Merge lp:~albertog/siesta/4.1-superc-gamma into lp:siesta/4.1

[Alberto Garcia]

Removed m_gamma module.
Clarified the relationship (or lack thereof) between 'gamma' in k-point sampling and 'gamma' meaning absence of auxiliary supercell.

HSX files always contain now indxuo information, even if it is trivial.

Note that for medium-sized borderline systems (say, the si64 box), using an auxiliary supercell
increases significantly the time spent in dfscf and rhoofd.

[lp:~albertog/siesta/4.1-superc-gamma]

932. By Alberto Garcia on 2018-06-26

Re-instatiate gamma arguments. Update modp. Update TS interfaces

(Thanks to Nick Papior)

The flow of 'gamma' (meaning Gamma-point sampling only) is now more
clear.

The new MODP1 now replaces the former MODP.

TranSiesta routines avoid the use of 'not_using_auxcell'.

=== modified file 'Src/Makefile'
--- Src/Makefile	2018-06-08 09:23:57 +0000
+++ Src/Makefile	2018-06-26 07:59:48 +0000
@@ -132,7 +132,7 @@
         molecularmechanics.o zm_broyden_optim.o \
         cell_broyden_optim.o remove_intramol_pressure.o \
         m_ntm.o m_dipol.o m_kinetic.o m_rmaxh.o \
-        m_forces.o m_stress.o m_eo.o m_spin.o m_gamma.o m_hsx.o m_fire.o setup_H0.o \
+        m_forces.o m_stress.o m_eo.o m_spin.o m_hsx.o m_fire.o setup_H0.o \
         get_kpoints_scale.o get_target_stress.o fire_optim.o zm_fire_optim.o \
         cell_fire_optim.o m_fire_para.o m_fire_mixing.o write_raw_efs.o \
         pdos2g.o pdos2k.o pdos3g.o pdos3k.o spinorbit.o moments.o \
@@ -549,8 +549,8 @@
 atomlwf.o: alloc.o atmfuncs.o mneighb.o onmod.o precision.o spatial.o sys.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o m_gamma.o m_spin.o parallel.o
-bands.o: parallelsubs.o precision.o siesta_geom.o sys.o writewave.o
+bands.o: files.o get_kpoints_scale.o m_spin.o parallel.o parallelsubs.o
+bands.o: precision.o siesta_geom.o sys.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
 basis_io.o: precision.o pseudopotential.o radial.o sys.o xml.o
@@ -631,7 +631,7 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o m_dminim.o m_energies.o m_eo.o
-compute_dm.o: m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
 compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
 compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
 compute_dm.o: sparse_matrices.o sys.o units.o
@@ -646,8 +646,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o parallel.o precision.o siesta_geom.o sys.o units.o zmatrix.o
@@ -673,13 +673,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o sys.o units.o vmat.o
 diag.o: alloc.o diag_option.o parallel.o precision.o sys.o
-diag2g.o: fermid.o parallel.o parallelsubs.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
-diag3g.o: fermid.o parallel.o parallelsubs.o precision.o sys.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
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o m_spin.o parallel.o parallelsubs.o precision.o sys.o
-diagg.o: writewave.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
 diagk.o: compute_norm.o fermid.o m_spin.o parallel.o parallelsubs.o precision.o
 diagk.o: sys.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o parallel.o parallelsubs.o precision.o
@@ -721,9 +723,9 @@
 fft1d.o: parallel.o precision.o sys.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: m_dipol.o m_energies.o m_forces.o m_gamma.o m_hsx.o
-final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
-final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: m_dipol.o m_energies.o m_forces.o m_hsx.o m_mpi_utils.o
+final_H_f_stress.o: m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o m_ts_io.o
+final_H_f_stress.o: m_ts_kpoints.o m_ts_options.o metaforce.o
 final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
 final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o sys.o units.o
@@ -790,8 +792,8 @@
 ldau_specs.o: precision.o pseudopotential.o radial.o sys.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o m_energies.o
-local_DOS.o: m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o parallel.o
-local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o sys.o
+local_DOS.o: m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o siesta_geom.o
+local_DOS.o: siesta_options.o sparse_matrices.o sys.o
 m_broyddj.o: alloc.o m_mpi_utils.o parallel.o precision.o sys.o
 m_broyddj_nocomm.o: alloc.o parallel.o precision.o sys.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -859,10 +861,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -965,7 +967,7 @@
 m_ts_electrode.o: precision.o sys.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -1157,15 +1159,14 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
-projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o m_eo.o
-projected_DOS.o: m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
-projected_DOS.o: siesta_options.o sparse_matrices.o sys.o units.o
+projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o m_eo.o m_spin.o
+projected_DOS.o: parallel.o precision.o siesta_geom.o siesta_options.o
+projected_DOS.o: sparse_matrices.o sys.o units.o
 propor.o: precision.o sys.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
 proximity_check.o: precision.o siesta_geom.o siesta_options.o units.o
@@ -1212,10 +1213,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: m_dipol.o m_energies.o m_gamma.o m_hsx.o m_mpi_utils.o
-setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
-setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
-setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o sys.o
+setup_hamiltonian.o: m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o m_ntm.o
+setup_hamiltonian.o: m_partial_charges.o m_rhog.o m_spin.o m_steps.o m_stress.o
+setup_hamiltonian.o: metaforce.o molecularmechanics.o parallel.o siesta_geom.o
+setup_hamiltonian.o: siesta_options.o sparse_matrices.o sys.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o parallel.o parallelsubs.o siesta_geom.o sys.o
@@ -1226,10 +1227,10 @@
 siesta2wannier90.o: parallel.o precision.o siesta_options.o sys.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -1261,7 +1262,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o m_check_walltime.o m_cite.o m_energies.o
-siesta_init.o: m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o m_mpi_utils.o
+siesta_init.o: m_eo.o m_fixed.o m_forces.o m_iostruct.o m_mpi_utils.o
 siesta_init.o: m_new_dm.o m_rmaxh.o m_spin.o m_steps.o m_supercell.o m_timer.o
 siesta_init.o: m_wallclock.o metaforce.o molecularmechanics.o object_debug.o
 siesta_init.o: parallel.o parallelsubs.o projected_DOS.o siesta_cmlsubs.o
@@ -1291,15 +1292,15 @@
 state_init.o: alloc.o atomlist.o class_Data2D.o class_SpData1D.o
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
-state_init.o: ioxv.o kpoint_grid.o ldau_specs.o m_energies.o m_eo.o m_gamma.o
-state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
-state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
-state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
-state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
-state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
-state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
-state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
-state_init.o: sys.o units.o write_subs.o zmatrix.o
+state_init.o: ioxv.o kpoint_grid.o ldau_specs.o m_energies.o m_eo.o m_mixing.o
+state_init.o: m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o m_pivot_methods.o
+state_init.o: m_rmaxh.o m_sparse.o m_sparsity_handling.o m_spin.o m_steps.o
+state_init.o: m_supercell.o m_test_io.o m_ts_charge.o m_ts_electype.o
+state_init.o: m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
+state_init.o: m_ts_sparse.o m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
+state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
+state_init.o: siesta_options.o sparse_matrices.o sys.o units.o write_subs.o
+state_init.o: zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Src/bands.F'
--- Src/bands.F	2018-04-25 11:33:32 +0000
+++ Src/bands.F	2018-06-26 07:59:48 +0000
@@ -360,7 +360,6 @@
       use densematrix,  only : Haux, Saux, psi
       use alloc,        only : re_alloc, de_alloc
       use files,        only : slabel, label_length
-      use m_gamma,      only : gamma
       use atomlist,     only : iaorb, iphorb
       use siesta_geom,  only : isa
       use atmfuncs,     only : symfio, cnfigfio, labelfis, nofis
@@ -396,7 +395,7 @@
       integer :: ik, il, io, ispin, iu, iu_wfs, iuo, naux, nhs, j
 
       logical :: SaveParallelOverK
-
+      
       real(dp)
      .  Dnew, qs(2), e1, e2, efs(2), emax, emin, Enew, eV, qk, qtot,
      .  path, temp, wk, Entropy
@@ -448,7 +447,7 @@
 
         rewind (iu_wfs)
 
-        write(iu_wfs) nk, gamma
+        write(iu_wfs) nk, .false. ! nk, Gamma, same file-format in WFS as for Gamma-point
         write(iu_wfs) nspin
         write(iu_wfs) no_u
         write(iu_wfs) (iaorb(j),labelfis(isa(iaorb(j))),

=== modified file 'Src/compute_dm.F'
--- Src/compute_dm.F	2018-04-11 12:04:08 +0000
+++ Src/compute_dm.F	2018-06-26 07:59:48 +0000
@@ -30,7 +30,6 @@
       use m_eo
       use m_spin,   only: spin
       use m_diagon, only: diagon
-      use m_gamma
       use parallel, only: IONode
       use parallel, only: SIESTA_worker
       use m_compute_ebs_shift, only: compute_ebs_shift
@@ -67,10 +66,6 @@
       real(dp)            :: buffer1
       integer             :: mpierr
 
-!       character(15)            :: filename, indexstr
-!       character(15), parameter :: fnameform = '(A,A,A)'
-
-
 !-------------------------------------------------------------------- BEGIN
 
       if (SIESTA_worker) call timer( 'compute_dm', 1 )
@@ -125,6 +120,12 @@
      $               "The PEXSI solver does not implement "//
      $               "non-coll spins or Spin-orbit yet")
          endif
+         if (ionode) then
+            ! This should never happen for large-scale calculations...
+            if (no_s /= no_u) call die(
+     $               "The PEXSI solver cannot work " //
+     $               "with an auxiliary supercell")
+         endif
          call pexsi_solver(iscf, no_u, no_l, spin%spinor,
      $              maxnh, numh, listhptr, listh,
      $              H, S, qtot, Dscf, Escf,
@@ -173,13 +174,13 @@
      &              no_l, maxnh, maxnh, no_u,
      &              numh, listhptr, listh, numh, listhptr, listh, 
      &              H, S, qtot, fixspin, qtots, temp, e1, e2,
-     &              gamma, xijo, indxuo, nkpnt, kpoint, kweight,
+     $              xijo, indxuo, gamma_SCF, nkpnt, kpoint, kweight,
      &              eo, qo, Dscf, Escf, ef, efs, Entropy, no_u,
      &              occtol, iscf, neigwanted)
         Ecorrec = 0.0_dp
         PreviousCallDiagon=.true.
       elseif (isolve .eq. SOLVE_ORDERN) then
-        if (.not. gamma) call die("Cannot do O(N) with k-points.")
+        if ( .not. gamma_SCF ) call die("Cannot do O(N) with k-points.")
         if ( spin%NCol .or. spin%SO )
      .      call die("Cannot do O(N) with non-coll spins or Spin-orbit")
         call ordern(usesavelwf, ioptlwf, na_u, no_u, no_l, lasto,
@@ -193,11 +194,18 @@
      &      call die('ERROR: Non-collinear spin calculations
      &                       not yet implemented with OMM!')
         H_kin => val(H_kin_1D)
-        if (gamma) then
+
+        ! Decide which version of OMM to use.
+        ! Test based on use of auxiliary supercell
+        ! It might still be possible to avoid the complex version
+        
+        if ( no_u == no_s ) then    ! Not using an auxiliary supercell
           call dminim(.false., PreviousCallDiagon, iscf, istp, no_l,
      &                 spin%H, no_u, maxnh, numh, listhptr, listh, Dscf,
      &                 eta, qtots, H, S, H_kin)
         else
+          ! When using an auxiliary supercell
+          ! (even for gamma point; not optimized yet)
           call zminim(.false., PreviousCallDiagon, iscf, istp, no_l,
      &                 spin%H, no_u, maxnh, numh, listhptr, listh, Dscf,
      &                 eta, qtots, no_s, xijo, indxuo, nkpnt, kpoint,
@@ -211,7 +219,7 @@
      &              no_l, maxnh, maxnh, no_u,
      &              numh, listhptr, listh, numh, listhptr, listh,
      &              H, S, qtot, fixspin, qtots, temp, e1, e2,
-     &              gamma, xijo, indxuo, nkpnt, kpoint, kweight,
+     $              xijo, indxuo, gamma_SCF, nkpnt, kpoint, kweight,
      &              eo, qo, Dscf, Escf, ef, efs, Entropy, no_u,
      &              occtol, iscf, neigwanted)
 
