()]["default_value"][0].is_boolean()) {
+ *type__ += 3;
+ }
+ if (dict[section][el.key()]["default_value"][0].is_string()) {
+ *type__ += 4;
+ }
  } else {
- if (dict[section][el.key()]["default_value"].is_number_integer())
- *type = 1;
- if (dict[section][el.key()]["default_value"].is_number_float())
- *type = 2;
- if (dict[section][el.key()]["default_value"].is_boolean())
- *type = 3;
- if (dict[section][el.key()]["default_value"].is_string())
- *type = 4;
+ if (dict[section][el.key()]["default_value"].is_number_integer()) {
+ *type__ = 1;
+ }
+ if (dict[section][el.key()]["default_value"].is_number_float()) {
+ *type__ = 2;
+ }
+ if (dict[section][el.key()]["default_value"].is_boolean()) {
+ *type__ = 3;
+ }
+ if (dict[section][el.key()]["default_value"].is_string()) {
+ *type__ = 4;
+ }
  }
- std::memcpy(key_name, el.key().c_str(), el.key().size());
+ std::memcpy(key_name__, el.key().c_str(), el.key().size());
  }
  elem++;
  }
 }
 
-/* @fortran begin function void sirius_option_get_description_usage  return the description and usage of a given option
- @fortran argument in required string section  name of the section
- @fortran argument in required string name  name of the option
- @fortran argument out required string desc_  description of the option
- @fortran argument out required string usage_  how to use the option
+/* @fortran begin function void sirius_option_get_description_usage return the description and usage of a given option
+ @fortran argument in required string section name of the section
+ @fortran argument in required string name name of the option
+ @fortran argument out required string desc description of the option
+ @fortran argument out required string usage how to use the option
  @fortran end */
-
-void sirius_option_get_description_usage(char * section, char * name, char *desc_, char *usage_)
+void sirius_option_get_description_usage(char const* section__, char const* name__, char* desc__, char* usage__)
 {
  const json &parser = sirius::get_options_dictionary();
 
- // ugly as hell but fortran is a piece of ....
- for ( char *p = section; *p; p++) *p = tolower(*p);
- // ugly as hell but fortran is a piece of ....
- // for ( char *p = name; *p; p++) *p = tolower(*p);
+ auto section = std::string(section__);
+ std::transform(section.begin(), section.end(), section.begin(), ::tolower);
+
+ auto name = std::string(name__);
 
  if (parser[section][name].count("description")) {
- std::string description = parser[section][name].value("description", "");
- std::copy(description.begin(), description.end(), desc_);
+ auto description = parser[section][name].value("description", "");
+  std::copy(description.begin(), description.end(), desc__);
  }
  if (parser[section][name].count("usage")) {
- std::string usage = parser[section][name].value("usage","");
- std::copy(usage.begin(), usage.end(), usage_);
+ auto usage = parser[section][name].value("usage", "");
+ std::copy(usage.begin(), usage.end(), usage__);
  }
 }
 
-/* @fortran begin function void sirius_option_get_int  return the default value of the option
- @fortran argument in required string section  name of the section of interest
- @fortran argument in required string name  name of the element
- @fortran argument out required int default_value  table containing the default values (if vector)
- @fortran argument out required int length  length of the table containing the default values
+/* @fortran begin function void sirius_option_get_int return the default value of the option
+ @fortran argument in required string section name of the section of interest
+ @fortran argument in required string name name of the element
+ @fortran argument out required int default_value table containing the default values (if vector)
+ @fortran argument out required int length length of the table containing the default values
  @fortran end */
 
-void sirius_option_get_int(char * section, char * name, int *default_value, int *length)
+void sirius_option_get_int(char const* section__, char const* name__, int *default_value__, int *length__)
 {
- const json &parser = sirius::get_options_dictionary();
+ auto const &parser = sirius::get_options_dictionary();
 
- // ugly as hell but fortran is a piece of ....
- for ( char *p = section; *p; p++) *p = tolower(*p);
- // ugly as hell but fortran is a piece of ....
- // for ( char *p = name; *p; p++) *p = tolower(*p);
- if (!parser[section][name].count("default_value"))
- std::cout << "default value is mossing" << std::endl;
+ auto section = std::string(section__);
+ std::transform(section.begin(), section.end(), section.begin(), ::tolower);
+
+ auto name = std::string(name__);
+
+ if (!parser[section][name].count("default_value")) {
+ std::cout << "default value is missing" << std::endl;
+ }
  if (parser[section][name]["default_value"].is_array()) {
  std::vector<int> v = parser[section][name]["default_value"].get<std::vector<int>>();
- *length = v.size();
- memcpy(default_value, &v[0], v.size() * sizeof(int));
+ *length__ = v.size();
+ std::memcpy(default_value__, &v[0], v.size() * sizeof(int));
  } else {
- *default_value = parser[section][name].value("default_value", -1);
+ *default_value__ = parser[section][name].value("default_value", -1);
  }
 }