Merge lp:~albertog/siesta/4.1-scf-first into lp:~nickpapior/siesta/4.1-scf-first

[Alberto Garcia]

I have written a longer explanation in the manual. In particular, I explicitly mention that atomically filled DMs will be mixed by default, something that might be important in some cases.

Besides, this case highlights a contradiction: atomically filled DMs are not idempotent, and yet we happily mix them.

In fact, I believe that the idempotency issue is a red herring. Our DM is a decimated version of the true DM: we only keep those elements for which S (actually H) is not zero. This is fine to compute the charge density, and even to compute things like Tr(H*DM) and similar constructs. But since our DM is not the true DM, it is not idempotent. Moreover, even if DM_1 and DM_2 are idempotent, their mixing will not be. The really important thing is that the *output* DM is the one to be used to compute things like the kinetic energy, and the *input* DM is only an intermediate tool to compute the Hamiltonian.

I have avoided to open the can of worms of the heuristics when mixing the Hamiltonian. I believe that we should soon offer the possibility of reading H from file.

[Alberto Garcia (albertog)]

I forgot to mention that I have removed the mention to idempotency in the warning given to the user when the "force" flag is enabled and the sparsity has changed. This matches my view on the reduced importance of the idempotency issue.

[Nick Papior (nickpapior)]

I think you made a branch of 4.1 (after 4.1-wfs merge), merged in 4.1-scf-first made changes and then committed. :(
I.e. it is difficult to merge in 4.1-scf-first since there are many unrelated changes.

Do you mind me updating 4.1-scf-first branch with what I think you changed in r1093?

[Nick Papior (nickpapior)]

PS. I think your changes looks extremely appropriate and well thought! Thanks!

[Nick Papior (nickpapior)]

Could you check r1086 on lp:~nickpapior/siesta/4.1-scf-first to see if all is good?

[Alberto Garcia (albertog)]

Yes, that is correct!

----- El 19 de Ago de 2019, a las 10:19, Nick Rubner Papior <email address hidden> escribió:

| Could you check r1086 on lp:~nickpapior/siesta/4.1-scf-first to see if all is
| good?
| --
| https://code.launchpad.net/~albertog/siesta/4.1-scf-first/+merge/371434
| You are the owner of lp:~albertog/siesta/4.1-scf-first.

=== modified file 'Docs/Contributors.txt'
--- Docs/Contributors.txt	2018-10-22 14:12:27 +0000
+++ Docs/Contributors.txt	2019-08-18 23:02:58 +0000
@@ -60,6 +60,7 @@
 Magnus Paulsson
 Oscar Paz
 Andrei Postnikov
+Roberto Robles
 Tristana Sondon
 Andrew Walker
 Andrew Walkingshaw

=== modified file 'Docs/siesta.tex'
--- Docs/siesta.tex	2019-08-16 10:13:21 +0000
+++ Docs/siesta.tex	2019-08-18 23:02:58 +0000
@@ -277,6 +277,7 @@
 Magnus Paulsson,
 Oscar Paz,
 Andrei Postnikov,
+Roberto Robles,
 Tristana Sondon,
 Andrew Walker,
 Andrew Walkingshaw,
@@ -4103,23 +4104,41 @@
   \fdfindex*{DM.MixSCF1}[|see SCF.Mix.First]
   \fdfdepend{SCF.Mix!First.Force}%
 
-  Whether the first SCF should be mixed or it uses the output as input
-  in the next SCF step. It is generally advised to set this to true,
-  at least when restarting calculations.
-
-  The general logic of mixing on the first method is determined by the
-  read matrices. If the sparsity pattern has changed between the read
-  matrix and the current matrix \siesta\ will default to \emph{not}
-  mix in the first step, regardless of this flag. To ensure mixing is
-  done in the first step \fdf{SCF.Mix!First.Force} should be set to
-  \fdftrue.
+  This flag is used to decide whether mixing (of the DM or H) should
+  be done in the first SCF step. If mixing is not performed the output
+  DM or H generated in the first SCF step is used as input in the next
+  SCF step. When mixing the DM, this ``reset'' has the effect of
+  avoiding potentially undesirable memory effects: for example, a DM
+  read from file which corresponds to a different structure might not
+  satisfy the correct symmetry, and mixing will not fix it. On the
+  other hand, when reusing a DM for a restart of an interrupted
+  calculation, a full reset might not be advised.
+
+  The value of this flag is one of the ingredients used by \siesta\ to
+  decide what to do. If \fdftrue (the default), mixing will be
+  performed in all cases, except when a DM has been read from file and
+  the sparsity pattern of the DM on file is different from the current
+  one.  To ensure that a first-step mixing is done even in this case,
+  \fdf{SCF.Mix!First.Force} should be set to \fdftrue.
+
+  If the flag is \fdffalse, no mixing in the first step will be
+  performed, except if overridden by \fdf{SCF.Mix!First.Force}.
   
+  Note that the default value for this flag has changed from the old
+  (pre-version 4) setting in \siesta\. The new setting is most
+  appropriate for the case of restarting calculations. On the other
+  hand, it means that mixing in the first scf step will also be
+  performed for the standard case in which the initial DM is built as
+  a (diagonal) superposition of atomic orbital occupation values. In
+  some cases (e.g. spin-orbit calculations) better results might be
+  obtained by avoiding this mixing.
+
 \end{fdflogicalT}
 
 \begin{fdflogicalF}{SCF.Mix!First.Force}
 
-  Force the mixing of the first step, regardless of what \siesta\ may
-  heuristically decide.
+  Force the mixing (of DM or H) in the first SCF step, regardless of
+  what \siesta\ may heuristically decide.
 
   This overrules \fdf{SCF.Mix!First}.
   
@@ -10915,6 +10934,12 @@
   in a \tbtrans\ calculation to achieve a converged transmission
   function.
 
+  \item%
+  Energies from \tsiesta\ are \emph{not} to be trusted since the open
+  boundaries complicates the energy calculation. Therefore you cannot
+  compare energies between different calculations and/or different
+  bias'.
+
 \end{itemize}
 
 \subsection{Electrodes}
@@ -12137,12 +12162,18 @@
   
 \end{fdfentry}
 
-\begin{fdfentry}{TS!Elecs!DM.Init}[string]<diagon|bulk>
+\begin{fdfentry}{TS!Elecs!DM.Init}[string]<bulk|diagon>
 
   The density matrix elements in the electrodes may be forcefully set
   to the bulk values by reading in the DM of the corresponding
-  electrode. This may be set to \fdf*{bulk} to forcefully set the bulk
-  values.
+  electrode. This is by default \fdf*{bulk} for non-bias calculation,
+  and otherwise defaults to \fdf*{diagon}.
+
+  This step is only required once since the DM will be constant in the
+  electrode regions and thus it will be propagated through the
+  \sysfile{TSDE} files without having to re-do this step.
+  If this is done (by default) in the 0 bias calculation it will also
+  be effective in the bias calculation.
 
   \note this will automatically be set to \fdf*{diagon} for
   non-equilibrium calculations. If bulk density matrix elements are

=== modified file 'Src/Makefile'
--- Src/Makefile	2019-05-21 09:18:42 +0000
+++ Src/Makefile	2019-08-18 23:02:58 +0000
@@ -434,7 +434,8 @@
 	 m_ts_cctype.o ts_init.o ts_show_regions.o m_ts_electype.o \
 	 m_ts_method.o m_ts_elec_se.o \
 	 m_ts_debug.o m_ts_tdir.o \
-	 m_ts_chem_pot.o m_transiesta.o m_ts_hartree.o m_ts_voltage.o
+	 m_ts_chem_pot.o m_transiesta.o m_ts_hartree.o m_ts_voltage.o \
+         ts_energies.o
 
 # contour objects
 TS_OBJS += m_ts_contour_eq.o m_ts_contour_neq.o m_ts_io_ctype.o \
@@ -647,8 +648,9 @@
 compute_ebs_shift.o: m_mpi_utils.o parallel.o precision.o
 compute_energies.o: atomlist.o class_SpData1D.o class_SpData2D.o dhscf.o
 compute_energies.o: files.o m_dipol.o m_energies.o m_mpi_utils.o m_ntm.o
-compute_energies.o: m_rhog.o m_spin.o precision.o siesta_geom.o
-compute_energies.o: siesta_options.o sparse_matrices.o
+compute_energies.o: m_rhog.o m_spin.o m_ts_global_vars.o precision.o
+compute_energies.o: siesta_geom.o siesta_options.o sparse_matrices.o
+compute_energies.o: ts_energies.o
 compute_max_diff.o: m_mpi_utils.o precision.o
 compute_norm.o: m_mpi_utils.o m_spin.o precision.o sparse_matrices.o
 compute_pw_matrix.o: alloc.o m_planewavematrix.o m_planewavematrixvar.o
@@ -683,11 +685,11 @@
 dhscf.o: vmat.o
 diag.o: alloc.o diag_option.o parallel.o precision.o sys.o
 diag2g.o: fermid.o intrinsic_missing.o parallel.o parallelsubs.o precision.o
-diag2g.o: sys.o
-diag2k.o: fermid.o parallel.o parallelsubs.o precision.o sys.o
+diag2g.o: sys.o writewave.o
+diag2k.o: fermid.o parallel.o parallelsubs.o precision.o sys.o writewave.o
 diag3g.o: fermid.o intrinsic_missing.o parallel.o parallelsubs.o precision.o
-diag3g.o: sys.o
-diag3k.o: fermid.o parallel.o parallelsubs.o precision.o sys.o
+diag3g.o: sys.o writewave.o
+diag3k.o: fermid.o parallel.o parallelsubs.o precision.o sys.o writewave.o
 diag_option.o: parallel.o precision.o
 diagg.o: alloc.o fermid.o intrinsic_missing.o m_spin.o parallel.o
 diagg.o: parallelsubs.o precision.o sys.o writewave.o
@@ -822,7 +824,7 @@
 m_dscfcomm.o: alloc.o parallel.o parallelsubs.o precision.o schecomm.o
 m_efield.o: atmfuncs.o m_cite.o m_ts_global_vars.o mesh.o parallel.o
 m_efield.o: precision.o siesta_cml.o siesta_geom.o sys.o units.o
-m_energies.o: precision.o
+m_energies.o: m_ts_global_vars.o precision.o
 m_eo.o: precision.o
 m_exp_coord.o: files.o m_os.o parallel.o precision.o units.o
 m_filter.o: bessph.o precision.o radfft.o sys.o
@@ -935,12 +937,13 @@
 m_test_io.o: precision.o
 m_timer.o: m_io.o m_walltime.o moreParallelSubs.o parallel.o precision.o sys.o
 m_transiesta.o: alloc.o class_OrbitalDistribution.o class_SpData1D.o
-m_transiesta.o: class_SpData2D.o class_Sparsity.o files.o m_interpolate.o
-m_transiesta.o: m_ts_charge.o m_ts_contour_eq.o m_ts_contour_neq.o
-m_transiesta.o: m_ts_electype.o m_ts_fullg.o m_ts_fullk.o m_ts_gf.o
-m_transiesta.o: m_ts_kpoints.o m_ts_method.o m_ts_mumpsg.o m_ts_mumpsk.o
-m_transiesta.o: m_ts_options.o m_ts_sparse.o m_ts_tri_common.o m_ts_tri_init.o
-m_transiesta.o: m_ts_trig.o m_ts_trik.o parallel.o precision.o units.o
+m_transiesta.o: class_SpData2D.o class_Sparsity.o files.o m_energies.o
+m_transiesta.o: m_interpolate.o m_ts_charge.o m_ts_contour_eq.o
+m_transiesta.o: m_ts_contour_neq.o m_ts_electype.o m_ts_fullg.o m_ts_fullk.o
+m_transiesta.o: m_ts_gf.o m_ts_kpoints.o m_ts_method.o m_ts_mumpsg.o
+m_transiesta.o: m_ts_mumpsk.o m_ts_options.o m_ts_sparse.o m_ts_tri_common.o
+m_transiesta.o: m_ts_tri_init.o m_ts_trig.o m_ts_trik.o parallel.o precision.o
+m_transiesta.o: units.o
 m_trialorbitalclass.o: precision.o units.o
 m_trimat_invert.o: class_TriMat.o intrinsic_missing.o m_pivot_array.o
 m_trimat_invert.o: precision.o
@@ -1321,6 +1324,10 @@
 timer.o: timer_tree.o
 timer_tree.o: m_walltime.o
 transition_rate.o: alloc.o fermid.o parallel.o parallelsubs.o precision.o sys.o
+ts_energies.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
+ts_energies.o: class_Sparsity.o geom_helper.o m_energies.o m_spin.o
+ts_energies.o: m_ts_electype.o m_ts_method.o m_ts_options.o parallel.o
+ts_energies.o: precision.o sparse_matrices.o
 ts_init.o: m_fixed.o m_os.o m_ts_cctype.o m_ts_charge.o m_ts_electrode.o
 ts_init.o: m_ts_electype.o m_ts_gf.o m_ts_global_vars.o m_ts_kpoints.o
 ts_init.o: m_ts_method.o m_ts_options.o parallel.o siesta_options.o
@@ -1346,7 +1353,7 @@
 write_subs.o: m_steps.o m_stress.o m_ts_global_vars.o parallel.o precision.o
 write_subs.o: siesta_cml.o siesta_geom.o siesta_options.o units.o zmatrix.o
 writewave.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-writewave.o: get_kpoints_scale.o kpoint_grid.o m_spin.o parallel.o
+writewave.o: get_kpoints_scale.o kpoint_grid.o m_spin.o m_spin.o parallel.o
 writewave.o: parallelsubs.o precision.o siesta_geom.o sys.o units.o
 xml.o: precision.o
 zm_broyden_optim.o: m_broyddj_nocomm.o parallel.o precision.o sys.o units.o
@@ -1506,6 +1513,7 @@
 t_spin.o: m_spin.o
 timer_options.o: timer.o
 trialorbitalclass.o: m_trialorbitalclass.o
+ts_energies_m.o: ts_energies.o
 version_info.o: version.o
 write_subs_energies.o: write_subs.o
 write_subs_positions.o: write_subs.o

=== modified file 'Src/alloc.F90'
--- Src/alloc.F90	2017-10-10 19:27:53 +0000
+++ Src/alloc.F90	2019-08-18 23:02:58 +0000
@@ -45,7 +45,7 @@
 ! Notice that, if the restore call is skipped, the new defaults will
 ! stay in effect until a new call to alloc_dafault is made.
 ! ==================================================================
-! SUBROUTINE alloc_report( level, unit, file, printNow, threshold )
+! SUBROUTINE alloc_report( level, unit, file, printNow, threshold, shutdown )
 !   Sets the output file for the allocation report
 ! INPUT (optional):
 !   integer      :: level     : Level (detail) of report
@@ -53,7 +53,8 @@
 !   character*(*):: file      : Output file name
 !   logical      :: printNow  : If present & true => print report now
 !   real(dp)     :: threshold : Memory threshold (in bytes) to print
-!                               the memory use of any given array 
+!                               the memory use of any given array
+!   logical      :: shutdown  : If present & true then close output unit.
 ! BEHAVIOR:
 !   The detail/extent of the report increses with the value of level:
 ! level=0 : no report at all (the default)
@@ -73,6 +74,13 @@
 ! reports are written consecutively in the same file, each with a 
 ! time stamp header.
 !   If threshold is not present, threshold=0 is assumed.
+!   When performing library invocations of this module in say
+! external methods it is vital to close units before exiting the
+! library to ensure that no dangling files are kept open.
+! To ensure the file is closed before return one can use
+! the shutdown=.true. argument to forcefully close (and free)
+! the unit used to report. If not present or .false. the unit
+! will be kept open.
 !   In parallel execution, the report sections that involve every
 ! reallocation (levels 1, 3, and 4) are written only by node 0.
 ! The section that is written upon request (level 2) is written

=== modified file 'Src/atmfuncs.f'
--- Src/atmfuncs.f	2016-04-29 07:31:13 +0000
+++ Src/atmfuncs.f	2019-08-18 23:02:58 +0000
@@ -23,11 +23,6 @@
 
       implicit none 
 !
-      type(species_info), pointer        :: spp
-      type(rad_func), pointer            :: op
-      type(rad_func), pointer            :: pp
-      type(rad_func), pointer            :: func   
-!
       character(len=79) message
       integer, parameter               :: max_l = 5
       integer, parameter               :: max_ilm = (max_l+1)*(max_l+1)
@@ -47,10 +42,8 @@
 
       public  :: orb_gindex, kbproj_gindex, vna_gindex, ldau_gindex
       private
-                          !
+      
       contains
-!
-!
 
       subroutine chk(name,is)
       character(len=*), intent(in) :: name
@@ -290,9 +283,10 @@
 C                    IO = 0 => Local pseudopotential
 C************************OUTPUT*****************************************
 C   INTEGER LOFIO  : Quantum number L of orbital or KB projector
+      type(species_info), pointer :: spp
 
       call chk('lofio',is)
-      
+
       spp => species(is)
       if (io.gt.0) then
          if (io.gt.spp%norbs)  call die("lofio: No such orbital")
@@ -320,6 +314,7 @@
 C                    IO = 0 => Local pseudopotential
 C************************OUTPUT*****************************************
 C   INTEGER MOFIO  : Quantum number m of orbital or KB projector
+      type(species_info), pointer :: spp
 
       call chk('mofio',is)
       
@@ -348,6 +343,7 @@
 C                    IO > 0 => Basis orbitals
 C************************OUTPUT*****************************************
 C   INTEGER ZETAFIO  : Zeta number of orbital
+      type(species_info), pointer :: spp
 
       call chk('mofio',is)
 
@@ -372,6 +368,7 @@
 C  Returns cutoff radius of Kleynman-Bylander projectors and
 C  atomic basis orbitals.
 C  Distances in Bohr
+      type(species_info), pointer :: spp
 
       call chk('rcut',is)
       
@@ -379,12 +376,10 @@
       if (io.gt.0) then
          if (io.gt.spp%norbs)  call die("rcut: No such orbital")
 
-         op => spp%orbnl(spp%orb_index(io))
-         rcut = op%cutoff
+         rcut = spp%orbnl(spp%orb_index(io))%cutoff
       else if (io.lt.0) then
          if (-io.gt.spp%nprojs)  call die("rcut: No such projector")
-         pp => spp%pjnl(spp%pj_index(-io))
-         rcut = pp%cutoff
+         rcut = spp%pjnl(spp%pj_index(-io))%cutoff
       else
          rcut = spp%vna%cutoff
       endif
@@ -424,6 +419,7 @@
       data (sym_label(i),i=17,25)
      .  / 'gxy(x2-y2)', 'gzy(3x2-y2)', 'gz2xy', 'gz3y', 'gz4',
      .    'gz3x', 'gz2(x2-y2)', 'gzx(x2-3y2)', 'gx4+y4' /
+      type(species_info), pointer :: spp
 
       call chk('rcut',is)
       
@@ -461,12 +457,12 @@
                                    ! io>0 => basis orbitals
 
 C If true, the orbital IO is a perturbative polarization orbital
+      type(species_info), pointer :: spp
 
       spp => species(is)
       if ( (io .gt. species(is)%norbs) .or.
      $     (io .le. 0))   call die("pol: Wrong io")
 
-      spp => species(is)
       pol = spp%orbnl_ispol(spp%orb_index(io))
       
       end function pol
@@ -483,6 +479,7 @@
 C                 Sum_lm( epsKB_l * <Psi|Phi_lm> * <Phi_lm|Psi'> )
 C  where Phi_lm is returned by subroutine PHIATM.
 C  Energy in Rydbergs.
+      type(species_info), pointer :: spp
 
       integer ik
 
@@ -504,13 +501,14 @@
 C Returns local part of neutral-atom Kleynman-Bylander pseudopotential.
 C Distances in Bohr,  Energies in Rydbergs
 C  2) Returns exactly zero when |R| > RCUT(IS,0)
+      type(rad_func), pointer :: func
 
       real(dp) rmod, dvdr
 
       call chk('vna_sub',is)
 
