ImportError: No module named sids about sisl HOT 9 CLOSED

You must have the sids package in your PYTHONPATH, i.e. if you do:

python setup.py install --prefix=~/SIDS_PATH

you must add this to your .bashrc or equivalent .profile:

export PYTHONPATH=$HOME/SIDS_PATH/lib/python2.7/site-packages:$PYTHONPATH

to enable the sids package.

from sisl.

Hi Nick, many thanks! I will try again! Cheers!

Jin

from sisl.

Hi Nick,

Although running "sgrid -h" displays all possible arguments, I am still a bit confused on how to use these parameters. Would you mind send me an example or a more detailed explanation document? Cheers!

Jin

from sisl.

Hi Jin,

I still need to finish the documentation for the executables.

However, here is a brief show of what you possibly need:

sgrid TotalPotential.grid.nc tp.cube

this will convert the grid in the potential file to a cube called tp.cube.
However, this will not automatically attach a geometry (atomic species and coordinates). To accomplish this, you need to use the -g or --geometry flag.
The argument of that flag may be any kind of siesta format for coordinates, fdf, xyz, XV etc.
Hence you can do:

sgrid -g RUN.fdf TotalPotential.grid.nc tp.cube

and the cube will also contain the corresponding atomic coordinates.

If you want the difference between two files, say TS=0V and TS=0.5V you can do this (assuming you are in the folder containing the grid file for TS=0.5V):

sgrid -g RUN.fdf -d ../TSrun_0/TotalPotential.grid.nc TotalPotential.grid.nc diff.cube

which then contains the difference cube. If you are using this for different spins, say with Rho.grid.nc, you can perform these:

sgrid -g RUN.fdf Rho.grid.nc[0] spin_up.cube
sgrid -g RUN.fdf Rho.grid.nc[1] spin_down.cube

where the square bracket denotes the spin-index in the NetCDF file. :)
I think this should cover the most basic need for now?

from sisl.

Hi Nick,

Many thanks for your kind instruction! I still encounter some difficulties.

When I ran the following command as you suggested,

sgrid -g 1Ben_free_0d00V.fdf TotalPotential.grid.nc ppp.cube
the system show
"
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 241, in
run()
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 168, in run
args.func(args)
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 218, in grid_action
g = sids.Grid.read(f, var, idx)
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/grid.py", line 424, in read
return get_sile(sile).read_grid(args,*kwargs)
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/io/siesta_grid.py", line 42, in read_grid
with self:
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/io/sile.py", line 237, in enter
import netCDF4
ImportError: No module named netCDF4
"
So I tried to load netCDF4.3.0 by using "module load netCDF 4.3.0" or write "export NETCDF_PREFIX=/apps/netcdf/4.3.0" in .bashrc. They don't fix the problem. Would you mind make your suggestions? Cheers!

Jin

from sisl.

You need to install the python package netcdf4-python, check the
requirements on the sids front page :)

Kind regards Nick Papior
On 2 Jan 2016 13:00, "jinxyu" [email protected] wrote:

Hi Nick,

Many thanks for your kind instruction! I still encounter some difficulties.

When I ran the following command as you suggested,

sgrid -g 1Ben_free_0d00V.fdf TotalPotential.grid.nc ppp.cube
the system show
"
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 241, in
run()
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 168, in run
args.func(args)
File "/home/566/jxy566/LOCAL_APPS/Python-2.7.6/bin/sgrid", line 218, in
grid_action
g = sids.Grid.read(f, var, idx)
File
"/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/grid.py",
line 424, in read
return get_sile(sile).read_grid(_args,_kwargs)
File
"/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/io/siesta_grid.py",
line 42, in read_grid
with self:
File
"/home/566/jxy566/LOCAL_APPS/Python-2.7.6/lib/python2.7/site-packages/sids/io/sile.py",
line 237, in *enter
import netCDF4
ImportError: No module named netCDF4
"
So I tried to load netCDF4.3.0 by using "module load netCDF 4.3.0" or
write "export NETCDF_PREFIX=/apps/netcdf/4.3.0" in .bashrc. They don't fix
the problem. Would you mind make your suggestions? Cheers!

Jin

—
Reply to this email directly or view it on GitHub
#2 (comment).

from sisl.

Hi Nick, many thanks!

Jin

from sisl.

I have updated the documentation for a small brief discussion of the sgrid command, if you have any questions or suggestions to the documentation, please let me know :)

http://zerothi.github.io/sids/bizstyle/scripts/sgrid.html

from sisl.

Dear Nick, many thanks!

Jin

On 04-Jan-16 9:28 AM, Nick R. Papior wrote:

I have updated the documentation for a small brief discussion of the
|sgrid| command, if you have any questions or suggestions to the
documentation, please let me know :)

http://zerothi.github.io/sids/bizstyle/scripts/sgrid.html

—
Reply to this email directly or view it on GitHub
#2 (comment).

from sisl.