Problems reading output from MF2005 model converted to mf6 despite successful intermediate steps. #1800

JJHelly · 2023-05-30T22:18:59Z

JJHelly
May 30, 2023

Aloha.
I am new to modflow and flopy but fairly experience in modeling with quite a few other systems. I suspect I'm stumbling over some well-known conventions that I don't know about yet so pls bear with me. Here's the problem AFAIK.

I've compiled and run mf2005, mf6, and mf6-mpi (including Petsc).
I've converted the Maui_fut model that I downloaded from the NSDI links and run it using mf2005.
I then converted it with mf5to6 and re-ran it using both mf6 and mf6-mpi (the salinity-related dataset, SWI2, was not converted so don't know the effects of that).
I am trying to load it into flopy so I can look at the inputs and outputs.

The latest roadblock is trying to read the sim in this way:

sim = flopy.mf6.MFSimulation.load('Maui_fut_mf6')

= RESTART: /Volumes/Pegasus32R6/Projects-300/Project-Water-Hawaii/Maui-Water-Balance/data/level1/USGS-Sutra-Data-Maui/Maui_fut_mf6/Maui/mf6/reader.py
loading simulation...
loading simulation name file...
WARNING: Block "packages" is not a valid block name for file type nam.
loading tdis package...
Traceback (most recent call last):
File "/Volumes/Pegasus32R6/Projects-300/Project-Water-Hawaii/Maui-Water-Balance/data/level1/USGS-Sutra-Data-Maui/Maui_fut_mf6/Maui/mf6/reader.py", line 24, in
sim = flopy.mf6.MFSimulation.load('Maui_fut_mf6')
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/flopy-3.3.7-py3.11.egg/flopy/mf6/modflow/mfsimulation.py", line 777, in load
for item in models:
TypeError: 'NoneType' object is not iterable

Any suggestions about how to proceed would be quite welcome.

J.

Answered by JJHelly

May 31, 2023

Aloha.

This quandry was solved with the help of Chris Langevin through the flopy Discussion page on github.
The cause was that I did not copy over the mfsim.nam file after running mf5to6. Once that was run, I did:

cp Maui_fut_mf6.* ../mf6/.

which only copied the originally-named model files to ./mf6 where I was then running python3 and, of course, that didn't work.
I was under the mis-apprehension that the Maui_fut_mf6.nam file was the only one needed and I was doing the following:

ln -s ./Maui_fut_mf6.nam mfsim.nam

Not realizing that there can be multiple *.nam files and that mf6 uses mfsim.nam as the top-level simulation file.
I don't know how I would have discovered this otherwise with…

View full answer

langevin-usgs · 2023-05-31T12:37:29Z

langevin-usgs
May 31, 2023
Maintainer

I went through the process myself, and this is how it worked for me. Couple of points:

I ran this on a Mac
I did not run the mf6 model, though that should not matter
You probably need to specify the sim_ws argument to load and give it the path to the folder containing the model
FYI, mf6 does not have the SWI package, so the results from mf6 will be quite a bit different

(base) mycomputer:input.islandwide.modflow langevin$ mf5to6

 Mf5to6 - Converter for MODFLOW (2005, NWT, LGR) to MODFLOW 6
 Version 6.5.0 Release Candidate 12/09/2022
Usage:  MF5to6  mf2005-name-file  mf6-base-name

Or enter name-file and base-name in response to prompts:

 Enter the name of a MODFLOW-2005, MODFLOW-LGR, or MODFLOW-NWT NAME file:                           
Maui_fut.nam
 Enter the base-name for MODFLOW 6 input:                                                           
mf6


 Converting model based on name file: Maui_fut.nam

 Processing BAS package input...
 Processing LPF package input...
 Processing OC package input...
 Processing GHB package input...
 Processing RCH package input...
 Processing WEL package input...
 Processing DRN package input...

 CONVERSION REPORT
 Original name file: Maui_fut.nam
 New name file: mf6.nam
 -------------------------------------
 Data       New       Volume Budget
 Source     Package   Table Text
 --------   -------   ----------------
 LPF        NPF       [no entry]
 GHB        GHB       HEAD DEP BOUNDS
 RCH        RCH       RECHARGE
 WEL        WEL       WELLS 
 DRN        DRN       DRAINS
 -------------------------------------

NOTES:

 1. In PCG package input, damping and/or relaxation is used. You may need to 
   use under relaxation in IMS input.

WARNINGS:

 Conversion of file type SWI2 is not yet supported.