@@ -220,7 +228,8 @@
       else if (TSrun) then
 
          call transiesta(iscf,spin%H, block_dist, sparse_pattern,
-     &        Gamma, ucell, nsc, isc_off, no_u, na_u, lasto, xa, maxnh,
+     &        no_u == no_s, ucell, nsc, isc_off, no_u, na_u,
+     &        lasto, xa, maxnh,
      &        H, S, Dscf, Escf, Ef, Qtot, .false., DE_NEGF )
 
          Ecorrec = 0._dp

=== modified file 'Src/compute_rhog.F'
--- Src/compute_rhog.F	2016-03-21 22:47:29 +0000
+++ Src/compute_rhog.F	2018-06-26 07:59:48 +0000
@@ -28,7 +28,6 @@
       use m_spin,         only: nspin, h_spin_dim
       use m_dipol
       use alloc, only: re_alloc, de_alloc
-      use m_gamma
       use files, only : filesOut_t    ! derived type for output file names
 
       implicit none

=== modified file 'Src/diag2g.F'
--- Src/diag2g.F	2018-04-14 23:14:53 +0000
+++ Src/diag2g.F	2018-06-26 07:59:48 +0000
@@ -20,6 +20,8 @@
       use parallel,        only : Node, Nodes, BlockSize
       use parallelsubs,    only : LocalToGlobalOrb,GlobalToLocalOrb
       use m_fermid,        only : fermid, stepf
+      use intrinsic_missing, only: MODP
+
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -155,18 +157,19 @@
 ! needed
 ! in those cases. 
       
-      Saux = dcmplx(0.0_dp, 0.0_dp)
-      Haux = dcmplx(0.0_dp, 0.0_dp)
       do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
         do j = 1,numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-           Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-           Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-           Haux(1,jo,1,io) = dcmplx(H(ind,1),   0.0_dp)
-           Haux(2,jo,2,io) = dcmplx(H(ind,2),   0.0_dp)
-           Haux(2,jo,1,io) = dcmplx(H(ind,3), H(ind,4))
-           Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
+          jo = MODP(jo,nuotot) ! To allow auxiliary supercells
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1),   0.0_dp)
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2),   0.0_dp)
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,3), H(ind,4))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
         enddo
       enddo
       
@@ -178,20 +181,22 @@
       if (ierror.gt.0) then
         call die('Terminating due to failed diagonalisation')
       elseif (ierror.lt.0) then
-!       Repeat diagonalisation with increased memory to handle clustering
-        Saux = dcmplx(0.0_dp, 0.0_dp)
-        Haux = dcmplx(0.0_dp, 0.0_dp)
+!     Repeat diagonalisation with increased memory to handle clustering
+
         do io = 1,nuo
+          Saux(:,:,:,io) = 0._dp
+          Haux(:,:,:,io) = 0._dp
           do j = 1,numh(io)
-            ind = listhptr(io) + j
-            jo = listh(ind)
-             Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-             Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-             Haux(1,jo,1,io) = dcmplx(H(ind,1),   0.0_dp)
-             Haux(2,jo,2,io) = dcmplx(H(ind,2),   0.0_dp)
-             Haux(2,jo,1,io) = dcmplx(H(ind,3), H(ind,4))
-             Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-          enddo
+           ind = listhptr(io) + j
+           jo = listh(ind)
+           jo = MODP(jo,nuotot) ! To allow auxiliary supercells
+           Saux(1,jo,1,io) = Saux(1,jo,1,io) +dcmplx( S(ind), 0.0_dp)
+           Saux(2,jo,2,io) = Saux(2,jo,2,io) +dcmplx( S(ind), 0.0_dp)
+           Haux(1,jo,1,io) = Haux(1,jo,1,io) +dcmplx(H(ind,1),   0.0_dp)
+           Haux(2,jo,2,io) = Haux(2,jo,2,io) +dcmplx(H(ind,2),   0.0_dp)
+           Haux(2,jo,1,io) = Haux(2,jo,1,io) +dcmplx(H(ind,3), H(ind,4))
+           Haux(1,jo,2,io) = Haux(1,jo,2,io) +dcmplx(H(ind,3),-H(ind,4))
+         enddo
         enddo
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .             2*neigwanted,iscf,ierror, 2*BlockSize)
@@ -264,6 +269,7 @@
             do j = 1,numd(io)
               ind = listdptr(io) + j
               jo = listd(ind)
+              jo = MODP(jo,nuotot) ! To allow auxiliary supercells
       
 !                 | ------- 1,1 -------     ------- 2,1 ------- |
 !                 | c_{j,up}^* c_{i,up}     c_{j,dn}^* c_{i,up) |

=== modified file 'Src/diag3g.F'
--- Src/diag3g.F	2017-08-06 11:17:47 +0000
+++ Src/diag3g.F	2018-06-26 07:59:48 +0000
@@ -17,6 +17,7 @@
       use parallel,        only : Node, Nodes, BlockSize
       use parallelsubs,    only : LocalToGlobalOrb,GlobalToLocalOrb
       use m_fermid,        only : fermid, stepf
+      use intrinsic_missing, only: MODP
 #ifdef MPI
       use mpi_siesta
 #endif
@@ -148,22 +149,19 @@
 ! D_{i,j}(1,2) = 0.5 ( D_{i,j}(1,2) + D_{i,j}(2,1)^* )
 ! can not be enforced here.
 
-      Saux = dcmplx(0.0_dp, 0.0_dp)
-      Haux = dcmplx(0.0_dp, 0.0_dp)
       do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
         do j = 1,numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-           Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-           Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-           Haux(1,jo,1,io) = dcmplx(H(ind,1), H(ind,5))
-           Haux(2,jo,2,io) = dcmplx(H(ind,2), H(ind,6))
-           Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-           Haux(2,jo,1,io) = dcmplx(H(ind,7), H(ind,8))
-        
-c           write(6,'(a,3i5,8f12.6)') 'io/jo/ind/H(ind,1:8) = ',
-c     .           io, jo, ind, H(ind,1:8)
-
+          jo = MODP(jo,nuotot) ! To allow auxiliary supercells
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1), H(ind,5))
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2), H(ind,6))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,7), H(ind,8))
         enddo
       enddo
       
@@ -176,20 +174,22 @@
         call die('Terminating due to failed diagonalisation')
       elseif (ierror.lt.0) then
 !       Repeat diagonalisation with increased memory to handle clustering
-        Saux = dcmplx(0.0_dp, 0.0_dp)
-        Haux = dcmplx(0.0_dp, 0.0_dp)
-        do io = 1,nuo
-          do j = 1,numh(io)
-            ind = listhptr(io) + j
-            jo = listh(ind)
-             Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-             Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-             Haux(1,jo,1,io) = dcmplx(H(ind,1), H(ind,5))
-             Haux(2,jo,2,io) = dcmplx(H(ind,2), H(ind,6))
-             Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-             Haux(2,jo,1,io) = dcmplx(H(ind,7), H(ind,8))
-          enddo
+      do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
+        do j = 1,numh(io)
+          ind = listhptr(io) + j
+          jo = listh(ind)
+          jo = MODP(jo,nuotot) ! To allow auxiliary supercells
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1), H(ind,5))
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2), H(ind,6))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,7), H(ind,8))
         enddo
+      enddo
+      
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .             2*neigwanted,iscf,ierror,2*BlockSize)
       endif
@@ -264,6 +264,7 @@
             do j = 1,numd(io)
               ind = listdptr(io) + j
               jo = listd(ind)
+              jo = MODP(jo,nuotot) ! To allow auxiliary supercells
 !------- 1,1 -----------------------------------------------------------
               D11  = caux(1,iio) * dconjg(caux(1,jo))
 !------- 2,2 -----------------------------------------------------------

=== modified file 'Src/diagg.F'
--- Src/diagg.F	2017-08-06 09:35:09 +0000
+++ Src/diagg.F	2018-06-26 07:59:48 +0000
@@ -90,6 +90,7 @@
       use m_fermid,      only : fermid, fermispin, stepf
       use m_spin,        only : spinor_dim, e_spin_dim
       use alloc
+      use intrinsic_missing, only: MODP
 
 #ifdef MPI
       use mpi_siesta
@@ -148,7 +149,7 @@
       
       do ispin = 1,spinor_dim
 
-         call timer( 'r-eigvec', 1 )
+        call timer( 'r-eigvec', 1 )
         call timer( 'r-buildHS', 1 )
 !$OMP parallel do default(shared), private(io,j,ind,jo)
         do io = 1,nuo
@@ -157,6 +158,7 @@
           do j = 1,numh(io)
             ind = listhptr(io) + j
             jo = listh(ind)
+            jo = MODP(jo,nuotot)   ! To allow auxiliary supercells
             Saux(jo,io) = Saux(jo,io) + S(ind)
             Haux(jo,io) = Haux(jo,io) + H(ind,ispin)
           enddo
@@ -182,6 +184,7 @@
             do j = 1,numh(io)
               ind = listhptr(io) + j
               jo = listh(ind)
+              jo = MODP(jo,nuotot) ! To allow auxiliary supercells
               Saux(jo,io) = Saux(jo,io) + S(ind)
               Haux(jo,io) = Haux(jo,io) + H(ind,ispin)
             enddo
@@ -298,6 +301,7 @@
                 do j = 1,numd(io)
                   ind = listdptr(io) + j
                   jo  = listd(ind)
+                  jo = MODP(jo,nuotot) ! To allow auxiliary supercells
                   Dnew(ind,ispin) = Dnew(ind,ispin) + qei*paux(jo)
                   Enew(ind,ispin) = Enew(ind,ispin) + eei*paux(jo)
                 enddo

=== modified file 'Src/diagon.F'
--- Src/diagon.F	2017-08-06 11:17:47 +0000
+++ Src/diagon.F	2018-06-26 07:59:48 +0000
@@ -15,7 +15,7 @@
       subroutine diagon(no, nspin, maxuo, maxnh, maxnd, 
      .                  maxo, numh, listhptr, listh, numd, 
      .                  listdptr, listd, H, S, qtot, fixspin, 
-     .                  qs, temp, e1, e2, gamma, xij, indxuo, nk, 
+     .                  qs, temp, e1, e2, xij, indxuo, gamma, nk, 
      .                  kpoint, wk, eo, qo, Dnew, Enew, ef, efs, 
      .                  Entropy, nuotot, occtol, iscf, neigwanted )
 C *********************************************************************
@@ -56,13 +56,13 @@
 C real*8  e1, e2              : Energy range for density-matrix states
 C                               (to find local density of states)
 C                               Not used if e1 > e2
-C logical gamma               : Only gamma point?
 C real*8  xij(3,maxnh)        : Vectors between orbital centers (sparse)
 C                               (not used if only gamma point)
 C integer indxuo(no)          : Index of equivalent orbital in unit cell
 C                               Unit cell orbitals must be the first in
 C                               orbital lists, i.e. indxuo.le.nuo, with
 C                               nuo the number of orbitals in unit cell
+C logical Gamma               : Whether only the Gamma point is sampled.
 C integer nk                  : Number of k points
 C real*8  kpoint(3,nk)        : k point vectors
 C real*8  wk(nk)              : k point weights (must sum one)
@@ -116,6 +116,7 @@
       implicit none
 
       real(dp), intent(in) :: H(:,:)
+      logical, intent(in) :: gamma
 
       integer
      .  iscf, maxnd, maxnh, maxuo, maxo, nk, no, nuotot,
@@ -133,7 +134,7 @@
      .  xij(3,maxnh), qs(:), efs(nspin)
      
       logical
-     .  fixspin, gamma, getD, getPSI
+     .  fixspin, getD, getPSI
 
       external
      .  diag2g, diag2k, diagsprl
@@ -146,12 +147,6 @@
 #endif
       integer            :: io, iuo, naux, nhs, npsi, nuo
       real(dp),  pointer :: aux(:)
-      integer,   pointer :: muo(:)
-
-#ifdef DEBUG
-      call write_debug( '    PRE diagon' )
-#endif
-
 C  ....................
 
