add function to update multiplicity and ADP when reading from a CIF string array

Python_API/Src/API_Atom_TypeDef.py

@@ -343,7 +343,12 @@ class AtomList(CFML_api.FortranBindedClass):
     """
     def __init__(self, string_array=None):
         CFML_api.FortranBindedClass.__init__(self)
+        self._mult = True
+        self._adp = True
         if string_array:
+            self._mult = False 
+            self._adp = False
+            
             dict = CFML_api.crysfml_api.atom_typedef_atomlist_from_CIF_string_array(string_array)
             self._set_fortran_address(dict["AtomList"])
               
@@ -366,7 +371,7 @@ class AtomList(CFML_api.FortranBindedClass):
     @property
     def natoms(self):
         """
-        total number of atoms in the list
+        Total number of atoms in the list
         """
         return CFML_api.crysfml_api.atom_typedef_get_natoms(self.get_fortran_address())["natoms"]
     
@@ -374,3 +379,29 @@ class AtomList(CFML_api.FortranBindedClass):
         """ Print the list of atoms. """
         
         CFML_api.crysfml_api.atom_typedef_write_atom_list(self.get_fortran_address())
+
+
+    def set_mult_occ_cif(self,spg):
+        """
+        Update the multiplicity and modify the occupancy when reading from a CIF array,
+        in order to be in agreement with the definitions of Sfac in CrysFML
+        This needs to be run when the AtomList is initialised from a CIF-like stringarray
+        rather than from the class CIFFile
+        """
+        if (self._mult == False):
+            CFML_api.crysfml_api.atom_typedef_atomlist_reset_occ_cif(self.get_fortran_address(),spg.get_fortran_address())
+            self._mult = True
+        else:
+            print("Warning: multiplicity and occupancy have already been set")
+
+    def set_all_anisotropic_displacement_parameters_cif(self,cell):
+        """
+        Update all Atom fields for Us, Bs and betas
+        This needs to be run when the AtomList is initialised from a CIF-like stringarray
+        rather than from the class CIFFile
+        """
+        if (self._adp == False):
+            CFML_api.crysfml_api.atom_typedef_atomlist_set_all_adp_cif(self.get_fortran_address(),cell.get_fortran_address())
+            self._adp = True
+        else:
+            print("Warning: Anisotropic Displacement Parameters have already been set")

Python_API/Src/Extensions/API_Atom_TypeDef.f90

@@ -4,6 +4,8 @@ module API_Atom_TypeDef
   use, intrinsic :: iso_c_binding
   use, intrinsic :: iso_fortran_env
 
+  use CFML_GlobalDeps, only : cp, eps
+
   use CFML_Atom_TypeDef, only: &
        Atom_List_type, &
        Atoms_Cell_type, &
@@ -13,9 +15,23 @@ module API_Atom_TypeDef
        Write_Atom_list, &
        Atom_type
 
+  Use CFML_Crystallographic_Symmetry, only: &
+       Get_Multip_Pos
+
+  use CFML_Crystal_Metrics, only: &
+       Convert_U_Betas, Convert_B_Betas
+
   use CFML_IO_Formats, only: &
        Read_Atom, Read_Cif_Atom
 
+  use API_Crystallographic_Symmetry, only: &
+       Space_Group_type_p, &
+       get_space_group_type_from_arg
+
+  use API_Crystal_Metrics, only: &
+       Crystal_Cell_type_p, &
+       get_cell_from_arg
+
   implicit none
 
   type Atom_type_p
@@ -178,6 +194,118 @@ contains
   end function atom_typedef_atomlist_from_CIF_string_array
 