-      v=0.0_dp
-      grv(1:3)=0.0_dp
+      v = 0.0_dp
+      grv(1:3) = 0.0_dp
 
       if (floating(is)) return
 
@@ -520,7 +518,7 @@
       if (rmod .gt. func%cutoff) return
 
       call rad_get(func,rmod,v,dvdr)
-      rmod=rmod+tiny20
+      rmod = rmod + tiny20
       grv(1:3) = dvdr * r(1:3)/rmod
  
       end subroutine vna_sub
@@ -535,13 +533,14 @@
 C Distances in Bohr, Energies in Rydbergs
 C Density in electrons/Bohr**3
 C  2) Returns exactly zero when |R| > Rchloc
+      type(rad_func), pointer :: func
 
       real(dp) :: rmod, dchdr
 
       call chk('psch',is)
 
-      ch=0.0_dp 
-      grch(1:3)=0.0_dp 
+      ch = 0.0_dp 
+      grch(1:3) = 0.0_dp 
 
       if (floating(is)) return
 
@@ -550,7 +549,7 @@
       if (rmod .gt. func%cutoff) return
 
       call rad_get(func,rmod,ch,dchdr)
-      rmod=rmod+tiny20
+      rmod = rmod + tiny20
       grch(1:3) = dchdr * r(1:3)/rmod
 
       end subroutine psch
@@ -565,19 +564,20 @@
 C in the xc potential.
 C Distances in Bohr, Energies in Rydbergs, Density in electrons/Bohr**3
 C  2) Returns exactly zero when |R| > Rcore
+      type(rad_func), pointer :: func
 
       real(dp) rmod, dchdr
 
       call chk('chcore_sub',is)
 
-      ch=0.0_dp
-      grch(1:3)=0.0_dp
+      ch = 0.0_dp
+      grch(1:3) = 0.0_dp
 
       if (floating(is)) return
 
       func => species(is)%core
       rmod = sqrt(sum(r*r))
-      rmod=rmod+tiny20                   ! Moved here. JMS, Dec.2012
+      rmod = rmod + tiny20                   ! Moved here. JMS, Dec.2012
       if (rmod .gt. func%cutoff) return
 
       call rad_get(func,rmod,ch,dchdr)
@@ -611,6 +611,8 @@
 C 5) Prints a message and stops when no data exits for IS and/or IO
 C 6) Returns exactly zero when |R| > RCUT(IS,IO)
 C 7) PHIATM with IO = 0 is strictly equivalent to VNA_SUB
+      type(species_info), pointer :: spp
+      type(rad_func), pointer :: func
 
       real(dp) rmod, phir, dphidr
       real(dp) rly(max_ilm), grly(3,max_ilm)
@@ -652,6 +654,7 @@
          ilm = l*l + l + m + 1
          call rlylm( l, r, rly, grly )
          phi = phir * rly(ilm)
+!GCC$ unroll 3
          do i = 1,3
             grphi(i)=dphidr*rly(ilm)*r(i)/rmod+phir*grly(i,ilm)
          enddo
@@ -687,6 +690,8 @@
 C    where epsKB_l is returned by function EPSKB
 C 6) Returns exactly zero when |R| > RCUT(IS,IO)
 C 7) RPHIATM with ITYPE = 0 is strictly equivalent to VNA_SUB
+      type(species_info), pointer :: spp
+      type(rad_func), pointer :: func
 
       real(dp) rmod, phir
       integer l, m, ik
@@ -734,16 +739,17 @@
       end subroutine rphiatm
 
 
-      subroutine all_phi( is, it, r, nphi, phi, grphi )
+      subroutine all_phi( is, it, r, maxnphi, nphi, phi, grphi )
       integer,   intent(in) :: is     ! Species index
       integer,   intent(in) :: it     ! Orbital-type switch:
                                       ! IT > 0 => Basis orbitals
                                       ! IT < 0 => KB projectors
       real(dp),  intent(in) :: r(3)   ! Point vector, relative to atom
+      integer,  intent(in) :: maxnphi ! Maximum number of phi's
       integer,  intent(out) :: nphi   ! Number of phi's
-      real(dp), intent(out) :: phi(:) ! Basis orbital, KB projector, or
+      real(dp), intent(out) :: phi(maxnphi) ! Basis orbital, KB projector, or
                                       !  local pseudopotential
-      real(dp), optional, intent(out) :: grphi(:,:) ! Gradient of phi
+      real(dp), optional, intent(out) :: grphi(3,maxnphi) ! Gradient of phi
 
 C  Returns Kleynman-Bylander local pseudopotential, nonlocal projectors,
 C  and atomic basis orbitals (and their gradients).
@@ -763,16 +769,15 @@
 C 6) Returns exactly zero when |R| > RCUT(IS,IO)
 C 8) If arrays phi or grphi are too small, returns with the required
 C    value of nphi
+      type(species_info), pointer :: spp
 
-      integer i, jlm, l, lmax, m, maxlm, n
+      integer i, jlm, l, lmax, m, maxlm
       double precision  rmod, phir, dphidr
       real(dp) rly(max_ilm), grly(3,max_ilm)
 
-      integer, parameter :: maxphi=100
-
-      integer :: ilm(maxphi)
-      double precision :: rmax(maxphi)
-      logical :: within(maxphi)
+      integer :: ilm(maxnphi)
+      double precision :: rmax(maxnphi)
+      logical :: within(maxnphi)
 
       call chk('all_phi',is)
       spp => species(is)
@@ -786,37 +791,24 @@
          call die("all_phi: Please use phiatm to get Vna...")
       endif
       
-      if (nphi.gt.maxphi) call die('all_phi: maxphi too small')
+      if (nphi.gt.maxnphi) call die('all_phi: maxphi too small')
 
       if (it.gt.0) then
          do i = 1, nphi
             l = spp%orb_l(i)
             m = spp%orb_m(i)
             ilm(i) = l*(l+1)+m+1
-            op => spp%orbnl(spp%orb_index(i))
-            rmax(i) = op%cutoff
+            rmax(i) = spp%orbnl(spp%orb_index(i))%cutoff
          enddo
       else
          do i = 1, nphi
-            pp => spp%pjnl(spp%pj_index(i))
-            rmax(i) = pp%cutoff
+            rmax(i) = spp%pjnl(spp%pj_index(i))%cutoff
             l = spp%pj_l(i)
             m = spp%pj_m(i)
             ilm(i) = l*(l+1)+m+1
          enddo
       endif
 
-!     Check size of output arrays
-      if (present(grphi)) then
-        if (size(grphi,1).ne.3)
-     .    call die('all_phi: incorrect first dimension of grphi')
-        n = min( size(phi), size(grphi,2) )
-      else
-        n = size(phi)
-      endif
-!     Return if the caller did not provide arrays large enough...
-      if (n.lt.nphi) return
-
 !     Initialize orbital values
       phi(1:nphi) = 0._dp
       if (present(grphi)) grphi(:,1:nphi) = 0._dp
@@ -841,14 +833,11 @@
         if (.not.within(i)) cycle i_loop
           
 !       Find radial part
-
         if (it.gt.0) then
-           func => spp%orbnl(spp%orb_index(i))
-        else 
-           func => spp%pjnl(spp%pj_index(i))
-        endif
-
-        call rad_get(func,rmod,phir,dphidr)
+          call rad_get(spp%orbnl(spp%orb_index(i)),rmod,phir,dphidr)
+        else
+          call rad_get(spp%pjnl(spp%pj_index(i)),rmod,phir,dphidr)
+        end if
 
 !       Multiply radial and angular parts
         jlm = ilm(i)
@@ -875,6 +864,7 @@
 C due to the overlap of the two 'local pseudopotential charge densities'
 C Distances in Bohr, Energies in Rydbergs
 C  2) Returns exactly zero when |R| > Rchloc
+      type(rad_func), pointer :: func
 
       integer ismx, ismn, indx
       real(dp) r_local
@@ -910,6 +900,7 @@
       integer, intent(in)  :: l    ! Angular momentum of the basis funcs
 C Returns the number of different basis functions
 C with the same angular momentum and for a given species
+      type(species_info), pointer :: spp
 
       integer i
 
@@ -930,7 +921,8 @@
 
 C Returns the number of different KB projectors
 C with the same angular momentum and for a given species
-      
+      type(species_info), pointer :: spp
+
       integer i
 
       call chk('nkbl_func',is)

=== modified file 'Src/bands.F'
--- Src/bands.F	2018-10-17 13:04:40 +0000
+++ Src/bands.F	2019-08-18 23:02:58 +0000
@@ -296,7 +296,8 @@
       end subroutine initbands
 
 
-      subroutine bands( no_s, nspin, maxspn, no_u, no_l, maxnh, maxk,
+      subroutine bands( no_s, spin,
+     .                  no_u, no_l,maxnh, maxk,
      .                  numh, listhptr, listh, H, S, ef, xij, indxuo,
      .                  writeb, nk, kpoint, ek, occtol, getPSI )
 
@@ -305,40 +306,39 @@
 C Written by J.Soler, August 1997 and August 1998.
 C Initialisation moved into a separate routine, JDG Jan 2000.
 C WFS options by A. Garcia, April 2012
+C Cleaned for tSpin by N. Papior, August 2019
 
 C **************************** INPUT **********************************
 C integer no_s                : Number of basis orbitals in supercell
-C integer nspin               : Number of spin components
-C integer maxspn              : Maximum number of spin components
-C                               nspin /= maxspn for spin-orbit
+C type(tSpin) spin            : Containing all spin-information
 C integer maxnh               : Maximum number of orbitals interacting
 C                               with any orbital
 C integer maxk                : Last dimension of kpoint and ek
-C integer numh(no_l)           : Number of nonzero elements of each row
+C integer numh(no_l)          : Number of nonzero elements of each row
 C                               of hamiltonian matrix
-C integer listhptr(no_l)       : Pointer to start of each row of the
+C integer listhptr(no_l)      : Pointer to start of each row of the
 C                               hamiltonian matrix
 C integer listh(maxlh)        : Nonzero hamiltonian-matrix element
 C                               column indexes for each matrix row
-C real*8  H(maxnh,nspin)      : Hamiltonian in sparse form
+C real*8  H(maxnh,spin%H)     : Hamiltonian in sparse form
 C real*8  S(maxnh)            : Overlap in sparse form
 C real*8  ef                  : Fermi energy
 C real*8  xij(3,maxnh)        : Vectors between orbital centers (sparse)
 C                               (not used if only gamma point)
 C integer no_u                : First dimension of ek
-C integer no_l               : Second dimension of H and S
-C integer indxuo(no_s)          : Index of equivalent orbital in unit cell
+C integer no_l                : Second dimension of H and S
+C integer indxuo(no_s)        : Index of equivalent orbital in unit cell
 C                               Unit cell orbitals must be the first in
 C                               orbital lists, i.e. indxuo.le.no_l, with
 C                               no_l the number of orbitals in unit cell
 C real*8  ef                  : Fermi energy
 C logical writeb              : This routine must write bands?
-C integer no_u              : Total number of orbitals in unit cell
+C integer no_u                : Total number of orbitals in unit cell
 C integer nk                  : Number of band k points
 C real*8  kpoint(3,maxk)      : k point vectors
 C real*8  occtol              : Occupancy threshold for DM build
 C *************************** OUTPUT **********************************
-C real*8  ek(no_u,maxspn,maxk) : Eigenvalues
+C real*8  ek(no_u,spin%spinor,maxk) : Eigenvalues
 C *************************** UNITS ***********************************
 C Lengths in atomic units (Bohr).
 C k vectors in reciprocal atomic units.
@@ -366,7 +366,7 @@
       use atmfuncs,     only : symfio, cnfigfio, labelfis, nofis
       use writewave,    only : wfs_filename
 
-      use m_spin,       only: NoMagn, SPpol, NonCol, SpOrb
+      use t_spin, only: tSpin
 
       use m_diag_option, only: ParallelOverK, Serial
       use m_diag, only: diag_init
@@ -374,13 +374,13 @@
 
       implicit          none
 
-      integer  ::   nspin
-      integer  ::   maxk, maxnh, maxspn, no_u, no_l, nk, no_s,
+      type(tSpin), intent(in) :: spin
+      integer  ::   maxk, maxnh, no_u, no_l, nk, no_s,
      .              indxuo(no_s), listh(maxnh), numh(no_l),
-     .              listhptr(*), nuo
+     .              listhptr(*)
       logical  ::   writeb
-      real(dp) ::   ef, ek(no_u,maxspn,maxk),
-     .              H(maxnh,nspin), kpoint(3,maxk),
+      real(dp) ::   ef, ek(no_u,spin%spinor,maxk),
+     .              H(maxnh,spin%H), kpoint(3,maxk),
      .              S(maxnh), xij(3,maxnh), occtol
       logical, intent(in) :: getPSI
 
@@ -394,7 +394,6 @@
       logical, parameter :: fixspin = .false.
 
       integer :: ik, il, io, ispin, iu, iu_wfs, iuo, naux, nhs, j
-
       logical :: SaveParallelOverK
       
       real(dp)
@@ -405,17 +404,10 @@
       real(dp), dimension(:), pointer :: aux => null()
 
       parameter ( eV = 1.d0 / 13.60580d0 )
+
       save Dnew, Enew, e1, e2, qk, qtot, temp, wk
-
       data Dnew, Enew, e1, e2, qk, qtot, temp, wk /8*0.d0/
 
-C Get number of local orbitals
-#ifdef MPI
-      call GetNodeOrbs(no_u,Node,Nodes,nuo)
-#else
-      nuo = no_u
-#endif
-
 C Start time counter
       call timer( 'bands', 1 )
 
@@ -430,12 +422,13 @@
       endif
 
 C     Allocate local arrays - only aux is relevant here
-      if ( nspin >=4 ) then
-         nhs  = 2 * (2*no_u) * (2*no_l)
+
+      if ( spin%Grid == 4 ) then
+         nhs = 2 * (2*no_u) * (2*no_l)
       else
          nhs = 2 * no_u*no_l
       endif
-      naux  = 2*no_u*5
+      naux = 2*no_u*5
       call allocDenseMatrix(nhs, nhs, nhs)
       call re_alloc( aux, 1, naux, 'aux', 'bands' )
 
@@ -448,7 +441,7 @@
         rewind (iu_wfs)
 
         write(iu_wfs) nk, .false. ! nk, Gamma, same file-format in WFS as for Gamma-point
-        write(iu_wfs) nspin
+        write(iu_wfs) spin%Grid
         write(iu_wfs) no_u
         write(iu_wfs) (iaorb(j),labelfis(isa(iaorb(j))),
      .            iphorb(j), cnfigfio(isa(iaorb(j)),iphorb(j)),
@@ -458,7 +451,7 @@
       endif
 
 C Find the band energies
-      if (NoMagn .or. SPpol) then
+      if ( spin%Grid < 4 ) then
 C fixspin and qs are not used in diagk, since getD=.false. ...
         qs(1) = 0.0_dp
         qs(2) = 0.0_dp
@@ -475,7 +468,7 @@
            call diag_init()
         end if
 
-        call diagk( nspin, no_l, no_s, maxspn, 
+        call diagk( spin%H, no_l, no_s, spin%spinor, 
      .              maxnh, maxnh, 
      .              no_u, numh, listhptr, listh, numh, listhptr,
      .              listh, H, S, getD, getPSI, fixspin, qtot, qs, temp,
@@ -487,29 +480,17 @@
         ParallelOverK = SaveParallelOverK
         if ( ParallelOverK ) Serial = .true.
 
-      elseif ( NonCol ) then
-         if (getPSI) then
-            if (node==0) then
-               write(6,*) "No WFS for non-colinear spin, yet..."
-            endif
-            RETURN
-         endif
+      elseif ( spin%NCol ) then
         call diag2k(no_l, no_s, maxnh, maxnh, no_u,
      .              numh, listhptr, listh, numh, listhptr,
-     .              listh, H, S, getD, qtot, temp, e1, e2,
+     .              listh, H, S, getD, getPSI, qtot, temp, e1, e2,
      .              xij, indxuo, nk, kpoint, wk,
      .              ek, qk, Dnew, Enew, ef, Entropy,
      .              Haux, Saux, psi, Haux, Saux, aux,
      .              no_u, occtol, 1, no_u )
 
-      elseif ( SpOrb ) then
-        if (getPSI) then
-           if (node==0) then
-              write(6,*) "No WFS for spin-orbit, yet..."
-           endif
-           return
-        end if
-        call diag3k(nuo, no_s, maxnh, maxnh, no_u, numh,
+      elseif ( spin%SO ) then
+        call diag3k(no_l, no_s, maxnh, maxnh, no_u, numh,
      .              listhptr, listh, numh, listhptr, listh,
      .              H, S, getD, getPSI, qtot, temp, e1, e2, xij,
      .              indxuo, nk, kpoint, wk, ek, qk, Dnew,
@@ -517,7 +498,7 @@
      .              Haux, Saux, psi, Haux, Saux, aux,
      .              no_u, occtol, 1, no_u )
       else
-        call die( 'bands: ERROR: incorrect value of nspin')
+        call die( 'bands: ERROR: incorrect value of spin%H')
       endif
 
 C Write bands
@@ -540,7 +521,7 @@
      .      path = path + sqrt( (kpoint(1,ik)-kpoint(1,ik-1))**2 +
      .                          (kpoint(2,ik)-kpoint(2,ik-1))**2 +
      .                          (kpoint(3,ik)-kpoint(3,ik-1))**2 )
-          do ispin = 1,maxspn
+          do ispin = 1, spin%spinor
             do io = 1, no_u
               emax = max( emax, ek(io,ispin,ik) )
               emin = min( emin, ek(io,ispin,ik) )
@@ -552,13 +533,14 @@
         write(iu,*) emin/eV, emax/eV
 
 C Write eigenvalues
-        if ( nspin <= 2 ) then
-          write(iu,*) no_u, maxspn, nk
-        else if ( nspin <= 8 ) then
-          write(iu,*) 2*no_u, 1, nk
-        else
-          call die( 'bands: ERROR: incorrect value of nspin' )
-        end if
+        if ( spin%Grid == 4 ) then
+          write(iu,*) 2*no_u, 1, nk     ! A single spin channel, double number of bands
+        else 
+          write(iu,*) no_u, spin%spinor, nk
+        endif
+
+        ! For non-collinear calculations, the ek array will contain the first no_u
+        ! bands in ek(:,1,ik), and the next no_u bands in ek(:,2,ik)   
         path = 0.d0
         do ik = 1,nk
           if (nlines .ge. 0) then
@@ -568,11 +550,11 @@
      .                            (kpoint(3,ik)-kpoint(3,ik-1))**2 )
             write(iu,'(f10.6,10f12.4,/,(10x,10f12.4))')
      .         path, ((ek(io,ispin,ik)/eV,io=1,no_u),
-     .         ispin=1,maxspn)
+     .         ispin=1,spin%spinor)
           else
             write(iu,'(3f9.5,8f12.4,/,(27x,8f12.4))')
      .        kpoint(1,ik), kpoint(2,ik), kpoint(3,ik),
-     .        ((ek(io,ispin,ik)/eV,io=1,no_u),ispin=1,maxspn)
+     .        ((ek(io,ispin,ik)/eV,io=1,no_u),ispin=1,spin%spinor)
           endif
         enddo
 

=== modified file 'Src/compute_dm.F'
--- Src/compute_dm.F	2018-11-02 09:03:25 +0000
+++ Src/compute_dm.F	2019-08-18 23:02:58 +0000
@@ -24,7 +24,7 @@
      &                    qtot, Qtots, no_l
       use sys, only: die, bye
       use Kpoint_grid
-      use m_energies,   only: Ebs, Ecorrec, Entropy, DE_NEGF
+      use m_energies,   only: Ebs, Ecorrec, Entropy
       use m_energies,   only: Ef, Efs
       use m_rmaxh
       use m_eo
@@ -231,7 +231,7 @@
          call transiesta(iscf,spin%H, block_dist, sparse_pattern,
      &        no_u == no_s, ucell, nsc, isc_off, no_u, na_u,
      &        lasto, xa, maxnh,
-     &        H, S, Dscf, Escf, Ef, Qtot, .false., DE_NEGF )
+     &        H, S, Dscf, Escf, Ef, Qtot, .false.)
 
