Merge pull request #61 from optados-developers/PR51

This adds "PDOS String Reads labels" functionallity
optados-developers · Nov 14, 2024 · bb8a1a9 · bb8a1a9
2 parents 7445701 + f3d8e73
commit bb8a1a9
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diff --git a/optados/documents/user_guide.tex b/optados/documents/user_guide.tex
@@ -16,6 +16,8 @@
 \def\red{\textcolor{red}}
 \usepackage{lscape}
 
+\usepackage{hyperref}
+
 %\parskip=2mm
 \newcommand{\kbf}{\mathbf{k}}
 \renewcommand{\d}{\mathrm{d}}
@@ -415,12 +417,18 @@ \section{Installation}
 
 Choose which compiler to use to make \optados. The valid values are:
 \begin{itemize}
-\item[{\bf --}]  \verb#g95# (default)
-\item[{\bf --}]  \verb#gfortran#
+\item[{\bf --}]  \verb#gfortran# (default)
 \item[{\bf --}]  \verb#ifort#
 \item[{\bf --}]  \verb#nag#
-\item[{\bf --}]  \verb#pathscale#
 \item[{\bf --}]  \verb#pgf90#
+\item[{\bf --}]  \verb#AOOC#
+\item[{\bf --}]  \verb#oneAPI#
+\end{itemize}
+
+The following are no longer supported but are provided for legacy systems:
+\begin{itemize}
+\item[{\bf --}]  \verb#g95# 
+\item[{\bf --}]  \verb#pathscale#
 \item[{\bf --}]  \verb#sun#
 \end{itemize}
 
@@ -741,6 +749,9 @@ \section{PDOS Parameters}
 \item[{\bf --}]  \verb#Si1(s;d)#     (decompose onto 's' and 'd' channels for
   atom Si1)
 \item[{\bf --}]  \verb#sum:C1:C3:C4-C8#  (decompose onto atoms C1, C2 and C4,C5,C6,C7,C8 and combine into the single projection)
+\item[{\bf --}]  \verb#``C:Exi'':H#  (decompose only onto site labelled C:Exi in \verb#seedname-out.cell# and Hydrogen sites)
+\item[{\bf --}]  \verb#``C'':H#  (decompose only onto Carbon sites that \textit{are not labelled} in \verb#seedname-out.cell# and Hydrogen sites. \textit{N.B} this is the same as  \verb#C:H# if no sites are labelled.)
+
 
 \end{itemize}
 

diff --git a/optados/src/electronic.f90 b/optados/src/electronic.f90
@@ -1149,9 +1149,8 @@ subroutine elec_pdos_read
 
     ! Band indices used in the read-in of the pdos
     real(kind=dp)                        :: dummyr1, dummyr2, dummyr3
-    integer                              :: dummyi, ib, ik, is
+    integer                              :: dummyi, ib, ik, is, iorbitals
     integer                              :: pdos_in_unit, ierr, inodes
-    logical                              :: full_debug_pdos_weights = .false.
     character(filename_len) :: pdos_filename
     real(kind=dp) :: time0, time1, file_version
     real(kind=dp), parameter :: file_ver = 1.0_dp
@@ -1181,14 +1180,15 @@ subroutine elec_pdos_read
       read (pdos_in_unit) pdos_mwab%nspins
       read (pdos_in_unit) pdos_mwab%norbitals
       read (pdos_in_unit) pdos_mwab%nbands
-      if (full_debug_pdos_weights) then
-        write (stdout, *) " ***** F U L L _ D E B U G _ P D O S _ W E I G H T S ***** "
-        write (stdout, *) "pdos_mwab%nkpoints= ", pdos_mwab%nkpoints
-        write (stdout, *) "pdos_mwab%nspins= ", pdos_mwab%nspins
-        write (stdout, *) "pdos_mwab%norbitals= ", pdos_mwab%norbitals
-        write (stdout, *) "pdos_mwab%nbands= ", pdos_mwab%nbands
-        write (stdout, *) "   **** ***** *****  ***** ***** *****  ***** ***** *****  "
-      end if
+      if (iprint > 3) then
+        write (stdout, *) " +==========================================================================+"
+        write (stdout, *) " |                          D E B U G   P D O S                             |"
+        write (stdout, *) " +==========================================================================+"
+        write (stdout, *) " pdos_mwab%nkpoints : ", pdos_mwab%nkpoints
+        write (stdout, *) " pdos_mwab%nspins   : ", pdos_mwab%nspins
+        write (stdout, *) " pdos_mwab%norbitals: ", pdos_mwab%norbitals
+        write (stdout, *) " pdos_mwab%nbands   : ", pdos_mwab%nbands
+      endif
 
