Merge branch 'master' of https://github.com/glwhart/enumlib

HISTORY.md

@@ -1,5 +1,8 @@
 # Revision History for `enumlib`
 
+## 2.0.2 (JJ)
+- Fixed functions in `enumlib/wrap` to reflect changes to `get_dvector_permutations`.
+
 ## 2.0.1 (GLWH)
 - Removed a bunch of print statements related to debugging of Rev. 2.0.0
 

README.md

@@ -88,8 +88,8 @@ be found in the ('enumlib/support/input') directory.
 Detailed directions on how to run the code for several of the example
 input files can be found in the `enumlib/support/EXAMPLES` file.
 
-There are also helper programs in the aux_src directory for making VASP POSCARs, pictures of
-2-D enumerations, etc.
+There are also helper programs in the `aux_src` directory for making VASP POSCARs, pictures of
+2D enumerations, etc.
 
 `makeStr.py` <-- Makes POSCARS for the desired enumerated structures.
 (`makeStr.x` from the fortran code has been superceded by this python script.)

aux_src/HNF_profiler.f90

@@ -3,7 +3,7 @@ Module HNF_profiler
 use derivative_structure_generator, only: get_all_HNFs, remove_duplicate_lattices, &
      & get_dvector_permutations
 use vector_matrix_utilities, only: minkowski_reduce_basis, norm, matrix_inverse, determinant
-use symmetry, only: make_primitive, get_lattice_pointGroup
+use symmetry, only: make_primitive, get_lattice_pointGroup, get_spaceGroup
 use enumeration_types
 implicit none
 public get_HNFs
@@ -15,7 +15,7 @@ Module HNF_profiler
   !!system.</parameter>
   !!<parameter name="atom_pos" regular="true">The atomic basis in
   !!cartesian coordinates.</parameter>
-  !!<parameter name="atom_types" regular="true">The atomic occupansies
+  !!<parameter name="atom_types" regular="true">The atomic occupancies
   !!for each atom in the cell (atom A = 0, B = 1 ....).</parameter>
   !!<parameter name="n_" regular="true">The determinant of the desired
   !!HNF.</parameter>
@@ -32,8 +32,9 @@ Module HNF_profiler
   !!<parameter name="pgs" regular="true">The size of the
   !!point-group for the superlattice.</parameter>
   subroutine get_HNFs(A, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_, eps_)
-    real(dp), intent(in) :: A(3,3), atom_pos(:,:)
-    integer, intent(in) :: atom_types(:)
+    real(dp), intent(in) :: A(3,3)
+    real(dp), allocatable :: atom_pos(:,:)
+    integer, intent(inout) :: atom_types(:)
     integer, intent(out) :: hnfs(100,3,3)
     real(dp), intent(out) :: r_mins(100), r_maxs(100)
     integer, intent(out) :: pgs(100), dets(100)
@@ -46,13 +47,19 @@ subroutine get_HNFs(A, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_
     type(RotPermList), pointer :: RPlist(:)
     integer, pointer :: all_hnfs(:,:,:), unq_hnfs(:,:,:), degeneracy_list(:)
     type(opList), pointer :: fixop(:)
-    real(dp), pointer :: latts(:,:,:), d(:,:), pg_Ops(:,:,:), atomPos(:,:)
+    real(dp), allocatable :: atomPos(:,:), d(:,:)
+    real(dp), pointer :: latts(:,:,:), pg_Ops(:,:,:)
     real(dp) :: reduced_latt(3,3), norms(3), inv_lat(3,3), prim_lat(3,3)
     integer :: temp_hnfs(100,3,3), det_fix, js(100), HNF(3,3),temp_mat(3,3)
     integer, pointer :: atomTypes(:)
     real(dp), allocatable, target :: temp_pos(:,:)
     integer, allocatable, target :: temp_types(:)
 
+    real(dp), allocatable :: sg_op(:,:,:)
+    real(dp), allocatable :: sg_fract(:,:)
+    logical               :: lattcoords
+    integer               :: nD
+
     ! It only makes sense to use this code for bulk crystals and not
     ! surfaces so we hardcode the LatDim to be 3.
     LatDim = 3
@@ -88,25 +95,36 @@ subroutine get_HNFs(A, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_
     ! Here we allocate temp variables for the atom types and positions
     ! and then associate them with pointers that will be passed into
     ! make_primitive. This is necessary because F90wrap cannot have
-    ! pointers declared in the subroutine call derictley and so we
+    ! pointers declared in the subroutine called directly and so we
     ! have to define the pointers internally. The pointers also can't
-    ! be set equal to the input variables becaus it causes segfaults
+    ! be set equal to the input variables because it causes segfaults
     ! when the code is run, hence the temporary variables.
     allocate(temp_pos(size(atom_pos,1),size(atom_pos,2)),temp_types(size(atom_types,1)))
     temp_pos = atom_pos
-    temp_types = atom_types 
-    atomPos => temp_pos
+    temp_types = atom_types
+    atomPos = temp_pos
     atomTypes => temp_types
     call make_primitive(prim_lat, atomTypes, atomPos, .False., eps_=eps)
 
