Python Netcdf Ioerror: Netcdf: Netcdf: Invalid Dimension Id Or Name

I am writing a script in python for handling NetCDF files, but I am facing some issues in creating variables, here is the part of the code: stepnumber_var = ofl.createVariable('ste

Solution 1:

This may be a case of a library trying to be "helpful" (see the end of my post for details, but I can't confirm it). To fix this, you should explicitly create dimensions for atom_number and step_number, by using the following before you create the variables (assuming I am understanding nSteps and nAtoms correctly):

ofl.createDimension("step_number", nSteps) ofl.createDimension("atom_number", nAtoms)

If you are new to netCDF, I might suggest looking at either the netcdf4-python package,

http://unidata.github.io/netcdf4-python/

of the netCDF package found in scipy:

http://docs.scipy.org/doc/scipy/reference/io.html

What might be going on: it looks like the issue is that when you create the variable step_number, the library is trying to be helpful by creating a step_number dimension with unlimited length. However, you can only have one unlimited dimension in a netcdf-3 file, so the helpful "trick" does not work.

Solution 2:

atomNumber_var.standard_name = "atom__number"

The atom__number has two "__" instead of one "_". I am not sure if this is your problem, but it may be something to look at.

I would also suggest making your netcdf file steps clearer. I like to break them down into 3 steps. I used an example of scientific data using ocean sst. You also have a section for creating dimensions, but you don't actually do it. This is more correctly create variable section.

1. Create Dimensions

2. Create Variable

3. Fill the variable

   from netCDF4 import Dataset
   ncfile = Dataset('temp.nc','w')
   lonsdim = latdata.shape    #Set dimension lengths
   latsdim = londata.shape   
   ################Create Dimensions###############
   latdim   = ncfile.createDimension('latitude', latsdim)
   londim   = ncfile.createDimension('longitude', lonsdim)
   ################Create Variables#################   The variables contain the dimensions previously set
   latitude  = ncfile.createVariable('latitude','f8',('latitude'))
   longitude = ncfile.createVariable('longitude','f8',('longitude'))
   oceantemp  = ncfile.createVariable('SST','f4' ('latitude','longitude'),fill_value=-99999.0)
   ###############
   Fill Variables
   ################
   latitude[:]    = latdata      #lat data to fill in
   longitude[:]   = londata      #lon data to fill in
   oceantemp[:,:]  = sst[:,:]    #some variable previous calculated

I hope this is helpful.