          Ecorrec = 0._dp
          Entropy = 0.0_dp

=== modified file 'Src/compute_energies.F90'
--- Src/compute_energies.F90	2017-12-21 15:49:49 +0000
+++ Src/compute_energies.F90	2019-08-18 23:02:58 +0000
@@ -55,6 +55,8 @@
 #ifdef MPI
       use m_mpi_utils,     only: globalize_sum
 #endif
+      use m_ts_global_vars, only: TSrun
+      use ts_energies_m, only: ts_compute_energies
 
       integer, intent(in)   :: iscf
 
@@ -85,6 +87,10 @@
       ! E0 = Ena + Ekin + Enl + Eso - Eions
 
       call update_DEna()
+      ! Also call transiesta
+      if ( TSrun ) then
+        call ts_compute_energies()
+      end if
       call update_Etot()
 
 
@@ -94,9 +100,13 @@
 
       if (mix_charge) then   ! possibly add mixH here
          EHarrs = 0.0_dp
+         NEGF_Eharrs = 0._dp
       else
          call compute_DEharr()
          Eharrs = Etot + DEharr
+         if ( TSrun ) then
+           NEGF_Eharrs = NEGF_Etot + NEGF_DEharr
+         end if
       endif
 
 ! Possible correction to Etot if mixing the DM. This is purely
@@ -218,6 +228,8 @@
       use class_dSpData1D, only : val
       use class_dSpData2D, only : val
       use sparse_matrices, only: H_kin_1D, H_vkb_1D, H_so_2D
+      use ts_energies_m, only: ts_compute_energies
+      use m_ts_global_vars, only: TSrun
 
       type(filesOut_t)  :: filesOut  ! blank output file names
       real(dp), pointer :: H_vkb(:), H_kin(:), H_so(:,:)
@@ -281,7 +293,12 @@
          Eso = buffer1
 #endif
       end if
-      
+
+      ! Also call transiesta
+      if ( TSrun ) then
+        call ts_compute_energies()
+      end if
+       
       ! E0 = Ena + Ekin + Enl + Eso - Eions
 
       ! Clarify: Ecorrec (from O(N))

=== modified file 'Src/delk.F90'
--- Src/delk.F90	2016-03-01 14:24:48 +0000
+++ Src/delk.F90	2019-08-18 23:02:58 +0000
@@ -386,7 +386,7 @@
                    r2sp = sum(dxsp**2)
                    if ( r2sp < r2cut(is) ) then
 !$OMP critical
-                      call all_phi( is, +1, dxsp, nphiloc, phia(:,isp) )
+                      call all_phi( is, +1, dxsp, maxoa, nphiloc, phia(:,isp) )
 !$OMP end critical
                    else
                       phia(:,isp) = 0.0_dp

=== modified file 'Src/dfscf.f'
--- Src/dfscf.f	2018-04-22 00:13:43 +0000
+++ Src/dfscf.f	2019-08-18 23:02:58 +0000
@@ -303,7 +303,7 @@
               dxsp(1:3,isp) = xdop(1:3,iop)+xdsp(1:3,isp)-dxa(1:3,ia)
               r2sp = dxsp(1,isp)**2 + dxsp(2,isp)**2 + dxsp(3,isp)**2
               if (r2sp.lt.r2cut(is)) then
-                call all_phi( is,+1, dxsp(:,isp), nphiloc,
+                call all_phi( is,+1, dxsp(:,isp), maxoa, nphiloc,
      .                        phia(:,isp), grada(:,:,isp))
               else
                 phia(:,isp) = 0.0_dp

=== modified file 'Src/dhscf.F'
--- Src/dhscf.F	2019-06-27 10:49:55 +0000
+++ Src/dhscf.F	2019-08-18 23:02:58 +0000
@@ -948,7 +948,7 @@
         call de_alloc( DRho_par, 'DRho_par','dhscf' )
 
         if ( debug_dhscf ) then
-           write(*,debug_fmt) Node,'DRho',
+           write(*,debug_fmt) Node,'Rho',
      &          (sqrt(sum(DRho(:,ispin)**2)),ispin=1,nspin)
         end if
 
@@ -1141,6 +1141,11 @@
       enddo
 !$OMP end parallel do
 
+      if ( debug_dhscf ) then
+        write(*,debug_fmt) Node,'DRho',
+     &      (sqrt(sum(DRho(:,ispin)**2)),ispin=1,nspin)
+      end if
+
 C ----------------------------------------------------------------------
 C Save electron density difference
 C ----------------------------------------------------------------------

=== modified file 'Src/diag2g.F'
--- Src/diag2g.F	2018-06-25 11:33:42 +0000
+++ Src/diag2g.F	2019-08-18 23:02:58 +0000
@@ -7,7 +7,7 @@
 !
       subroutine diag2g( nuo, no, maxnh, maxnd, maxo,
      .                   numh, listhptr, listh, numd, listdptr,
-     .                   listd, H, S, getD, qtot, temp, e1, e2,
+     .                   listd, H, S, getD, getPSI, qtot, temp, e1, e2,
      .                   eo, qo, Dnew, Enew, ef, Entropy, 
      .                   Haux, Saux, psi, caux, 
      .                   nuotot, occtol, iscf, neigwanted)
@@ -19,6 +19,8 @@
       use sys
       use parallel,        only : Node, Nodes, BlockSize
       use parallelsubs,    only : LocalToGlobalOrb,GlobalToLocalOrb
+      use writewave,       only : writew
+      use iso_c_binding,   only : c_loc, c_f_pointer
       use m_fermid,        only : fermid, stepf
       use intrinsic_missing, only: MODP
 
@@ -100,16 +102,19 @@
       real(dp) Entropy, eo(maxo*2), H(maxnh,4), qo(maxo*2)
       real(dp) qtot, S(maxnh), temp, occtol
       
-      complex(dp), dimension(2,nuotot,2*nuo) :: psi
+      complex(dp), dimension(2,nuotot,2*nuo), target :: psi
       complex(dp), dimension(2,nuotot,2,nuo) :: Haux, Saux
-      complex(dp), dimension(2,nuotot) :: caux
-      logical               getD
+      complex(dp), dimension(2,nuotot), target :: caux
+      logical               getD, getPSI
       
 !     Internal variables .............................................
 
+      real(dp), pointer :: psi_real_1d(:)
+      real(dp), pointer :: aux(:)
+      
       integer           BNode, BTest, ie, ierror, iie, iio
       integer           ind, io, j, jo, nd, iuo, juo
-      real(dp)          ee, pipj, qe, t
+      real(dp)          ee, pipj, qe, t, k(3)
       complex(dp) :: cicj, D11, D22, D12, D21
 #ifdef MPI
       integer MPIerror
@@ -201,6 +206,14 @@
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .             2*neigwanted,iscf,ierror, 2*BlockSize)
       endif
+
+      if (getPSI) then
+         k(1:3) = 0.0d0
+         call c_f_pointer( c_loc(psi), psi_real_1d, [size(psi)*2] )
+         call writew(nuotot,nuo,1,k,1,
+     &        eo,psi_real_1d,gamma=.true.,
+     $        non_coll=.true., blocksize=2*BlockSize)
+      endif
       
 !     Check if we are done
       if (.not.getD) goto 1001

=== modified file 'Src/diag2k.F'
--- Src/diag2k.F	2018-04-14 23:14:53 +0000
+++ Src/diag2k.F	2019-08-18 23:02:58 +0000
@@ -7,7 +7,7 @@
 !
       subroutine diag2k( nuo, no, maxnh, maxnd, maxo,
      .                   numh, listhptr, listh, numd, listdptr, 
-     .                   listd, H, S, getD, qtot, temp, e1, e2,
+     .                   listd, H, S, getD, getPsi, qtot, temp, e1, e2,
      .                   xij, indxuo, nk, kpoint, wk,
      .                   eo, qo, Dnew, Enew, ef, Entropy,
      .                   Haux, Saux, psi, Dk, Ek, caux, 
@@ -20,7 +20,9 @@
       use sys
       use parallel,      only : Node, Nodes, BlockSize
       use parallelsubs,  only : LocalToGlobalOrb
+      use writewave,     only : writew
       use m_fermid,      only : fermid, stepf
+      use iso_c_binding, only : c_loc, c_f_pointer
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -79,8 +81,8 @@
 C integer iscf                : SCF cycle number
 C integer neigwanted          : Number of eigenvalues wanted
 C *************************** OUTPUT **********************************
-C real*8 eo(maxo*4,nk)        : Eigenvalues
-C real*8 qo(maxo*4,nk)        : Occupations of eigenstates
+C real*8 eo(maxo*2,nk)        : Eigenvalues
+C real*8 qo(maxo*2,nk)        : Occupations of eigenstates
 C real*8 Dnew(maxnd,4)        : Output Density Matrix
 C real*8 Enew(maxnd,4)        : Output Energy-Density Matrix
 C real*8 ef                   : Fermi energy
@@ -116,11 +118,15 @@
       integer :: neigwanted
 
       complex(dp), dimension(2,nuotot,2,nuo) :: Haux, Saux, Dk, Ek
-      complex(dp), dimension(2,nuotot,2*nuo) :: psi
-      complex(dp), dimension(2,nuotot) :: caux
-      logical               getD
+      complex(dp), dimension(2,nuotot,2*nuo), target :: psi
+      complex(dp), dimension(2,nuotot), target       :: caux
+      logical, intent(in) ::        getD, getPsi
       
 !     Internal variables .............................................
+
+      ! For interface compliance using c_f_pointer
+      real(dp),    pointer :: aux(:)
+      real(dp),    pointer :: psi_real(:)
       
       integer  BNode, BTest, ie, ierror, iie, ik, ind, io, iio
       integer  iuo, j, jo, juo, neigneeded
@@ -170,6 +176,9 @@
 !
 ! 1. Hermiticity imposes H_{i,j}^{is,js}=H_{j,i}^{js,is}^*
 
+      ! Jump point for bands and wfs output only
+      if (getPSI .and. (.not. GetD)) goto 10
+      
 !     Find eigenvalues at every k point
       do ik = 1,nk
       
@@ -214,10 +223,10 @@
         endif
       enddo
       
-!-----------------------------------------------------------------------
-!     Check if we are done
-!-----------------------------------------------------------------------
-      if (.not.getD) goto 1001
+      ! Check if we are done (i.e.: pure bands only)
+      if (.not.getD .and. .not. getPSI) then
+         RETURN
+      end if
 !-----------------------------------------------------------------------
       
 !     Find new Fermi energy and occupation weights
@@ -240,16 +249,23 @@
       Dnew(:,:) = 0.0_dp
       Enew(:,:) = 0.0_dp
       
-!     Find maximum eigenvector that is required for this k point 
+ 10   continue      ! ---- Start here for (getPsi and (not getDM))
+
       do ik = 1,nk
-        neigneeded = 0
-        ie = 2*nuotot
-        do while (ie.gt.0.and.neigneeded.eq.0)
-          qe = qo(ie,ik)
-          if (abs(qe).gt.occtol) neigneeded = ie
-          ie = ie - 1
-        enddo
-      
+         !  Find maximum eigenvector index that is required for this k point 
+         if (getPSI) then
+             ! We do not have info about occupation
+             neigneeded = neigwanted
+          else
+             neigneeded = 0
+             ie = 2*nuotot    ! for mixed spins
+             do while (ie.gt.0.and.neigneeded.eq.0)
+                qe = qo(ie,ik)
+                if (abs(qe).gt.occtol) neigneeded = ie
+                ie = ie - 1
+             enddo
+          endif
+          
 !       Find eigenvectors 
         Saux = dcmplx(0.0_dp,0.0_dp)
         Haux = dcmplx(0.0_dp,0.0_dp)
@@ -310,8 +326,25 @@
           call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,caux,psi,
      .               neigneeded,iscf,ierror,2*BlockSize)
         endif
-      
-!-----------------------------------------------------------------------	     
+
+              
+        if (getPSI) then
+           if (.not. getD) then
+              ! Fill in the missing eigenvalue information
+              ! This is useful if we are requesting WFS in a "bands" setting
+              call c_f_pointer(c_loc(caux),aux,[2*nuotot])
+              call kludge_copy(2*nuotot,eo(1,ik),aux)
+           endif
+           call c_f_pointer(c_loc(psi),psi_real,[2*size(psi)])
+           call writew(nuotot,nuo,ik,kpoint(1,ik),1, ! last '1' is 'spin-block number'
+     .                 eo(1,ik),       ! energies
+     .                 psi_real,gamma=.false.,non_coll=.true.,
+     $                 blocksize=2*BlockSize)
+        endif
+
+        if (.not. getD) CYCLE   ! process new k-point
+
+!-----------------------------------------------------------------------
 !     Store the products of eigenvectors in matrices Dk and Ek
 !     WARNING: Dk and Ek may be EQUIVALENCE'd to Haux and Saux
 !-----------------------------------------------------------------------	     
@@ -445,13 +478,22 @@
 
         enddo
         enddo
-      enddo
+      enddo  ! over k-points
 
- 1001 continue
-      
 #ifdef DEBUG
       call write_debug( '    POS diag2k' )
 #endif
+            
+      CONTAINS
+            ! Work around shape of aux array
+      subroutine kludge_copy(n,a,b)
+      integer, intent(in) :: n
+      real(dp), intent(out) :: a(n)
+      real(dp), intent(in)  :: b(n)
+!$OMP parallel workshare default(shared)
+      a(1:n) = b(1:n)
+!$OMP end parallel workshare
+      end subroutine kludge_copy
 
       end subroutine diag2k
       

=== modified file 'Src/diag3g.F'
--- Src/diag3g.F	2018-06-25 11:33:42 +0000
+++ Src/diag3g.F	2019-08-18 23:02:58 +0000
@@ -5,7 +5,7 @@
 !  or http://www.gnu.org/copyleft/gpl.txt.
 ! See Docs/Contributors.txt for a list of contributors.
 !
-      subroutine diag3g( nuo, no, maxuo, maxnh, maxnd, maxo,
+      subroutine diag3g( nuo, no, maxnh, maxnd, maxo,
      .                   numh, listhptr, listh, numd, listdptr,
      .                   listd, H, S, getD, getPSI, qtot, temp, e1, e2,
      .                   eo, qo, Dnew, Enew, ef, Entropy,
@@ -16,8 +16,10 @@
       use sys
       use parallel,        only : Node, Nodes, BlockSize
       use parallelsubs,    only : LocalToGlobalOrb,GlobalToLocalOrb
+      use writewave,       only : writew
       use m_fermid,        only : fermid, stepf
       use intrinsic_missing, only: MODP
+      use iso_c_binding,   only : c_loc, c_f_pointer
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -33,7 +35,6 @@
 C **************************** INPUT **********************************
 C integer nuo                 : Number of basis orbitals on local node
 C integer no                  : Number of basis orbitals
-C integer maxuo               : Maximum number of basis  orbitals
 C integer maxnh               : Maximum number of orbitals interacting  
 C integer maxnd               : First dimension of Dnew and Enew
 C integer maxo                : First dimension of eo and qo
@@ -86,7 +87,7 @@
 !     Indices is and js are for spin components 
 !     Indices iuo and juo are for orbital components:
 ! *********************************************************************
-      integer maxo, maxuo, maxnd, maxnh
+      integer maxo, maxnd, maxnh
       integer no, nuo, nuotot, iscf, neigwanted
       
       integer listh(maxnh), numh(nuo), listhptr(nuo)
@@ -96,7 +97,8 @@
       real(dp) Entropy, eo(maxo*2), H(maxnh,8), qo(maxo*2)
       real(dp) qtot, S(maxnh), temp, occtol
       
-      complex(dp), dimension(2,nuotot,2*nuo) :: psi
+      complex(dp), dimension(2,nuotot,2*nuo), target :: psi
+      real(dp), pointer                              :: psi_real_1d(:)
       complex(dp), dimension(2,nuotot,2,nuo) :: Haux, Saux
       complex(dp), dimension(2,nuotot) :: caux
       logical               getD, getPSI
@@ -105,7 +107,7 @@
       
       integer           BNode, BTest, ie, ierror, iie, iio
       integer           ind, io, j, jo, nd, iuo, juo
-      real(dp)          ee, qe, t
+      real(dp)          ee, qe, t, k(3)
       complex(dp)       D11, D22, D12, D21
 #ifdef MPI
       integer MPIerror
@@ -193,7 +195,20 @@
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .             2*neigwanted,iscf,ierror,2*BlockSize)
       endif
-      
+
+      if (getPSI) then
+         k(1:3) = 0.0d0
+
+          ! We do not have info about occupation
+          ! In the current implementation, neigneeded
+          ! is ALWAYS nuotot.
+          ! This is because writewave expects the full spectrum
+         call c_f_pointer( c_loc(psi), psi_real_1d, [size(psi)*2] )
+         call writew(nuotot,nuo,1,k,1,
+     &        eo,psi_real_1d,gamma=.true.,
+     $        non_coll=.true.,blocksize=2*BlockSize)
+      endif
+
 !     Check if we are done
       if (.not.getD) return
       

=== modified file 'Src/diag3k.F'
--- Src/diag3k.F	2017-08-06 11:17:47 +0000
+++ Src/diag3k.F	2019-08-18 23:02:58 +0000
@@ -18,7 +18,9 @@
       use sys
       use parallel,      only : Node, Nodes, BlockSize
       use parallelsubs,  only : LocalToGlobalOrb
+      use writewave,     only : writew
       use m_fermid,      only : fermid, stepf
+      use iso_c_binding, only : c_f_pointer, c_loc
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -114,12 +116,14 @@
       integer :: neigwanted
       
       complex(dp), dimension(2,nuotot,2,nuo) :: Haux, Saux, Dk, Ek
-      complex(dp), dimension(2,nuotot,2*nuo) :: psi
-      complex(dp), dimension(2,nuotot) :: caux
-      logical               getD, getPSI
-      
-!     TEMPOS, INTERNAL VARIABLES etc.
-      
+      complex(dp), dimension(2,nuotot,2*nuo), target :: psi
+      complex(dp), dimension(2,nuotot), target :: caux
+      logical, intent(in) ::               getD, getPSI
+      
+
+      real(dp),    pointer :: aux(:)
+      real(dp), pointer  :: psi_real(:)
+
       integer  BNode, BTest, ie, ierror, iie, ik, ind, io, iio
       integer  iuo, j, jo, juo, neigneeded
       real(dp) ee, qe, t
@@ -175,6 +179,9 @@
 !
 !
 