       allocate (pdos_orbital%species_no(pdos_mwab%norbitals), stat=ierr)
       if (ierr /= 0) call io_error(" Error : cannot allocate pdos_orbital")
@@ -1200,6 +1200,18 @@ subroutine elec_pdos_read
       read (pdos_in_unit) pdos_orbital%species_no(1:pdos_mwab%norbitals)
       read (pdos_in_unit) pdos_orbital%rank_in_species(1:pdos_mwab%norbitals)
       read (pdos_in_unit) pdos_orbital%am_channel(1:pdos_mwab%norbitals)
+      if (iprint > 3) then
+        write (stdout, *)
+        write (stdout, *) " +--------------------------------------------------------------------------+"
+        write (stdout, *) "                                   pdos_orbital%                           "
+        write (stdout, *) "       species_no                 rank_in_species                am_channel"
+        write (stdout, *) " +--------------------------------------------------------------------------+"
+        do iorbitals = 1, pdos_mwab%norbitals
+          write (stdout, '(10x,i5,25x,i5,25x,i5)') pdos_orbital%species_no(iorbitals), pdos_orbital%rank_in_species(iorbitals), &
+          & pdos_orbital%am_channel(iorbitals)
+        end do
+        write (stdout, *) " +==========================================================================+ "
+      end if
       !-------------------------------------------------------------------------!
     end if
     call comms_bcast(pdos_mwab%norbitals, 1)
@@ -1235,7 +1247,7 @@ subroutine elec_pdos_read
             read (pdos_in_unit) dummyi ! this is the spin number
             read (pdos_in_unit) nbands_occ(ik, is)
             do ib = 1, nbands_occ(ik, is)
-              if (full_debug_pdos_weights) then
+              if (iprint > 3) then
                 write (stdout, *) " ***** F U L L _ D E B U G _ P D O S _ W E I G H T S ***** "
                 write (stdout, *) ib, ik, is
                 write (stdout, *) "   **** ***** *****  ***** ***** *****  ***** ***** *****  "

diff --git a/optados/src/parameters.f90 b/optados/src/parameters.f90
@@ -36,7 +36,7 @@ module od_parameters
 
   use od_constants, only: dp
   use od_io, only: stdout, maxlen
-  use od_cell, only: atoms_label, num_atoms, num_species, atoms_symbol, &
+  use od_cell, only: atoms_label, num_atoms, num_species, atoms_symbol, atoms_label, &
        & atoms_species_num, atoms_pos_frac, atoms_pos_cart, num_crystal_symmetry_operations
 
   implicit none
@@ -549,6 +549,7 @@ subroutine param_write_atomic_coord
     implicit none
 
     integer :: nat, nsp, atom_counter
+    character(len=maxlen) :: temp_symb
 
     ! System
 
@@ -558,14 +559,20 @@ subroutine param_write_atomic_coord
       if (iprint > 2) then
         write (stdout, '(1x,a)') '+----------------------------------------------------------------------------+'
         if (lenconfac .eq. 1.0_dp) then
-          write (stdout, '(1x,a)') '|   Site       Fractional Coordinate          Cartesian Coordinate (Ang)     |'
+          write (stdout, '(1x,a)') '|      Site            Fractional Coordinate     Cartesian Coordinate (Ang)  |'
         else
-          write (stdout, '(1x,a)') '|   Site       Fractional Coordinate          Cartesian Coordinate (Bohr)    |'
+          write (stdout, '(1x,a)') '|      Site            Fractional Coordinate     Cartesian Coordinate (Bohr)  |'
         end if
         write (stdout, '(1x,a)') '+----------------------------------------------------------------------------+'
         do nsp = 1, num_species
           do nat = 1, atoms_species_num(nsp)
-            write (stdout, '(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|', atoms_symbol(nsp), nat, &
+            ! Use the atoms species unless atom label is present
+            if (trim(atoms_symbol(nsp)) .ne. trim(atoms_label(nsp))) then
+              temp_symb = atoms_label(nsp)
+            else
+              temp_symb = atoms_symbol(nsp)
+            endif
+            write (stdout, '(1x,a1,1x,a7,1x,i3,7x,3F8.4,3x,a1,1x,3F8.4,4x,a1)') '|', trim(temp_symb), nat, &
               atoms_pos_frac(:, nat, nsp), '|', atoms_pos_cart(:, nat, nsp)*lenconfac, '|'
           end do
         end do