Merge lp:~nickpapior/siesta/merge-OSSO-fixes into lp:~albertog/siesta/merge-OSSO

[Nick Papior]

Fixed minor issues and comments from me.

[Alberto Garcia (albertog)]

Good. Thanks!

review: Approve

=== modified file 'Docs/siesta.tex'
--- Docs/siesta.tex	2018-04-20 08:00:21 +0000
+++ Docs/siesta.tex	2018-04-20 13:37:02 +0000
@@ -2242,7 +2242,7 @@
 The default is \emph{one} KB projector from each angular momentum,
 constructed from the nodeless eigenfunction.
 
-For full spin--orbit calculations, the program generates $lj$
+For full spin-orbit calculations, the program generates $lj$
 projectors using the $l+1/2$ and $l-1/2$ components of the
 (relativistic) pseudopotentials. In this case the specification of the
 reference energies for projectors is not changed: only $l$ is
@@ -3258,7 +3258,7 @@
     coordinates rigidly to have them positive, by using
     \fdf{AtomicCoordinatesOrigin}.  See the
     \program{Sies2arc}\index{Sies2arc@\textsc{Sies2arc}} utility in the
-    \program{Util/} directory for generating \sysfile*{.arc} files for CERIUS animation.
+    \program{Util/} directory for generating \sysfile*{arc} files for CERIUS animation.
 
   \end{fdflogicalF}
 
@@ -3728,12 +3728,12 @@
 
     \option[spin-orbit]%
     \fdfindex*{Spin:spin-orbit}%
-    Performs calculations including the spin--orbit coupling. By default the 
-    off--site SO option is set to \fdftrue. To perform an on--site SO calculations 
-    this option has to be {\bf spin-orbit+onsite}. This requires the
+    Performs calculations including the spin-orbit coupling. By default the 
+    off-site SO option is set to \fdftrue. To perform an on-site SO calculations 
+    this option has to be \fdf*{spin-orbit+onsite}. This requires the
     pseudopotentials to be relativistic.
 
-    See Sect.~\ref{sec:spin-orbit} for further specific spin--orbit options.
+    See Sect.~\ref{sec:spin-orbit} for further specific spin-orbit options.
 
   \end{fdfoptions}
 
@@ -3778,48 +3778,49 @@
 \end{fdflogicalF}
 
 
-\subsection{Spin--Orbit coupling}
+\subsection{Spin-Orbit coupling}
 \label{sec:spin-orbit}
 
 \siesta\ includes the posibility to perform fully relativistic
 calculations by means of the inclusion in the total Hamiltonian not
 only the Darwin and velocity correction terms~(Scalar--Relativistic
-calculations), but also the spin--orbit~(SO) contribution. There are 
-two approaches regarding the SO formalism: on--site and off--site.
-Within the on--site approximation only the intra--atomic SO contribution is taken 
-into account. In the off--site scheme additional neighboring 
-interactions are also included in the SO term. By default, the off--site SO 
-formalism is switched on, being necessary to change the \fdf{Spin} flag 
-in the input file if the on--site approximation wants to be used. See 
-\fdf{Spin} on how to handle the spin--orbit coupling. 
+calculations), but also the spin-orbit~(SO) contribution. There are
+two approaches regarding the SO formalism: on-site and off-site.
+Within the on-site approximation only the intra-atomic SO
+contribution is taken into account. In the off-site scheme additional
+neighboring interactions are also included in the SO term. By default,
+the off-site SO formalism is switched on, being necessary to change
+the \fdf{Spin} flag in the input file if the on-site approximation
+wants to be used. See \fdf{Spin} on how to handle the spin-orbit
+coupling.
 
-The on--site spin-orbit scheme in this version of \siesta\ has been implemented by
-Dr. Ram\'on Cuadrado based on the original on--site SO formalism and
+The on-site spin-orbit scheme in this version of \siesta\ has been implemented by
+Dr. Ram\'on Cuadrado based on the original on-site SO formalism and
 implementation developed by Prof. Jaime Ferrer and his collaborators \textit{et al}~(L
 Fern\'andez--Seivane, M Oliveira, S Sanvito, and J Ferrer, Journal of
-Physics: Condensed Matter, {\bf 18}, 7999 (2006); L Fern\'andez--Seivane 
-and Jaime Ferrer, Phys. Rev. Lett. {\bf 99}, 183401 (2007)).
+Physics: Condensed Matter, \textbf{18}, 7999 (2006); L Fern\'andez--Seivane 
+and Jaime Ferrer, Phys. Rev. Lett. \textbf{99}, 183401 (2007)).
 