+      ! Jump point for bands and wfs output only
+      if (getPSI .and. (.not. GetD)) goto 10
+      
 !     Find eigenvalues at every k point
 
       do ik = 1,nk
@@ -214,11 +221,11 @@
           call die('Terminating due to failed diagonalisation')
         endif
       enddo
-      
-!-----------------------------------------------------------------------
-!     Check if we are done
-!-----------------------------------------------------------------------
-      if (.not.getD) return
+
+      ! Check if we are done (i.e.: pure bands only)
+      if (.not.getD .and. .not. getPSI) then
+         RETURN
+      end if
 !-----------------------------------------------------------------------
       
 !     Find new Fermi energy and occupation weights
@@ -240,16 +247,23 @@
 !     New density and energy-density matrices of unit-cell orbitals
       Dnew(:,:) = 0.0_dp
       Enew(:,:) = 0.0_dp
+
+ 10   continue   ! ---- Start here for (getPsi and (not getDM))
       
-!     Find maximum eigenvector that is required for this k point 
       do ik = 1,nk
-        neigneeded = 0
-        ie = 2*nuotot  ! for mixed spins
-        do while (ie.gt.0.and.neigneeded.eq.0)
-          qe = qo(ie,ik)
-          if (abs(qe).gt.occtol) neigneeded = ie
-          ie = ie - 1
-        enddo
+         !  Find maximum eigenvector index that is required for this k point 
+         if (getPSI) then
+             ! We do not have info about occupation
+             neigneeded = neigwanted
+         else
+             neigneeded = 0
+             ie = 2*nuotot      ! for mixed spins
+             do while (ie.gt.0.and.neigneeded.eq.0)
+                qe = qo(ie,ik)
+                if (abs(qe).gt.occtol) neigneeded = ie
+                ie = ie - 1
+             enddo
+         endif
       
 !       Find eigenvectors 
         Saux = dcmplx(0.0_dp,0.0_dp)
@@ -314,6 +328,22 @@
      .               neigneeded,iscf,ierror, 2*BlockSize)
         endif
       
+          if (getPSI) then
+             if (.not. getD) then
+                ! Fill in the missing eigenvalue information
+                ! This is useful if we are requesting WFS in a "bands" setting
+                call c_f_pointer(c_loc(caux),aux,[2*nuotot])
+                call kludge_copy(2*nuotot,eo(1,ik),aux)
+             endif
+             call c_f_pointer(c_loc(psi),psi_real,[2*size(psi)])
+             call writew(nuotot,nuo,ik,kpoint(1,ik),1,     ! last '1' is 'spin-block number'
+     .                   eo(1,ik),                         ! energies
+     .                   psi_real,gamma=.false.,non_coll=.true.,
+     $                   blocksize=2*BlockSize)
+          endif
+
+          if (.not. getD) CYCLE   ! process new k-point
+
 !***********************************************************************
 ! BUILD NEW DENSITY MATRIX
 !***********************************************************************
@@ -429,8 +459,18 @@
         enddo
       enddo
       
-!***********************************************************************      
-      return
+      CONTAINS
+            ! Work around shape of aux array
+      subroutine kludge_copy(n,a,b)
+      integer, intent(in) :: n
+      real(dp), intent(out) :: a(n)
+      real(dp), intent(in)  :: b(n)
+!$OMP parallel workshare default(shared)
+      a(1:n) = b(1:n)
+!$OMP end parallel workshare
+      end subroutine kludge_copy
+
       end subroutine diag3k
 !***********************************************************************      
+
       

=== modified file 'Src/diagg.F'
--- Src/diagg.F	2018-06-25 11:33:42 +0000
+++ Src/diagg.F	2019-08-18 23:02:58 +0000
@@ -91,7 +91,7 @@
       use m_spin,        only : spinor_dim, e_spin_dim
       use alloc
       use intrinsic_missing, only: MODP
-
+      use iso_c_binding, only : c_f_pointer, c_loc
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -117,10 +117,9 @@
      &  qo(maxo,spinor_dim), qtot, qs(spinor_dim), S(maxnh), temp, 
      &  efs(spinor_dim), occtol
      
-      real(dp)
-     &  Haux(nuotot,nuo), Saux(nuotot,nuo), 
-     &  psi(nuotot,maxuo,spinor_dim) 
-
+      real(dp) Haux(nuotot,nuo), Saux(nuotot,nuo)
+      real(dp), target :: psi(nuotot,maxuo,spinor_dim) 
+      real(dp), pointer :: psi_real_1d(:)
       real(dp), dimension(1), parameter :: wk = (/ 1.0_dp /)
       integer, parameter                :: nk = 1
 
@@ -203,8 +202,11 @@
           do ix = 1,3
             k(ix) = 0.0d0
           enddo
+          call c_f_pointer(c_loc(psi(:,:,ispin)),psi_real_1d,
+     $                     [size(psi,1)*size(psi,2)])
           call writew(nuotot,nuo,1,k,ispin,
-     &                eo(1,ispin),psi(1,1,ispin),.true.)
+     &                eo(1,ispin),psi_real_1d,gamma=.true.,
+     $                non_coll=.false.,blocksize=BlockSize)
         endif
 
       enddo

=== modified file 'Src/diagk.F'
--- Src/diagk.F	2017-08-06 09:35:09 +0000
+++ Src/diagk.F	2019-08-18 23:02:58 +0000
@@ -101,6 +101,7 @@
       use writewave,     only : writew
       use m_fermid,      only : fermid, fermispin, stepf
       use m_spin,        only : spinor_dim, e_spin_dim
+      use iso_c_binding, only : c_loc, c_f_pointer
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -143,6 +144,7 @@
       real(dp) :: qp1, qp2, eqp1, eqp2
 
       real(dp), pointer :: lpsi(:,:)
+      real(dp), pointer :: psi_real_1d(:)
 
       logical, allocatable :: done_juo(:)
 C     ....................
@@ -347,8 +349,10 @@
                 ! This is useful if we are requesting WFS in a "bands" setting
                 call kludge_copy(nuotot,eo(1,ispin,ik),aux)
              endif
+             call c_f_pointer(c_loc(psi),psi_real_1d,[size(psi)])
              call writew(nuotot,nuo,ik,kpoint(1,ik),ispin,
-     .                 aux,psi,.false.)
+     .                 aux,psi_real_1d,gamma=.false.,non_coll=.false.,
+     $                 blocksize=BlockSize)
           endif
 
           if (getD) then

=== modified file 'Src/diagon.F'
--- Src/diagon.F	2018-11-02 09:03:25 +0000
+++ Src/diagon.F	2019-08-18 23:02:58 +0000
@@ -266,7 +266,7 @@
        if (gamma) then
         call diag2g( nuo, no, maxnh, maxnd, maxo, numh,
      .               listhptr, listh, numd, listdptr, listd,
-     .               H, S, getD, qtot, temp, e1, e2, eo, qo, 
+     .               H, S, getD, getPSI, qtot, temp, e1, e2, eo, qo, 
      .               Dnew, Enew, ef, Entropy,
      .               Haux, Saux, psi, aux,
      .               nuotot, occtol, iscf, neigwanted )
@@ -281,7 +281,7 @@
        else
         call diag2k( nuo, no, maxnh, maxnd, maxo, numh,
      .               listhptr, listh, numd, listdptr, listd,
-     .               H, S, getD, qtot, temp, e1, e2, xij,
+     .               H, S, getD, getPsi, qtot, temp, e1, e2, xij,
      .               indxuo, nk, kpoint, wk, eo, qo, Dnew,
      .               Enew, ef, Entropy, 
      .               Haux, Saux, psi, Haux, Saux, aux,
@@ -289,7 +289,7 @@
        endif
       elseif ( spin%SO ) then
         if (gamma) then
-          call diag3g( nuo, no, maxuo, maxnh, maxnd, maxo, numh,
+          call diag3g( nuo, no, maxnh, maxnd, maxo, numh,
      .                 listhptr, listh, numd, listdptr, listd,
      .                 H, S, getD, getPSI, qtot, temp, e1, e2, eo, qo,
      .                 Dnew, Enew, ef, Entropy, 

=== modified file 'Src/ioeig.f'
--- Src/ioeig.f	2018-05-08 11:36:55 +0000
+++ Src/ioeig.f	2019-08-18 23:02:58 +0000
@@ -19,10 +19,10 @@
 
       implicit          none
 
-      integer,  intent(in) :: no
-      integer,  intent(in) :: nspin
+      integer,  intent(in) :: no     ! no_u: number of orbitals in unit cell
+      integer,  intent(in) :: nspin  ! 'nspin_grid': 1, 2, or 4
       integer,  intent(in) :: nk
-      integer,  intent(in) :: maxo
+      integer,  intent(in) :: maxo   ! no_u again
       integer,  intent(in) :: nspinor
       integer,  intent(in) :: maxk
       real(dp), intent(in) :: ef
@@ -45,11 +45,17 @@
 
       write(iu,"(e17.9)") ef/eV
       if ( nspin > nspinor ) then
-        write(iu,"(tr1,i10,i2,tr1,i10)")   no*2, 1, nk
+        ! NC/SOC case: a single block of wavefunctions (without spin tag)
+        ! nspin (4) will be used here to signal NC/SOC to utilities such as 
+        ! Eig2DOS
+        write(iu,"(tr1,i10,i2,tr1,i10)")   no*2, nspin, nk
       else
         write(iu,"(tr1,i10,i2,tr1,i10)")   no, min(nspin,2), nk
       end if
       do ik = 1,nk
+        ! This statement will correctly print eo in the NC/SOC case,
+        ! as the eigenvalues take up two complete 'io' columns,
+        ! and nspinor = 2. 
         write(iu,"(i10,10(tr1,e17.9),/,(tr10,10(tr1,e17.9)))")
      .          ik, ((eo(io,is,ik)/eV,io=1,no),is=1,nspinor)
       enddo
@@ -83,7 +89,7 @@
             if ( is == 1 .and. nspinor > 1 ) then
                call cmlAddProperty(xf=mainXML, value="up", 
      .              dictRef="siesta:spin")
-            else if ( nspinor > 1 ) then
+            else if ( nspinor > 1) then
                call cmlAddProperty(xf=mainXML, value="down", 
      .              dictRef="siesta:spin")
             end if

=== modified file 'Src/iosockets.F90'
--- Src/iosockets.F90	2018-11-27 11:01:23 +0000
+++ Src/iosockets.F90	2019-08-18 23:02:58 +0000
@@ -181,6 +181,8 @@
   if (IOnode) then
     if (leqi(master,"i-pi") .and. trim(header)=="POSDATA") then 
       call readbuffer(socket, c, 9)
+      ! Please see below for the cell array
+      ! If this is to be used, it should *ALSO* be transposed!
       call readbuffer(socket, aux, 9)    ! not used in siesta
       master_xunit = ipi_xunit
       master_eunit = ipi_eunit
@@ -201,7 +203,15 @@
                  MPI_Comm_World, MPIerror)
   call MPI_Bcast(c,9, MPI_Double_Precision,0, MPI_Comm_World, MPIerror)
 #endif
-  cell = RESHAPE( c, (/3,3/) )
+  ! I-Pi assumes row-major order of *only* the cell parameters
+  ! So we need to transpose the cell
+  ! This is a very bad practice since the same is happening in
+  ! ASE I-pi implementation.
+  ! The cell is transposed when transfering, but not the coordinates.
+  ! Essentially one could leave out *any* transposes in all implementations
+  ! and it would work! However, this is now a legacy implementation
+  ! that should not be changed, neither in I-pi, nor ASE.
+  cell = TRANSPOSE( RESHAPE( c, (/3,3/) ) )
 
 ! Read and check number of atoms
   if (ionode) then

=== modified file 'Src/m_energies.F90'
--- Src/m_energies.F90	2018-07-03 13:43:29 +0000
+++ Src/m_energies.F90	2019-08-18 23:02:58 +0000
@@ -47,7 +47,18 @@
   real(dp):: Eldau      
   real(dp):: DEldau
 
-  real(dp) :: DE_NEGF  ! NEGF total energy contribution = - e * \sum_i N_i \mu_i
+  real(dp) :: NEGF_DE  ! NEGF total energy contribution = - e * \sum_i N_i \mu_i
+  ! Generally we should only calculate energies in the regions where we are updating elements
+  ! As such we need a specific energy for the NEGF part
+  ! Their meaning is directly transferable to the above listed energies (in the updating regions)
+  real(dp) :: NEGF_Ebs
+  real(dp) :: NEGF_Ekin
+  real(dp) :: NEGF_Enl
+  real(dp) :: NEGF_Eso
+  real(dp) :: NEGF_DEharr
+  real(dp) :: NEGF_Eharrs
+  real(dp) :: NEGF_Etot
+  real(dp) :: NEGF_FreeE
 
 contains
 
@@ -85,7 +96,17 @@
     Eso = 0._dp
     Eldau = 0._dp      
     DEldau = 0._dp
-    DE_NEGF = 0._dp
+
+    ! NEGF part
+    NEGF_DE = 0._dp
+    NEGF_Ebs = 0._dp
+    NEGF_Ekin = 0._dp
+    NEGF_Enl = 0._dp
+    NEGF_Eso = 0._dp
+    NEGF_DEharr = 0._dp
+    NEGF_Eharrs = 0._dp
+    NEGF_Etot = 0._dp
+    NEGF_FreeE = 0._dp
 
   end subroutine init_Energies
 
@@ -102,27 +123,36 @@
   subroutine update_E0()
 
     E0 = Ena + Ekin + Enl + Eso - Eions
-    
+
   end subroutine update_E0
   
   subroutine update_Etot()
+    use m_ts_global_vars, only: TSrun
     
     ! DUext (external electric field) -- should it be in or out?
     Etot = Ena + Ekin + Enl + Eso - Eions + &
-         DEna + DUscf + DUext + Exc + &
-         Ecorrec + Emad + Emm + Emeta + Eldau
-    ! Commented out the NEGF contribution to the total energy
-    ! We know it is wrong, but we estimate it. See output
-    !    Etot = Etot + DE_NEGF
+        DEna + DUscf + DUext + Exc + &
+        Ecorrec + Emad + Emm + Emeta + Eldau
 
+    if ( TSrun ) then
+      NEGF_Etot = Ena + NEGF_Ekin + NEGF_Enl + NEGF_Eso - Eions + &
+          DEna + DUscf + DUext + Exc + Ecorrec + Emad + Emm + Emeta + &
+          Eldau + NEGF_DE
+    end if
+    
   end subroutine update_Etot
 
   !> @param kBT the temperature in energy
   subroutine update_FreeE( kBT )
+    use m_ts_global_vars, only: TSrun
     real(dp), intent(in) :: kBT
 
     FreeE = Etot - kBT * Entropy
 
+    if ( TSrun ) then
+      NEGF_FreeE = NEGF_Etot - kBT * Entropy
+    end if
+
   end subroutine update_FreeE
 
   !> @param kBT the temperature in energy

=== modified file 'Src/m_io_yaml.F90'
--- Src/m_io_yaml.F90	2018-05-30 08:58:52 +0000
+++ Src/m_io_yaml.F90	2019-08-18 23:02:58 +0000
@@ -174,7 +174,6 @@
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "DEna", DEna
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "DUscf", DUscf
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "DUext", DUext
-    write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "Enegf", DE_NEGF
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "Exc", Exc
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "Ecorrec", Ecorrec
     write(unit=yaml_fd, fmt='(2X,A,":",1X,E24.8)') "Emadel", Emad

=== modified file 'Src/m_mixing.F90'
--- Src/m_mixing.F90	2019-06-20 10:46:56 +0000
+++ Src/m_mixing.F90	2019-08-18 23:02:58 +0000
@@ -423,25 +423,46 @@
 
          ! Do options so that a pulay option may refer to
          ! the actual names of the constants
+         
          if ( m%m == MIX_PULAY ) then
-
-            ! The linear mixing weight
-            if ( leqi(opt,'weight.linear') &
-                 .or. leqi(opt,'w.linear') ) then
-               
-               m%rv(1) = fdf_breals(pline,1)
-
-            else if ( leqi(opt,'svd.cond') ) then
-
-               ! This is only applicable to the Pulay
-               ! mixing scheme...
-               
-               m%rv(I_SVD_COND) = fdf_bvalues(pline,1)
-               
-            end if
-
+           if ( leqi(opt,'weight.linear') &
+               .or. leqi(opt,'w.linear') ) then
+             
+             m%rv(1) = fdf_breals(pline,1)
+             if ( m%rv(1) <= 0._dp .or. 1._dp < m%rv(1) ) then
+               call die("m_mixing: Mixing weight should be 0 < weight <= 1")
+             end if
+             
+           else if ( leqi(opt,'svd.cond') ) then
+             m%rv(I_SVD_COND) = fdf_bvalues(pline,1)
+           end if
+           
+         else if ( m%m == MIX_BROYDEN ) then
+           
+           ! The linear mixing weight
+           if ( leqi(opt,'weight.linear') &
+               .or. leqi(opt,'w.linear') ) then
+             
+             m%rv(1) = fdf_breals(pline,1)
+             if ( m%rv(1) <= 0._dp .or. 1._dp < m%rv(1) ) then
+               call die("m_mixing: Linear mixing weight should be 0 < weight <= 1")
+             end if
+
+           else if ( leqi(opt,'weight.prime') &
+               .or. leqi(opt,'w.prime') ) then
+             
+             m%rv(2) = fdf_breals(pline,1)
+             if ( m%rv(2) < 0._dp .or. 1._dp < m%rv(2) ) then
+               call die("m_mixing: Prime weight should be 0 <= weight <= 1")
+             end if
+
+           else if ( leqi(opt,'svd.cond') ) then
+             
+             m%rv(I_SVD_COND) = fdf_bvalues(pline,1)
+             
+           end if
+           
          end if
-
          
          ! Generic options for all advanced methods...
          if ( leqi(opt,'next.p') ) then
@@ -473,6 +494,10 @@
     type(tMixer), intent(inout) :: mix
     integer :: n
 
+    if ( mix%w <= 0._dp .or. 1._dp < mix%w ) then
+      call die("m_mixing: Mixing weight should be: 0 < weight <= 1")
+    end if
+
     ! Correct amount of history in the mixing.
     if ( 0 < mix%restart .and. &
          mix%restart < mix%n_hist ) then
@@ -518,7 +543,7 @@
        
        ! allocate temporary array
        mix%n_hist = max(2, mix%n_hist)
-       n = 1 + mix%n_hist
+       n = 2 + mix%n_hist
        allocate(mix%rv(I_SVD_COND:n))
        mix%rv(1:n) = mix%w
 
@@ -702,7 +727,7 @@
     type(tMixer), intent(in), target :: mixers(:)
 
     type(tMixer), pointer :: m
-    character(len=50) :: fmt
+    character(len=64) :: fmt
 
     logical :: bool
     integer :: i
@@ -795,9 +820,13 @@
           write(*,'(2a,t50,''= '',i0)') trim(fmt), &
                '    History steps',m%n_hist
           write(*,'(2a,t50,''= '',f12.6)') trim(fmt), &
-               '    Jacobian weight',m%w
-          write(*,'(2a,t50,''= '',f12.6)') trim(fmt), &
-               '    Weight prime',m%rv(1)
+               '    Linear mixing weight',m%rv(1)
+          write(*,'(2a,t50,''= '',f12.6)') trim(fmt), &
+               '    Inverse Jacobian weight',m%w
+          write(*,'(2a,t50,''= '',f12.6)') trim(fmt), &
+               '    Weight prime',m%rv(2)
+          write(*,'(2a,t50,''= '',e10.4)') trim(fmt), &
+               '    SVD condition',m%rv(I_SVD_COND)
           if ( m%rv(I_P_NEXT) > 0._dp ) then
              write(*,'(2a,t50,''= '',f6.4)') trim(fmt), &
                   '    Step mixer parameter',m%rv(I_P_NEXT)
@@ -921,8 +950,11 @@
        ! For Broyden this is the inverse Jacobian
        write(*,'(t3,a,f6.4)') 'weight ', m%w
        select case ( m%m )
-       case ( MIX_PULAY, MIX_BROYDEN )
-          write(*,'(t3,a,f6.4)') 'weight.linear ', m%rv(1)
+       case ( MIX_PULAY )
+         write(*,'(t3,a,f6.4)') 'weight.linear ', m%rv(1)
+       case ( MIX_BROYDEN )
+         write(*,'(t3,a,f6.4)') 'weight.linear ', m%rv(1)
+         write(*,'(t3,a,f6.4)') 'weight.prime ', m%rv(2)
        end select
           
        if ( m%n_hist > 0 ) then
@@ -1685,7 +1717,7 @@
       ! This is the modified Broyden algorithm...
 