 C Get Node number and calculate local orbital range
@@ -164,7 +159,8 @@
 C Start time counter ................................................
       call timer( 'diagon', 1 )
 
-C Check internal dimensions ..........................................
+C     Check internal dimensions ..........................................
+      
       if ( spin%none .or. spin%Col ) then
        if (gamma) then
         nhs  = nuotot * nuo
@@ -195,36 +191,9 @@
 
 
 C Allocate local arrays
-      nullify(aux,muo)
+      nullify(aux)
       call re_alloc( aux,  1, naux, 'aux',  'diagon' )
-      call re_alloc( muo,  1, nuo,  'muo',  'diagon' )
-
-
-C Check indxuo
-      do iuo = 1,nuo
-        muo(iuo) = 0
-      enddo
-      do io = 1,no
-        iuo = indxuo(io)
-        if (iuo.le.0 .or. iuo.gt.nuotot) then
-          if (Node.eq.0)
-     $        write(6,*) 'diagon: ERROR: invalid index: io, indxuo =',
-     .                     io, indxuo(io)
-          call die()
-        endif
-        call GlobalToLocalOrb(indxuo(io),Node,Nodes,iuo)
-        if (iuo.gt.0) then
-          muo(iuo) = muo(iuo) + 1
-        endif
-      enddo
-      do iuo = 1,nuo
-        if (muo(iuo) .ne. muo(1)) then
-          if (Node.eq.0)
-     $      write(6,'(/,2a,3i6)') 'diagon: ERROR: inconsistent indxuo',
-     .             '. iuo, muo(iuo), muo(1) =', iuo, muo(iuo), muo(1)
-          call die()
-        endif
-      enddo
+
 
 C Call apropriate routine
       getD = .true.
@@ -337,13 +306,10 @@
 
 C Free local arrays
       call de_alloc( aux, name='aux', routine='diagon' )
-      call de_alloc( muo, name='muo', routine='diagon' )
 
 C Stop time counter
       call timer( 'diagon', 2 )
-#ifdef DEBUG
-      call write_debug( '    POS diagon' )
-#endif
+
       CONTAINS
       
       subroutine output_kpoint_occupation() ! CC RC It seems ok for osSO

=== modified file 'Src/final_H_f_stress.F'
--- Src/final_H_f_stress.F	2018-06-08 16:37:51 +0000
+++ Src/final_H_f_stress.F	2018-06-26 07:59:48 +0000
@@ -50,7 +50,6 @@
       use m_dipol
       use m_forces,          only: fa
       use alloc, only: re_alloc, de_alloc
-      use m_gamma
       use m_hsx, only: write_hsx
       use sys, only: die
       use fdf
@@ -98,6 +97,7 @@
 #endif
       character(len=label_length+13) :: fname
       integer :: io_istep, io_ia1
+      logical :: not_using_auxcell
 #ifdef CDF
 #ifdef NCDF_4
       type(dict) :: dic_save
@@ -105,6 +105,8 @@
 #endif
 !------------------------------------------------------------------------- BEGIN
 
+      not_using_auxcell = (no_s == no_u)
+      
 !     Initialize Hamiltonian ........................................
       call re_alloc(H_tmp, 1,maxnh, 1, spin%H,
      $             'H_tmp','final_H_f_stress')
@@ -288,7 +290,7 @@
 ! This call could be moved to a more appropriate place
 !
       if (savehs) then
-         call write_hsx( gamma, no_u, no_s, spin%H, indxuo,
+         call write_hsx( no_u, no_s, spin%H, indxuo,
      &        maxnh, numh, listhptr, listh, H, S, Qtot,
      &        Temp, xijo)
       endif
@@ -306,7 +308,7 @@
          ! This is "pure" MD and we only write consecutive numbers
          ! Together with this you cannot also save FC
          fname = fname_TSHS(slabel, istep = istep )
-         call ts_write_tshs(fname, .false., Gamma, ts_Gamma,
+         call ts_write_tshs(fname, .false., not_using_auxcell, ts_Gamma,
      &        ucell, nsc, isc_off, na_u, no_s, spin%H, 
      &        ts_kscell, ts_kdispl, 
      &        xa, lasto, 
@@ -325,7 +327,8 @@
             !  6 = +z
             call FC_index(istep,ia1,io_istep,io_ia1)
             fname = fname_TSHS(slabel,istep = io_istep, ia1 = io_ia1)
-            call ts_write_tshs(fname, .false., Gamma, ts_Gamma,
+            call ts_write_tshs(fname, .false.,
+     &           not_using_auxcell, ts_Gamma,
      &           ucell, nsc, isc_off, na_u, no_s, spin%H, 
      &           ts_kscell, ts_kdispl, 
      &           xa, lasto, 
@@ -333,7 +336,8 @@
      &           Ef, Qtot, Temp, io_istep, io_ia1)
          else
             fname = fname_TSHS(slabel)
-            call ts_write_tshs(fname, .false., Gamma, ts_Gamma,
+            call ts_write_tshs(fname, .false.,
+     &           not_using_auxcell, ts_Gamma,
      &           ucell, nsc, isc_off, na_u, no_s, spin%H,
      &           ts_kscell, ts_kdispl, 
      &           xa, lasto,

=== modified file 'Src/intrinsic_missing.F90'
--- Src/intrinsic_missing.F90	2018-03-23 08:38:08 +0000
+++ Src/intrinsic_missing.F90	2018-06-26 07:59:48 +0000
@@ -231,12 +231,7 @@
   elemental function MODP(a,p)
     integer, intent(in) :: a,p
     integer :: MODP
-    if ( a > p ) then
-       MODP = MOD(a,p)
-       if ( MODP == 0 ) MODP = p
-    else
-       MODP = a
-    end if
+    MODP = MOD(a-1,p) + 1
   end function MODP
 
 ! Function to return the unique COUNT of an integer array.

=== modified file 'Src/local_DOS.F'
--- Src/local_DOS.F	2018-02-27 14:03:49 +0000
+++ Src/local_DOS.F	2018-06-26 07:59:48 +0000
@@ -36,7 +36,6 @@
       use m_spin,         only: nspin
       use m_spin,         only: spinor_dim 
       use m_diagon,       only: diagon
-      use m_gamma
       use m_dhscf,        only: dhscf
       implicit none
 
@@ -79,7 +78,7 @@
           call diagon(no_s, spinor_dim, no_l, maxnh, maxnh, no_u,
      .                numh, listhptr, listh, numh, listhptr, listh, 
      .                H, S, qtot, fixspin, qtots, temp, e1, e2,
-     .                gamma, xijo, indxuo, nkpnt, kpoint, kweight,
+     .                xijo, indxuo, gamma_SCF, nkpnt, kpoint, kweight,
      .                eo, qo, Dscf, Escf, ef, efs, dummy_Entrop, no_u,
      .                occtol, dummy_iscf, neigwanted)
 

=== removed file 'Src/m_gamma.F90'
--- Src/m_gamma.F90	2016-01-25 16:00:16 +0000
+++ Src/m_gamma.F90	1970-01-01 00:00:00 +0000
@@ -1,18 +0,0 @@
-! ---
-! 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.
-! ---
-module m_gamma
-	implicit none
-
-  public
-
-  logical:: gamma      ! Gamma point (k=0) in BZ only?
-
-end module m_gamma
-
-
-

=== modified file 'Src/m_hsx.F'
--- Src/m_hsx.F	2017-10-10 19:27:53 +0000
+++ Src/m_hsx.F	2018-06-26 07:59:48 +0000
@@ -8,7 +8,7 @@
       module m_hsx
       public :: write_hsx
       CONTAINS
-      subroutine write_hsx( gamma, no_u, no_s, nspin, indxuo, maxnh, 
+      subroutine write_hsx( no_u, no_s, nspin, indxuo, maxnh, 
      .                 numh, listhptr, listh, H, S, qtot, temp, xij)
 C *********************************************************************
 C Saves the hamiltonian and overlap matrices, and other data required
@@ -16,8 +16,6 @@
 C Writen by J.Soler July 1997.
 C Note because of the new more compact method of storing H and S
 C this routine is NOT backwards compatible
-C *************************** INPUT **********************************
-C logical       gamma         : Is only gamma point used?
 C ******************** INPUT or OUTPUT (depending on task) ***********
 C integer no_u                : Number of basis orbitals per unit cell
 C integer no_s                : Number of basis orbitals per supercell
@@ -36,7 +34,6 @@
 C real*8  qtot                : Total number of electrons
 C real*8  temp                : Electronic temperature for Fermi smearing
 C real*8  xij(3,maxnh)        : Vectors between orbital centers (sparse)
-C                               (not read/written if only gamma point)
 
 C
 C  Modules
@@ -59,7 +56,10 @@
 
       implicit          none
 
-      logical           gamma
+      ! This really means that supercell info is supported by default
+      logical, parameter ::  gamma = .false. 
+      logical, parameter ::  write_xijk = .true.
+
       integer           maxnh, no_u, no_s, nspin
       integer           indxuo(no_s), listh(maxnh), numh(*), listhptr(*)
       real(dp)          H(maxnh,nspin), S(maxnh),
@@ -78,7 +78,6 @@
       real(dp), dimension(:),   allocatable :: buffer
       real(dp), dimension(:,:), allocatable :: buffer2
 #endif
-      logical    baddim, gammaonfile, write_xijk
 
       call timer("writeHSX",1)
       
@@ -101,14 +100,14 @@
 C Write overall data
           write(iu) no_u, no_s, nspin, maxnhtot
 
-C Read logical
+C Write logical (always .false.)
           write(iu) gamma
 
 C Allocate local array for global numh
           allocate(numhg(no_u))
           call memory('A','I',no_u,'iohs')
 
-C Write out indxuo
+C Write out indxuo always
           if (.not.gamma) then
             write(iu) (indxuo(ih),ih=1,no_s)
           endif
@@ -272,9 +271,7 @@
           write(iu) qtot,temp
         endif
 
