Merge branch 'feature-python_api-wyckoff' into 'master'

Feature python api wyckoff

See merge request scientific-software/crysfml!16

Author: Elisa Rebolini

Python_API/Src/API_Crystallographic_Symmetry.py

@@ -307,4 +307,39 @@ def str_orbit(self):
         ret = []
         for k in range(48):
             ret.append(CFML_api.crysfml_api.crystallographic_symmetry_get_wyckoff_str_orbit(self.get_fortran_address(), k+1)["str_orbit"])
-        return ret
+        return ret
+
+
+
+def multiplicity_pos(pos, spg: SpaceGroup):
+    """
+    Return the multiplicity of a real space point given the Shubnikov/space group.
+    ...
+    Parameters
+    ----------
+    pos : np.array[dtype='float32', ndim=q]
+       x,y,z coordinates 
+    spg : CMFL_api.crysfml_api.SpaceGroup
+
+    Returns:
+    int: Multiplicity of the point
+
+    """
+    return CFML_api.crysfml_api.crystallographic_symmetry_get_multip_pos_crys(pos, spg.get_fortran_address())["mult"]
+
+
+def occupancy_site(pos, spg):
+    """
+    Return the occupancy foctor given the position and Shubnikov/space group.
+    ...
+    Parameters
+    ----------
+    pos : np.array[dtype='float32', ndim=1]
+       x,y,z coordinates 
+    spg : CMFL_api.crysfml_api.SpaceGroup
+
+    Returns:
+    float: occupancy factor (site multiplicity/multiplicity)
+
+    """
+    return CFML_api.crysfml_api.crystallographic_symmetry_get_occ_site(pos, spg.get_fortran_address())["occ"]

Python_API/Src/API_Reflections_Utilities.py

@@ -16,6 +16,26 @@
 import CFML_api.FortranBindedClass
 
 class ReflectionList(CFML_api.FortranBindedClass):
+    """ 
+    A class used to describe the reflection list type(Reflection_List_Type) in CFML.
+
+    ... 
+    Attributes
+    ----------
+    cell : CMFL_api.crysfml_api.Cell
+    spg : CMFL_api.crysfml_api.SpaceGroup
+    lfriedel : boolean
+    job : CMFL_api.crysfml_api.JobInfo
+
+    Methods
+    -------
+    print_description
+        Prints the reflection lsit
+    compute_structure_factors
+        Compute the structure factor for each reflection of the list
+    
+    """
+    
     def __init__(self, cell, spg, lfriedel, job):
         CFML_api.FortranBindedClass.__init__(self)
         (stlmin, stlmax) = job.range_stl
@@ -38,12 +58,28 @@ def nref(self):
         return CFML_api.crysfml_api.reflections_utilities_get_nref(self.get_fortran_address())["nref"]
 
     def compute_structure_factors(self, space_group, atom_list, job):
-                            
+        """
+        Compute all structure factors 
+        ...
+        Parameters
+        ----------
+        space_group : CMFL_api.crysfml_api.SpaceGroup
+        atom_list :  CMFL_api.crysfml_api.AtomList
+        job : CMFL_api.crysfml_api.JobInfo
+        """
         CFML_api.crysfml_api.structure_factors_structure_factors(
             atom_list.get_fortran_address(), space_group.get_fortran_address(),
             self.get_fortran_address(), job.get_fortran_address())
-        
 
+        
+    def print_description(self):
+        """
+        Write the list of reflections and structure factors
+        """
+        print("\n")
+        CFML_api.crysfml_api.reflections_utilities_write_reflist_info(self.get_fortran_address())
+        
+        
 class Reflection(CFML_api.FortranBindedClass):
     """ Class for a given Reflection in CFML
 

Python_API/Src/Extensions/API_Crystallographic_Symmetry.f90

@@ -17,7 +17,16 @@ module API_Crystallographic_Symmetry
   use, intrinsic :: iso_c_binding
   use, intrinsic :: iso_fortran_env
 
-  use CFML_Crystallographic_Symmetry, only: Space_Group_Type, set_SpaceGroup, Write_SpaceGroup, Sym_Oper_Type, Wyckoff_Type, Wyck_Pos_Type
+  use CFML_GlobalDeps,       only : Cp
+  use CFML_Crystallographic_Symmetry, only: &
+       Space_Group_Type, &
+       set_SpaceGroup, &
+       Write_SpaceGroup, &
+       Sym_Oper_Type, &
+       Wyckoff_Type, &
+       Wyck_Pos_Type, &
+       Get_Multip_Pos, &
+       Get_Occ_Site
 
   implicit none
 
@@ -1515,4 +1524,107 @@ function crystallographic_symmetry_get_wyckoff_str_orbit(self_ptr, args_ptr) res
 