       ! Retrieve the previous weights
-      w => mix%rv(2:1+nh)
+      w => mix%rv(3:2+nh)
       select case ( mix%v )
       case ( 2 ) ! Unity Broyden
          
@@ -1779,9 +1811,9 @@
 
       ! Add the diagonal term
       ! This should also prevent it from being
-      ! singular (unless mix%w == 0)
+      ! singular (unless mix%rv(2) == 0)
       do i = 1 , nh
-         A(i,i) = mix%rv(1) ** 2 + A(i,i)
+         A(i,i) = mix%rv(2) ** 2 + A(i,i)
       end do
 
       ! Calculate the inverse
@@ -2006,7 +2038,7 @@
          
       end if
 
-      ! Get the linear mixing term...
+      ! Get the inverse Jacobian term...
       G = mix%w
 
       ! if debugging print out the different variables
@@ -2242,7 +2274,7 @@
 
       ! Update weights (if necessary)
       if ( nh > 1 ) then
-         do i = 2 , nh
+         do i = 3 , nh + 1
             mix%rv(i) = mix%rv(i+1)
          end do
       end if

=== modified file 'Src/m_new_dm.F90'
--- Src/m_new_dm.F90	2019-08-16 10:13:21 +0000
+++ Src/m_new_dm.F90	2019-08-18 23:02:58 +0000
@@ -335,7 +335,7 @@
     ! Determine how the mixing of the first step should be performed
     !
     ! The idea is that one will allow mixing on the first SCF step
-    ! only for atomicly filled orbitals. This will in most cases
+    ! only for atomically filled orbitals. This will in most cases
     ! be a good initial choice, while in certain systems (spin-orbit)
     ! it may not be so good.
     ! Subsequently for any MD steps beyond the initial step, we will not
@@ -352,8 +352,8 @@
       mix_scf_first = .true.
       if ( IONode .and. init_method < 0 ) then
         ! Warn the user about this
-        write(*,"(a)") "Mixing first iteration is *forced* although the sparsity pattern has changed..."
-        write(*,"(a)") "Mixing non-compatible matrices may result in non-idempotency problems."
+        write(*,"(a)") "Mixing first scf iteration is *forced* although the sparsity pattern has changed..."
+        write(*,"(a)") "Mixing non-compatible matrices might result in problems."
         write(*,"(a)") "Please use a linear mixer for the first few steps to remove history effects."
       end if
     else if ( mix_scf_first .and. init_method < 0 ) then

=== modified file 'Src/m_spin.F90'
--- Src/m_spin.F90	2019-01-13 16:11:47 +0000
+++ Src/m_spin.F90	2019-08-18 23:02:58 +0000
@@ -355,6 +355,8 @@
        write(*,'(a)') repeat('#',60)
        write(*,'(a,t16,a,t60,a)') '#','Spin-orbit coupling is in beta','#'
        write(*,'(a,t13,a,t60,a)') '#','Several options may not be compatible','#'
+       call message("WARNING","This spin-orbit implementation uses a local approximation.")
+       call message("WARNING","You are strongly advised to use the newer version.")
        write(*,'(a)') repeat('#',60)
     end if
 

=== modified file 'Src/m_transiesta.F90'
--- Src/m_transiesta.F90	2019-02-13 17:39:22 +0000
+++ Src/m_transiesta.F90	2019-08-18 23:02:58 +0000
@@ -48,7 +48,7 @@
        sp_dist, sparse_pattern, &
        no_aux_cell, ucell, nsc, isc_off, no_u, na_u, lasto, xa, n_nzs, &
        H, S, DM, EDM, Ef, &
-       Qtot, Fermi_correct, DE_NEGF)
+       Qtot, Fermi_correct)
 
     use units, only : eV
     use alloc, only : re_alloc, de_alloc
@@ -75,6 +75,8 @@
     use m_ts_gf, only : read_Green
     use m_interpolate
 
+    use m_energies, only: NEGF_DE
+
 ! ********************
 ! * INPUT variables  *
 ! ********************
@@ -94,7 +96,6 @@
     real(dp), intent(in) :: Qtot
     real(dp), intent(inout) :: Ef
     logical, intent(in) :: Fermi_correct
-    real(dp), intent(inout) :: DE_NEGF
 
 ! ******************** IO descriptors ************************
     integer, allocatable :: uGF(:)
@@ -127,7 +128,7 @@
     ! Note that this will *only* be updated in case V /= 0.
     ! This energy corresponds to the non-equilibrium energies:
     !   e \sum_i N_i * \mu_i
-    DE_NEGF = 0._dp
+    NEGF_DE = 0._dp
 
     if ( TSiscf == 1 ) then
        ! We need to initialize TRANSIESTA
@@ -256,14 +257,14 @@
                   nq, uGF, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           else
              call ts_fullk(N_Elec,Elecs, &
                   nq, uGF, &
                   ucell, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           end if
        else if ( ts_method == TS_BTD ) then
           if ( ts_Gamma ) then
@@ -271,14 +272,14 @@
                   nq, uGF, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           else
              call ts_trik(N_Elec,Elecs, &
                   nq, uGF, &
                   ucell, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           end if
 #ifdef SIESTA__MUMPS
        else if ( ts_method == TS_MUMPS ) then
@@ -287,14 +288,14 @@
                   nq, uGF, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           else
              call ts_mumpsk(N_Elec,Elecs, &
                   nq, uGF, &
                   ucell, nspin, na_u, lasto, &
                   sp_dist, sparse_pattern, &
                   no_u, n_nzs, &
-                  H, S, DM, EDM, Ef, DE_NEGF)
+                  H, S, DM, EDM, Ef, NEGF_DE)
           end if
 #endif
        else

=== modified file 'Src/m_ts_options.F90'
--- Src/m_ts_options.F90	2019-06-11 08:38:16 +0000
+++ Src/m_ts_options.F90	2019-08-18 23:02:58 +0000
@@ -375,7 +375,7 @@
 
     ! Whether we should always set the DM to bulk
     ! values (by reading in from electrode DM)
-    if ( TS_scf_mode == 1 ) then
+    if ( TS_scf_mode == 1 .or. .not. IsVolt ) then
        chars = 'bulk'
     else
        chars = 'diagon'

=== modified file 'Src/mixer.F'
--- Src/mixer.F	2018-11-27 11:01:23 +0000
+++ Src/mixer.F	2019-08-18 23:02:58 +0000
@@ -30,7 +30,8 @@
       use m_mixing_scf, only: scf_mix
       use m_mixing, only: mixing
       
-      use m_spin,           only: h_spin_dim, SpOrb
+      use m_spin,           only: spin
+
       use parallel,         only: IONode
 
       implicit none
@@ -42,6 +43,7 @@
 
       real(dp)              :: dtmp
       integer               :: iiscf, i, is
+      integer :: nspin_mix
 
       external :: mulliken
 !-------------------------------------------------------------------- BEGIN
@@ -52,15 +54,17 @@
          ! Mix Hamiltonian
          Xin => Hold
          Xout => H
+         nspin_mix = spin%H
       else
          ! Mix density matrix
          Xin => Dold
          Xout => Dscf
+         nspin_mix = spin%DM
       end if
 
 
       ! Create residual function to minimize
-      allocate(F(maxnh,h_spin_dim))
+      allocate(F(maxnh,nspin_mix))
 
 !$OMP parallel default(shared), private(dtmp,i)
 
@@ -103,15 +107,15 @@
       ! Upon exit Xout contains the mixed quantity
       select case ( mix_spin )
       case ( MIX_SPIN_ALL )
-         call mixing( scf_mix, maxnh, h_spin_dim, Xin, F, Xout)
+         call mixing( scf_mix, maxnh, nspin_mix, Xin, F, Xout)
       case ( MIX_SPIN_SPINOR )
-         call mixing( scf_mix, maxnh, h_spin_dim, Xin, F, Xout,
+         call mixing( scf_mix, maxnh, nspin_mix, Xin, F, Xout,
      &        nsub=2)
       case ( MIX_SPIN_SUM )
-         call mixing( scf_mix, maxnh, h_spin_dim, Xin, F, Xout,
+         call mixing( scf_mix, maxnh, nspin_mix, Xin, F, Xout,
      &        nsub=1)
       case ( MIX_SPIN_SUM_DIFF )
-         call mixing( scf_mix, maxnh, h_spin_dim, Xin, F, Xout,
+         call mixing( scf_mix, maxnh, nspin_mix, Xin, F, Xout,
      &        nsub=2)
       end select
 
@@ -148,31 +152,23 @@
       ! Correctly handle mixed quantity
       ! move over mixed quantity to "input"
       if ( mix_scf_first ) then
-         
-         ! always allow mixing
-!$OMP do
-         do is = 1 , size(Xin, 2)
-            do i = 1 , size(Xin, 1)
-               Xin(i,is) = Xout(i,is)
-            end do
-         end do
-!$OMP end do nowait
-         
+
+        ! always allow mixing
+        ! I.e. we do nothing
+        
       else if ( iscf == 1 ) then
          
-         ! We are not allowed to mix the first SCF
-         ! Remember that Xout contains the MIXED
-         ! quantity and F is the current residual
-         ! hence:
-         !   Xout = Xin + F
+        ! We are not allowed to mix the first SCF
+        ! Remember that Xout contains the MIXED
+        ! quantity and F is the current residual
+        ! hence for no mixing we re-create Xout:
+        !   Xout = Xin + F
 !$OMP do
-         do is = 1 , size(Xin, 2)
-            do i = 1 , size(Xin, 1)
-               Xin(i,is) = Xin(i,is) + F(i,is)
-               ! we require that Xin == Xout:
-               Xout(i,is) = Xin(i,is)
-            end do
-         end do
+        do is = 1 , nspin_mix
+          do i = 1 , size(Xin, 1)
+            Xout(i,is) = Xin(i,is) + F(i,is)
+          end do
+        end do
 !$OMP end do nowait
 
       end if
@@ -188,7 +184,7 @@
 
       if (muldeb .and. (.not. MixH) ) then 
          if (IONode) write (6,"(/a)") 'Using DM after mixing:'
-         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 'Src/print_spin.F90'
--- Src/print_spin.F90	2018-04-11 09:52:01 +0000
+++ Src/print_spin.F90	2019-08-18 23:02:58 +0000
@@ -2,10 +2,10 @@
   !
   ! Prints spin in output and CML files
   !
-  use m_spin,          only: nspin
+  use m_spin,          only: spin
   use atomlist,        only: no_l
   use sparse_matrices, only: listhptr, numh
-  use sparse_matrices, only: S, Dscf
+  use sparse_matrices, only: S, Dscf   ! Dscf could have 1, 2, 4, or 8 components
   use siesta_cml
   use parallel,        only: IOnode
   use precision,       only: dp
@@ -15,58 +15,73 @@
 
   implicit none
   
-  real(dp), intent(out)  :: qspin(4)
+  real(dp), intent(out)  :: qspin(spin%Grid)
 
   integer  :: ispin, io, j, ind
   real(dp) :: qaux
   real(dp) :: Stot        ! Total spin magnitude
   real(dp) :: Svec(3)     ! Total spin vector
 #ifdef MPI
-  real(dp) :: qtmp(4)
-#endif
-
-  if (nspin .ge. 2) then
-     do ispin = 1,nspin
-        qspin(ispin) = 0.0_dp
-        do io = 1,no_l
-           do j = 1,numh(io)
-              ind = listhptr(io)+j
-              qspin(ispin) = qspin(ispin) + Dscf(ind,ispin) * S(ind)
-           enddo
-        enddo
-     enddo
-
-#ifdef MPI
-     !       Global reduction of spin components
-     call globalize_sum(qspin(1:nspin),qtmp(1:nspin))
-     qspin(1:nspin) = qtmp(1:nspin)
-#endif
-
-     if (nspin .eq. 2) then
-
-        if (IOnode) then
-           Svec(1) = 0.0_dp
-           Svec(2) = 0.0_dp
-           Svec(3) = qspin(1) - qspin(2)
-           Stot = Svec(3)
-           write(6,'(5x,a,f10.5,2f10.1,f10.5)') 'spin moment: S , {S} = ', Stot, Svec
-        endif
-        if (cml_p) call cmlAddProperty(xf=mainXML,            &
-             value=qspin(1)-qspin(2), dictref='siesta:stot', &
-             units='siestaUnits:spin')
-
-     elseif (nspin .eq. 4) then
-
-        call spnvec( nspin, qspin, qaux, Stot, Svec )
-        if (IONode) then
-           write(6,'(5x,a,4f10.5)') 'spin moment: S , {S} = ', Stot, Svec
-           if (cml_p) then
-              call cmlAddProperty(xf=mainXML, value=Stot,  &
-                   dictref='siesta:stot', units='siestaUnits:spin')
-              call cmlAddProperty(xf=mainXML, value=Svec,  &
-                   dictref='siesta:svec', units='siestaUnits:spin')
-           endif !cml_p
-        endif
-     endif
+  real(dp) :: qtmp(spin%Grid)
+#endif
+
+  qspin(:) = 0.0_dp
+
+  if ( spin%Grid < 2 ) return
+
+  if ( spin%SO ) then
+     
+    do io = 1,no_l
+      do j = 1,numh(io)
+        ind = listhptr(io)+j
+        ! In the SOC case, hermitify Dscf
+        qspin(1:2) = qspin(1:2) + dscf(ind,1:2) * S(ind)
+        qspin(3) = qspin(3) + 0.5_dp*(dscf(ind,3)+dscf(ind,7)) * S(ind)
+        qspin(4) = qspin(4) + 0.5_dp*(dscf(ind,4)+dscf(ind,8)) * S(ind)
+      end do
+    end do
+
+  else
+     
+    do io = 1,no_l
+      do j = 1,numh(io)
+        ind = listhptr(io)+j
+        qspin(:) = qspin(:) + Dscf(ind,:) * S(ind)
+      end do
+    end do
+     
   endif
+#ifdef MPI
+  ! Global reduction of spin components
+  call globalize_sum(qspin(1:spin%Grid),qtmp(1:spin%Grid))
+  qspin(1:spin%Grid) = qtmp(1:spin%Grid)
+#endif
+
+  ! We are left with printing out to stdout
+  if ( .not. IONode ) return
+  
+  if ( spin%Grid == 2) then
+
+    Svec(1) = 0.0_dp
+    Svec(2) = 0.0_dp
+    Svec(3) = qspin(1) - qspin(2)
+    Stot = Svec(3)
+    write(6,'(5x,a,f10.5,2f10.1,f10.5)') 'spin moment: S , {S} = ', Stot, Svec
+    if (cml_p) call cmlAddProperty(xf=mainXML,            &
+        value=qspin(1)-qspin(2), dictref='siesta:stot', &
+        units='siestaUnits:spin')
+    
+  else if ( spin%Grid == 4 ) then
+
+    call spnvec( spin%Grid, qspin, qaux, Stot, Svec )
+    write(6,'(5x,a,4f10.5)') 'spin moment: S , {S} = ', Stot, Svec
+    if (cml_p) then
+      call cmlAddProperty(xf=mainXML, value=Stot,  &
+          dictref='siesta:stot', units='siestaUnits:spin')
+      call cmlAddProperty(xf=mainXML, value=Svec,  &
+          dictref='siesta:svec', units='siestaUnits:spin')
+    end if !cml_p
+
+  end if
+
 end subroutine print_spin

=== modified file 'Src/read_options.F90'
--- Src/read_options.F90	2019-08-16 10:13:21 +0000
+++ Src/read_options.F90	2019-08-18 23:02:58 +0000
@@ -445,9 +445,9 @@
 
   ! Density Matrix Mixing  (proportion of output DM in new input DM)
   wmix = fdf_get('DM.MixingWeight',0.25_dp)
-  if (ionode) then
-     write(6,6) 'redata: New DM Mixing Weight',wmix
-  endif
+!!$  if (ionode) then
+!!$     write(6,6) 'redata: New DM Mixing Weight',wmix
+!!$  endif
 
   if (cml_p) then
      call cmlAddParameter( xf=mainXML,name='DM.MixingWeight', &

=== modified file 'Src/rhoofd.F90'
--- Src/rhoofd.F90	2016-09-13 13:22:20 +0000
+++ Src/rhoofd.F90	2019-08-18 23:02:58 +0000
@@ -294,7 +294,7 @@
                  r2sp = sum(dxsp**2)
                  if ( r2sp < r2cut(is) ) then
 !$OMP critical
-                    call all_phi( is, +1, dxsp, nphiloc, phia(:,isp) )
+                    call all_phi( is, +1, dxsp, maxoa, nphiloc, phia(:,isp) )
 !$OMP end critical
                  else
                     phia(:,isp) = 0.0_dp

=== modified file 'Src/rhoofdsp.f'
--- Src/rhoofdsp.f	2016-01-25 16:00:16 +0000
+++ Src/rhoofdsp.f	2019-08-18 23:02:58 +0000
@@ -306,7 +306,8 @@
                 dxsp(:) = xdsp(:,isp) + xdop(:,iop) - dxa(:,ia)
                 r2sp = sum(dxsp**2)
                 if (r2sp.lt.r2cut(is)) then
-                  call all_phi( is, +1, dxsp, nphiloc, phia(:,isp) )
+                  call all_phi( is, +1, dxsp, maxoa,
+     &                nphiloc, phia(:,isp) )
                 else
                   phia(:,isp) = 0.0_dp
                 endif

=== modified file 'Src/siesta_analysis.F'
--- Src/siesta_analysis.F	2018-06-25 11:33:42 +0000
+++ Src/siesta_analysis.F	2019-08-18 23:02:58 +0000
@@ -46,8 +46,7 @@
       use m_energies
       use m_steps, only: final
       use m_ntm
-      use m_spin,         only: nspin, spinor_dim, h_spin_dim
-      use m_spin,         only: SpOrb, NonCol, SPpol, NoMagn
+      use m_spin,         only: spin
       use m_dipol
       use m_eo
       use m_forces,          only: fa
@@ -68,15 +67,15 @@
 
       real(dp)          :: dummy_str(3,3)
       real(dp)          :: dummy_strl(3,3)
-      real(dp)          :: qspin(4)         ! Local
+      real(dp)          :: qspin(spin%Grid)         ! Local
 
-      real(dp)          :: polxyz(3,nspin)  ! Autom., small
-      real(dp)          :: polR(3,nspin)    ! Autom., small
+      real(dp)          :: polxyz(3,spin%Grid)  ! Autom., small
+      real(dp)          :: polR(3,spin%Grid)    ! Autom., small
       real(dp)          :: qaux
       real(dp), pointer :: ebk(:,:,:)       ! Band energies
 
       integer           :: j, ix, ind, ik, io, ispin
-      integer           :: wfs_band_min, wfs_band_max
+      integer           :: wfs_band_min, wfs_band_max, max_n_states
       real(dp)          :: g2max, current_ef
       type(filesOut_t)  :: filesOut  ! blank output file names
 
@@ -127,7 +126,7 @@
 
       if (fdf_get("Read-H-from-file",.false.)) then
          if (SIESTA_worker) then
-            call read_spmatrix(maxnh, no_l, h_spin_dim, numh,
+            call read_spmatrix(maxnh, no_l, spin%H, numh,
      .           listhptr, listh, H, found, userfile="H_IN")
             if (.not. found) call die("Could not find H_IN")
             current_ef = ef
@@ -137,7 +136,7 @@
 
 #ifdef SIESTA__PEXSI
       if (fdf_get("PEXSI.DOS",.false.)) then
-         call pexsi_dos(no_u, no_l, spinor_dim,
+         call pexsi_dos(no_u, no_l, spin%spinor,
      $        maxnh, numh, listhptr, listh, H, S, qtot, ef)
          
       endif
@@ -263,6 +262,17 @@
 !        latest DM, although this is probably too much).
 !        See the logic in siesta_forces.
 