-        write_xijk = .TRUE.
-
-        if (write_xijk) then
+        if (write_xijk) then           ! Always
 #ifdef MPI
 C Allocate buffer array
           if (Node .eq. 0) then

=== modified file 'Src/m_ncdf_siesta.F90'
--- Src/m_ncdf_siesta.F90	2018-02-27 14:03:49 +0000
+++ Src/m_ncdf_siesta.F90	2018-06-26 07:59:48 +0000
@@ -42,7 +42,6 @@
     use fdf, only : fdf_get, leqi
     use class_Sparsity
     use files, only : slabel
-    use m_gamma, only : Gamma
     use atomlist, only: no_u, no_s, lasto, Qtot
     use siesta_geom, only: na_u, nsc
     use sparse_matrices, only: sparse_pattern

=== modified file 'Src/m_transiesta.F90'
--- Src/m_transiesta.F90	2018-04-04 13:22:33 +0000
+++ Src/m_transiesta.F90	2018-06-26 07:59:48 +0000
@@ -46,7 +46,7 @@
 
   subroutine transiesta(TSiscf,nspin, &
        sp_dist, sparse_pattern, &
-       Gamma, ucell, nsc, isc_off, no_u, na_u, lasto, xa, n_nzs, &
+       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)
 
@@ -82,7 +82,7 @@
     integer, intent(in)  :: nspin
     type(OrbitalDistribution), intent(inout) :: sp_dist
     type(Sparsity), intent(inout) :: sparse_pattern
-    logical, intent(in)  :: Gamma
+    logical, intent(in)  :: no_aux_cell
     real(dp), intent(in) :: ucell(3,3)
     integer, intent(in)  :: nsc(3), no_u, na_u
     integer, intent(in) :: isc_off(3,product(nsc))
@@ -134,7 +134,7 @@
        ! local sparsity pattern...
        converged = IsVolt .or. TS_RHOCORR_METHOD == TS_RHOCORR_FERMI
        call ts_sparse_init(slabel,converged, N_Elec, Elecs, &
-            ucell, nsc, na_u, xa, lasto, sp_dist, sparse_pattern, Gamma, &
+            ucell, nsc, na_u, xa, lasto, sp_dist, sparse_pattern, no_aux_cell, &
             isc_off)
 
        if ( ts_method == TS_BTD ) then

=== modified file 'Src/pdos.F'
--- Src/pdos.F	2018-05-08 11:36:55 +0000
+++ Src/pdos.F	2018-06-26 07:59:48 +0000
@@ -8,7 +8,7 @@
       subroutine pdos( NO, nspin, maxspn, NO_L, MAXNH, 
      .                 MAXO, NUMH, LISTHPTR, LISTH, H, S, 
      .                 E1, E2, SIGMA, NHIST,
-     .                 GAMMA, XIJ, INDXUO, NK, KPOINT, WK, EO, NO_U )
+     .                 XIJ, INDXUO, GAMMA, NK, KPOINT, WK, EO, NO_U )
 C **********************************************************************
 C Subroutine to calculate the projected density of states on the
 C atomic orbitals for a given eigenvalue spectra
@@ -37,13 +37,13 @@
 C                               Not used if e1 > e2
 C REAL*8  SIGMA               : Width of the gaussian to expand the eigenvalues
 C INTEGER NHIST               : Number of subdivisions of the histogram
-C LOGICAL GAMMA               : Only gamma point?
 C REAL*8  XIJ(3,MAXNH)        : Vectors between orbital centers (sparse)
 C                               (not used if only gamma point)
 C INTEGER INDXUO(NO)          : Index of equivalent orbital in unit cell
 C                               Unit cell orbitals must be the first in
 C                               orbital lists, i.e. indxuo.le.nuo, with
 C                               nuo the nuber of orbitals in the unit cell
+C logical Gamma               : whether only the Gamma point is sampled
 C INTEGER NK                  : Number of k points
 C REAL*8  KPOINT(3,NK)        : k point vectors
 C REAL*8  WK(NK)              : k point weights (must sum one)
@@ -80,6 +80,7 @@
      .  NO, NSPIN, MAXSPN, NO_L, MAXNH, NK, NHIST, 
      .  MAXO, NO_U
 
+      logical, intent(in) :: Gamma
       integer 
      .  NUMH(*), LISTH(MAXNH), LISTHPTR(*), INDXUO(NO)
 
@@ -87,9 +88,6 @@
      .  H(MAXNH,NSPIN), S(MAXNH), E1, E2, SIGMA,  
      .  XIJ(3,MAXNH), KPOINT(3,NK), WK(NK), EO(MAXO,MAXSPN,NK)
 
-      logical
-     .  gamma
-
 C Dynamic arrays -------------------------------------------------------
       real(dp), dimension(:,:)  , pointer :: DTOT
       real(dp), dimension(:,:,:), pointer :: DPR

=== modified file 'Src/pdos2g.F'
--- Src/pdos2g.F	2018-04-17 20:18:03 +0000
+++ Src/pdos2g.F	2018-06-26 07:59:48 +0000
@@ -100,19 +100,19 @@
      &     routine='pdos2g')
 
 C Initialize auxiliary variables
-      Haux=dcmplx(0.0_dp,0.0_dp)
-      Saux=dcmplx(0.0_dp,0.0_dp)
-
       do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
         do j = 1,numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-            Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-            Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-            Haux(1,jo,1,io) = dcmplx(H(ind,1),   0.0_dp)
-            Haux(2,jo,2,io) = dcmplx(H(ind,2),   0.0_dp)
-            Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-            Haux(2,jo,1,io) = dcmplx(H(ind,3), H(ind,4))
+          jo = indxuo(jo)
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1),   0.0_dp)
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2),   0.0_dp)
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,3), H(ind,4))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
         enddo
       enddo
 
@@ -123,19 +123,20 @@
         call die('Terminating due to failed diagonalisation')
       elseif (ierror .lt. 0) then
 C Repeat diagonalisation with increased memory to handle clustering
-        Saux = dcmplx(0.0_dp, 0.0_dp)
-        Haux = dcmplx(0.0_dp, 0.0_dp)
         do io = 1,nuo
+          Saux(:,:,:,io) = 0._dp
+          Haux(:,:,:,io) = 0._dp
           do j = 1,numh(io)
-            ind = listhptr(io) + j
-            jo = listh(ind)
-             Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-             Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-             Haux(1,jo,1,io) = dcmplx(H(ind,1),   0.0_dp)
-             Haux(2,jo,2,io) = dcmplx(H(ind,2),   0.0_dp)
-             Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-             Haux(2,jo,1,io) = dcmplx(H(ind,3), H(ind,4))
-          enddo
+           ind = listhptr(io) + j
+           jo = listh(ind)
+           jo = indxuo(jo)
+           Saux(1,jo,1,io) = Saux(1,jo,1,io) +dcmplx( S(ind), 0.0_dp)
+           Saux(2,jo,2,io) = Saux(2,jo,2,io) +dcmplx( S(ind), 0.0_dp)
+           Haux(1,jo,1,io) = Haux(1,jo,1,io) +dcmplx(H(ind,1),   0.0_dp)
+           Haux(2,jo,2,io) = Haux(2,jo,2,io) +dcmplx(H(ind,2),   0.0_dp)
+           Haux(2,jo,1,io) = Haux(2,jo,1,io) +dcmplx(H(ind,3), H(ind,4))
+           Haux(1,jo,2,io) = Haux(1,jo,2,io) +dcmplx(H(ind,3),-H(ind,4))
+         enddo
         enddo
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .                         2*nuotot,1,ierror,2*BlockSize)
@@ -147,7 +148,8 @@
         do j = 1, numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-          Spr(jo,io) = S(ind)
+          jo = indxuo(jo)
+          Spr(jo,io) = Spr(jo,io) + S(ind)
         enddo
       enddo
 

=== modified file 'Src/pdos3g.F'
--- Src/pdos3g.F	2018-04-18 10:18:19 +0000
+++ Src/pdos3g.F	2018-06-26 07:59:48 +0000
@@ -95,25 +95,25 @@
       delta = (E2 - E1)/nhist
 
 C Initialize auxiliary variables
-      Haux=dcmplx(0.0_dp,0.0_dp)
-      Saux=dcmplx(0.0_dp,0.0_dp)
 
       call re_alloc(Spr, 1, nuotot, 1, nuo, name='Spr',
      &     routine='pdos3g')
 
       do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
         do j = 1,numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-            Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-            Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-            Haux(1,jo,1,io) = dcmplx(H(ind,1), H(ind,5))
-            Haux(2,jo,2,io) = dcmplx(H(ind,2), H(ind,6))
-            Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-            Haux(2,jo,1,io) = dcmplx(H(ind,7), H(ind,8))
+          jo = indxuo(jo)
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1), H(ind,5))
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2), H(ind,6))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,7), H(ind,8))
         enddo
       enddo
-
 C Diagonalize at the Gamma point
       call cdiag( Haux, Saux, 2*nuotot, 2*nuo, 2*nuotot,
      .            eo, psi, 2*nuotot, 1, ierror, 2*BlockSize )
@@ -121,20 +121,21 @@
         call die('Terminating due to failed diagonalisation')
       elseif (ierror .lt. 0) then
 C Repeat diagonalisation with increased memory to handle clustering
-        Saux = dcmplx(0.0_dp, 0.0_dp)
-        Haux = dcmplx(0.0_dp, 0.0_dp)
-        do io = 1,nuo
-          do j = 1,numh(io)
-            ind = listhptr(io) + j
-            jo = listh(ind)
-             Saux(1,jo,1,io) = dcmplx(  S(ind),   0.0_dp)
-             Saux(2,jo,2,io) = dcmplx(  S(ind),   0.0_dp)
-             Haux(1,jo,1,io) = dcmplx(H(ind,1), H(ind,5))
-             Haux(2,jo,2,io) = dcmplx(H(ind,2), H(ind,6))
-             Haux(1,jo,2,io) = dcmplx(H(ind,3),-H(ind,4))
-             Haux(2,jo,1,io) = dcmplx(H(ind,7), H(ind,8))
-          enddo
+      do io = 1,nuo
+        Saux(:,:,:,io) = 0._dp
+        Haux(:,:,:,io) = 0._dp
+        do j = 1,numh(io)
+          ind = listhptr(io) + j
+          jo = listh(ind)
+          jo = indxuo(jo)
+          Saux(1,jo,1,io) = Saux(1,jo,1,io) + dcmplx( S(ind), 0.0_dp)
+          Saux(2,jo,2,io) = Saux(2,jo,2,io) + dcmplx( S(ind), 0.0_dp)
+          Haux(1,jo,1,io) = Haux(1,jo,1,io) + dcmplx(H(ind,1), H(ind,5))
+          Haux(2,jo,2,io) = Haux(2,jo,2,io) + dcmplx(H(ind,2), H(ind,6))
+          Haux(1,jo,2,io) = Haux(1,jo,2,io) + dcmplx(H(ind,3),-H(ind,4))
+          Haux(2,jo,1,io) = Haux(2,jo,1,io) + dcmplx(H(ind,7), H(ind,8))
         enddo
+      enddo
         call cdiag(Haux,Saux,2*nuotot,2*nuo,2*nuotot,eo,psi,
      .                         2*nuotot,1,ierror,2*BlockSize)
       endif
@@ -145,7 +146,8 @@
         do j = 1, numh(io)
           ind = listhptr(io) + j
           jo = listh(ind)
-          Spr(jo,io) = S(ind)
+          jo = indxuo(jo)
+          Spr(jo,io) = Spr(jo,io) + S(ind)
         enddo
       enddo
 