   end function crystallographic_symmetry_get_wyckoff_str_orbit
 
+
+
+  function crystallographic_symmetry_get_multip_pos_crys(self_ptr, args_ptr) result(r) bind(c)
+
+    type(c_ptr), value :: self_ptr
+    type(c_ptr), value :: args_ptr
+    type(c_ptr) :: r
+    type(tuple) :: args
+    type(dict) :: retval
+    integer :: num_args
+    integer :: ierror
+
+    type(Space_Group_type_p) :: spg
+    type(object)                         :: pos_obj
+    type(ndarray)                        :: pos_nd
+    real(kind=cp), dimension(:), pointer :: pos_p
+
+    integer :: mult
+    
+    r = C_NULL_PTR   ! in case of an exception return C_NULL_PTR
+    ! use unsafe_cast_from_c_ptr to cast from c_ptr to tuple
+    call unsafe_cast_from_c_ptr(args, args_ptr)
+    ! Check if the arguments are OK
+    ierror = args%len(num_args)
+    ! we should also check ierror, but this example does not do complete error checking for simplicity
+    if (num_args /= 2) then
+       call raise_exception(TypeError, "get_multip_pos_crys expects exactly 2 arguments")
+       call args%destroy
+       return
+    endif
+
+    ! Doing boring stuff
+    ierror = args%getitem(pos_obj, 0)        !pos -> x,y,z
+    ierror = cast(pos_nd, pos_obj)
+    ierror = pos_nd%get_data(pos_p)
+
+    call get_space_group_type_from_arg(args, spg, 1)
+    
+    mult = Get_Multip_Pos(pos_p, spg%p)
+    !write(*,*) "f90 mult",mult
+
+    ierror = dict_create(retval)
+    ierror = retval%setitem("mult", mult)
+    
+    r = retval%get_c_ptr()
+
+    call args%destroy
+    call pos_obj%destroy
+    
+    
+  end function crystallographic_symmetry_get_multip_pos_crys
+
+
+  function crystallographic_symmetry_get_occ_site(self_ptr, args_ptr) result(r) bind(c)
+
+    type(c_ptr), value :: self_ptr
+    type(c_ptr), value :: args_ptr
+    type(c_ptr) :: r
+    type(tuple) :: args
+    type(dict) :: retval
+    integer :: num_args
+    integer :: ierror
+
+    type(Space_Group_type_p) :: spg
+    type(object)                         :: pos_obj
+    type(ndarray)                        :: pos_nd
+    real(kind=cp), dimension(:), pointer :: pos_p
+
+    real(kind=cp) :: occ
+    
+    r = C_NULL_PTR   ! in case of an exception return C_NULL_PTR
+    ! use unsafe_cast_from_c_ptr to cast from c_ptr to tuple
+    call unsafe_cast_from_c_ptr(args, args_ptr)
+    ! Check if the arguments are OK
+    ierror = args%len(num_args)
+    ! we should also check ierror, but this example does not do complete error checking for simplicity
+    if (num_args /= 2) then
+       call raise_exception(TypeError, "get_multip_pos_crys expects exactly 2 arguments")
+       call args%destroy
+       return
+    endif
+
+    ! Doing boring stuff
+    ierror = args%getitem(pos_obj, 0)        !pos -> x,y,z
+    ierror = cast(pos_nd, pos_obj)
+    ierror = pos_nd%get_data(pos_p)
+
+    call get_space_group_type_from_arg(args, spg, 1)
+    
+    occ= Get_Occ_site(pos_p, spg%p)
+    !write(*,*) "f90 mult",mult
+
+    ierror = dict_create(retval)
+    ierror = retval%setitem("occ", occ)
+    
+    r = retval%get_c_ptr()
+
+    call args%destroy
+    call pos_obj%destroy
+    
+    
+  end function crystallographic_symmetry_get_occ_site
+
 end module API_Crystallographic_Symmetry

Python_API/Src/Extensions/API_Reflections_Utilities.f90

@@ -24,7 +24,8 @@ module API_Reflections_Utilities
        Reflection_Type, &
        Reflection_List_Type, &
        Hkl_uni, &
-       get_maxnumref
+       get_maxnumref, &
+       Write_RefList_Info
 
   use API_Crystallographic_Symmetry, only: &
        Space_Group_Type_p, &
@@ -143,6 +144,42 @@ function reflections_utilities_get_nref(self_ptr, args_ptr) result(r) bind(c)
 
   end function reflections_utilities_get_nref
 
+   ! @brief Print the list of reflections and structure factors to standard output
+  function reflections_utilities_write_reflist_info(self_ptr, args_ptr) result(r) bind(c)
+
+    type(c_ptr), value :: self_ptr
+    type(c_ptr), value :: args_ptr
+    type(c_ptr) :: r
+    
+    type(tuple) :: args
+    type(dict)  :: retval
+    integer     :: num_args
+    integer     :: ierror
+
+    type(Reflection_List_Type_p)   :: reflist_p
+
+    r = C_NULL_PTR      
+    call unsafe_cast_from_c_ptr(args, args_ptr)
+    
+    ierror = args%len(num_args)
+    
+    if (num_args /= 1) then
+       call raise_exception(TypeError, "write_reflist_info expects exactly 1 argument")
+       call args%destroy
+       return
+    endif
+    
+    call get_reflection_list_from_arg(args, reflist_p)
+
+    call Write_RefList_Info(reflist_p%p)
+
+    ierror = dict_create(retval)
+    r = retval%get_c_ptr()
+
+    call args%destroy
+
+  end function reflections_utilities_write_reflist_info
+
 
   function reflections_utilities_hkl_uni_reflist(self_ptr, args_ptr) result(r) bind(c)
 