-    call get_dvector_permutations(prim_lat, d, dRPList, LatDim, eps)
+    ! Get the space group of the parent lattice.
+    lattcoords = .false.
+    call get_spaceGroup(prim_lat, atom_types, atom_pos, sg_op, sg_fract, &
+                 & lattcoords, eps)
+
+    ! The number of active sites is the same as the number of atoms.
+    nD = size(atom_pos,2)
+
+    call get_dvector_permutations(prim_lat, d, nD, sg_op, sg_fract, dRPList, &
+                                  LatDim, eps)
     call matrix_inverse(prim_lat, inv_lat)
 
     do i=n_min,n_max
-       ! Find all the HFNs then remove those that are equivalent.
+       ! Find all the HNFs then remove those that are equivalent.
        call get_all_HNFs(i, all_hnfs)
-       call remove_duplicate_lattices(all_hnfs, LatDim, prim_lat, d, dRPList, unq_hnfs, &
-            fixop, RPList, latts, degeneracy_list,eps)
+
+       call remove_duplicate_lattices(all_hnfs, LatDim, prim_lat, sg_op, &
+            sg_fract, d, dRPList, unq_hnfs, fixop, RPList, latts, &
+            degeneracy_list,eps)
        count_i = 0
        max_rmin = 0
        temp_hnfs = 0
@@ -136,7 +154,7 @@ subroutine get_HNFs(A, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_
              js(count_i) = j
           end if
        end do
-       
+
        do j=1,count_i
           ! We repeat the minkowski reduction here to get the rmax
           ! value and retrieve the point group for the lattice. Later
@@ -154,11 +172,11 @@ subroutine get_HNFs(A, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_
           r_maxs(n_hnfs) = this_rmax
           dets(n_hnfs) = i
           pgs(n_hnfs) = size(pg_Ops,3)
-          if (n_hnfs==100) exit 
+          if (n_hnfs==100) exit
        end do
        deallocate(latts, unq_hnfs, RPList, fixOp)
        js = 0
-       if (n_hnfs==100) exit 
+       if (n_hnfs==100) exit
     end do
   end subroutine get_HNFs
 

aux_src/README.md

@@ -1,40 +1,41 @@
-##BRIEF DESCRIPTION
+### BRIEF DESCRIPTION
 
 ## Description of aux_src files
 
-These files contain program's that can be useful for some users and need should be maintained but are not necessary for the main code, enum.x, to run. A description of what each file does follows:
+These files contain programs that can be useful for some users and need should be maintained but are not necessary for the main code, `enum.x`, to run. A description of what each file does follows:
 
-#makestr.f90:
-makestr.f90 is used for making POSCARs, it is accessed and used in the src directory by typing
+# makestr.f90:
+`makestr.f90` is used for making `POSCAR`s. It is accessed and used in the src directory by typing
 `make makestr.x`
 
-#make2Dplot.f90: This program is used to make a 2D plot of the
+# make2Dplot.f90:
+This program is used to make a 2D plot of the
 enumeration results. It can also be compiled in the src directory by
-typing `make 2Dplot.x`. This program relies on splot.f which won't
+typing `make 2Dplot.x`. This program relies on `splot.f` which won't
 compile with gfortran. To use this program compile with ifort.
 
-#convert_structure_to_enumformat.f90:
+# convert_structure_to_enumformat.f90:
 This program is designed to convert a structures.in file to structure.enum.out file. It can be compiled in the src directory using `make convert_structures_to_enumformat.x`
 
-#HNF_counter.f90:
+# HNF_counter.f90:
 
-#compare_two_enum_files.f90:
+# compare_two_enum_files.f90:
 It can be compiled from the src directory using `make compare_enum_files.x`
 
-#cwrapper.f90:
+# cwrapper.f90:
 This prgram provides an interface for C++.
 