=== modified file 'Src/post_scf_work.F'
--- Src/post_scf_work.F	2018-02-27 14:03:49 +0000
+++ Src/post_scf_work.F	2018-06-26 07:59:48 +0000
@@ -41,7 +41,6 @@
       use m_compute_dm,   only : PreviousCallDiagon
       use m_eo
       use Kpoint_grid
-      use m_gamma
       implicit none
 
       ! MD-step, SCF-step
@@ -52,12 +51,8 @@
       type(Pair_Geometry_dSpData2D)  :: pair
       type(Geometry)                :: geom
 
-#ifdef DEBUG
-      call write_debug( '    PRE post_scf_work' )
-#endif
-
       call timer( 'PostSCF', 1 )
-!
+
 !     If converged, make one last iteration to find forces and stress
 
 !     If we use the minimization routine, the energy-density
@@ -81,15 +76,17 @@
      &                no_l, maxnh, maxnh, no_u,
      &                numh, listhptr, listh, numh, listhptr, listh, 
      &                H, S, qtot, fixspin, qtots, temp, 1.0_dp, -1.0_dp,
-     &                gamma, xijo, indxuo, nkpnt, kpoint, kweight,
+     &                xijo, indxuo, gamma_SCF, nkpnt, kpoint, kweight,
      &                eo, qo, Dscf, Escf, ef, efs, Entropy, no_u,
      &                occtol, iscf, neigwanted)
           Ecorrec = 0.0_dp
         else
-          if (gamma) then
+            if ( no_u == no_s ) then ! Not using an auxiliary supercell
             call dminim(.true., .false., iscf, istp, no_l, nspin, no_u,
      &                  maxnh, numh, listhptr, listh, Escf, eta, qtots)
           else
+            ! When using an auxiliary supercell
+            ! (even for gamma point; not optimized yet)
             call zminim(.true., .false., iscf, istp, no_l, nspin, no_u,
      &                  maxnh, numh, listhptr, listh, Escf, eta, qtots,
      &                  no_s, xijo, indxuo, nkpnt, kpoint, kweight)

=== modified file 'Src/projected_DOS.F'
--- Src/projected_DOS.F	2018-01-04 18:48:03 +0000
+++ Src/projected_DOS.F	2018-06-26 07:59:48 +0000
@@ -69,7 +69,6 @@
       use parallel,    only: IOnode
       use m_eo
       use m_spin,      only: h_spin_dim, spinor_dim
-      use m_gamma
       use units,       only: eV
       
       implicit none
@@ -122,7 +121,7 @@
          call pdos( no_s, h_spin_dim, spinor_dim, no_l, 
      .        maxnh,
      .        no_u, numh, listhptr, listh, H, S,
-     .        e1, e2, sigma, nhist, gamma_pdos, xijo, indxuo, 
+     .        e1, e2, sigma, nhist, xijo, indxuo, gamma_PDOS,
      .        nkpnt_pdos, kpoints_pdos, kweight_pdos, eo,
      .        no_u)
       else
@@ -131,7 +130,8 @@
      .        maxnh,
      .        no_u, numh, listhptr, listh, H, S,
      .        e1, e2, sigma, nhist,
-     .        gamma, xijo, indxuo, nkpnt, kpoint, kweight, eo,
+     .        xijo, indxuo, gamma_SCF,
+     .        nkpnt, kpoint, kweight, eo,
      .        no_u)
       endif
 

=== modified file 'Src/setup_hamiltonian.F'
--- Src/setup_hamiltonian.F	2018-03-30 23:16:29 +0000
+++ Src/setup_hamiltonian.F	2018-06-26 07:59:48 +0000
@@ -43,7 +43,6 @@
       use m_spin,         only: spin
       use m_dipol
       use alloc, only: re_alloc, de_alloc
-      use m_gamma
       use m_hsx, only: write_hsx
       use sys, only: die, bye
       use m_partial_charges, only: want_partial_charges
@@ -256,7 +255,7 @@
 ! Only in HSX format now.  Use Util/HSX/hsx2hs to generate an HS file
 
       if (savehs .or. write_coop) then
-         call write_hsx( gamma, no_u, no_s, spin%H, indxuo,
+         call write_hsx( no_u, no_s, spin%H, indxuo,
      &        maxnh, numh, listhptr, listh, H, S, qtot,
      &        temp, xijo)
       endif

=== modified file 'Src/siesta_analysis.F'
--- Src/siesta_analysis.F	2018-04-09 21:33:05 +0000
+++ Src/siesta_analysis.F	2018-06-26 07:59:48 +0000
@@ -15,7 +15,7 @@
 
       subroutine siesta_analysis( relaxd )
       USE band, only: nbk, bk, maxbk, bands
-      USE writewave, only: nwk, wfk, wwave
+      USE writewave, only: nwk, wfk, wwave, gamma_wavefunctions
       USE writewave, only: setup_wfs_list, wfs_filename
       USE m_ksvinit, only: nkpol, kpol, wgthpol
       use m_ksv
@@ -35,7 +35,6 @@
      &                    iphkb, no_u, no_s, iza, iphorb, rmaxo, indxua
       use atomlist, only: qtot
       use fdf
-      use writewave,    only: wwave
       use siesta_cml
       use files,        only : slabel
       use files,        only : filesOut_t   ! derived type for output file names
@@ -52,7 +51,6 @@
       use m_dipol
       use m_eo
       use m_forces,          only: fa
-      use m_gamma 
       use alloc,             only: re_alloc, de_alloc
       use basis_enthalpy,    only: write_basis_enthalpy
       use m_partial_charges, only: want_partial_charges
@@ -275,7 +273,7 @@
         call wwave( no_s, h_spin_dim, spinor_dim, no_u, no_l, maxnh, 
      &              nwk,
      &              numh, listhptr, listh, H, S, Ef, xijo, indxuo,
-     &              nwk, wfk, no_u, gamma, occtol )
+     &              gamma_wavefunctions, nwk, wfk, no_u, occtol )
       endif
 
 
@@ -295,7 +293,7 @@
          call wwave( no_s, h_spin_dim, spinor_dim, no_u, no_l, maxnh, 
      .        nkpnt,
      .        numh, listhptr, listh, H, S, Ef, xijo, indxuo,
-     .        nkpnt, kpoint, no_u, gamma, occtol)
+     .        gamma_SCF, nkpnt, kpoint, no_u, occtol)
       endif
 
 !     Compute bands

=== modified file 'Src/siesta_init.F'
--- Src/siesta_init.F	2018-06-07 20:08:23 +0000
+++ Src/siesta_init.F	2018-06-26 07:59:48 +0000
@@ -57,7 +57,6 @@
       use m_rmaxh
       use m_forces 
       use m_eo
-      use m_gamma
       use m_fixed,            only: init_fixed, print_fixed
       use m_ioxv,             only: xv_file_read
       use m_projected_DOS,    only: init_projected_DOS
@@ -115,7 +114,7 @@
       integer :: i, is, ispin, n_dm_items
       integer :: neigmin      ! Min. number of eigenstates (per k point)
       integer :: ns           ! Number of species
-      logical :: user_wants_supercell
+      logical :: user_wants_supercell, not_using_auxcell
       real(dp) :: walltime_m, walltime_s
 
       integer :: World_Group
@@ -567,7 +566,7 @@
 !     not early, in order to decide whether to use an 
 !     auxiliary supercell for the calculation of matrix elements.
       call setup_Kpoint_grid( ucell )
-      gamma = gamma_scf
+      not_using_auxcell = gamma_scf
 
       ! Read in diagonalization routines
       ! Note that only the sampled BZ is responsible for
@@ -580,7 +579,7 @@
 !     the auxiliary supercell is needed for a non-gamma calculation
       call init_projected_DOS( )
       if (do_pdos) then
-        gamma = gamma .and. gamma_pdos
+        not_using_auxcell = not_using_auxcell.and. gamma_pdos
       endif
 
       nullify(eo,qo)
@@ -590,13 +589,13 @@
      &              'siesta_init')
 
       call setup_bands( )
-      gamma = gamma .and. gamma_bands
+      not_using_auxcell = not_using_auxcell .and. gamma_bands
 
       call setup_wf_kpoints( )
-      gamma = gamma .and. gamma_wavefunctions
+      not_using_auxcell = not_using_auxcell .and. gamma_wavefunctions
 
       call estimate_pol_kpoints( ucell )
-      gamma = gamma .and. gamma_polarization
+      not_using_auxcell = not_using_auxcell .and. gamma_polarization
 !      print *, "gamma, gamma_pol: ", gamma, gamma_polarization
 !
 !     User can request that the calculation is done with an explicit
@@ -604,12 +603,12 @@
 !     the gamma point
 !
       user_wants_supercell = fdf_get( 'ForceAuxCell', .false. )
-      if (user_wants_supercell) gamma = .false.
+      if (user_wants_supercell) not_using_auxcell = .false.
 
 !     Find required supercell
 !     2*rmaxh is used to guarantee that two given orbitals in the
 !     supercell can only overlap once
-      if (gamma) then
+      if (not_using_auxcell) then
         nsc(1:3) = 1
       else
         ! Discussion with Jose-Soler we get this size ! NPA

=== modified file 'Src/state_init.F'
--- Src/state_init.F	2018-05-15 09:48:18 +0000
+++ Src/state_init.F	2018-06-26 07:59:48 +0000
@@ -13,7 +13,7 @@
       CONTAINS
 
       subroutine state_init( istep )
-      use Kpoint_grid,       only: setup_Kpoint_grid, nkpnt
+      use Kpoint_grid,       only: setup_Kpoint_grid, nkpnt, gamma_scf
       use m_os,              only: file_exist
       use m_new_dm,          only: new_dm
       use m_proximity_check, only: proximity_check
@@ -66,7 +66,6 @@
       use m_normalize_dm, only: normalize_dm
 
       use m_eo
-      use m_gamma
       use files,             only: slabel
       use m_mpi_utils,       only: globalize_or
       use m_mpi_utils,       only: globalize_sum
@@ -129,15 +128,15 @@
 
       type(dData2D) :: tmp_2D
       real(dp) :: dummy_qspin(8)
-
+      logical  :: not_using_auxcell
 
 !------------------------------------------------------------------- BEGIN
       call timer( 'IterGeom', 1 )
-#ifdef DEBUG
-      call write_debug( '  PRE state_init' )
-#endif
+
       call timer( 'state_init', 1 )
 
+      not_using_auxcell = (no_s == no_u)
+      
       istp = istp + 1
 
       if (IOnode) then
@@ -245,7 +244,7 @@
       endif
 
       if ( cell_can_change .and.
-     &     (istep.ne.inicoor) .and. (.not.gamma) ) then
+     &     (istep.ne.inicoor) .and. (.not.gamma_scf) ) then
 
 !       Will print k-points also
         call setup_Kpoint_grid( ucell )
@@ -258,7 +257,7 @@
      &                 'state_init' )
 
