[SIESTA-L] Fwd: transport in ballistic regime for nano structures

[Zara Nosh]

Dear all,
I have a question about the studying the transport in nanostructures in the
ballistic regimes.

As  screening reduces in nano structures and e-e interaction is more
important than balk materials, how much ignoring the e-e interactions is
acceptable or reasonable?
Would please any one introduce some comparisons between experimental
results and theory results (in ballistic regimes)?

I really appreciate your help in advance.
-Zara

[SIESTA-L] Error in the compilation of tbtrans with netcdf4

[Ankita Joshi]

Hi all users,

While compiling tbtrans with netcdf4, I faced following error. Could somebody 
help in the compilation of tbtrans with netcdf4?

Compilation architecture to be used: unknown
If that is not what you want, give the correct
value to the variable SIESTA_SYS in your shell environment.

==> Incorporating information about present compilation (compiler and flags)
make[1]: Entering directory 
`/home/ANKITA/SOFTWARE/siesta-4.1-b2_transiesta/Util/TS/TBtrans'
gfortran -c -O2 -fPIC -ftree-vectorize -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4 
-DTBTRANS compinfo.F90
make[1]: Leaving directory 
`/home/ANKITA/SOFTWARE/siesta-4.1-b2_transiesta/Util/TS/TBtrans'
gfortran -O2 -fPIC -ftree-vectorize -o tbtrans \
 precision.o sys.o m_io.o alloc.o memoryinfo.o memory.o pxf.o 
moreParallelSubs.o m_mpi_utils.o reclat.o idiag.o minvec.o parallel.o io.o 
files.o cellsubs.o sorting.o kpoint_convert.o timestamp.o m_wallclock.o 
m_spin.o cdiag.o m_diagon_opt.o zheevds.o debugmpi.o find_kgrid.o die.o 
m_walltime.o timer_tree.o m_timer.o timer.o class_OrbitalDistribution.o 
class_Sparsity.o class_Data1D.o class_Data2D.o class_SpData1D.o 
class_SpData2D.o class_TriMat.o m_uuid.o object_debug.o m_char.o cross.o m_os.o 
intrinsic_missing.o geom_helper.o m_io_s.o m_sparse.o m_handle_sparse.o 
m_iodm.o m_integrate.o m_interpolate.o m_mat_invert.o m_iterator.o fdf_extra.o 
create_Sparsity_SC.o create_Sparsity_Union.o m_region.o m_sparsity_handling.o 
m_pivot_array.o m_pivot.o m_pivot_methods.o m_ncdf_io.o m_geom_aux.o 
m_geom_objects.o m_geom_box.o m_geom_coord.o m_geom_square.o m_geom_plane.o 
m_ts_electype.o m_ts_method.o m_ts_chem_pot.o m_ts_electrode.o m_ts_elec_se.o 
m_ts_gf.o m_ts_cctype.o m_ts_sparse_helper.o m_ts_io.o m_ts_iodm.o 
m_ts_io_ctype.o m_ts_debug.o m_ts_io_contour.o m_gauss_quad.o m_ts_contour_eq.o 
m_ts_contour_neq.o m_gauss_fermi_inf.o m_gauss_fermi_30.o m_gauss_fermi_28.o 
m_gauss_fermi_26.o m_gauss_fermi_24.o m_gauss_fermi_22.o m_gauss_fermi_20.o 
m_gauss_fermi_19.o m_gauss_fermi_18.o m_gauss_fermi_17.o m_ts_aux.o 
m_ts_tri_scat.o m_trimat_invert.o m_ts_trimat_invert.o m_ts_tri_common.o 
m_ts_rgn2trimat.o m_ts_sparse.o m_ts_tdir.o m_ts_pivot.o nag.o version.o 
m_verbosity.o tbt_init.o tbt_end.o tbt_reinit.o m_tbt_hs.o m_tbt_regions.o 
m_tbt_options.o m_tbt_tri_init.o m_tbt_contour.o m_tbt_kpoint.o m_tbt_gf.o 
m_tbtrans.o m_tbt_trik.o m_tbt_tri_scat.o m_tbt_proj.o m_tbt_diag.o m_tbt_dH.o 
m_tbt_sigma_save.o m_tbt_save.o m_tbt_kregions.o m_tbt_sparse_helper.o 
tbtrans.o \
 libfdf.a libncdf.a libfdict.a -lnetcdff -lnetcdf -lhdf5_fortran -lhdf5 -lz
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_i0':
nf_ncdf.f90:(.text+0xaf85): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_i0':
nf_ncdf.f90:(.text+0xb1d9): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_z0':
nf_ncdf.f90:(.text+0x107d8): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
nf_ncdf.f90:(.text+0x10a6d): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_z0':
nf_ncdf.f90:(.text+0x10d1e): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
nf_ncdf.f90:(.text+0x10ead): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_c0':
nf_ncdf.f90:(.text+0x16439): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
nf_ncdf.f90:(.text+0x166ce): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_c0':
nf_ncdf.f90:(.text+0x1697e): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
nf_ncdf.f90:(.text+0x16b0d): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_d0':
nf_ncdf.f90:(.text+0x191e5): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_d0':
nf_ncdf.f90:(.text+0x1944d): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_s0':
nf_ncdf.f90:(.text+0x1bb27): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_s0':
nf_ncdf.f90:(.text+0x1bd8d): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_inq_var_h0':
nf_ncdf.f90:(.text+0x1e465): undefined reference to 
`__netcdf_MOD_nf90_inq_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_def_fill_h0':
nf_ncdf.f90:(.text+0x1e6bb): undefined reference to 
`__netcdf_MOD_nf90_def_var_fill_fourbyteint'
libncdf.a(nf_ncdf.o): In function `__nf_ncdf_MOD_ncdf_def_var_logical':