-The off--site scheme has been implemented by
+The off-site scheme has been implemented by
 Dr. Ram\'on Cuadrado and Dr. Jorge I. Cerd\'a based on their initial 
 work~(R. Cuadrado and J. I. Cerd\'a ``Fully relativistic pseudopotential 
 formalism under an atomic orbital basis: spin-orbit splittings and 
-magnetic anisotropies'', J. Phys.: Condens. Matter {\bf 24}, 086005 (2012); 
+magnetic anisotropies'', J. Phys.: Condens. Matter \textbf{24}, 086005 (2012); 
 ``In-plane/out-of-plane disorder influence on the magnetic anisotropy of 
 Fe$_{1-y}$Mn$_y$Pt-L1(0) bulk alloy'', R. Cuadrado, Kai Liu, Timothy 
-J. Klemmer and R. W. Chantrell, Applied Physics Letters, {\bf 108}, 
+J. Klemmer and R. W. Chantrell, Applied Physics Letters, \textbf{108}, 
 123102 (2016)).  
 
 The inclusion of the SO term in the Hamiltonian (and in the Density
-Matrix) causes an increase in the number of non--zero elements in their
-off--diagonal parts, i.e., for some $(\mu,\nu)$ pair of basis
-orbitals, H$^{\sigma\sigma'}_{\mu\nu}$~(DM$^{\sigma\sigma'}_{\mu\nu}$)
-[$\sigma,\sigma'$=$\uparrow,\downarrow$] will be $\neq$0. This is
+Matrix) causes an increase in the number of non-zero elements in their
+off-diagonal parts, i.e., for some $(\mu,\nu)$ pair of basis
+orbitals, $\mathbf H^{\sigma\sigma'}_{\mu\nu}$ ($\mathbf{DM}^{\sigma\sigma'}_{\mu\nu}$)
+[$\sigma,\sigma'=\uparrow,\downarrow$] will be $\neq0$. This is
 mainly due to the fact that the $\mathbf L\cdot\mathbf S$ operator
-will promote the mixing between different spin--up/down components.
-In addition, these H$^{\sigma\sigma'}_{\mu\nu}$~(and
-DM$^{\sigma\sigma'}_{\mu\nu}$) elements will be complex, in contrast
-with typical polarized/non--polarized calculations where these
+will promote the mixing between different spin-up/down components.
+In addition, these $\mathbf H^{\sigma\sigma'}_{\mu\nu}$ (and
+$\mathbf{DM}^{\sigma\sigma'}_{\mu\nu}$) elements will be complex, in contrast
+with typical polarized/non-polarized calculations where these
 matrices are purely real. Since the spin-up and spin-down manifolds
 are essentially mixed, the solver has to deal with matrices whose
 dimensions are twice as large as for the collinear (unmixed) spin
@@ -3828,13 +3829,13 @@
 
 
 Unless explicitly advised the following type of calculation can be carried out 
-regardless of whether on--site or off--site approximation is employed: 
+regardless of whether on-site or off-site approximation is employed: 
 \begin{itemize}
   % 
   \item Selfconsistent calculations for gamma point as well as for
   bulks.
   %
-  \item Structure optimizations %% only supported by the off--site SO
+  \item Structure optimizations %% only supported by the off-site SO
     %% formalism *** Why ?
   %
   %%% *** Incompatible... \item LDA+U calculations~(See Sect.\ref{sec:lda+u} for further info).
@@ -3855,35 +3856,35 @@
   % 
 \end{itemize}
 