 Program terminated normally, but see warning(s) above.

(base) mycomputer:input.islandwide.modflow langevin$ ls
Maui_fut.bas			Maui_fut.rch			mf6.drn				mf6.tdis
Maui_fut.dis			Maui_fut.swi2			mf6.ghb				mf6.wel
Maui_fut.drn			Maui_fut.wel			mf6.ic				mf6_conversion_messages.txt
Maui_fut.ghb			RUN_MF2005.BAT			mf6.ims				mfsim.nam
Maui_fut.lpf			fut_rch.dat			mf6.nam				usgs.model.reference
Maui_fut.nam			maui_kani.dat			mf6.npf
Maui_fut.oc			maui_kh.dat			mf6.oc
Maui_fut.pcg			mf6.dis				mf6.rch
(base) mycomputer:input.islandwide.modflow langevin$ ls
Maui_fut.bas			Maui_fut.rch			mf6.drn				mf6.tdis
Maui_fut.dis			Maui_fut.swi2			mf6.ghb				mf6.wel
Maui_fut.drn			Maui_fut.wel			mf6.ic				mf6_conversion_messages.txt
Maui_fut.ghb			RUN_MF2005.BAT			mf6.ims				mfsim.nam
Maui_fut.lpf			fut_rch.dat			mf6.nam				usgs.model.reference
Maui_fut.nam			maui_kani.dat			mf6.npf
Maui_fut.oc			maui_kh.dat			mf6.oc
Maui_fut.pcg			mf6.dis				mf6.rch
(base) mycomputer:input.islandwide.modflow langevin$ conda activate modflow6
(modflow6) mycomputer:input.islandwide.modflow langevin$ ipython
Python 3.10.9 | packaged by conda-forge | (main, Feb  2 2023, 20:26:08) [Clang 14.0.6 ]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.11.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import flopy

In [2]: sim = flopy.mf6.MFSimulation.load(sim_ws='.')
loading simulation...
  loading simulation name file...
  loading tdis package...
  loading model gwf6...
    loading package dis...
    loading package ic...
WARNING: Block "options" is not a valid block name for file type ic.
    loading package npf...
    loading package oc...
    loading package ghb...
    loading package rch...
    loading package wel...
    loading package drn...
  loading solution package mf6...

In [3]:

I was also able to run this:

In [3]: sim.gwf[0].plot()
Out[3]: 
[<Axes: title={'center': ' top'}>,
 <Axes: title={'center': 'botm layer 1'}>,
 <Axes: title={'center': 'idomain layer 1'}>,
 <Axes: title={'center': 'strt layer 1'}>,
 <Axes: title={'center': 'icelltype layer 1'}>,
 <Axes: title={'center': 'k layer 1'}>,
 <Axes: title={'center': ' ghb_0 location stress period 1 layer 1'}>,
 <Axes: title={'center': 'RECHARGE stress period 1'}>,
 <Axes: title={'center': ' wel_0 location stress period 1 layer 1'}>,
 <Axes: title={'center': ' drn_0 location stress period 1 layer 1'}>]

In [4]: import matplotlib

In [5]: import matplotlib.pyplot as plt

In [6]: plt.show()

and get this and a few other figures:

1 reply

JJHelly May 31, 2023
Author

Aloha. No joy. Followed your procedure but it doesn't work for me. Also, your process didn't seem to need a 'mfsim.nam' file whereas mine does; as well as modflowsim.tdis. Don't know when you ran this but I wonder why the differences. This doesn't seem to match the documentation for flopy.

Any thoughts?