@@ -666,7 +703,8 @@ function reflections_utilities_get_B(self_ptr, args_ptr) result(r) bind(c)
     call args%destroy
 
   end function reflections_utilities_get_B
-  
+
+ 
 
 
 end module API_Reflections_Utilities

Python_API/Src/Extensions/API_init.f90

@@ -56,7 +56,9 @@ module API_init
        crystallographic_symmetry_get_wyckoff_site, &
        crystallographic_symmetry_get_wyckoff_norb, &
        crystallographic_symmetry_get_wyckoff_str_orig, &
-       crystallographic_symmetry_get_wyckoff_str_orbit
+       crystallographic_symmetry_get_wyckoff_str_orbit, &
+       crystallographic_symmetry_get_multip_pos_crys, &
+       crystallographic_symmetry_get_occ_site
 
   use API_IO_Formats, only: &
        IO_formats_readn_set_xtal_structure, &
@@ -174,6 +176,7 @@ module API_init
        reflections_utilities_hkl_uni_reflist, &
        reflections_utilities_del_reflection_list, &
        reflections_utilities_get_nref, &
+       reflections_utilities_write_reflist_info, &
        reflections_utilities_del_reflection, &
        reflections_utilities_get_item, &
        reflections_utilities_get_H, &
@@ -257,9 +260,17 @@ function init() result(m)
     type(c_ptr) :: m
     integer :: ierror
     ierror = forpy_initialize()
-    
-    call method_table%init(200)
 
+
+
+    !--------------------------
+    !Total number of method in the binding
+    !--------------------------
+    call method_table%init(203)
+
+
+
+    
     !--------------------------
     ! Error Messages (1)
     !--------------------------
@@ -268,9 +279,13 @@ function init() result(m)
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(error_messages))  ! address of Fortran function to add
 
+
+
+    
     !--------------------------
     ! Diffraction Patterns (43)
     !--------------------------
+    
     call method_table%add_method("diffraction_patterns_compute_powder_pattern", &                  ! method name
          "compute the powder diffraction pattern from some experimental conditions and a set of reflections", &  !doc-string
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
@@ -486,9 +501,12 @@ function init() result(m)
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(diffraction_patterns_get_nd))  ! address of Fortran function to add
 
+
+    
     !--------------------------
-    ! Crystallographic Symmetry (37)
+    ! Crystallographic Symmetry (39)
     !--------------------------
+    
     call method_table%add_method("crystallographic_symmetry_set_spacegroup", &                  ! method name
          "Creates the space group", &  !doc-string
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
@@ -674,6 +692,15 @@ function init() result(m)
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(crystallographic_symmetry_get_wyckoff_str_orbit))  ! address of Fortran function to add
 
+    call method_table%add_method("crystallographic_symmetry_get_multip_pos_crys", &                  ! method name
+         "Mutiplicity of an x,y,z point for a given Space Group", &  !doc-string
+         METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
+         c_funloc(crystallographic_symmetry_get_multip_pos_crys))  ! address of Fortran function to add
+    call method_table%add_method("crystallographic_symmetry_get_occ_site", &                  ! method name
+         "Occupancy factor of an x,y,z point for a given Space Group", &  !doc-string
+         METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
+         c_funloc(crystallographic_symmetry_get_occ_site))  ! address of Fortran function to add
+
 
     !--------------------------
     ! IO formats (35)
@@ -1085,8 +1112,11 @@ function init() result(m)
          "Lm_xyz getter", &  !doc-string
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(atom_typedef_get_Lm_xyz))  ! address of Fortran function to add
+
+
+    
     !--------------------------
-    ! Reflection Utilities (13)
+    ! Reflection Utilities (14)
     !--------------------------
     call method_table%add_method("reflections_utilities_hkl_uni_reflist", &                  ! method name
          "Return the list of reflections", &  !doc-string
@@ -1102,6 +1132,11 @@ function init() result(m)
          "nref getter", &  !doc-string
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(reflections_utilities_get_nref))  ! address of Fortran function to add
+
+    call method_table%add_method("reflections_utilities_write_reflist_info", &                  ! method name
+         "print reflist info", &  !doc-string
+         METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
+         c_funloc(reflections_utilities_write_reflist_info))  ! address of Fortran function to add
 
     call method_table%add_method("reflections_utilities_del_reflection", &                  ! method name
          "Reflection deallocation", &  !doc-string