-Note: Due to the small SO contribution to the total
-energy, the level of precision required to perform a proper fully
-relativistic calculation during the selfconsistent process is quite
-demanding. The following values must be carefully converged and
-checked for each specific system to assure that the results are
-accurate enough: \fdf{SCF.H!Tolerance} during the
-selfconsistency~(typically between 10$^{-3}$eV -- 10$^{-4}$eV), 
-\fdf{ElectronicTemperature},
-\textbf{k}--point sampling and high values of
-\fdf{MeshCutoff}~(specifically for extended solids). In general, one
-can say that a good calculation will have high number of \textbf{k}--points,
-low \fdf{ElectronicTemperature}, extremely small \fdf{SCF.H!Tolerance}
-and high values of \fdf{MeshCutoff}.  We encourage the user to test
-carefully these options for each system. An additional point to take
-into account is the mixing scheme employed. You are encouraged to use 
-\fdf{SCF.Mix} \fdf*{hamiltonian} (currently is set up by default) 
-instead of density matrix mixing, since it speeds up the convergence. 
-The pseudopotentials have to be properly generated and tested for each 
-specific system and they have to be in their fully relativistic form,
-together with the non--linear core corrections. Finally it is worth to 
-mention that the selfconsistent convergence for some non--highly symmetric 
-magnetizations directions with respect to the physical symmetry axis 
+Note: Due to the small SO contribution to the total energy, the level
+of precision required to perform a proper fully relativistic
+calculation during the selfconsistent process is quite demanding. The
+following values must be carefully converged and checked for each
+specific system to assure that the results are accurate enough:
+\fdf{SCF.H!Tolerance} during the selfconsistency (typically between
+$10^{-3}\,\mathrm{eV}$ -- $10^{-4}\,\mathrm{eV}$),
+\fdf{ElectronicTemperature}, \textbf{k}--point sampling and high
+values of \fdf{MeshCutoff}~(specifically for extended solids). In
+general, one can say that a good calculation will have high number of
+\textbf{k}--points, low \fdf{ElectronicTemperature}, extremely small
+\fdf{SCF.H!Tolerance} and high values of \fdf{MeshCutoff}.  We
+encourage the user to test carefully these options for each system. An
+additional point to take into account is the mixing scheme
+employed. You are encouraged to use \fdf{SCF.Mix:hamiltonian}
+(currently is set up by default) instead of density matrix mixing,
+since it speeds up the convergence.  The pseudopotentials have to be
+properly generated and tested for each specific system and they have
+to be in their fully relativistic form, together with the non-linear
+core corrections. Finally it is worth to mention that the
+selfconsistent convergence for some non-highly symmetric
+magnetizations directions with respect to the physical symmetry axis
 could still be difficult.
 
 \begin{fdfentry}{Spin!OrbitStrength}[real]<1.0>
 
   It allows to vary the strength of the 
-  spin--orbit interaction from zero to any positive value. It can be
-  used for both the on--site and off-site SOC flavors, but only for
+  spin-orbit interaction from zero to any positive value. It can be
+  used for both the on-site and off-site SOC flavors, but only for
   debugging and testing purposes, as the only physical value is 1.0.
 
 \end{fdfentry}
@@ -3902,29 +3903,6 @@
 
 \end{fdflogicalF}
 
-% *** The following items should not be relevant.
-
-%%For the off--site SO approximation some mandatory flags have to set 
-%%up to \fdffalse\ in the fdf file: 
-
-%%\begin{fdflogicalT}{PAO!OldStylePolOrbs}
-
-%%  By default is set up to \fdftrue, however it has to set up to \fdffalse.
-
-%%\end{fdflogicalT}
-
-%%\begin{fdflogicalT}{DM.MixSCF1}
-
-%%  By default is set up to \fdftrue, however it has to set up to \fdffalse.
-
-%%\end{fdflogicalT}
-
-%%\begin{fdflogicalT}{Restricted.Radial.Grid}
-
-%%  By default is set up to \fdftrue, however it has to set up to \fdffalse.
-
-%%\end{fdflogicalT}
-
 
 
 \subsection{The self-consistent-field loop}
@@ -5049,7 +5027,7 @@
   \index{reading saved data!density matrix}
   
   Instructs to read the density matrix stored in file
-  \sysfile{.DM} by a previous run.
+  \sysfile{DM} by a previous run.
   
   \siesta\ will continue even if \sysfile*{DM} is not found.
 
@@ -9067,8 +9045,8 @@
 Enable an experimental timer which is based on wall time on the master
 node and is aware of the tree-structure of the timed sections. At the
 end of the program, a report is generated in the output file, and a
-{\tt time.json} file in JSON format is also written. \index{JSON
-  timing report@{\bf JSON timing report}} This file can be used by
+\file{time.json} file in JSON format is also written. \index{JSON
+  timing report@\textbf{JSON timing report}} This file can be used by
 third-party scripts to process timing data.
 