 
+  !---- Modify occupation factors and set multiplicity of atoms
+  !---- in order to be in agreement with the definitions of Sfac in CrysFML
+  function atom_typedef_atomlist_reset_occ_cif(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(Atom_List_Type_p) :: a_p
+    type(Space_Group_type_p) :: spg
+
+    real(kind=cp),dimension(6):: pos
+    integer :: i
+    
+    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, "update_occ_cif expects exactly 1 argument")
+       call args%destroy
+       return
+    endif
+    
+    ! Doing boring stuff
+    call get_atom_list_type_from_arg(args, a_p, 0)
+    call get_space_group_type_from_arg(args, spg, 1)
+
+    do i=1,a_p%p%natoms
+       pos(1:3)=a_p%p%atom(i)%x
+       a_p%p%atom(i)%Mult = Get_Multip_Pos(pos(1:3),SpG%p)
+       ! This step is needed for CIF file only as the convention is different!
+       a_p%p%atom(i)%Occ = a_p%p%atom(i)%Occ*real(a_p%p%atom(i)%Mult)/max(1.0,real(SpG%p%Multip))
+       if(a_p%p%atom(i)%occ < eps) a_p%p%atom(i)%occ=real(a_p%p%atom(i)%Mult)/max(1.0,real(SpG%p%Multip))
+    enddo
+
+    ierror = dict_create(retval)
+    r = retval%get_c_ptr()
+
+    call args%destroy
+    
+    
+  end function atom_typedef_atomlist_reset_occ_cif
+
+
+  function atom_typedef_atomlist_set_all_adp_cif(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(Atom_List_Type_p) :: a_p
+    type(Crystal_Cell_type_p) :: cell
+
+    integer :: i
+    
+    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, "update_occ_cif expects exactly 1 argument")
+       call args%destroy
+       return
+    endif
+    
+    ! Doing boring stuff
+    call get_atom_list_type_from_arg(args, a_p, 0)
+    call get_cell_from_arg(args, cell, 1)
+
+    do i=1,a_p%p%natoms
+       select case (A_p%p%atom(i)%thtype)
+             case ("isotr")
+                A_p%p%atom(i)%biso= A_p%p%atom(i)%ueq*78.95683521
+
+             case ("aniso")
+                select case (A_p%p%atom(i)%Utype)
+                   case ("u_ij")
+                      A_p%p%atom(i)%u(1:6) =  Convert_U_Betas(A_p%p%atom(i)%u(1:6),Cell%p)
+                   case ("b_ij")
+                      A_p%p%atom(i)%u(1:6) = Convert_B_Betas(A_p%p%atom(i)%u(1:6),Cell%p)
+                end select
+                A_p%p%atom(i)%Utype="beta"
+
+             case default
+                A_p%p%atom(i)%biso = A_p%p%atom(i)%ueq*78.95683521
+                A_p%p%atom(i)%thtype = "isotr"
+          end select
+    enddo
+
+    ierror = dict_create(retval)
+    r = retval%get_c_ptr()
+
+    call args%destroy
+    
+    
+  end function atom_typedef_atomlist_set_all_adp_cif
+
+  
+
   function atom_typedef_set_item(self_ptr, args_ptr) result(r) bind(c)
 
     type(c_ptr), value :: self_ptr
@@ -1762,6 +1890,7 @@ contains
     type(dict) :: retval
     integer :: num_args
     integer :: ierror
+    
     type(Atom_Type_p) :: atom_type_pointer
   
     type(ndarray) :: Lm_xyz
@@ -1787,4 +1916,7 @@ contains
     call args%destroy
     
   end function atom_typedef_get_Lm_xyz
+
+
+  
 end module API_Atom_TypeDef

Python_API/Src/Extensions/API_init.f90

@@ -130,6 +130,8 @@ module API_init
   use API_Atom_TypeDef, only: &
        atom_typedef_del_atom_list, &
        atom_typedef_atomlist_from_CIF_string_array, &
+       atom_typedef_atomlist_reset_occ_cif, &
+       atom_typedef_atomlist_set_all_adp_cif, &
        atom_typedef_get_item, &
        atom_typedef_get_natoms, &
        atom_typedef_atom_from_string, &
@@ -269,7 +271,7 @@ CONTAINS
     !--------------------------
     !Total number of method in the binding
     !--------------------------
-    call method_table%init(206)
+    call method_table%init(208)
 
 
 
@@ -884,7 +886,7 @@ CONTAINS
          c_funloc(IO_Formats_set_bkg))  ! address of Fortran function to add
     
     !--------------------------
-    ! Atom Typedef (45)
+    ! Atom Typedef (47)
     !--------------------------
     call method_table%add_method("atom_typedef_del_atom_list", &                  ! method name
          "Delete an atom list", &  !doc-string
@@ -895,6 +897,16 @@ CONTAINS
          "Create an atom list from an array of CIF lines", &  !doc-string
          METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
          c_funloc(atom_typedef_atomlist_from_CIF_string_array))  ! address of Fortran function to add
+
+    call method_table%add_method("atom_typedef_atomlist_reset_occ_cif", & ! method name
+         "Set mult and occ according to Sfac convention", &  !doc-string
+         METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
+         c_funloc(atom_typedef_atomlist_reset_occ_cif))  ! address of Fortran function to add
+
+    call method_table%add_method("atom_typedef_atomlist_set_all_adp_cif", & ! method name
+         "Set all Atom fields for Us, Bs and betas", &  !doc-string
+         METH_VARARGS, &                  ! this method takes arguments but no keyword arguments
+         c_funloc(atom_typedef_atomlist_set_all_adp_cif))  ! address of Fortran function to add
     
     call method_table%add_method("atom_typedef_set_item", &                  ! method name
          "Set an item in the atom list", &  !doc-string