+!     Setup the number of states depending on the used method
+!     For polarized calculations we use no_u and separate spin-channels.
+!     For NC/SO we have mixed spin-channels and separating makes no
+!     sense.
+      if ( spin%Grid == 4 ) then
+!       We are NC/SO
+        max_n_states = no_u * 2
+      else
+        max_n_states = no_u
+      end if
+
 !     Find and print wavefunctions at selected k-points
 !**   This uses H,S, and xa
       if (nwk.gt.0) then
@@ -270,7 +280,7 @@
         if (IONode) print "(a)",
      $              "Writing WFSX for selected k-points in "
      $                           // trim(wfs_filename)
-        call wwave( no_s, h_spin_dim, spinor_dim, no_u, no_l, maxnh, 
+        call wwave( no_s, spin, no_u, no_l, maxnh, 
      &              nwk,
      &              numh, listhptr, listh, H, S, Ef, xijo, indxuo,
      &              gamma_wavefunctions, nwk, wfk, no_u, occtol )
@@ -278,19 +288,20 @@
 
 
 !**   This uses H,S, and xa
-      if (write_coop) then
+      if ( write_coop ) then
         ! Output the wavefunctions for the kpoints in the SCF set
         ! Note that we allow both a band number and an energy range
         ! The user is responsible for using appropriate values.
         wfs_band_min = fdf_get("WFS.BandMin",1)
-        wfs_band_max = fdf_get("WFS.BandMax",no_u)
-        call setup_wfs_list(nkpnt,no_u,wfs_band_min,wfs_band_max,
+        wfs_band_max = fdf_get("WFS.BandMax",max_n_states)
+        call setup_wfs_list(nkpnt,max_n_states,
+     $                      wfs_band_min,wfs_band_max,
      $                      use_scf_weights=.true.,
      $                      use_energy_window=.true.)
          wfs_filename = trim(slabel)//".fullBZ.WFSX"
          if (IONode) print "(a)", "Writing WFSX for COOP/COHP in " 
      $                           // trim(wfs_filename)
-         call wwave( no_s, h_spin_dim, spinor_dim, no_u, no_l, maxnh, 
+         call wwave( no_s, spin, no_u, no_l, maxnh, 
      .        nkpnt,
      .        numh, listhptr, listh, H, S, Ef, xijo, indxuo,
      .        gamma_SCF, nkpnt, kpoint, no_u, occtol)
@@ -299,82 +310,101 @@
 !     Compute bands
 !**   This uses H,S, and xa
       nullify( ebk )
-      call re_alloc( ebk, 1, no_u, 1, spinor_dim, 1, maxbk,
-     &               'ebk', 'siesta_analysis' )
-
-      if (nbk.gt.0) then
+      if ( spin%Grid == 4 ) then
+        call re_alloc( ebk, 1, no_u*2, 1, 1, 1, maxbk,
+     &      'ebk', 'siesta_analysis' )
+      else
+        call re_alloc( ebk, 1, no_u, 1, spin%spinor, 1, maxbk,
+     &      'ebk', 'siesta_analysis' )
+      end if
+      
+      if ( nbk > 0 ) then
         if (IONode) print "(a)", "Computing bands..."
         getPSI = fdf_get('WFS.Write.For.Bands', .false.)
         if (getPSI) then
-           wfs_filename = trim(slabel)//".bands.WFSX"
-         if (IONode) print "(a)", "Writing WFSX for bands in "
-     $                           // trim(wfs_filename)
-           wfs_band_min = fdf_get("WFS.BandMin",1)
-           wfs_band_max = fdf_get("WFS.BandMax",no_u)
-           call setup_wfs_list(nbk,no_u,wfs_band_min,wfs_band_max,
-     $          use_scf_weights=.false.,
-     $          use_energy_window=.false.)
-        endif
-        call bands( no_s, h_spin_dim, spinor_dim, no_u, no_l, maxnh, 
+          wfs_filename = trim(slabel)//".bands.WFSX"
+          if (IONode) print "(a)", "Writing WFSX for bands in "
+     $        // trim(wfs_filename)
+          wfs_band_min = fdf_get("WFS.BandMin",1)
+          wfs_band_max = fdf_get("WFS.BandMax",max_n_states)
+          call setup_wfs_list(nbk,max_n_states,
+     $        wfs_band_min,wfs_band_max,
+     $        use_scf_weights=.false.,
+     $        use_energy_window=.false.)
+        end if
+        call bands( no_s, spin, no_u, no_l, maxnh, 
      .              maxbk,
      .              numh, listhptr, listh, H, S, Ef, xijo, indxuo,
-     .              .true., nbk, bk, ebk, occtol, getPSI )
-        if (IOnode) then
+     .      .true., nbk, bk, ebk, occtol, getPSI )
+
+        if ( IOnode ) then
           if ( writbk ) then
-            write(6,'(/,a,/,a4,a12)')
-     &       'siesta: Band k vectors (Bohr**-1):', 'ik', 'k'
+            write(6,'(/,a,/,a4,tr1,a12)')
+     &          'siesta: Band k vectors (Bohr**-1):', 'ik', 'k'
             do ik = 1,nbk
-              write(6,'(i4,3f12.6)') ik, (bk(ix,ik),ix=1,3)
-            enddo
-          endif
+              write(6,'(i4,3(tr1,f12.6))') ik, (bk(ix,ik),ix=1,3)
+            end do
+          end if
         
           if ( writb ) then
-            write(6,'(/,a,/,a4,a3,a7)')
-     &       'siesta: Band energies (eV):', 'ik', 'is', 'eps'
-            do ispin = 1, spinor_dim
+            if ( spin%Grid == 4 ) then
+              write(6,'(/,a,/,a4,tr1,a9)')
+     &            'siesta: Band energies (eV):', 'ik', 'eps'
               do ik = 1,nbk
-                write(6,'(i4,i3,10f7.2)')
-     &            ik, ispin, (ebk(io,ispin,ik)/eV,io=1,min(10,no_u))
-                if (no_u.gt.10) write(6,'(7x,10f7.2)')
-     &              (ebk(io,ispin,ik)/eV,io=11,no_u)
+                write(6,'(i4,10(tr1,f9.4))')
+     &              ik, (ebk(io,1,ik)/eV,io=1,min(10,2*no_u))
+                if ( 2*no_u > 10 ) write(6,'(4x,10(tr1,f9.4))')
+     &              (ebk(io,1,ik)/eV,io=11,no_u*2)
+              end do
+
+            else
+              write(6,'(/,a,/,a4,a3,tr1,a9)')
+     &            'siesta: Band energies (eV):', 'ik', 'is', 'eps'
+              do ispin = 1, spin%spinor
+                do ik = 1,nbk
+                  write(6,'(i4,i3,10(tr1,f9.4))')
+     &                ik, ispin, (ebk(io,ispin,ik)/eV,io=1,min(10,no_u))
+                  if ( no_u > 10 ) write(6,'(7x,10(tr1,f9.4))')
+     &                (ebk(io,ispin,ik)/eV,io=11,no_u)
+                enddo
               enddo
-            enddo
+            end if
           endif
+          
         endif
       endif
 
 !     Print eigenvalues
-      if (IOnode .and. writeig) then
-        if ((isolve.eq.SOLVE_DIAGON .or.
-     &       ((isolve.eq.SOLVE_MINIM) .and. minim_calc_eigenvalues))
-     &      .and. no_l.lt.1000) then
-          if ( h_spin_dim <= 2 ) then
-            write(6,'(/,a,/,a4,a3,a7)')
-     &       'siesta: Eigenvalues (eV):', 'ik', 'is', 'eps'
-            do ik = 1,nkpnt
-              do ispin = 1,spinor_dim
-                write(6,'(i4,i3,10f7.2)')
+      if ( IOnode .and. writeig .and. no_l < 1000 .and. 
+     &    (isolve.eq.SOLVE_DIAGON .or.
+     &    (isolve.eq.SOLVE_MINIM .and. minim_calc_eigenvalues)) ) then
+
+        if ( spin%Grid == 4 ) then
+          write(6,'(/,a)') 'siesta: Eigenvalues (eV):'
+          do ik = 1,nkpnt
+            write(6,'(a,i6)') 'ik =', ik
+            write(6,'(10(tr1,f9.4))') (eo(io,1,ik)/eV,io=1,2*neigwanted)
+          end do
+
+        else
+          write(6,'(/,a,/,a4,a3,tr1,a9)')
+     &        'siesta: Eigenvalues (eV):', 'ik', 'is', 'eps'
+          do ik = 1,nkpnt
+            do ispin = 1, spin%spinor
+              write(6,'(i4,i3,10(tr1,f9.4))')
      &            ik,ispin,(eo(io,ispin,ik)/eV,io=1,min(10,neigwanted))
-                if (no_u.gt.10) write(6,'(7x,10f7.2)')
+              if (no_u.gt.10) write(6,'(7x,10(tr1,f9.4))')
      &            (eo(io,ispin,ik)/eV,io=11,neigwanted)
-              enddo
-            enddo
-          else
-            write(6,'(/,a)') 'siesta: Eigenvalues (eV):'
-            do ik = 1,nkpnt
-              write(6,'(a,i6)') 'ik =', ik
-              write(6,'(10f7.2)')
-     &          ((eo(io,ispin,ik)/eV,io=1,neigwanted),ispin=1,2)
-            enddo
-          endif
-          write(6,'(a,f15.6,a)') 'siesta: Fermi energy =', ef/eV, ' eV'
-        endif
+            end do
+          end do
+        end if
+        write(6,'(a,f15.6,a)') 'siesta: Fermi energy =', ef/eV, ' eV'
       endif
 
       if (((isolve.eq.SOLVE_DIAGON).or.
      &     ((isolve.eq.SOLVE_MINIM).and.minim_calc_eigenvalues))
      &     .and.IOnode)
-     &     call ioeig(eo,ef,neigwanted,nspin,nkpnt,no_u,spinor_dim,
+     &     call ioeig(eo,ef,neigwanted,spin%H,nkpnt,no_u,spin%spinor,
      &     nkpnt,kpoint, kweight)
 
 
@@ -430,7 +460,7 @@
 !     Calculation of the bulk polarization using the Berry phase
 !     formulas by King-Smith and Vanderbilt
       if (nkpol.gt.0 .and. .not.bornz) then
-        if (NonCol .or. SpOrb) then
+        if ( spin%NCol .or. spin%SO ) then
           if (IOnode) then
             write(6,'(/a)')
      .       'siesta_analysis: bulk polarization implemented only for'
@@ -439,7 +469,7 @@
           endif
         else
          call KSV_pol(na_u, na_s, xa_last, rmaxo, scell_last, 
-     &               ucell_last,no_u, no_l, no_s, nspin, qspin, 
+     &               ucell_last,no_u, no_l, no_s, spin%Grid, qspin, 
      &               maxnh, nkpol, numh, listhptr, listh, 
      &               H, S, xijo, indxuo, isa, iphorb, 
      &               iaorb, lasto, shape,
@@ -449,7 +479,7 @@
 
 !     Calculation of the optical conductivity
       call optical(na_u, na_s, xa_last, scell_last, ucell_last,
-     &             no_u, no_l, no_s, nspin, qspin,
+     &             no_u, no_l, no_s, spin%Grid, qspin,
      &             maxnh, numh, listhptr, listh, H, S, xijo,
      $             indxuo, ebk, ef, temp,
      &             isa, iphorb, iphKB, lasto, lastkb, shape )
@@ -479,7 +509,7 @@
         g2max = g2cut
         dummy_str  = 0.0
         dummy_strl = 0.0
-        call dhscf( nspin, no_s, iaorb, iphorb, no_l,
+        call dhscf( spin%Grid, no_s, iaorb, iphorb, no_l,
      .              no_u, na_u, na_s, isa, xa_last, indxua, 
      &              ntm, 0, 0, 0, filesOut, 
      &              maxnh, numh, listhptr, listh, Dscf, Datm,

=== modified file 'Src/siesta_dicts.F90'
--- Src/siesta_dicts.F90	2018-09-06 10:00:24 +0000
+++ Src/siesta_dicts.F90	2019-08-18 23:02:58 +0000
@@ -316,8 +316,19 @@
          ('E.spin_orbit'.kvp.Eso)
     variables = variables // &
          ('E.ldau'.kvp.Eldau)
-    variables = variables // &
-         ('E.negf'.kvp.DE_NEGF)
+    
+    variables = variables // &
+         ('E.negf.dN'.kvp.NEGF_DE)
+    variables = variables // &
+         ('E.negf.spin_orbit'.kvp.NEGF_Eso)
+    variables = variables // &
+         ('E.negf.harris'.kvp.NEGF_Eharrs)
+    variables = variables // &
+         ('E.negf.total'.kvp.NEGF_Etot)
+    variables = variables // &
+         ('E.negf.kinetic'.kvp.NEGF_Ekin)
+    variables = variables // &
+         ('E.negf.band_structure'.kvp.NEGF_Ebs)
 
     ! Add the number of charges to the system
     variables = variables // &

=== modified file 'Src/siesta_forces.F'
--- Src/siesta_forces.F	2018-09-24 07:27:11 +0000
+++ Src/siesta_forces.F	2019-08-18 23:02:58 +0000
@@ -84,7 +84,6 @@
       use m_pexsi, only: pexsi_finalize_scfloop
 #endif     
 
-      use m_energies,            only: DE_NEGF
       use m_ts_options, only : N_Elec
       use m_ts_method
       use m_ts_global_vars,      only: TSmode, TSinit, TSrun
@@ -380,7 +379,7 @@
               call transiesta(iscf,spin%H, 
      &             block_dist, sparse_pattern, Gamma_Scf, ucell, nsc,
      &             isc_off, no_u, na_u, lasto, xa, maxnh, H, S,
-     &             Dscf, Escf, Ef, Qtot, .true., DE_NEGF) 
+     &             Dscf, Escf, Ef, Qtot, .true.) 
            
               ! We will not have not converged as we have just
               ! changed the Fermi-level

=== modified file 'Src/spher_harm.f'
--- Src/spher_harm.f	2017-02-19 19:26:15 +0000
+++ Src/spher_harm.f	2019-08-18 23:02:58 +0000
@@ -68,12 +68,15 @@
       PARAMETER (TINY=1.e-14_dp, ZERO=0._dp, HALF=0.5_dp, ONE=1._dp,
      .           TWO=2._dp, THREE=3._dp, SIX=6._dp)
 
+      real(dp), parameter :: pi = 3.14159265358979323846264338327950_dp
+      real(dp), parameter :: pi4 = 4 * pi
+
 C Internal variables
       INTEGER
-     .  I, ILM, ILM0, L, LMXMX, M, MS
+     .  I, ILM, ILM0, L, LMXMX, M
       REAL(DP)
      .  C(0:MAXLP1*MAXLP1), COSM, COSMM1, COSPHI,
-     .  ZP(0:MAXLP1,0:MAXLP1), FAC, FOURPI, GY(3),
+     .  ZP(0:MAXLP1,0:MAXLP1), FAC, GY(3),
      .  P(0:MAXLP1,0:MAXLP1),
      .  RL(-1:MAXL), RSIZE, RX, RY, RZ, RXY,
      .  SINM, SINMM1, SINPHI, YY
@@ -83,11 +86,10 @@
 C Evaluate normalization constants once and for all
       IF (LMAX.GT.LMXMX) THEN
          IF (LMAX.GT.MAXL) call die('YLM: MAXL too small')
-         FOURPI=TWO**4*ATAN(ONE)
          DO 20 L=0,LMAX
             ILM0=L*L+L
             DO 15 M=0,L
-               FAC=(2*L+1)/FOURPI
+               FAC=(2*L+1)/pi4
                DO 10 I=L-M+1,L+M
                   FAC=FAC/I
    10          CONTINUE
@@ -202,27 +204,25 @@
       SINM=ZERO
       DO 90 M=0,LMAX
         DO 80 L=M,LMAX
-          DO 75 MS = -1,1,2
-            IF (MS.EQ.-1) THEN
-              ILM=L*L+L-M
-              YY=C(ILM)*P(L,M)*SINM
-              GY(1)=(-ZP(L,M))*RX *RZ *SINM - P(L,M)*M*COSM*SINPHI/RXY
-              GY(2)=(-ZP(L,M))*RY *RZ *SINM + P(L,M)*M*COSM*COSPHI/RXY
-              GY(3)= ZP(L,M)*RXY*RXY*SINM
-            ELSE
-              ILM=L*L+L+M
-              YY=C(ILM)*P(L,M)*COSM
-              GY(1)=(-ZP(L,M))*RX *RZ *COSM + P(L,M)*M*SINM*SINPHI/RXY
-              GY(2)=(-ZP(L,M))*RY *RZ *COSM - P(L,M)*M*SINM*COSPHI/RXY
-              GY(3)= ZP(L,M)*RXY*RXY*COSM
-            ENDIF
-            GY(1)= GY(1)*C(ILM)/RSIZE
-            GY(2)= GY(2)*C(ILM)/RSIZE
-            GY(3)= GY(3)*C(ILM)/RSIZE
-            RLY(ILM)=RL(L)*YY
-            GRLY(1,ILM)= RX*L*RL(L-1)*YY + RL(L)*GY(1)
-            GRLY(2,ILM)= RY*L*RL(L-1)*YY + RL(L)*GY(2)
-            GRLY(3,ILM)= RZ*L*RL(L-1)*YY + RL(L)*GY(3)
+          ILM=L*L+L-M
+          GY(1)=(-ZP(L,M))*RX *RZ *SINM - P(L,M)*M*COSM*SINPHI/RXY
+          GY(2)=(-ZP(L,M))*RY *RZ *SINM + P(L,M)*M*COSM*COSPHI/RXY
+          GY(3)= ZP(L,M)*RXY*RXY*SINM
+          YY=C(ILM)*P(L,M)*SINM
+          RLY(ILM)=RL(L)*YY
+          GRLY(1,ILM)= RX*L*RL(L-1)*YY + RL(L)*GY(1)*C(ILM)/RSIZE
+          GRLY(2,ILM)= RY*L*RL(L-1)*YY + RL(L)*GY(2)*C(ILM)/RSIZE
+          GRLY(3,ILM)= RZ*L*RL(L-1)*YY + RL(L)*GY(3)*C(ILM)/RSIZE
+          
+          ILM=L*L+L+M
+          GY(1)=(-ZP(L,M))*RX *RZ *COSM + P(L,M)*M*SINM*SINPHI/RXY
+          GY(2)=(-ZP(L,M))*RY *RZ *COSM - P(L,M)*M*SINM*COSPHI/RXY
+          GY(3)= ZP(L,M)*RXY*RXY*COSM
+          YY=C(ILM)*P(L,M)*COSM
+          RLY(ILM)=RL(L)*YY
+          GRLY(1,ILM)= RX*L*RL(L-1)*YY + RL(L)*GY(1)*C(ILM)/RSIZE
+          GRLY(2,ILM)= RY*L*RL(L-1)*YY + RL(L)*GY(2)*C(ILM)/RSIZE
+          GRLY(3,ILM)= RZ*L*RL(L-1)*YY + RL(L)*GY(3)*C(ILM)/RSIZE
    75     CONTINUE
    80   CONTINUE
         COSMM1=COSM