   \note, if used with the PEXSI solver (see Sec.~\ref{SolverPEXSI})
@@ -10620,9 +10598,9 @@
 
 \begin{fdflogicalF}{TDED.Saverho}
 
-If \fdftrue\ the instantaneous time-dependent density is saved to
-\texttt{ <istep>}.\texttt{TDRho}\index{TDRho@{\bf TDRho}} after every
-\fdf{TDED.Nsaverho} number of steps.
+  If \fdftrue\ the instantaneous time-dependent density is saved to
+  \file{<istep>.TDRho} after every \fdf{TDED.Nsaverho} number of
+  steps.
 
 \end{fdflogicalF}
 

=== modified file 'Src/bands.F'
--- Src/bands.F	2017-10-19 09:19:20 +0000
+++ Src/bands.F	2018-04-20 13:37:02 +0000
@@ -366,7 +366,6 @@
       use atmfuncs,     only : symfio, cnfigfio, labelfis, nofis
       use writewave,    only : wfs_filename
 
-!      use m_spin,       only: NoMagn, SPpol, NonCol, SpOrb
       use m_spin,       only: spin 
 
       use m_diag_option, only: ParallelOverK, Serial

=== modified file 'Src/dfscf.f'
--- Src/dfscf.f	2018-02-21 12:52:06 +0000
+++ Src/dfscf.f	2018-04-20 13:37:02 +0000
@@ -71,12 +71,8 @@
       use parallel,      only: Nodes, Node
       use sys,           only: die
       use parallelsubs,  only: GlobalToLocalOrb
-!      use m_spin,        only: NonCol, SpOrb
-!      use m_spin,        only: h_spin_dim, spinor_dim
 
-! CC RC  Added  for the offSpOrb
       use m_spin,        only: spin
-! CC RC  Added  for the offSpOrb
 
       implicit none
 
@@ -354,14 +350,12 @@
         ! done with nspin=4 (grid_nspin)?
         V(1:nsp,1:nspin) = Vscf(1:nsp,ip,1:nspin)
 
-!! CC RC  Added  for the offSpOrb
 C     Factor two for nondiagonal elements for non-collinear spin
-        if( spin%SO ) then
+        if ( spin%SO ) then
          V(1:nsp,7:8) = V(1:nsp,3:4)
-        elseif( spin%NCol ) then 
+        else if ( spin%NCol ) then 
          V(1:nsp,3:4) = 2.0_dp * V(1:nsp,3:4)
-        endif
-!! CC RC  Added  for the offSpOrb
+        end if
 
 C     Loop on first orbital of mesh point
         do ic = 1,nc

=== modified file 'Src/m_spin.F90'
--- Src/m_spin.F90	2018-04-19 12:47:26 +0000
+++ Src/m_spin.F90	2018-04-20 13:37:02 +0000
@@ -184,18 +184,14 @@
        spin%NCol = .true.
        
     else if ( leqi(opt, 'spin-orbit') .or. leqi(opt, 'S-O') .or. &
-         leqi(opt, 'SOC') .or. leqi(opt, 'SO') ) then
+         leqi(opt, 'SOC') .or. leqi(opt, 'SO') .or. &
+         leqi(opt, 'spin-orbit+offsite') .or. leqi(opt, 'S-O+offsite') .or. &
+         leqi(opt, 'SOC+offsite') .or. leqi(opt, 'SO+offsite') ) then
        ! Spin-orbit defaults to the off-site implementation
        
        spin%SO = .true.
        spin%SO_offsite = .true.
 
-    else if ( leqi(opt, 'spin-orbit+offsite') .or. leqi(opt, 'S-O+offsite') .or. &
-         leqi(opt, 'SOC+offsite') .or. leqi(opt, 'SO+offsite') ) then
-       
-       spin%SO = .true.
-       spin%SO_offsite = .true.
-
     else if ( leqi(opt, 'spin-orbit+onsite') .or. leqi(opt, 'S-O+onsite') .or. &
          leqi(opt, 'SOC+onsite') .or. leqi(opt, 'SO+onsite') ) then
        
@@ -207,12 +203,12 @@
        call die('Spin: unknown flag, please assert the correct input.')
     end if
 
-    if (spin%SO_offsite) then
+    if ( spin%SO_offsite ) then
        call add_citation("10.1088/0953-8984/24/8/086005")
-    endif
-    if (spin%SO_onsite) then
+    end if
+    if ( spin%SO_onsite ) then
        call add_citation("10.1088/0953-8984/18/34/012")
-    endif
+    end if
     
     ! Note that, in what follows,
     !   spinor_dim = min(h_spin_dim,2)
@@ -242,9 +238,10 @@
        spin%Col  = .false.
        spin%NCol = .false.
        spin%SO   = .true.
+       ! off/on MUST already be set!
 