 !       Find required supercell
-        if (gamma) then
+        if (not_using_auxcell) then
            nsc(1:3) = 1
         else
            do i = 1 , 3
@@ -340,14 +339,14 @@
       call delete(xij_2D) ! as xijo will be reallocated
       nullify(xijo)
       call hsparse( negl, scell, nsc, na_s, isa, xa, lasto,
-     &              lastkb, iphorb, iphKB, maxnh, gamma,
+     &              lastkb, iphorb, iphKB, maxnh, not_using_auxcell,
      $              set_xijo=.true., folding=folding1,
      $              diagonal_folding=diag_folding1,
      $              debug_folding=fdf_get('debug-folding',.false.))
 !
       call globalize_or(diag_folding1,diag_folding)
       call globalize_or(folding1,folding)
-      if (diag_folding .and. gamma) then
+      if (diag_folding .and. not_using_auxcell) then
          call message("WARNING","Gamma-point calculation " //
      $         "with interaction between periodic images")
          call message("WARNING",
@@ -358,7 +357,7 @@
      $                              "'force-aux-cell T'")
 
       else if (folding) then
-         if (gamma) then
+         if (not_using_auxcell) then
                call message("INFO","Gamma-point calculation " //
      $                      "with multiply-connected orbital pairs")
                call message("INFO",
@@ -449,7 +448,7 @@
       xijo => val(xij_2D)
 
       ! Calculate the super-cell offsets...
-      if ( Gamma ) then
+      if ( not_using_auxcell ) then
          ! Here we create the super-cell offsets
          call re_alloc(isc_off,1,3,1,1)
          isc_off(:,:) = 0
@@ -467,7 +466,7 @@
          ! Force the creation of the full sparsity pattern
          call ts_sparse_init(slabel,IsVolt, N_Elec, Elecs, 
      &        ucell, nsc, na_u, xa, lasto, block_dist, sparse_pattern, 
-     &        Gamma, isc_off)
+     &        not_using_auxcell, isc_off)
 
          ! create the tri-diagonal matrix
          call ts_tri_analyze( block_dist, sparse_pattern , N_Elec,
@@ -580,7 +579,7 @@
          ! We include H as S, well-knowing that we only write one of
          ! them, there is no need to allocate space for no reason!
          call ts_write_tshs(fname, 
-     &        .true., Gamma, ts_Gamma_file,
+     &        .true., not_using_auxcell, ts_Gamma_file,
      &        ucell, nsc, isc_off, na_u, no_s, spin%H,
      &        ts_kscell_file, ts_kdispl_file,
      &        xa, lasto, 

=== modified file 'Src/writewave.F'
--- Src/writewave.F	2018-06-08 14:34:39 +0000
+++ Src/writewave.F	2018-06-26 07:59:48 +0000
@@ -386,7 +386,7 @@
       subroutine wwave( no, nspin, maxspn, maxo, maxuo, maxnh, 
      .                  maxk,
      .                  numh, listhptr, listh, H, S, ef, xij, indxuo,
-     .                  nk, kpoint, nuotot, gamma, occtol)
+     .                  gamma, nk, kpoint, nuotot, occtol)
 C *********************************************************************
 C Finds wavefunctions at selected k-points.
 C Written by P. Ordejon, June 2003
@@ -415,10 +415,10 @@
 C                               Unit cell orbitals must be the first in
 C                               orbital lists, i.e. indxuo.le.nuo, with
 C                               nuo the number of orbitals in unit cell
+C logical Gamma               : whether only the Gamma-point is sampled
 C integer nk                  : Number of band k points
 C real*8  kpoint(3,maxk)      : k point vectors
 C integer nuotot              : Total number of orbitals in unit cell
-C logical gamma               : Indicates if this is a Gamma point run
 C real*8  occtol              : Occupancy threshold for DM build
 C *************************** OUTPUT **********************************
 C None; output is dumped to wave functions file SystemLabel.WFSX
@@ -448,11 +448,11 @@
 
       implicit          none
 
+      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(*)
-      logical           gamma
       real(dp)          ef, H(:,:), kpoint(3,maxk), 
      .                  S(maxnh), xij(3,maxnh), occtol
 
@@ -470,7 +470,6 @@
      .  temp, wk, Entropy
 
 C Dynamic arrays
-      integer,  allocatable :: muo(:)
       logical, parameter :: getD = .false.
       logical, parameter :: getPSI = .true.
       real(dp), allocatable :: aux(:)
@@ -525,45 +524,11 @@
       call re_alloc(Saux,1,nhs,name='Saux',routine='densematrix')
       call re_alloc(psi,1,nhs,name='psi',routine='densematrix')
 
-CC RC  ek has different arguments here than in 3.1.1 version that it is:
-C      allocate(ek(maxspn,nuo,nuotot)) and the next call to memory
       allocate(ek(nuotot,maxspn,nk))
       call memory('A','D',maxspn*nk*nuotot,'writewave')
       naux = 2*nuotot*5
       allocate(aux(naux))
       call memory('A','D',naux,'writewave')
-      allocate(muo(nuotot))
-      call memory('A','I',nuotot,'writewave')
-
-C Check indxuo 
-      do iuo = 1,nuotot
-        muo(iuo) = 0
-      enddo
-      do io = 1,no
-        iuo = indxuo(io)
-        if (indxuo(io).le.0 .or. indxuo(io).gt.nuotot) then
-          if (Node.eq.0) then
-            write(6,*) 'writewave: invalid index: io, indxuo =',
-     .        io, indxuo(io)
-            call die('writewave: invalid indxuo')
-          else
-            call die()
-          endif
-        endif
-        muo(iuo) = muo(iuo) + 1
-      enddo
-      do iuo = 1,nuotot
-        if (muo(iuo) .ne. muo(1)) then
-          if (Node.eq.0) then
-          write(6,'(/,2a,3i6)') 'writewave: ERROR: inconsistent indxuo.'
-     .     ,' iuo, muo(iuo), muo(1) =', iuo, muo(iuo), muo(1)
-            call die('writewave: ERROR: inconsistent indxuo.')
-          else
-            call die()
-          endif
-        endif
-      enddo
-
 
 C Open file
 
@@ -602,7 +567,6 @@
 
 C Call appropriate diagonalization routine
 
-CC RC Added for on-site SO
       if (NoMagn .or. SPpol) then
        if (gamma) then
          call diagg( h_spin_dim, nuo, maxuo, maxnh, maxnh, 
@@ -621,7 +585,7 @@
      &               "WF info generation"
              end if
              ParallelOverK = .false.
-             Serial = Nodes == 1
+             Serial = (Nodes == 1)
              call diag_init()
           end if
 
@@ -638,7 +602,7 @@
          if ( ParallelOverK ) Serial = .true.
          
        endif
-CC RC Added for on-site SO
+
       elseif (NonCol) then
         if (gamma) then
           call diag2g( nuo, no, maxuo, maxnh, maxnh, maxo, numh,
@@ -677,8 +641,6 @@
 
 
 C Free local arrays 
-      call memory('D','I',size(muo),'writewave')
-      deallocate(muo)
       call memory('D','D',size(aux),'writewave')
       deallocate(aux)
       call memory('D','D',size(ek),'writewave')
@@ -716,7 +678,7 @@
       logical gamma
 
 C  Internal variables .............................................
-      integer  BNode, ntot, iie, iw, indwf, j, ind, iu
+      integer  BNode, iie, iw, indwf, j, ind, iu
 
       integer number_of_wfns
       integer, allocatable  :: ind_wfn(:)
@@ -746,21 +708,6 @@
      .        status='old')
       endif
 
-C Check that the total number of orbitals is correct
-
-#ifdef MPI
-      if (Nodes.gt.1) then
-        call MPI_AllReduce(nuo,ntot,1,MPI_integer,MPI_sum,
-     .    MPI_Comm_World,MPIerror)
-      else
-        ntot = nuo
-      endif
-#else
-      ntot = nuo
-#endif
-
-      if (ntot .ne. nuotot) call die('Inconsistent number of orbitals')
-
       if (wfs_energy_window) then  
          allocate(ind_wfn(nwflist(ik)))
          number_of_wfns = 0
@@ -810,7 +757,10 @@
       do iw = 1,nwflist(ik)
         indwf = iwf(ik,iw)
 
-C Determine which node handles this wavefunction
+        ! Determine which node handles this wavefunction
+        ! Note that the distribution is block cyclic,
+        ! so the same 'orbital' helper functions apply
+
         call WhichNodeOrb(indwf,Nodes,BNode)
 
         if (Node .eq. 0 .and. debug) then
@@ -820,7 +770,7 @@
 
         if (Node.eq.BNode) then
 
-C Determine the index of the orbital in the local node
+C Determine the index of the wavefunction in the local node
 
           call GlobalToLocalOrb( indwf, BNode, Nodes, iie)
 
@@ -830,12 +780,12 @@
 C must be handled differently
 
           if (gamma) then
-            do j = 1,ntot
+            do j = 1,nuotot
               ind = j + (iie-1)*nuotot 
               aux(1,j) = real(psi(ind),kind=sp)
             enddo
           else
-            do j = 1,ntot
+            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)
@@ -862,12 +812,12 @@
         endif
 #endif
 
-C eigenvector is now stored in aux in all processors, and can be printed
+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,ntot)
+          write(iu) (aux(1:,j), j=1,nuotot)
        endif
 
       enddo

=== modified file 'Util/COOP/Makefile'
--- Util/COOP/Makefile	2018-06-08 09:23:57 +0000
+++ Util/COOP/Makefile	2018-06-26 07:59:48 +0000
@@ -88,7 +88,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -140,10 +140,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -155,8 +155,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -183,13 +183,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -231,11 +233,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -304,8 +306,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -374,10 +376,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -481,7 +483,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -674,14 +676,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -731,11 +732,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -748,10 +748,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -782,7 +782,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -814,14 +814,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/COOP/dm_creator.F90'
--- Util/COOP/dm_creator.F90	2016-01-25 16:00:16 +0000
+++ Util/COOP/dm_creator.F90	2018-06-26 07:59:48 +0000
@@ -178,7 +178,6 @@
   ! Will pick up atoms, zval, and thus N_electrons
 
   call read_hs_file(trim(sflnm)//".HSX")
-  if (gamma_wfsx .neqv. gamma) STOP "Gamma mismatch"
 
   ztot = 0.0_dp
   do ia = 1, na_u
@@ -326,7 +325,7 @@
 
   ! * Curves
 
-     if (gamma) then
+     if (gamma_wfsx) then
         allocate(wf(1,1:no_u))
      else
         allocate(wf(2,1:no_u))
@@ -378,7 +377,7 @@
                                 !AG: Corrected:  (qcos, qsin) = conjg(C_1)*(C_2)
                                 ! We might want to avoid recomputing this
 
-                                if (gamma) then
+                                if (gamma_wfsx) then
                                    qcos = wf(1,io1)*wf(1,io2) 
                                    qsin = 0.0_dp
                                 else

=== modified file 'Util/COOP/fat.f90'
--- Util/COOP/fat.f90	2016-05-05 13:00:27 +0000
+++ Util/COOP/fat.f90	2018-06-26 07:59:48 +0000
@@ -197,7 +197,6 @@
   ! but the total charge is read as qtot.
 
   call read_hs_file(trim(sflnm)//".HSX")
-  if (gamma_wfsx .neqv. gamma) STOP "Gamma mismatch"
 
   if (energies_only) STOP
 
@@ -340,7 +339,7 @@
      nbands = max_band - min_band + 1
      allocate(eig(nbands,nspin), fat(nbands,nspin))
 
-     if (gamma) then
+     if (gamma_wfsx) then
         allocate(wf(1,1:no_u))
      else
         allocate(wf(2,1:no_u))
@@ -469,7 +468,7 @@
                                 !AG: Corrected:  (qcos, qsin) = conjg(C_1)*(C_2)
                                 ! We might want to avoid recomputing this
 
