modflowpy
feature: Separate input and out files in different directories
Is your feature request related to a problem? Please describe.
Models tend to get big with many input and output files. Therefore, distributing files in directories and sub-directories can be helpful to organize a project. All examples I found so far use a flat directory structure, i.e. all input and output files are in one directory.
This is my attempt to separate input and output files.
This is the directory structure after running mf6:
├── input
│ ├── rivercond.chd
│ ├── rivercond.dis
│ ├── rivercond.dis.grb
│ ├── rivercond.ic
│ ├── rivercond.ims
│ ├── rivercond.nam
│ ├── rivercond.npf
│ ├── rivercond.oc
│ ├── rivercond.riv
│ └── rivercond.tdis
├── mfsim.lst
├── mfsim.nam
└── output
├── rivercond.cbc
└── rivercond.hds
The content of mfsim.nam:
BEGIN options
MEMORY_PRINT_OPTION all
END options
BEGIN timing
TDIS6 input/rivercond.tdis
END timing
BEGIN models
gwf6 input/rivercond.nam rivercond
END models
BEGIN exchanges
END exchanges
BEGIN solutiongroup 1
ims6 input/rivercond.ims rivercond
END solutiongroup 1
rivercond.oc:
BEGIN options
BUDGET FILEOUT output/rivercond.cbc
HEAD FILEOUT output/rivercond.hds
END options
BEGIN period 1
SAVE head all
SAVE budget all
PRINT budget all
END period 1
rivercond.nam:
BEGIN options
PRINT_INPUT
SAVE_FLOWS
END options
BEGIN packages
DIS6 input/rivercond.dis dis
NPF6 input/rivercond.npf npf
IC6 input/rivercond.ic ic
RIV6 input/rivercond.riv river
CHD6 input/rivercond.chd chd_0
OC6 input/rivercond.oc oc
END packages
This works. I guess this could be extend into a deeper structure that would allow to use the same input files for multiple models. For example, these models could share files for the model geometry and use specific files for some boundary conditions that are different for each model (variant).
Looking at the source of flopy, it seems that it always assumes a flat structure (i.e. all files in one directory) for model post processing such as plotting. I this correct?
Describe the solution you'd like
A flexible directory structure, that allows to distribute input and output files to specified directories would help to organize large models and scenario runs that modify only small parts of the input. Maybe this already possible but I don't know how to do it.
Describe alternatives you've considered
See problem description above.
Additional context
Test runs done with MF 6.6.
Further to this idea is to use consistent filenames regardless of model name. For instance, a model with a groundwater-flow simulation could look like this:
Part of mfsim.nam:
BEGIN models
gwf6 input/gwf.nam rivercond
END models
Part of input/gwf.nam:
BEGIN packages
DIS6 input/gwf.dis dis
NPF6 input/gwf.npf npf
IC6 input/gwf.ic ic
RIV6 input/gwf.riv river
CHD6 input/gwf.chd chd_0
OC6 input/gwf.oc oc
END packages
and if there were a groundwater-transport component, the gwt.nam, gwt.dis, etc. files would be in the input directory.
However, there are many exceptions where there is more than one package per model (e.g. two WEL packages wells1.wel and wells2.wel), or nested groundwater-flow models (e.g. parent.nam and child.nam). So this simple approach is sometime too simple to use broadly.
One side observation is that input/rivercond.dis.grb is an output file that can only be suppressed with NOGRB. I'm not sure how to convince mf6 to output it separately.
Thanks for your suggestion. I tend to use the naming pattern gwf_modelname_suffix.*´, gwt_modelname_suffix., gwe_modelname_suffix.´ etc. modelname is also the name of the base directory. Once parameterized with flopy, this should have the same benefits as using the same name stems for all model files across models. I realized that the *.dis.rgb file appears in the input directory. My approach would be a post-run cleanup step, moving to output. But flopy doesn't know this and would not find this file. :(
Just an FYI that it is possible now to organize individual models of a simulation into folders, and do this with flopy. There is an example of this for two flow models and two transport models located here. The example makes use of the flopy model method set_model_relative_path(). The result of that test is to create a folder structure like the following:
In this case, the mfsim.nam file has relative paths to the individual model name files:
# File generated by Flopy version 3.10.0.dev1 on 03/03/2025 at 09:31:21.
BEGIN options
END options
BEGIN timing
TDIS6 test_mf6model_0-adv01a_gwtgwt_0.tdis
END timing
BEGIN models
gwf6 flow1/flow1.nam flow1
gwf6 flow2/flow2.nam flow2
gwt6 transport1/transport1.nam transport1
gwt6 transport2/transport2.nam transport2
END models
BEGIN exchanges
GWF6-GWF6 flow1_flow2.gwfgwf flow1 flow2
GWT6-GWT6 transport1_transport2.gwtgwt transport1 transport2
GWF6-GWT6 flow1_transport1.gwfgwt flow1 transport1
GWF6-GWT6 flow2_transport2.gwfgwt flow2 transport2
END exchanges
BEGIN solutiongroup 1
ims6 flow.ims flow1 flow2
ims6 transport.ims transport1 transport2
END solutiongroup 1
One thing to keep in mind here is that all file names should be specified relative to the directory where mf6 was run. So this results in a model name file that looks like:
# File generated by Flopy version 3.10.0.dev1 on 03/03/2025 at 09:31:21.
BEGIN options
SAVE_FLOWS
END options
BEGIN packages
DIS6 flow1/flow1.dis dis
IC6 flow1/flow1.ic ic
NPF6 flow1/flow1.npf npf
WEL6 flow1/flow1.wel wel-1
OC6 flow1/flow1.oc oc
END packages
I like @mwtoews idea to have a simple and straightforward way to have all files named and organized in an intuitive manner. I also can see benefit to organizing input and output into separate folders as suggested by @pya. File management has been tricky and error prone with flopy in the past. I think there may be some things we could do on the MODFLOW side to help with some of this, perhaps along the line of MODFLOW issue #157.
@christianlangevin Thanks for your comment. I was not aware of set_model_relative_path(). This seems the way to go. Much better than writing your own pre- and post-file-moving tools.