=== added file 'Src/ts_energies.F90'
--- Src/ts_energies.F90	1970-01-01 00:00:00 +0000
+++ Src/ts_energies.F90	2019-08-18 23:02:58 +0000
@@ -0,0 +1,206 @@
+!
+! Copyright (C) 1996-2016	The SIESTA group
+!  This file is distributed under the terms of the
+!  GNU General Public License: see COPYING in the top directory
+!  or http://www.gnu.org/copyleft/gpl.txt.
+! See Docs/Contributors.txt for a list of contributors.
+!
+! This code segment has been fully created by:
+! Nick Papior Andersen, 2019, [e-mail]
+! Please conctact the author, prior to re-using this code.
+
+! Module for calculating energy contributions for the transiesta
+! calculations.
+! Effectively many of the energy contributions stem from Hamiltonian
+! and/or DM elements.
+! However, in TranSiesta we only update/use a subset of the full
+! matrices. As such the energies should only be calculated
+! on the used elements rather than the full.
+!
+! There are many more elements that need to be split, while currently
+! we only calculate a subset of what is actually needed.
+! The main problem in calculating NEGF energies is:
+!  1. the open-boundary problem, and
+!  2. how to handle real-space energies such as Exc from dhscf.
+module ts_energies_m
+
+  implicit none
+
+contains
+
+  subroutine ts_compute_energies()
+
+    use precision, only: dp
+    use m_ts_options, only: N_Elec, Elecs
+    use m_spin, only: spin
+
+    use sparse_matrices, only: dit => block_dist
+    use sparse_matrices, only: n_nzs => maxnh
+    use sparse_matrices, only: Dold, Dscf, H
+    use sparse_matrices, only: H_kin_1D, H_vkb_1D, H_so_2D
+    use sparse_matrices, only: sp => sparse_pattern
+    
+    use m_ts_method
+    use parallel, only : Node
+#ifdef MPI
+    use mpi_siesta
+#endif
+    use class_OrbitalDistribution
+    use class_Sparsity
+    use class_dSpData1D
+    use class_dSpData2D
+
+    use geom_helper, only : UCORB
+    use m_ts_electype, only: Elec
+    use m_energies, only: NEGF_Ebs, NEGF_Ekin, NEGF_Eso, NEGF_Etot, NEGF_Enl
+    use m_energies, only: NEGF_DEharr
+
+! **********************
+! * LOCAL variables    *
+! **********************
+    integer, pointer :: l_ncol(:), l_ptr(:), l_col(:)
+    integer :: no_lo, no_u, lio, io, ind, jo, ir, jr, r, ispin
+    real(dp), pointer :: H_vkb(:), H_kin(:), H_so(:,:)
+    real(dp) :: Etmp(5,0:1+1+N_Elec*2)
+#ifdef MPI
+    real(dp) :: tmp(5,0:1+1+N_Elec*2)
+    integer :: MPIerror
+#endif
+
+    H_vkb => val(H_vkb_1D)
+    H_kin => val(H_kin_1D)
+    if ( spin%SO ) then
+      H_so => val(H_so_2D)
+    end if
+
+    ! Retrieve information about the sparsity pattern
+    call attach(sp, &
+        n_col=l_ncol,list_ptr=l_ptr,list_col=l_col, &
+        nrows=no_lo,nrows_g=no_u)
+    
+    ! Initialize energies
+    Etmp(:,:) = 0._dp
+    
+!$OMP parallel do default(shared), &
+!$OMP&private(lio,io,ir,ind,jo,jr,r,ispin), &
+!$OMP&reduction(+:Etmp)
+    do lio = 1 , no_lo
+
+      ! obtain the global index of the orbital.
+      io = index_local_to_global(dit,lio,Node)
+      ir = orb_type(io)
+      
+      ! Loop number of entries in the row... (index frame)
+      do ind = l_ptr(lio) + 1 , l_ptr(lio) + l_ncol(lio)
+        
+        ! as the local sparsity pattern is a super-cell pattern,
+        ! we need to check the unit-cell orbital
+        ! The unit-cell column index
+        jo = UCORB(l_col(ind),no_u)
+        jr = orb_type(jo)
+        
+        if      ( all((/ir,jr/) == TYP_BUFFER) ) then
+          r = 1 ! buffer
+        else if ( any((/ir,jr/) == TYP_BUFFER) ) then
+          r = 0 ! other
+        else if ( all((/ir,jr/) == TYP_DEVICE) ) then
+          r = 2 ! device
+        else if ( any((/ir,jr/) == TYP_DEVICE) ) then
+          r = 4+(ir+jr-1)*2 ! device/electrode
+        else if ( ir == jr ) then
+          r = 3+(ir-1)*2 ! electrode/electrode
+        else
+          r = 0 ! other
+        end if
+
+        ! Ebs
+        if ( spin%SO ) then
+          Etmp(1,r) = Etmp(1,r) + H(ind,1) * Dscf(ind,1) &
+              + H(ind,2) * Dscf(ind,2) &
+              + H(ind,3) * Dscf(ind,7) &
+              + H(ind,4) * Dscf(ind,8) &
+              - H(ind,5) * Dscf(ind,5) &
+              - H(ind,6) * Dscf(ind,6) &
+              + H(ind,7) * Dscf(ind,3) &
+              + H(ind,8) * Dscf(ind,4)
+        else if ( spin%NCol ) then
+          Etmp(1,r) = Etmp(1,r) + H(ind,1) * Dscf(ind,1) &
+              + H(ind,2) * Dscf(ind,2) &
+              + (H(ind,3) * Dscf(ind,3) &
+              + H(ind,4) * Dscf(ind,4) ) * 2
+        else
+          Etmp(1,r) = Etmp(1,r) + sum(H(ind,:) * Dscf(ind,:) )
+        end if
+
+        do ispin = 1, spin%spinor
+          ! Ekin
+          Etmp(2,r) = Etmp(2,r) + H_kin(ind) * Dscf(ind,ispin)
+          ! Enl
+          Etmp(3,r) = Etmp(3,r) + H_vkb(ind) * Dscf(ind,ispin)
+        end do
+
+        ! Eso
+        if ( spin%SO ) then
+          Etmp(4,r) = Etmp(4,r) + H_so(ind,1)*Dscf(ind,7) + H_so(ind,2)*Dscf(ind,8) &
+              + H_so(ind,5)*Dscf(ind,3) + H_so(ind,6)*Dscf(ind,4) &
+              - H_so(ind,3)*Dscf(ind,5) - H_so(ind,4)*Dscf(ind,6)
+
+        end if
+
+        ! DEharr
+        if ( spin%SO ) then
+          Etmp(5,r) = Etmp(5,r) + H(ind,1) * ( Dscf(ind,1) - Dold(ind,1) )  &
+                          + H(ind,2) * ( Dscf(ind,2) - Dold(ind,2) )  &
+                          + H(ind,3) * ( Dscf(ind,7) - Dold(ind,7) )  &
+                          + H(ind,4) * ( Dscf(ind,8) - Dold(ind,8) )  &
+                          - H(ind,5) * ( Dscf(ind,5) - Dold(ind,5) )  &
+                          - H(ind,6) * ( Dscf(ind,6) - Dold(ind,6) )  &
+                          + H(ind,7) * ( Dscf(ind,3) - Dold(ind,3) )  &
+                          + H(ind,8) * ( Dscf(ind,4) - Dold(ind,4) )
+        else if ( spin%NCol ) then
+          Etmp(5,r) = Etmp(5,r) + H(ind,1) * ( Dscf(ind,1) - Dold(ind,1) )  &
+              + H(ind,2) * ( Dscf(ind,2) - Dold(ind,2) )  &
+              + 2.0_dp * H(ind,3) * ( Dscf(ind,3) - Dold(ind,3) )  &
+              + 2.0_dp * H(ind,4) * ( Dscf(ind,4) - Dold(ind,4) )
+        else
+          do ispin = 1, spin%spinor
+            Etmp(5,r) = Etmp(5,r) + H(ind,ispin) * (Dscf(ind,ispin) - Dold(ind,ispin))
+          end do
+        end if
+
+      end do
+    end do
+!$OMP end parallel do
+
+    ! Now add the *other* contributions
+    do ir = 1, N_Elec
+      if ( Elecs(ir)%DM_update >= 1 ) then
+        ! add cross-terms
+        r = 4 + (TYP_DEVICE+ir - 1) * 2
+        Etmp(:,2) = Etmp(:,2) + Etmp(:,r)
+      end if
+      if ( Elecs(ir)%DM_update == 2 ) then
+        r = 3 + (ir - 1) * 2
+        ! add diagonal electrode terms
+        Etmp(:,2) = Etmp(:,2) + Etmp(:,r)
+      end if
+    end do
+
+#ifdef MPI
+    call MPI_AllReduce(Etmp(1,2),tmp(1,2),size(Etmp, 1), &
+        MPI_Double_Precision,MPI_SUM, MPI_Comm_World,MPIerror)
+    Etmp(:,2) = tmp(:,2)
+#endif
+
+    ! Copy data over
+    NEGF_Ebs = Etmp(1,2)
+    NEGF_Ekin = Etmp(2,2)
+    NEGF_Enl = Etmp(3,2)
+    NEGF_Eso = Etmp(4,2)
+    NEGF_DEharr = Etmp(5,2)
+
+  end subroutine ts_compute_energies
+
+end module ts_energies_m
+
+  

=== modified file 'Src/vmat.F90'
--- Src/vmat.F90	2016-06-22 08:57:57 +0000
+++ Src/vmat.F90	2019-08-18 23:02:58 +0000
@@ -339,7 +339,7 @@
                    r2sp = sum(dxsp**2)
                    if ( r2sp < r2cut(is) ) then
 !$OMP critical
-                      call all_phi( is, +1, dxsp, nphiloc, phia(:,isp) )
+                      call all_phi( is, +1, dxsp, maxoa, nphiloc, phia(:,isp) )
 !$OMP end critical
                    else
                       phia(:,isp) = 0.0_dp

=== modified file 'Src/vmatsp.f'
--- Src/vmatsp.f	2016-01-25 16:00:16 +0000
+++ Src/vmatsp.f	2019-08-18 23:02:58 +0000
@@ -309,7 +309,8 @@
                 enddo
                 r2sp = sum(dxsp**2)
                 if (r2sp.lt.r2cut(is)) then
-                  call all_phi( is, +1, dxsp, nphiloc, phia(:,isp) )
+                  call all_phi( is, +1, dxsp, maxoa,
+     &                nphiloc, phia(:,isp) )
                 else
                   phia(:,isp) = 0.0_dp
                 endif

=== modified file 'Src/write_subs.F'
--- Src/write_subs.F	2017-11-23 14:17:27 +0000
+++ Src/write_subs.F	2019-08-18 23:02:58 +0000
@@ -296,7 +296,7 @@
       use units
       use m_energies 
       use m_spin
-      use m_ts_global_vars, only: TSinit, TSrun
+      use m_ts_global_vars, only: TSrun
       implicit none
 
       integer              :: iscf
@@ -304,16 +304,10 @@
       real(dp), intent(in) :: dHmax ! Max. change in H elements
 
       character(len=64) :: fmt
-      character(len=6) :: scf_name
 
       logical              :: first_scf_step
       integer              :: i
 
-      scf_name = 'scf'
-      if ( TSrun ) then
-         scf_name = 'ts-scf'
-      end if
-      
       first_scf_step = (iscf == 1)
       ! Only print out full decomposition at very beginning and end.
       if ((istp==1.and.first_scf_step).or.final) then
@@ -329,7 +323,6 @@
      .     'siesta: DEna    =', DEna/eV,
      .     'siesta: DUscf   =', DUscf/eV,
      .     'siesta: DUext   =', DUext/eV,
-     .     'siesta: Enegf   =', DE_NEGF/eV,
      .     'siesta: Exc     =', Exc/eV,
      .     'siesta: eta*DQ  =', Ecorrec/eV,
      .     'siesta: Emadel  =', Emad/eV,
@@ -339,6 +332,18 @@
      .     'siesta: Eharris =', (Eharrs+Ekinion)/eV,
      .     'siesta: Etot    =', (Etot+Ekinion)/eV,
      .     'siesta: FreeEng =', (FreeE+Ekinion)/eV
+        if ( TSrun ) then
+        write(6,'(a,f17.6)')
+     .     'transiesta: E-dN      =', NEGF_DE/eV,
+     .     'transiesta: Band Stru =', NEGF_Ebs/eV,
+     .     'transiesta: Kinetic   =', NEGF_Ekin/eV,
+     .     'transiesta: Ion-elec  =', (Enascf+NEGF_Enl+DUscf-
+     .      Uscf-Uatm)/eV,
+     .     'transiesta: Eso       =', NEGF_Eso/eV,
+     .     'transiesta: Eharris   =', (NEGF_Eharrs+Ekinion)/eV,
+     .     'transiesta: Etot      =', (NEGF_Etot+Ekinion)/eV,
+     .     'transiesta: FreeEng   =', (NEGF_FreeE+Ekinion)/eV
+        end if
         if (cml_p) then
           call cmlStartPropertyList(mainXML,
      .         title='Energy Decomposition')
@@ -372,9 +377,6 @@
           call cmlAddProperty(xf=mainXML, value=DUext/eV, 
      .         units='siestaUnits:eV', 
      .         dictref='siesta:DUext', fmt='r6')
-          call cmlAddProperty(xf=mainXML, value=DE_NEGF/eV, 
-     .         units='siestaUnits:eV', 
-     .         dictref='siesta:Enegf', fmt='r6')
           call cmlAddProperty(xf=mainXML, value=Exc/eV, 
      .         units='siestaUnits:eV', 
      .         dictref='siesta:Exc', fmt='r6')
@@ -402,6 +404,29 @@
           call cmlAddProperty(xf=mainXML, value=(FreeE+Ekinion)/eV, 
      .         units='siestaUnits:eV', 
      .         dictref='siesta:FreeEK', fmt='r6')
+
+          if ( TSrun ) then
+          ! NEGF energies
+          call cmlAddProperty(xf=mainXML, value=NEGF_DE/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:EdN-GF', fmt='r6')
+          call cmlAddProperty(xf=mainXML, value=NEGF_Ebs/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:Ebs-GF', fmt='r6')
+          call cmlAddProperty(xf=mainXML, value=NEGF_Ekin/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:Ekin-GF', fmt='r6')
+          call cmlAddProperty(xf=mainXML,
+     .         value=(NEGF_Eharrs+Ekinion)/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:EharrsK-GF', fmt='r6')
+          call cmlAddProperty(xf=mainXML, value=(NEGF_Etot+Ekinion)/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:EtotK-GF', fmt='r6')
+          call cmlAddProperty(xf=mainXML, value=(NEGF_FreeE+Ekinion)/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:FreeEK-GF', fmt='r6')
+          end if
           call cmlEndPropertyList(mainXML)
         endif
       endif
@@ -414,6 +439,11 @@
           call cmlAddProperty(xf=mainXML, value=Eharrs/eV, 
      .         units="siestaUnits:eV", 
      .         dictRef="siesta:Eharrs", fmt="r7")
+          if ( TSrun ) then
+          call cmlAddProperty(xf=mainXML, value=NEGF_Eharrs/eV, 
+     .         units="siestaUnits:eV", 
+     .         dictRef="siesta:Eharrs-GF", fmt="r7")
+          end if
           if ( .not. harrisfun ) then
              ! store dDmax and dHmax
              call cmlAddProperty(xf=mainXML, value=dDmax, 
@@ -438,6 +468,14 @@
              call cmlAddProperty(xf=mainXML, value=FreeE/eV, 
      .             units="siestaUnits:eV", 
      .             dictRef="siesta:FreeE", fmt="r7")
+             if ( TSrun ) then
+             call cmlAddProperty(xf=mainXML, value=NEGF_Etot/eV, 
+     .             units="siestaUnits:eV", 
+     .             dictRef="siesta:Etot-GF", fmt="r7")
+             call cmlAddProperty(xf=mainXML, value=NEGF_FreeE/eV, 
+     .             units="siestaUnits:eV", 
+     .             dictRef="siesta:FreeE-GF", fmt="r7")
+             end if
              if ( fixspin ) then
                 call cmlAddProperty(xf=mainXML, value=Efs(1)/eV, 
      .               units="siestaUnits:eV", 
@@ -455,25 +493,49 @@
              end if
           endif
 
-          if ( fixspin ) then
-             if ( (iscf == 1) .or. muldeb ) then
-                write(6,'(/,a12,3a16,4a10)')
-     .           'iscf', 'Eharris(eV)', 'E_KS(eV)', 'FreeEng(eV)', 
-     .           'dDmax', 'Ef_up', 'Ef_dn(eV)','dHmax(eV)'
-             end if
-             write(6,'(a8,i4,3f16.6,4f10.6)')
-     .  trim(scf_name)//': ',iscf, Eharrs/eV, Etot/eV, FreeE/eV, 
-     .           dDmax, Efs(1:2)/eV, dHmax/eV
-          else                  ! fixspin
-             if ( (iscf == 1) .or. muldeb ) then
-                write(6,'(/,a12,3a16,3a10)')
-     .           'iscf', 'Eharris(eV)', 'E_KS(eV)', 'FreeEng(eV)', 
-     .           'dDmax','Ef(eV)','dHmax(eV)'
-             end if
-             write(6,'(a8,i4,3f16.6,3f10.6)')
-     .  trim(scf_name)//': ',iscf, Eharrs/eV, Etot/eV, FreeE/eV, 
-     .           dDmax, Ef      /eV, dHmax/eV
-          end if                ! fixspin
+          if ( TSrun ) then
+            if ( fixspin ) then
+              if ( (iscf == 1) .or. muldeb ) then
+                write(6,'(/,a12,3a16,4a10)')
+     .              'iscf', 'Eharris(eV)', 'E_KS(eV)', 'FreeEng(eV)',
+     .              'dDmax', 'Ef_up', 'Ef_dn(eV)','dHmax(eV)'
+              end if
+              write(6,'(a8,i4,3f16.6,4f10.6)')
+     .            'ts-scf: ',iscf, NEGF_Eharrs/eV, NEGF_Etot/eV,
+     .            NEGF_FreeE/eV,
+     &            dDmax, Efs(1:2)/eV, dHmax/eV
+            else                ! fixspin
+              if ( (iscf == 1) .or. muldeb ) then
+                write(6,'(/,a12,3a16,3a10)')
+     .              'iscf', 'Eharris(eV)', 'E_KS(eV)','FreeEng(eV)',
+     .              'dDmax','Ef(eV)','dHmax(eV)'
+              end if
+              write(6,'(a8,i4,3f16.6,3f10.6)')
+     .            'ts-scf: ',iscf, NEGF_Eharrs/eV, NEGF_Etot/eV,
+     .            NEGF_FreeE/eV,
+     &            dDmax, Ef /eV, dHmax/eV
+            end if              ! fixspin
+          else ! not NEGF
+            if ( fixspin ) then
+              if ( (iscf == 1) .or. muldeb ) then
+                write(6,'(/,a12,3a16,4a10)')
+     .              'iscf', 'Eharris(eV)', 'E_KS(eV)', 'FreeEng(eV)', 
+     .              'dDmax', 'Ef_up', 'Ef_dn(eV)','dHmax(eV)'
+              end if
+              write(6,'(a8,i4,3f16.6,4f10.6)')
+     .            'scf: ',iscf, Eharrs/eV, Etot/eV,
+     &            FreeE/eV,dDmax, Efs(1:2)/eV, dHmax/eV
+            else                ! fixspin
+              if ( (iscf == 1) .or. muldeb ) then
+                write(6,'(/,a12,3a16,3a10)')
+     .              'iscf', 'Eharris(eV)', 'E_KS(eV)', 'FreeEng(eV)', 
+     .              'dDmax','Ef(eV)','dHmax(eV)'
+              end if
+              write(6,'(a8,i4,3f16.6,3f10.6)')
+     .            'scf: ',iscf, Eharrs/eV, Etot/eV,
+     &            FreeE/eV,dDmax, Ef      /eV, dHmax/eV
+            end if              ! fixspin
+          end if
           
        elseif ((isolve==SOLVE_ORDERN) .or. (isolve==SOLVE_MINIM)) then
           
@@ -503,12 +565,21 @@
      .    'siesta: ',      'Eldau   =', Eldau/eV,
      .    'siesta: ',      'Eso     =', Eso/eV,
      .    'siesta: ',   'Ext. field =', DUext/eV,
-     .    'siesta: ',      'Enegf   =', DE_NEGF/eV,
      .    'siesta: ',  'Exch.-corr. =', Exc/eV,
      .    'siesta: ', 'Ion-electron =', (Enascf+Enl+DUscf-Uscf-Uatm)/eV,
      .    'siesta: ',      'Ion-ion =', (Ena+Uatm-Enaatm-Eions)/eV,
      .    'siesta: ',      'Ekinion =', Ekinion/eV,
      .    'siesta: ',        'Total =', (Etot+Ekinion)/eV
+        if ( TSrun ) then
+        write(6,'(a,a15,f15.6)')
+     .    'transiesta: ',    'E-dN  =', NEGF_DE/eV,
+     .    'transiesta: ','Band Stru =', NEGF_Ebs/eV,
+     .    'transiesta: ',  'Kinetic =', NEGF_Ekin/eV,
+     .    'transiesta: ', 'Ion-elec =', (Enascf+NEGF_Enl+DUscf-
+     .      Uscf-Uatm)/eV,
+     .    'transiesta: ',      'Eso =', NEGF_Eso/eV,
+     .    'transiesta: ',    'Total =', (NEGF_Etot+Ekinion)/eV
+        end if
         if ( fixspin ) then
            write(6,'(a,a15,f15.6)')
      .          'siesta: ', 'Fermi_up =', Efs(1)/eV,
@@ -537,9 +608,6 @@
           call cmlAddProperty(xf=mainXML, value=DUext/eV, 
      .         units='siestaUnits:eV', 
      .         dictref='siesta:DUext', fmt='r7')
-          call cmlAddProperty(xf=mainXML, value=DE_NEGF/eV, 
-     .         units='siestaUnits:eV', 
-     .         dictref='siesta:Enegf', fmt='r7')
           call cmlAddProperty(xf=mainXML, value=Exc/eV,   
      .         units='siestaUnits:eV', 
      .         dictref='siesta:Exc', fmt='r7')
@@ -557,6 +625,26 @@
           call cmlAddProperty(xf=mainXML, value=(Etot+Ekinion)/eV,
      .         units='siestaUnits:eV', 
      .         dictref='siesta:Etot', fmt='r7')
+
+          if ( TSrun ) then
+          ! NEGF energies
+          call cmlAddProperty(xf=mainXML, value=NEGF_DE/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:EdN-GF', fmt='r7')
+          call cmlAddProperty(xf=mainXML, value=NEGF_Ebs/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:Ebs-GF', fmt='r7')
+          call cmlAddProperty(xf=mainXML, value=NEGF_Ekin/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:Ekin-GF', fmt='r7')
+          call cmlAddProperty(xf=mainXML, 
+     .         value=(Enascf+NEGF_Enl+DUscf-Uscf-Uatm)/eV, 
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:I-e-GF', fmt='r7')
+          call cmlAddProperty(xf=mainXML, value=(NEGF_Etot+Ekinion)/eV,
+     .         units='siestaUnits:eV', 
+     .         dictref='siesta:Etot-GF', fmt='r7')
+          end if
           call cmlEndPropertyList(mainXML)
         endif !cml_p
       endif !final