-                                if (gamma) then
+                                if (gamma_wfsx) then
                                    qcos = wf(1,io1)*wf(1,io2) 
                                    qsin = 0.0_dp
                                 else

=== modified file 'Util/COOP/io_hs.f90'
--- Util/COOP/io_hs.f90	2016-01-25 16:00:16 +0000
+++ Util/COOP/io_hs.f90	2018-06-26 07:59:48 +0000
@@ -22,6 +22,7 @@
   real(sp), allocatable  :: buff3(:,:)
 
   integer numx, ind
+  logical lacking_indxuo
 
   write(6,"(1x,a)",advance='no') trim(fname)
   open(hs_u,file=trim(fname),status='old',form='unformatted')
@@ -32,14 +33,20 @@
   if (nnao /= nao) STOP "norbs inconsistency"
   no_u = nao
 
-  read(hs_u,iostat=iostat) gamma
-  if (iostat /= 0) STOP "gamma"
-  IF (DEBUG) PRINT *, "GAMMA=", gamma
-  if (.not. gamma) then
+  ! In modern versions of HSX files this should be always .false., that is,
+  ! files always include the indxuo array, even if it is trivial.
+  
+  read(hs_u,iostat=iostat) lacking_indxuo
+  if (iostat /= 0) STOP "lacking_indxuo"
+  IF (DEBUG) PRINT *, "LACKING_INDXUO=", lacking_indxuo
+
+  if (.not. lacking_indxuo) then
+     ! read it
      allocate(indxuo(no_s))
      read(hs_u) (indxuo(i),i=1,no_s)
   else
      allocate(indxuo(no_u))
+     ! build it
      do i=1,no_u
         indxuo(i) = i
      enddo

=== modified file 'Util/COOP/main_vars.f90'
--- Util/COOP/main_vars.f90	2016-05-05 13:00:27 +0000
+++ Util/COOP/main_vars.f90	2018-06-26 07:59:48 +0000
@@ -84,7 +84,6 @@
   logical,   allocatable :: ref_mask(:)
 
   !
-  logical :: gamma
   real(dp) :: r_dummy(3), dummy_weight, ztot
   integer  :: idummy
   !

=== modified file 'Util/COOP/mprop.f90'
--- Util/COOP/mprop.f90	2016-01-25 16:00:16 +0000
+++ Util/COOP/mprop.f90	2018-06-26 07:59:48 +0000
@@ -301,7 +301,6 @@
   ! but the total charge is read as qtot.
 
   call read_hs_file(trim(sflnm)//".HSX")
-  if (gamma_wfsx .neqv. gamma) STOP "Gamma mismatch"
 
   ztot = 0.0_dp
   do ia = 1, na_u
@@ -517,7 +516,7 @@
 
   ! * Curves
 
-     if (gamma) then
+     if (gamma_wfsx) then
         allocate(wf(1,1:no_u))
      else
         allocate(wf(2,1:no_u))
@@ -676,7 +675,7 @@
                                 !AG: Corrected:  (qcos, qsin) = conjg(C_1)*(C_2)
                                 ! We might want to avoid recomputing this
 
-                                if (gamma) then
+                                if (gamma_wfsx) then
                                    qcos = wf(1,io1)*wf(1,io2) 
                                    qsin = 0.0_dp
                                 else