hellyj@Music-Room mf6 % ls
Maui_fut_mf6.dis Maui_fut_mf6.ims Maui_fut_mf6.rch
Maui_fut_mf6.drn Maui_fut_mf6.nam Maui_fut_mf6.tdis
Maui_fut_mf6.ghb Maui_fut_mf6.npf Maui_fut_mf6.wel
Maui_fut_mf6.ic Maui_fut_mf6.oc Maui_fut_mf6_conversion_messages.txt
hellyj@Music-Room mf6 % ln -s Maui_fut_mf6.nam mfsim.nam
hellyj@Music-Room mf6 % python3
Python 3.11.3 (v3.11.3:f3909b8bc8, Apr 4 2023, 20:12:10) [Clang 13.0.0 (clang-1300.0.29.30)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import flopy
sim = flopy.mf6.MFSimulation.load(sim_ws='.')
loading simulation...
loading simulation name file...
WARNING: Block "packages" is not a valid block name for file type nam.
loading tdis package...
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/flopy-3.3.7-py3.11.egg/flopy/mf6/mfpackage.py", line 2628, in load
fd_input_file = open(
^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/Volumes/Pegasus32R6/Projects-300/Project-Water-Hawaii/Maui-Water-Balance/data/level1/USGS-Sutra-Data-Maui/Maui_fut_mf6/mf6/modflowsim.tdis'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/flopy-3.3.7-py3.11.egg/flopy/mf6/modflow/mfsimulation.py", line 758, in load
instance._tdis_file.load(strict)
File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/flopy-3.3.7-py3.11.egg/flopy/mf6/mfpackage.py", line 2637, in load
raise MFDataException(
flopy.mf6.mfbase.MFDataException: An error occurred in package "None". The error occurred while loading package file in the "load" method.
Additional Information:
(1) File /Volumes/Pegasus32R6/Projects-300/Project-Water-Hawaii/Maui-Water-Balance/data/level1/USGS-Sutra-Data-Maui/Maui_fut_mf6/mf6/modflowsim.tdis of type tdis could not be opened.

mbakker7 · 2023-05-31T13:39:09Z

mbakker7
May 31, 2023
Collaborator

Just a heads up, we are working on a new (and improved) SeaWaterIntrusion (SWI) package for MF6, but this will take probably at least a year to finish. Initial results look great however, so stay tuned.

1 reply

JJHelly May 31, 2023
Author

Good to know.
Mahalo.