=== modified file 'Src/writewave.F'
--- Src/writewave.F	2018-10-17 13:04:40 +0000
+++ Src/writewave.F	2019-08-18 23:02:58 +0000
@@ -40,15 +40,23 @@
       USE alloc, only: re_alloc
       USE sys, only: die
       USE atomlist, only: no_u
+      USE m_spin, only: spin
 
       implicit none
 
+      integer :: max_n_states
+      
       ! Find number of k-points for wavefunction printout
 
       nullify(wfk)
 
       nwk = 0
-      call initwave( no_u, nwk, wfk )
+      if ( spin%Grid == 4 ) then
+        max_n_states = 2 * no_u
+      else
+        max_n_states = no_u
+      end if
+      call initwave( max_n_states, nwk, wfk )
 
       if (nwk .eq. 0) then
          gamma_wavefunctions = .true.
@@ -96,7 +104,7 @@
          call die("WFS.BandMin < 1")
       endif
       if (wfs_band_max > norb) then
-         call die("WFS.BandMax > number of orbitals")
+         call die("WFS.BandMax > maximum number of states")
       endif
       if (wfs_band_max < wfs_band_min) then
          call message("WARNING","WFS.BandMax < WFS.BandMin." //
@@ -126,7 +134,7 @@
 C Based on initband routine by J.Soler
 C Written by P. Ordejon, June 2003
 C **************************** INPUT **********************************
-C integer norb           : Number of orbitals
+C integer norb           : Number of orbitals (actually max number of bands)
 C *************************** OUTPUT **********************************
 C integer nk             : Number k points to compute wavefunctions
 C real*8  kpoint(3,maxk) : k point vectors
@@ -383,7 +391,7 @@
 
       end subroutine initwave
 
-      subroutine wwave( no, nspin, maxspn, maxo, maxuo, maxnh, 
+      subroutine wwave( no, spin, maxo, maxuo, maxnh, 
      .                  maxk,
      .                  numh, listhptr, listh, H, S, ef, xij, indxuo,
      .                  gamma, nk, kpoint, nuotot, occtol)
@@ -391,10 +399,10 @@
 C Finds wavefunctions at selected k-points.
 C Written by P. Ordejon, June 2003
 C from routine 'bands' written by J.M.Soler
+C Changed to use tSpin, N. Papior, August 2019
 C **************************** INPUT **********************************
 C integer no                  : Number of basis orbitals
-C integer nspin  = h_spin_dim : Number of spin components of H, D
-C integer maxspn = spinor_dim : Second dimension of ek
+C tSpin spin                  : Contains spin information
 C integer maxo                : First dimension of ek
 C integer maxuo               : Second dimension of H and S
 C integer maxnh               : Maximum number of orbitals interacting  
@@ -406,7 +414,7 @@
 C                               hamiltonian matrix
 C integer listh(maxlh)        : Nonzero hamiltonian-matrix element  
 C                               column indexes for each matrix row
-C real*8  H(maxnh,nspin)      : Hamiltonian in sparse form
+C real*8  H(maxnh,spin%H)     : Hamiltonian in sparse form
 C real*8  S(maxnh)            : Overlap in sparse form
 C real*8  ef                  : Fermi energy
 C real*8  xij(3,maxnh)        : Vectors between orbital centers (sparse)
@@ -438,7 +446,7 @@
       use atmfuncs,     only : symfio, cnfigfio, labelfis, nofis
       use atomlist,     only : iaorb, iphorb
       use siesta_geom,  only : isa
-      use m_spin,       only : NoMagn, SPpol, NonCol, SpOrb
+      use t_spin, only: tSpin
       use units, only : eV
 
 #ifdef MPI
@@ -449,12 +457,12 @@
 
       implicit          none
 
+      type(tSpin), intent(in) :: spin
       logical, intent(in) :: Gamma
       integer           maxk, maxnh, maxo, maxuo, nk, no, 
-     .                  h_spin_dim, spinor_dim, nspin, maxspn,
      .                  nuotot, indxuo(no), listh(maxnh), numh(*), 
      .                  listhptr(*)
-      real(dp)          ef, H(:,:), kpoint(3,maxk), 
+      real(dp)          ef, H(maxnh,spin%H), kpoint(3,maxk), 
      .                  S(maxnh), xij(3,maxnh), occtol
 
       external          io_assign, io_close, memory
@@ -480,9 +488,7 @@
       data Dnew, Enew, e1, e2, qk, qtot, temp, wk /8*0.d0/
 
       logical :: SaveParallelOverK
-
-      h_spin_dim=size(H,dim=2)
-
+      
 
 C Get local number of orbitals
 #ifdef MPI
@@ -505,26 +511,17 @@
       endif
 
 C Check spin
-      if (h_spin_dim .gt. 2) then
-        if (Node.eq.0) then
-          write(6,'(/,a,/,a)')
-     .       'writewave: WARNING: wavefunctions printed is only '
-          write(6,'(/,a,/,a)')
-     .       '           implemented for nspin = 1 or 2'
-        endif
-        goto 999
-      endif
 
 C Allocate local arrays - only aux is relevant here
-      if ( h_spin_dim >= 4 ) then
+      if ( spin%Grid == 4 ) then
          nhs = 2 * (2*nuotot) * (2*nuo)
       else
          nhs = 2 * nuotot * nuo
       endif
       call allocDenseMatrix(nhs, nhs, nhs) 
 
-      allocate(ek(nuotot,maxspn,nk))
-      call memory('A','D',maxspn*nk*nuotot,'writewave')
+      allocate(ek(nuotot,spin%spinor,nk))
+      call memory('A','D',nuotot*spin%spinor*nk,'writewave')
       naux = 2*nuotot*5
       allocate(aux(naux))
       call memory('A','D',naux,'writewave')
@@ -543,12 +540,12 @@
           write(6,'(a)') 'writewave: Wave Functions Coefficients'
           write(6,*)
           write(6,'(a26,2x,i6)') 'Number of k-points = ', nk
-          write(6,'(a26,2x,i6)') 'Number of Spins = ', maxspn
+          write(6,'(a26,2x,i6)') 'Number of Spins = ', spin%Grid
           write(6,'(a26,2x,i6)') 'Number of basis orbs = ',nuotot
           write(6,*)
         endif
         write(iu) nk, gamma
-        write(iu) maxspn
+        write(iu) spin%Grid   ! This will be 1, 2, or 4
         write(iu) nuotot
         write(iu) (iaorb(j),labelfis(isa(iaorb(j))),
      .            iphorb(j), cnfigfio(isa(iaorb(j)),iphorb(j)),
@@ -566,9 +563,9 @@
 
 C Call appropriate diagonalization routine
 
-      if (NoMagn .or. SPpol) then
+      if ( spin%Grid <= 2 ) then
        if (gamma) then
-         call diagg( h_spin_dim, nuo, maxuo, maxnh, maxnh, 
+         call diagg( spin%H, nuo, maxuo, maxnh, maxnh, 
      .               maxo, numh, listhptr, listh, numh, listhptr, 
      .               listh, H, S, getD, getPSI,
      .               fixspin, qtot, qs, temp,
@@ -588,7 +585,7 @@
              call diag_init()
           end if
 
-         call diagk( h_spin_dim, nuo, no, maxspn, maxnh, maxnh,
+         call diagk( spin%H, nuo, no, spin%spinor, maxnh, maxnh,
      .               maxo, numh, listhptr, listh, numh, listhptr, 
      .               listh, H, S, getD, getPSI,
      .               fixspin, qtot, qs, temp,
@@ -602,16 +599,16 @@
          
        endif
 
-      elseif (NonCol) then
+      elseif ( spin%NCol) then
         if (gamma) then
-          call diag2g( nuo, no, maxuo, maxnh, maxnh, maxo, numh,
+          call diag2g( nuo, no, maxnh, maxnh, maxo, numh,
      .                 listhptr, listh, numh, listhptr, listh,
      .                 H, S, getD, getPSI, qtot, temp, e1, e2, ek, qk,
      .                 Dnew, Enew, ef, Entropy,
      .                 Haux, Saux, psi, aux,
      .                 nuotot, occtol, 1, nuotot )
         else
-          call diag2k( nuo, no, maxuo, maxnh, maxnh, maxo, numh,
+          call diag2k( nuo, no, maxnh, maxnh, maxo, numh,
      .                 listhptr, listh, numh, listhptr, listh,
      .                 H, S, getD, getPSI, qtot, temp, e1, e2, xij,
      .                 indxuo, nk, kpoint, wk, ek, qk, Dnew,
@@ -619,18 +616,18 @@
      .                 Haux, Saux, psi, Haux, Saux, aux,
      .                 nuotot, occtol, 1, nuotot )
         endif
-      elseif (SpOrb) then
+      elseif ( spin%SO ) then
         if (gamma) then
           call diag3g( nuo, no, maxnh, maxnh, maxo, numh,
      .                 listhptr, listh, numh, listhptr, listh,
-     .                 H, S, getD, qtot, temp, e1, e2, ek, qk,
+     .                 H, S, getD, getPSI, qtot, temp, e1, e2, ek, qk,
      .                 Dnew, Enew, ef, Entropy,
      .                 Haux, Saux, psi, aux,
      .                 nuotot, occtol, 1, nuotot )
         else
-          call diag3k( nuo, no, maxuo, maxnh, maxnh, maxo, numh,
+          call diag3k( nuo, no, maxnh, maxnh, maxo, numh,
      .                 listhptr, listh, numh, listhptr, listh,
-     .                 H, S, getD, qtot, temp, e1, e2, xij,
+     .                 H, S, getD, getPsi, qtot, temp, e1, e2, xij,
      .                 indxuo, nk, kpoint, wk, ek, qk, Dnew,
      .                 Enew, ef, Entropy,
      .                 Haux, Saux, psi, Haux, Saux, aux,
@@ -653,15 +650,16 @@
       end subroutine wwave
 
 
-      subroutine writew(nuotot,nuo,ik,k,ispin,eo,psi,gamma)
+      subroutine writew(nuotot,nuo,ik,k,ispin,eo,psi,
+     $                  gamma,non_coll,blocksize)
 
       use precision
       use sys
       use parallel,     only : Node, Nodes
+      use parallel,     only : Module_Blocksize=>BlockSize
       use parallelsubs, only : GlobalToLocalOrb, WhichNodeOrb
       use units,        only : eV
       use kpoint_grid,  only : kweight
-
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -673,16 +671,17 @@
 #endif
 
       integer, intent(in)  ::  nuotot, nuo, ispin, ik
-      real(dp), intent(in) ::  eo(*), psi(*), k(3)
+      logical, intent(in)  ::  non_coll, gamma
+      real(dp), intent(in) ::  eo(*), k(3)
+      real(dp), intent(in) ::  psi(:)
+      integer, intent(in)  ::  blocksize
 
-      logical gamma
 
 C  Internal variables .............................................
       integer  BNode, iie, iw, indwf, j, ind, iu
-
+      integer  :: blocksize_saved
       integer number_of_wfns
       integer, allocatable  :: ind_wfn(:)
-
       real(dp)  :: kpoint_weight
       real(SP), dimension(:,:), allocatable :: aux   !! NOTE SP
 
@@ -692,12 +691,17 @@
 
 C Allocate auxiliary arrays
 
-      if (gamma) then
-         allocate(aux(1,nuotot))
-         call memory('A','D',nuotot,'writewave')
+      if (non_coll) then
+         allocate(aux(4,nuotot))
+         call memory('A','D',4*nuotot,'writewave')
       else
-         allocate(aux(2,nuotot))
-         call memory('A','D',2*nuotot,'writewave')
+         if (gamma) then
+            allocate(aux(1,nuotot))
+            call memory('A','D',nuotot,'writewave')
+         else
+            allocate(aux(2,nuotot))
+            call memory('A','D',2*nuotot,'writewave')
+         endif
       endif
 
 C Find file name, and open for Node 0
@@ -733,7 +737,11 @@
         if (wwf) then
           write(6,*)
           write(6,'(a22,2x,i6,2x,3f10.6)') 'k-point = ',ik, k(1:3)
-          write(6,'(a22,2x,i6)') 'Spin component = ',ispin
+          if (non_coll) then
+             write(6,'(a22,2x,i6)') 'Spin component (non-collinear)= ',0
+          else
+             write(6,'(a22,2x,i6)') 'Spin component = ',ispin
+          endif
           write(6,'(a22,2x,i6)') 'Num. wavefunctions = ',nwflist(ik)
           write(6,'(a)') 'Use readwfsx utility to print '
      $                   // "wavefunction coefficients from WFSX file"
@@ -748,14 +756,26 @@
         write(iu) nwflist(ik)
       endif
 
-C Loop over wavefunctions that should be printed
-
+      ! Loop over wavefunctions that should be stored
+
+      ! The effective blocksize to use is passed as an argument.
+      ! Module_blocksize is the variable in the 'parallel' module that
+      ! holds the value that all the helper functions (WhichNodeOrb,
+      ! GetNodeOrb, etc) see.  Hence, we must temporarily set
+      ! Module_blocksize to the passed blocksize.
+
+      ! Examples: non-collinear calculations need a wf blocksize double
+      ! the 'orbital' one
+
+      blocksize_saved = Module_blocksize
+      Module_blocksize = blocksize
+      
       if (Node .eq. 0 .and. debug) then
          print *, " -*- Will print ", nwflist(ik), " wfns."
          print *, " -*- ", iwf(ik,1:nwflist(ik))
       endif
       do iw = 1,nwflist(ik)
-        indwf = iwf(ik,iw)
+         indwf = iwf(ik,iw)
 
         ! Determine which node handles this wavefunction
         ! Note that the distribution is block cyclic,
@@ -770,30 +790,44 @@
 
         if (Node.eq.BNode) then
 
-C Determine the index of the wavefunction in the local node
-
+          ! Determine the index of the wavefunction in the local node
           call GlobalToLocalOrb( indwf, BNode, Nodes, iie)
 
-C Save wavefunction in aux array
-
-C psi has different structure in diagk and diagg, so the indexing
-C must be handled differently
-
-          if (gamma) then
-            do j = 1,nuotot
-              ind = j + (iie-1)*nuotot 
-              aux(1,j) = real(psi(ind),kind=sp)
-            enddo
-          else
-            do j = 1,nuotot
-              ind = 1+(j-1)*2+(iie-1)*2*nuotot
-              aux(1,j) = real(psi(ind),kind=sp)
-              aux(2,j) = real(psi(ind+1),kind=sp)
-            enddo
-          endif
-
-        endif
-
+          ! Save wavefunction in aux array
+
+          ! Despite being passed as a one-dimensional array, psi has
+          ! different underlying structures for different cases, so the
+          ! indexing must be handled differently
+
+          if (.not. non_coll) then
+             if (gamma) then
+                ! Real functions
+                do j = 1,nuotot
+                   ind = j + (iie-1)*nuotot 
+                   aux(1,j) = real(psi(ind),kind=sp)
+                enddo
+             else
+                ! Complex functions: two reals per orbital coefficient
+                do j = 1,nuotot
+                   ind = 1+(j-1)*2+(iie-1)*2*nuotot
+                   aux(1,j) = real(psi(ind),kind=sp)
+                   aux(2,j) = real(psi(ind+1),kind=sp)
+                enddo
+             endif
+          else                  ! non-collinear case, including SOC
+             ! Each 'orbital' coefficient is actually four reals: complex up/down
+             ! (spinor)
+             do j = 1,nuotot
+                ind = 1 + (j-1)*4 + (iie-1)*4*nuotot 
+                aux(1,j) = real(psi(ind),kind=sp)
+                aux(2,j) = real(psi(ind+1),kind=sp)
+                aux(3,j) = real(psi(ind+2),kind=sp)
+                aux(4,j) = real(psi(ind+3),kind=sp)
+             enddo
+          endif  !  non-coll or not
+
+       endif          ! Node == BNode
+       
 #ifdef MPI
 C Pass the wf to the master node
         if (BNode.ne.0) then
@@ -815,19 +849,22 @@
 C eigenvector is now stored in aux in Node 0, and can be printed
 
         if (Node .eq. 0) then
-          write(iu) indwf
-          write(iu) eo(indwf)/eV
-          write(iu) (aux(1:,j), j=1,nuotot)
-       endif
+           write(iu) indwf
+           write(iu) eo(indwf)/eV
+           write(iu) (aux(1:,j), j=1,nuotot)
+        endif
 
       enddo
-
+      
 C Close output file
 
       if (Node .eq. 0) then
         call io_close(iu)
       endif
 
+      ! Restore blocksize value in module
+      Module_blocksize = blocksize_saved
+
 C Deallocate auxiliary arrays
 
       call memory('D','D',size(aux),'writewave')

=== added file 'Tests/Pseudos/Bi.psf'
--- Tests/Pseudos/Bi.psf	1970-01-01 00:00:00 +0000
+++ Tests/Pseudos/Bi.psf	2019-08-18 23:02:58 +0000
@@ -0,0 +1,3061 @@
+ Bi pb rel pcec
+ ATM3.3    12-FEB-13 Troullier-Martins                       
+ 6s 2.00r r= 1.98/6p 3.00r r= 1.98/5d10.00r r= 1.48/5f 0.00r r= 2.47/  
+   4  3 1216  0.298644840562E-04  0.125000000000E-01   15.0000000000    
+ Radial grid follows
+  0.375648965487E-06  0.756023013283E-06  0.114118157761E-05  0.153118484027E-05
+  0.192609374007E-05  0.232596998233E-05  0.273087604852E-05  0.314087520605E-05
+  0.355603151811E-05  0.397640985372E-05  0.440207589786E-05  0.483309616171E-05
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