=== modified file 'Util/Denchar/Src/Makefile'
--- Util/Denchar/Src/Makefile	2018-06-08 09:23:57 +0000
+++ Util/Denchar/Src/Makefile	2018-06-26 07:59:48 +0000
@@ -157,7 +157,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -214,10 +214,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -229,8 +229,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -257,13 +257,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -305,11 +307,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -378,8 +380,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -448,10 +450,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -555,7 +557,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -748,14 +750,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -805,11 +806,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -822,10 +822,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -856,7 +856,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -888,14 +888,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/Gen-basis/Makefile'
--- Util/Gen-basis/Makefile	2018-06-08 09:23:57 +0000
+++ Util/Gen-basis/Makefile	2018-06-26 07:59:48 +0000
@@ -152,7 +152,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -204,10 +204,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -219,8 +219,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -247,13 +247,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -295,11 +297,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -368,8 +370,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -438,10 +440,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -545,7 +547,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -738,14 +740,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -795,11 +796,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -812,10 +812,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -846,7 +846,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -878,14 +878,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/Grimme/Makefile'
--- Util/Grimme/Makefile	2018-06-08 09:23:57 +0000
+++ Util/Grimme/Makefile	2018-06-26 07:59:48 +0000
@@ -90,7 +90,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -142,10 +142,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -157,8 +157,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -185,13 +185,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -233,11 +235,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -306,8 +308,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -376,10 +378,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -483,7 +485,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -676,14 +678,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -733,11 +734,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -750,10 +750,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -784,7 +784,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -816,14 +816,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/Helpers/Makefile'
--- Util/Helpers/Makefile	2018-06-08 09:23:57 +0000
+++ Util/Helpers/Makefile	2018-06-26 07:59:48 +0000
@@ -93,7 +93,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -145,10 +145,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -160,8 +160,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -188,13 +188,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -236,11 +238,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -309,8 +311,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -379,10 +381,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -486,7 +488,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -679,14 +681,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -736,11 +737,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -753,10 +753,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -787,7 +787,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -819,14 +819,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/STM/ol-stm/Src/Makefile'
--- Util/STM/ol-stm/Src/Makefile	2018-06-08 09:23:57 +0000
+++ Util/STM/ol-stm/Src/Makefile	2018-06-26 07:59:48 +0000
@@ -170,7 +170,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -227,10 +227,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -242,8 +242,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -270,13 +270,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -318,11 +320,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -391,8 +393,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -461,10 +463,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -568,7 +570,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -761,14 +763,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -818,11 +819,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -835,10 +835,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -869,7 +869,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -901,14 +901,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/SpPivot/Makefile'
--- Util/SpPivot/Makefile	2018-06-08 09:23:57 +0000
+++ Util/SpPivot/Makefile	2018-06-26 07:59:48 +0000
@@ -99,7 +99,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -156,10 +156,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -171,8 +171,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -199,13 +199,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -247,11 +249,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -320,8 +322,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -390,10 +392,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -497,7 +499,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -690,14 +692,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -747,11 +748,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -764,10 +764,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -798,7 +798,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -830,14 +830,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/TS/TBtrans/Makefile'
--- Util/TS/TBtrans/Makefile	2018-06-08 09:23:57 +0000
+++ Util/TS/TBtrans/Makefile	2018-06-26 07:59:48 +0000
@@ -355,7 +355,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -412,10 +412,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -427,8 +427,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -455,13 +455,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -503,11 +505,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -576,8 +578,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -646,10 +648,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -753,7 +755,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -946,14 +948,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -1003,11 +1004,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -1020,10 +1020,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -1054,7 +1054,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -1086,14 +1086,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/TS/ts2ts/Makefile'
--- Util/TS/ts2ts/Makefile	2018-06-08 09:23:57 +0000
+++ Util/TS/ts2ts/Makefile	2018-06-26 07:59:48 +0000
@@ -92,7 +92,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -149,10 +149,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -164,8 +164,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -192,13 +192,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -240,11 +242,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -313,8 +315,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -383,10 +385,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -490,7 +492,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -683,14 +685,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -740,11 +741,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -757,10 +757,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -791,7 +791,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -823,14 +823,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/TS/tshs2tshs/Makefile'
--- Util/TS/tshs2tshs/Makefile	2018-06-08 09:23:57 +0000
+++ Util/TS/tshs2tshs/Makefile	2018-06-26 07:59:48 +0000
@@ -158,7 +158,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -215,10 +215,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -230,8 +230,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -258,13 +258,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -306,11 +308,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -379,8 +381,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -449,10 +451,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -556,7 +558,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -749,14 +751,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -806,11 +807,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -823,10 +823,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -857,7 +857,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -889,14 +889,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Util/VCA/Makefile'
--- Util/VCA/Makefile	2018-06-08 09:23:57 +0000
+++ Util/VCA/Makefile	2018-06-26 07:59:48 +0000
@@ -123,7 +123,7 @@
 atomlwf.o: spatial.o
 automatic_cell.o: atm_types.o atmfuncs.o parallel.o precision.o units.o
 bands.o: alloc.o atmfuncs.o atomlist.o densematrix.o diag.o diag_option.o
-bands.o: files.o get_kpoints_scale.o local_sys.o m_gamma.o m_spin.o parallel.o
+bands.o: files.o get_kpoints_scale.o local_sys.o m_spin.o parallel.o
 bands.o: parallelsubs.o precision.o siesta_geom.o writewave.o
 basis_enthalpy.o: atmfuncs.o atomlist.o precision.o siesta_geom.o units.o
 basis_io.o: atm_types.o atmparams.o atom_options.o basis_types.o chemical.o
@@ -175,10 +175,10 @@
 coceri.o: files.o periodic_table.o precision.o units.o
 compute_dm.o: atomlist.o class_SpData1D.o compute_ebs_shift.o diagon.o
 compute_dm.o: iodmhs_netcdf.o kpoint_grid.o local_sys.o m_dminim.o m_energies.o
-compute_dm.o: m_eo.o m_gamma.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o
-compute_dm.o: m_steps.o m_transiesta.o m_ts_global_vars.o m_zminim.o
-compute_dm.o: normalize_dm.o ordern.o parallel.o precision.o siesta_geom.o
-compute_dm.o: siesta_options.o sparse_matrices.o units.o
+compute_dm.o: m_eo.o m_hsx.o m_pexsi_driver.o m_rmaxh.o m_spin.o m_steps.o
+compute_dm.o: m_transiesta.o m_ts_global_vars.o m_zminim.o normalize_dm.o
+compute_dm.o: ordern.o parallel.o precision.o siesta_geom.o siesta_options.o
+compute_dm.o: sparse_matrices.o units.o
 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
@@ -190,8 +190,8 @@
 compute_pw_matrix.o: parallel.o precision.o siesta2wannier90.o
 compute_pw_matrix.o: sparse_matrices.o
 compute_rhog.o: alloc.o atomlist.o dhscf.o files.o m_dipol.o m_energies.o
-compute_rhog.o: m_gamma.o m_ntm.o m_spin.o m_stress.o siesta_geom.o
-compute_rhog.o: siesta_options.o sparse_matrices.o
+compute_rhog.o: m_ntm.o m_spin.o m_stress.o siesta_geom.o siesta_options.o
+compute_rhog.o: sparse_matrices.o
 conjgr.o: precision.o
 conjgr_old.o: precision.o
 coor.o: alloc.o local_sys.o parallel.o precision.o siesta_geom.o units.o
@@ -218,13 +218,15 @@
 dhscf.o: meshdscf.o meshsubs.o moremeshsubs.o parallel.o parsing.o precision.o
 dhscf.o: rhofft.o rhoofd.o siesta_options.o units.o vmat.o
 diag.o: alloc.o diag_option.o local_sys.o parallel.o precision.o
-diag2g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag2g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag2g.o: precision.o
 diag2k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
-diag3g.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
+diag3g.o: fermid.o intrinsic_missing.o local_sys.o parallel.o parallelsubs.o
+diag3g.o: precision.o
 diag3k.o: fermid.o local_sys.o parallel.o parallelsubs.o precision.o
 diag_option.o: parallel.o precision.o
-diagg.o: alloc.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
-diagg.o: precision.o writewave.o
+diagg.o: alloc.o fermid.o intrinsic_missing.o local_sys.o m_spin.o parallel.o
+diagg.o: parallelsubs.o precision.o writewave.o
 diagk.o: compute_norm.o fermid.o local_sys.o m_spin.o parallel.o parallelsubs.o
 diagk.o: precision.o writewave.o
 diagk_file.o: fermid.o iowfs_netcdf.o local_sys.o parallel.o parallelsubs.o
@@ -266,11 +268,11 @@
 fft1d.o: local_sys.o parallel.o precision.o
 final_H_f_stress.o: alloc.o atomlist.o class_SpData2D.o compute_max_diff.o
 final_H_f_stress.o: dnaefs.o files.o grdsam.o kinefsm.o ldau.o ldau_specs.o
-final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_gamma.o
-final_H_f_stress.o: m_hsx.o m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o
-final_H_f_stress.o: m_stress.o m_ts_io.o m_ts_kpoints.o m_ts_options.o
-final_H_f_stress.o: metaforce.o molecularmechanics.o naefs.o nlefsm.o overfsm.o
-final_H_f_stress.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+final_H_f_stress.o: local_sys.o m_dipol.o m_energies.o m_forces.o m_hsx.o
+final_H_f_stress.o: m_mpi_utils.o m_ncdf_siesta.o m_ntm.o m_spin.o m_stress.o
+final_H_f_stress.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o metaforce.o
+final_H_f_stress.o: molecularmechanics.o naefs.o nlefsm.o overfsm.o parallel.o
+final_H_f_stress.o: siesta_geom.o siesta_options.o sparse_matrices.o
 final_H_f_stress.o: spinorbit.o units.o
 find_kgrid.o: alloc.o minvec.o parallel.o precision.o units.o
 fire_optim.o: alloc.o m_fire.o m_mpi_utils.o parallel.o precision.o
@@ -339,8 +341,8 @@
 ldau_specs.o: parallel.o precision.o pseudopotential.o radial.o units.o
 listsc.o: alloc.o
 local_DOS.o: atomlist.o dhscf.o diagon.o files.o kpoint_grid.o local_sys.o
-local_DOS.o: m_energies.o m_eo.o m_forces.o m_gamma.o m_ntm.o m_spin.o
-local_DOS.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
+local_DOS.o: m_energies.o m_eo.o m_forces.o m_ntm.o m_spin.o parallel.o
+local_DOS.o: siesta_geom.o siesta_options.o sparse_matrices.o
 m_broyddj.o: alloc.o local_sys.o m_mpi_utils.o parallel.o precision.o
 m_broyddj_nocomm.o: alloc.o local_sys.o parallel.o precision.o
 m_broyden_mixing.o: alloc.o m_broyddj.o m_mpi_utils.o parallel.o precision.o
@@ -409,10 +411,10 @@
 m_ncdf_io.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ncdf_io.o: class_Sparsity.o m_io_s.o parallel.o precision.o
 m_ncdf_siesta.o: atm_types.o atmparams.o atomlist.o class_Sparsity.o files.o
-m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_gamma.o m_kinetic.o
-m_ncdf_siesta.o: m_ncdf_io.o m_ntm.o m_spin.o m_stress.o m_ts_electype.o
-m_ncdf_siesta.o: m_ts_kpoints.o m_ts_options.o parallel.o precision.o radial.o
-m_ncdf_siesta.o: siesta_geom.o siesta_options.o sparse_matrices.o timestamp.o
+m_ncdf_siesta.o: kpoint_grid.o m_energies.o m_forces.o m_kinetic.o m_ncdf_io.o
+m_ncdf_siesta.o: m_ntm.o m_spin.o m_stress.o m_ts_electype.o m_ts_kpoints.o
+m_ncdf_siesta.o: m_ts_options.o parallel.o precision.o radial.o siesta_geom.o
+m_ncdf_siesta.o: siesta_options.o sparse_matrices.o timestamp.o
 m_new_dm.o: alloc.o atomlist.o class_Data2D.o class_Fstack_Data1D.o
 m_new_dm.o: class_Fstack_Pair_Geometry_SpData2D.o class_Geometry.o
 m_new_dm.o: class_OrbitalDistribution.o class_Pair_Geometry_SpData2D.o
@@ -516,7 +518,7 @@
 m_ts_electrode.o: parallel.o precision.o units.o
 m_ts_electype.o: class_OrbitalDistribution.o class_SpData1D.o class_SpData2D.o
 m_ts_electype.o: class_Sparsity.o create_Sparsity_SC.o geom_helper.o
-m_ts_electype.o: intrinsic_missing.o m_geom_box.o m_geom_plane.o
+m_ts_electype.o: intrinsic_missing.o m_char.o m_geom_box.o m_geom_plane.o
 m_ts_electype.o: m_handle_sparse.o m_iodm.o m_os.o m_region.o m_ts_chem_pot.o
 m_ts_electype.o: m_ts_io.o m_ts_io_ctype.o m_ts_iodm.o parallel.o precision.o
 m_ts_electype.o: units.o
@@ -709,14 +711,13 @@
 post_scf_work.o: atomlist.o class_Fstack_Pair_Geometry_SpData2D.o
 post_scf_work.o: class_Geometry.o class_Pair_Geometry_SpData2D.o compute_dm.o
 post_scf_work.o: diagon.o final_H_f_stress.o kpoint_grid.o m_dminim.o
-post_scf_work.o: m_energies.o m_eo.o m_gamma.o m_spin.o m_steps.o m_zminim.o
-post_scf_work.o: mneighb.o parallel.o siesta_geom.o siesta_options.o
-post_scf_work.o: sparse_matrices.o
+post_scf_work.o: m_energies.o m_eo.o m_spin.o m_steps.o m_zminim.o mneighb.o
+post_scf_work.o: parallel.o siesta_geom.o siesta_options.o sparse_matrices.o
 print_spin.o: atomlist.o m_mpi_utils.o m_spin.o parallel.o precision.o
 print_spin.o: siesta_cml.o sparse_matrices.o
 printmatrix.o: alloc.o
 projected_DOS.o: alloc.o atomlist.o kpoint_grid.o kpoint_pdos.o local_sys.o
-projected_DOS.o: m_eo.o m_gamma.o m_spin.o parallel.o precision.o siesta_geom.o
+projected_DOS.o: m_eo.o m_spin.o parallel.o precision.o siesta_geom.o
 projected_DOS.o: siesta_options.o sparse_matrices.o units.o
 propor.o: local_sys.o precision.o
 proximity_check.o: chemical.o m_ts_global_vars.o mneighb.o parallel.o
@@ -766,11 +767,10 @@
 setup_H0.o: siesta_geom.o siesta_options.o sparse_matrices.o spinorbit.o
 setup_hamiltonian.o: alloc.o atmfuncs.o atomlist.o class_SpData1D.o
 setup_hamiltonian.o: class_SpData2D.o dhscf.o files.o ldau.o ldau_specs.o
-setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_gamma.o m_hsx.o
-setup_hamiltonian.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_rhog.o
-setup_hamiltonian.o: m_spin.o m_steps.o m_stress.o metaforce.o
-setup_hamiltonian.o: molecularmechanics.o parallel.o siesta_geom.o
-setup_hamiltonian.o: siesta_options.o sparse_matrices.o
+setup_hamiltonian.o: local_sys.o m_dipol.o m_energies.o m_hsx.o m_mpi_utils.o
+setup_hamiltonian.o: m_ntm.o m_partial_charges.o m_rhog.o m_spin.o m_steps.o
+setup_hamiltonian.o: m_stress.o metaforce.o molecularmechanics.o parallel.o
+setup_hamiltonian.o: siesta_geom.o siesta_options.o sparse_matrices.o
 setup_ordern_indexes.o: alloc.o domain_decom.o parallel.o spatial.o
 shaper.o: atmfuncs.o mneighb.o precision.o
 show_distribution.o: atomlist.o local_sys.o parallel.o parallelsubs.o
@@ -783,10 +783,10 @@
 siesta2wannier90.o: siesta_options.o
 siesta_analysis.o: alloc.o atomlist.o bands.o basis_enthalpy.o dhscf.o files.o
 siesta_analysis.o: flook_siesta.o kpoint_grid.o ksv.o ksvinit.o local_DOS.o
-siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_gamma.o
-siesta_analysis.o: m_iodm_old.o m_mpi_utils.o m_ntm.o m_partial_charges.o
-siesta_analysis.o: m_pexsi_dos.o m_pexsi_local_dos.o m_spin.o m_steps.o
-siesta_analysis.o: parallel.o projected_DOS.o siesta2wannier90.o siesta_cml.o
+siesta_analysis.o: m_dipol.o m_energies.o m_eo.o m_forces.o m_iodm_old.o
+siesta_analysis.o: m_mpi_utils.o m_ntm.o m_partial_charges.o m_pexsi_dos.o
+siesta_analysis.o: m_pexsi_local_dos.o m_spin.o m_steps.o parallel.o
+siesta_analysis.o: projected_DOS.o siesta2wannier90.o siesta_cml.o
 siesta_analysis.o: siesta_geom.o siesta_options.o sparse_matrices.o units.o
 siesta_analysis.o: write_subs.o writewave.o zmatrix.o
 siesta_cmlsubs.o: files.o m_uuid.o parallel.o siesta_cml.o timestamp.o
@@ -817,7 +817,7 @@
 siesta_init.o: class_Fstack_Pair_Geometry_SpData2D.o densematrix.o
 siesta_init.o: diag_option.o files.o flook_siesta.o ioxv.o kpoint_grid.o
 siesta_init.o: kpoint_pdos.o ksvinit.o local_sys.o m_check_walltime.o m_cite.o
-siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_gamma.o m_iostruct.o
+siesta_init.o: m_energies.o m_eo.o m_fixed.o m_forces.o m_iostruct.o
 siesta_init.o: m_mpi_utils.o m_new_dm.o m_rmaxh.o m_spin.o m_steps.o
 siesta_init.o: m_supercell.o m_timer.o m_wallclock.o metaforce.o
 siesta_init.o: molecularmechanics.o object_debug.o parallel.o parallelsubs.o
@@ -849,14 +849,14 @@
 state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
 state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
 state_init.o: ioxv.o kpoint_grid.o ldau_specs.o local_sys.o m_energies.o m_eo.o
-state_init.o: m_gamma.o m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o
-state_init.o: m_os.o m_pivot_methods.o m_rmaxh.o m_sparse.o
-state_init.o: m_sparsity_handling.o m_spin.o m_steps.o m_supercell.o
-state_init.o: m_test_io.o m_ts_charge.o m_ts_electype.o m_ts_global_vars.o
-state_init.o: m_ts_io.o m_ts_kpoints.o m_ts_options.o m_ts_sparse.o
-state_init.o: m_ts_tri_init.o normalize_dm.o overlap.o parallel.o
-state_init.o: proximity_check.o siesta_cml.o siesta_dicts.o siesta_geom.o
-state_init.o: siesta_options.o sparse_matrices.o units.o write_subs.o zmatrix.o
+state_init.o: m_mixing.o m_mixing_scf.o m_mpi_utils.o m_new_dm.o m_os.o
+state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
+state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
+state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
+state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
+state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
+state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
+state_init.o: units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'version.info'
--- version.info	2018-06-19 11:00:00 +0000
+++ version.info	2018-06-26 07:59:48 +0000
@@ -1,1 +1,1 @@
-siesta-4.1--933
+siesta-4.1--933--gamma-932