JJHelly · 2023-05-31T17:15:54Z

JJHelly
May 31, 2023
Author

That's great. I'll try to reproduce what you did. Mahalo for responding. J. ------------------------------------------------------------------------------------------------------------------------------------------------------------ John Helly / San Diego Supercomputer Center / Scripps Institution of Oceanography https://www.sdsc.edu/~hellyj / 808 205 9882 / 760 8408660 On May 31, 2023, at 02:37, langevin-usgs ***@***.***> wrote: I went through the process myself, and this is how it worked for me. Couple of points: 1. I ran this on a Mac 2. I did not run the mf6 model, though that should not matter 3. You probably need to specify the sim_ws argument to load and give it the path to the folder containing the model 4. FYI, mf6 does not have the SWI package, so the results from mf6 will be quite a bit different (base) mycomputer:input.islandwide.modflow langevin$ mf5to6 Mf5to6 - Converter for MODFLOW (2005, NWT, LGR) to MODFLOW 6 Version 6.5.0 Release Candidate 12/09/2022 Usage: MF5to6 mf2005-name-file mf6-base-name Or enter name-file and base-name in response to prompts: Enter the name of a MODFLOW-2005, MODFLOW-LGR, or MODFLOW-NWT NAME file: Maui_fut.nam Enter the base-name for MODFLOW 6 input: mf6 Converting model based on name file: Maui_fut.nam Processing BAS package input... Processing LPF package input... Processing OC package input... Processing GHB package input... Processing RCH package input... Processing WEL package input... Processing DRN package input... CONVERSION REPORT Original name file: Maui_fut.nam New name file: mf6.nam ------------------------------------- Data New Volume Budget Source Package Table Text -------- ------- ---------------- LPF NPF [no entry] GHB GHB HEAD DEP BOUNDS RCH RCH RECHARGE WEL WEL WELLS DRN DRN DRAINS ------------------------------------- NOTES: 1. In PCG package input, damping and/or relaxation is used. You may need to use under relaxation in IMS input. WARNINGS: Conversion of file type SWI2 is not yet supported. Program terminated normally, but see warning(s) above. (base) mycomputer:input.islandwide.modflow langevin$ ls Maui_fut.bas Maui_fut.rch mf6.drn mf6.tdis Maui_fut.dis Maui_fut.swi2 mf6.ghb mf6.wel Maui_fut.drn Maui_fut.wel mf6.ic mf6_conversion_messages.txt Maui_fut.ghb RUN_MF2005.BAT mf6.ims mfsim.nam Maui_fut.lpf fut_rch.dat mf6.nam usgs.model.reference Maui_fut.nam maui_kani.dat mf6.npf Maui_fut.oc maui_kh.dat mf6.oc Maui_fut.pcg mf6.dis mf6.rch (base) mycomputer:input.islandwide.modflow langevin$ ls Maui_fut.bas Maui_fut.rch mf6.drn mf6.tdis Maui_fut.dis Maui_fut.swi2 mf6.ghb mf6.wel Maui_fut.drn Maui_fut.wel mf6.ic mf6_conversion_messages.txt Maui_fut.ghb RUN_MF2005.BAT mf6.ims mfsim.nam Maui_fut.lpf fut_rch.dat mf6.nam usgs.model.reference Maui_fut.nam maui_kani.dat mf6.npf Maui_fut.oc maui_kh.dat mf6.oc Maui_fut.pcg mf6.dis mf6.rch (base) mycomputer:input.islandwide.modflow langevin$ conda activate modflow6 (modflow6) mycomputer:input.islandwide.modflow langevin$ ipython Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:26:08) [Clang 14.0.6 ] Type 'copyright', 'credits' or 'license' for more information IPython 8.11.0 -- An enhanced Interactive Python. Type '?' for help. In [1]: import flopy In [2]: sim = flopy.mf6.MFSimulation.load(sim_ws='.') loading simulation... loading simulation name file... loading tdis package... loading model gwf6... loading package dis... loading package ic... WARNING: Block "options" is not a valid block name for file type ic. loading package npf... loading package oc... loading package ghb... loading package rch... loading package wel... loading package drn... loading solution package mf6... In [3]: I was also able to run this: In [3]: sim.gwf[0].plot() Out[3]: [<Axes: title={'center': ' top'}>, <Axes: title={'center': 'botm layer 1'}>, <Axes: title={'center': 'idomain layer 1'}>, <Axes: title={'center': 'strt layer 1'}>, <Axes: title={'center': 'icelltype layer 1'}>, <Axes: title={'center': 'k layer 1'}>, <Axes: title={'center': ' ghb_0 location stress period 1 layer 1'}>, <Axes: title={'center': 'RECHARGE stress period 1'}>, <Axes: title={'center': ' wel_0 location stress period 1 layer 1'}>, <Axes: title={'center': ' drn_0 location stress period 1 layer 1'}>] In [4]: import matplotlib In [5]: import matplotlib.pyplot as plt In [6]: plt.show() and get this and a few other figures: [image]<https://urldefense.com/v3/__https://user-images.githubusercontent.com/3372403/242275658-258790ee-db89-4bf4-8b18-f7f9886b6dba.png__;!!Mih3wA!FXTfNqC3sM4ErHT9isgQCV7suoyT0RZy8UlblR-l7bW-5W7SUaNkpRdgHTZ1aANTofPUuCg6i4vofSuIEnilyI7p$> — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/modflowpy/flopy/discussions/1800*discussioncomment-6049532__;Iw!!Mih3wA!FXTfNqC3sM4ErHT9isgQCV7suoyT0RZy8UlblR-l7bW-5W7SUaNkpRdgHTZ1aANTofPUuCg6i4vofSuIEjb_UqOH$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AZ3YXQGJZQLMQ2MXW5YORLLXI43RJANCNFSM6AAAAAAYUT4JQ4__;!!Mih3wA!FXTfNqC3sM4ErHT9isgQCV7suoyT0RZy8UlblR-l7bW-5W7SUaNkpRdgHTZ1aANTofPUuCg6i4vofSuIEmju3bf-$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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JJHelly · 2023-05-31T22:18:49Z

JJHelly
May 31, 2023
Author

Aloha.

This quandry was solved with the help of Chris Langevin through the flopy Discussion page on github.
The cause was that I did not copy over the mfsim.nam file after running mf5to6. Once that was run, I did:

cp Maui_fut_mf6.* ../mf6/.

which only copied the originally-named model files to ./mf6 where I was then running python3 and, of course, that didn't work.
I was under the mis-apprehension that the Maui_fut_mf6.nam file was the only one needed and I was doing the following:

ln -s ./Maui_fut_mf6.nam mfsim.nam

Not realizing that there can be multiple *.nam files and that mf6 uses mfsim.nam as the top-level simulation file.
I don't know how I would have discovered this otherwise without a complete course in Modflow but I will peruse the manual to see if there is something I could have read to understand this part of the architecture.

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Problems reading output from MF2005 model converted to mf6 despite successful intermediate steps. #1800

JJHelly May 30, 2023

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langevin-usgs May 31, 2023 Maintainer

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