        ! should be moved...
-       TRSym      = .false.
+       TRSym = .false.
 
     else if ( spin%NCol ) then
        ! Non-collinear case
@@ -257,13 +254,15 @@
        spin%spinor = 2
 
        ! Flags
-       spin%none = .false.
-       spin%Col  = .false.
-       spin%NCol = .true.
-       spin%SO   = .false.
+       spin%none       = .false.
+       spin%Col        = .false.
+       spin%NCol       = .true.
+       spin%SO         = .false.
+       spin%SO_onsite  = .false.
+       spin%SO_offsite = .false.
 
        ! should be moved...
-       TRSym      = .false.
+       TRSym = .false.
 
     else if ( spin%Col ) then
        ! Collinear case
@@ -276,13 +275,15 @@
        spin%spinor = 2
 
        ! Flags
-       spin%none = .false.
-       spin%Col  = .true.
-       spin%NCol = .false.
-       spin%SO   = .false.
+       spin%none       = .false.
+       spin%Col        = .true.
+       spin%NCol       = .false.
+       spin%SO         = .false.
+       spin%SO_onsite  = .false.
+       spin%SO_offsite = .false.
 
        ! should be moved...
-       TRSym      = .true.
+       TRSym = .true.
 
     else if ( spin%none ) then
        ! No spin configuration...
@@ -295,13 +296,15 @@
        spin%spinor = 1
 
        ! Flags
-       spin%none = .true.
-       spin%Col  = .false.
-       spin%NCol = .false.
-       spin%SO   = .false.
+       spin%none       = .true.
+       spin%Col        = .false.
+       spin%NCol       = .false.
+       spin%SO         = .false.
+       spin%SO_onsite  = .false.
+       spin%SO_offsite = .false.
 
        ! should be moved...
-       TRSym      = .true.
+       TRSym = .true.
 
     end if
 

=== modified file 'Src/rhoofd.F90'
--- Src/rhoofd.F90	2018-04-15 22:13:08 +0000
+++ Src/rhoofd.F90	2018-04-20 13:37:02 +0000
@@ -331,12 +331,6 @@
 !          Retrieve phi values
            if ( spin%SO_offsite ) then 
               Clocal(:,ic) = phia(iphi,:)
-!            if(ip.lt.10) then
-!             write(6,*) ' ip/nc/Clocal(1,:) = ', ip, nc, Clocal(1,:)   
-!            else
-!             stop 'Stopping in rhoofd...'
-!            endif
-
            else
               Clocal(:,ic) = dsqrt(2._dp) * phia(iphi,:)
            end if
@@ -389,13 +383,6 @@
 !          Retrieve phi values
            if ( spin%SO_offsite ) then 
               Clocal(:,ic) = phi(:,imp)
-!            if(ip.lt.5) then
-!             write(6,*) ' ip/nc/Clocal(1,:) = ', ip, nc, Clocal(1,:)
-!            else
-!             stop 'Stopping in rhoofd...'
-!            endif
-
-
            else
               Clocal(:,ic) = dsqrt(2._dp) * phi(:,imp)
            end if

=== modified file 'Src/state_analysis.F'
--- Src/state_analysis.F	2018-04-19 09:00:15 +0000
+++ Src/state_analysis.F	2018-04-20 13:37:02 +0000
@@ -22,7 +22,7 @@
      &                          CartesianForce_to_ZmatForce
       use atomlist,      only : iaorb, iphorb, amass, no_u, lasto
       use atomlist,      only : indxuo
-      use m_spin,        only : SpOrb
+      use m_spin,        only : spin
       use m_fixed,       only : fixed
       use sparse_matrices
       use siesta_geom
@@ -167,7 +167,7 @@
       endif
 
 !     Population and moment analysis 
-      if ( SpOrb .and. orbmoms) then
+      if ( spin%SO .and. orbmoms) then
          call moments( 1, na_u, no_u, maxnh, numh, listhptr,
      .           listh, S, Dscf, isa, lasto, iaorb, iphorb,
      .           indxuo )

=== modified file 'version.info'
--- version.info	2018-04-20 09:41:55 +0000
+++ version.info	2018-04-20 13:37:02 +0000
@@ -1,1 +1,1 @@
-trunk-687--merge-OSSO-694
+trunk-687--merge-OSSO-694--fixes-1