-#find_structure_in_list.f90:
+# find_structure_in_list.f90:
 It can be compiled from the src directory using `make find_structure_in_list.x`
-ih
-#makePerovStr.f90:
+
+# makePerovStr.f90:
 This program reads in a file in struct_enum.out format and writes out a VASP-like structue file. It can be compiled from the src directory using `make makeperovstr.x`
 
-#makeStr2D.f90:
+# makeStr2D.f90:
 This program reads in a file in struct_enum.out format and writes out a VASP-like structue file for a surface calculation. It can be compiled in the src directory using `make makestr.2d`
 
-#random_lattice_driver.f90:
+# random_lattice_driver.f90:
 
 If you have questions, email or call: gus.hart@gmail.com, 801-422-7444
 
-For in-depth examples, please see the `EXAMPLES` file in the `support` directory.
+For in-depth examples, please see the `EXAMPLES` file in the `support` directory.

src/derivative_structure_generator.f90

@@ -21,8 +21,8 @@ MODULE derivative_structure_generator
 private
 public get_all_HNFs, remove_duplicate_lattices, get_SNF, get_all_2D_HNFs,&
      &  gen_multilattice_derivatives, find_permutation_of_group,&
-     get_dvector_permutations, get_rotation_perms_lists, do_rotperms_form_groups,&
-     & mixed_radix_counter
+     & get_dvector_permutations, get_rotation_perms_lists,&
+     & do_rotperms_form_groups, mixed_radix_counter
 
 CONTAINS
 

wrap/f90wrap_HNF_profiler.f90

@@ -4,10 +4,10 @@ subroutine f90wrap_get_hnfs(a, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs,
     dets, n0, n1, n2, n_, eps_)
     use hnf_profiler, only: get_hnfs
     implicit none
-    
+
     real(8), intent(in), dimension(3,3) :: a
-    real(8), intent(in), dimension(n0,n1) :: atom_pos
-    integer, intent(in), dimension(n2) :: atom_types
+    real(8), intent(in), dimension(n0,n1), allocatable :: atom_pos(:,:)
+    integer, intent(inout), dimension(n2) :: atom_types
     integer, dimension(100,3,3), intent(inout) :: hnfs
     real(8), dimension(100), intent(inout) :: r_mins
     real(8), dimension(100), intent(inout) :: r_maxs
@@ -26,4 +26,3 @@ subroutine f90wrap_get_hnfs(a, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs,
 end subroutine f90wrap_get_hnfs
 
 ! End of module hnf_profiler defined in file ../aux_src/HNF_profiler.f90
-

wrap/supercell.py

@@ -8,11 +8,11 @@ def get_supers(atoms,n_=None,eps_=None):
     n_ (default 100) multiples of the parent cell.
 
     Args:
-        atoms (quipy.atoms.Atoms): an atoms object that the supercell 
+        atoms (quipy.atoms.Atoms): an atoms object that the supercell
             matrices will be found for.
         n_ (int): optional maximum number of multiples to find.
         eps_ (float): optional floating point tolerance.
-    
+
     Returns:
         (hnfs,rmin) the integer matrices that create unique supercells of the parent,
             and the rmin_values that match.
@@ -30,8 +30,8 @@ def get_supers(atoms,n_=None,eps_=None):
     u_atoms = np.unique(atoms_nums)
     atom_types = []
     for i in atoms_nums:
-        atom_types.append(np.where(u_atoms==i)[0][0])    
-    
+        atom_types.append(np.where(u_atoms==i)[0][0])
+
     Hnf_Profiler.get_hnfs(np.transpose(atoms.cell), np.transpose(atoms.positions),
                           atom_types, hnfs, rmin, rmax, pgs, dets, n_=n_, eps_=eps_)
     # We have more entries than needed. We only want to keep the non-zero ones.
@@ -43,20 +43,20 @@ def get_supers(atoms,n_=None,eps_=None):
 class Hnf_Profiler(f90wrap.runtime.FortranModule):
     """
     Module hnf_profiler
-    
-    
+
+
     Defined at ../aux_src/HNF_profiler.f90 lines 1-141
-    
+
     """
     @staticmethod
     def get_hnfs(a, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_=None, \
         eps_=None):
         """
         get_hnfs(a, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets[, n_, eps_])
-        
-        
+
+
         Defined at ../aux_src/HNF_profiler.f90 lines 34-141
-        
+
         Parameters
         ----------
         a : float array
@@ -69,13 +69,13 @@ def get_hnfs(a, atom_pos, atom_types, hnfs, r_mins, r_maxs, pgs, dets, n_=None,
         dets : int array
         n_ : int
         eps_ : float
-        
+
         """
         _supercell.f90wrap_get_hnfs(a=a, atom_pos=atom_pos, atom_types=atom_types, \
             hnfs=hnfs, r_mins=r_mins, r_maxs=r_maxs, pgs=pgs, dets=dets, n_=n_, \
             eps_=eps_)
-    
+
     _dt_array_initialisers = []
-    
+
 
 hnf_profiler = Hnf_Profiler()