[SIESTA-L] Resume Siesta Calculations

[Ajay_Khanna]

Hello Everyone, I want to know how we can resume siesta calculations if it is
stopped by some physical means like power cut or electricity fluctuations.

I was performing some calculations, and that took around 12 days, but at the
very last moment my ups break down. I want to resume those calculations;
please help in this regards.

Thank you
Ajay Khanna
M.Sc. Chemistry
National Institute of Technology, India

Re: [SIESTA-L] Different initial spin configurations in v3.2 and v4.1

[Nick Papior]

Please see whether this bug-report has corrected your problems.
The bug-report highlights that this is only a matter of printing the
initial spin configuration, not how the actual spin-configuration is "seen"
by siesta.
https://bugs.launchpad.net/siesta/+bug/1648053

2017-03-06 17:27 GMT+01:00 Pouya Partovi-Azar :

> Hello everyone,
>
> I’m doing a spin polarized calculation on a system consisting of hydrogen,
> carbon an nitrogen. I just encountered a strange behavior when comparing
> the outputs of SIESTA v3.2 and v4.1. I have attached the input files used
> for the calculations and the outputs generated by the code.
>
> If I set “DM.InitSpinAF  .false.” I expect to have 18 in "initdm: Initial
> spin polarization (Qup-Qdown)” according to the order in the atomic
> coordinates block (+3+5*(+2)+5*(+1)=18). I get the number 18 in v3.2 output
> file, but not in v4.1, where I get 5!
>
> Now, when I set “DM.InitSpinAF  .false.” I would expect to get 2 in
> "initdm: Initial spin polarization (Qup-Qdown)” (+3-2+2-2+2-2+1-1+1-1+1=2),
> which again I get correctly in v3.2. However, in v4.1 I get 1!
>
> Theses inconsistencies do not affect the final spin polarization of the
> system I have considered in these calculations, but there are, of course,
> systems where different initial spin configurations result in different
> final spins, and consequently different band structures, density of states,
> and transport properties for different spins.
>
> Does anyone know the main reason behind this difference in two SIESTA
> versions? How to solve it? By the way, the corresponding manuals do not
> specify anything about possible differences in two versions.
>
> Thanks in advance,
> Pouya
>
> PS: In the case of v4.1, I sometimes even get fractional numbers as
> initial spin configurations!
>
>
>
>


-- 
Kind regards Nick