Potential bug in 4-d variable output for standard memory mode

[anewman89]

When running vic2netcdf, an error occurs when outputting 4-d variables (e.g. soil moisture) using the standard memory mode.

I used the "standard" option and got an error. If I tried to include soil moisture in the configuration file I got the following error when the code tries to write to the netcdf files after it loads all the files in the current chunk:

Traceback (most recent call last):
File "./bin/vic_utils", line 5, in
pkg_resources.run_script('tonic==0.0.0.dev-2bf5167', 'vic_utils')
File "/glade/apps/opt/python/2.7.7/gnu-westmere/4.8.2/lib/python2.7/site-packages/pkg_resources.py", line 534, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/glade/apps/opt/python/2.7.7/gnu-westmere/4.8.2/lib/python2.7/site-packages/pkg_resources.py", line 1441, in run_script
exec(script_code, namespace, namespace)
File "./lib/python2.7/site-packages/tonic-0.0.0.dev_2bf5167-py2.7.egg/EGG-INFO/scripts/vic_utils", line 221, in
File "./lib/python2.7/site-packages/tonic-0.0.0.dev_2bf5167-py2.7.egg/EGG-INFO/scripts/vic_utils", line 197, in main
File "build/bdist.linux-x86_64/egg/tonic/models/vic/vic2netcdf.py", line 546, in _run
File "build/bdist.linux-x86_64/egg/tonic/models/vic/vic2netcdf.py", line 896, in vic2nc
File "build/bdist.linux-x86_64/egg/tonic/models/vic/vic2netcdf.py", line 459, in nc_add_data_standard
File "netCDF4.pyx", line 3267, in netCDF4.Variable.setitem (netCDF4.c:39658)
ValueError: total size of new array must be unchanged

I traced it back to line ~448:

self.f.variables[name][:, i, ys, xs]

is looking for something that is 2-dimensional while

p.df[sn].values[self.slice]

is only 1 dimensional with a length set at the number of time steps going into the current netcdf file. If I removed soil moisture in the configuration file, I got this option to output properly, so it is an issue with 4-d variables.

[anewman89]

@bartnijssen Does this issue give enough description, have proper formatting, etc?