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Bugs in mtlkt.py #402

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gdefilippis opened this issue Oct 1, 2018 · 6 comments
Closed

Bugs in mtlkt.py #402

gdefilippis opened this issue Oct 1, 2018 · 6 comments

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@gdefilippis
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gdefilippis commented Oct 1, 2018

  1. Lines 167 - 174 should be replaced by:
self.coldlak = [Util2d(model, (nlkinit,), np.float32, coldlak,
                             name='coldlak', locat=self.unit_number[0],
                             array_free_format=False)]

This is because you would get an error at line 190, saying that the method append cannot be used if self.coldlak is an Util2d object instead of a list.

  1. Line 227 should be replaced by:
for coldlak in self.coldlak:
    f_lkt.write(coldlak.get_file_entry())

This is because in the .lkt file you would get coldlak values for the first species only

  1. Line 446 should be replaced by:
for icomp in range(1, ncomp): 
@langevin-usgs
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Thanks @gdefilippis, we are taking a look.

@emorway-usgs
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emorway-usgs commented Oct 9, 2018 via email

@gdefilippis
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I have a model I used to integrate the LKT package in the QGIS-based FREEWAT interface (www.freewat.eu), which uses flopy for writing codes input files.
The flow model, including 3 lakes, is reasonable, meaning that it runs successfully and it is based on a real-world case study. The transport model has been set with totally unreasonable concentration values, because I used it just to test if the .lkt file was written correctly.
I hope you can benefit from this anyway.

Thank you,
Giovanna
lkt_test.zip

jdhughes-usgs pushed a commit that referenced this issue Oct 12, 2018
…e lakes (#412)

* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test
@emorway-usgs
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@gdefilippis If you pull the latest changes on the develop branch, your problem should be working with the changes made under pull request #412 Thanks for your patience. Let us know if something doesn't look quite right.

langevin-usgs pushed a commit that referenced this issue Oct 15, 2018
* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* Adding new example notebook for MT3D-USGS that uses SFT, LKT, and UZT, including connections between them

* Fixed a typo, added link for docs/notebook_examples.md in a reasonable section of the document

* An errant capital letter in the new notebook, switched to lowercase
jdhughes-usgs pushed a commit that referenced this issue Oct 18, 2018
#414)

* update(ModflowFlwob and ModflowHob): added "no_print", "options", and "filenames" kwargs.

*  refactor(modpath): refactor MODPATH 7 particle classes

Refactor MODPATH 7 particle classes to make a clear distinction between
particle groups and particle data (locations, etc.).

* Changes to LKT for dealing with multi-species simulations that include lakes (#412)

* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* refactor(modpath): refactor particledata (#416)

Refactor ParticleData (input style 1) so that it is the same as the 
node template (input style 3). Refactor NodeParticleTemplates 
particles into a single class. Add starting particle location data 
input style 2.

* New jupyter notebook for MT3D-USGS (#415)

* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* Adding new example notebook for MT3D-USGS that uses SFT, LKT, and UZT, including connections between them

* Fixed a typo, added link for docs/notebook_examples.md in a reasonable section of the document

* An errant capital letter in the new notebook, switched to lowercase

* docs: update documentation (#417)

Update docstrings for MFGridFile class. Update README.md and
CONTRIBUTING.md. Update pre-commit.py to use develop branch for
branches with "-" or ":" in the branch name (it is assumed these
are bug fix or feature branches for the develop branch.

* refactor(lgrutil.py) : redesign of the hidden lgrutil gem

Unfortunately, this breaks backward compatibility (if anyone was using this).  But the new implementation should be a little easier to use.  Still  need to implement ghost nodes.

* Removed old newline character before "NOPRINT".

* docs: update docstrings (#418)

Update docstrings for HeadObservation, ModflowHobs, and ModflowFlwob
classes.

Closed #406

* docs: update docstrings (#419)

Update docstrings for sphinx.

* refactor(Modflow): Forgive loading models with an incomplete BAS6 package (#420)

* raise IOError if external file does not exist

* remove requirement that BAS6 needs to be loaded in full

* update(ModflowFlwob and ModflowHob): add condition test to check for user-specified output file names.

* update(ModflowFlwob and ModflowHob): reworked additional code again after refactorization of upstream branch.

* update(ModflowFlwob and ModflowHob): reordered kwargs in __init__ to reflect order in docstring.

* update(ModflowFlwob and ModflowHob): reworked additional code again after refactorization of upstream branch.

* update(ModflowFlwob and ModflowHob): pass list of filenames to Package.__init__() to achieve desired output file names.

* update(ModflowFlwob and ModflowHob): updated HOB test and added new code to test FLWOBS.

* update(ModflowFlwob and ModflowHob): pass mf executable name to new model upon load.
@jdhughes-usgs
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@emorway-usgs should this issue be closed?

jdhughes-usgs pushed a commit that referenced this issue Oct 30, 2018
* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* Adding new example notebook for MT3D-USGS that uses SFT, LKT, and UZT, including connections between them

* Fixed a typo, added link for docs/notebook_examples.md in a reasonable section of the document

* An errant capital letter in the new notebook, switched to lowercase

* Removing variable MXUZCON from mtuzt.py.  Variable was in pre-release versions of MT3D-USGS, but didn't make the final cut and was never removed from flopy until now.  Fixes and closes issue #423

* Indexes needed adjusting after removing un-used variable from Item 2 in UZT input file.

* Fixing another index issue brought about by the removal of MXUZCON
@gdefilippis
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Dear all,
I am sorry for delay.
I tested this new version and it works fine.
Thank you,
Giovanna

langevin-usgs pushed a commit that referenced this issue Mar 18, 2019
* Explicit cast to np.array isn't preserved

* Fixes issue in LAK package _init_ routines when only a single lake is active

* Previous alteration worked for one lake, but didn't handle one stage for multiple lakes.  This should account for that condition

* Fix mis-statement

* LMT: Lacking support for keyword 'ALL' following Package_Flows keyword

* Add precision for variable thkmin

* PERLEN variable getting trucated by use of "G" (general form) when number of significant digits was > 4.

* Switching printing of PERLEN in BTN from 10.6G to 10G

* Fix for issue #402 including a new test for checking mtlkt.py

* Remove apostrophe from comment (interferes with Travis build)

* Rename test, another recent commit had the same name

* Remove argument from call to test

* Adding new example notebook for MT3D-USGS that uses SFT, LKT, and UZT, including connections between them

* Fixed a typo, added link for docs/notebook_examples.md in a reasonable section of the document

* An errant capital letter in the new notebook, switched to lowercase

* Removing variable MXUZCON from mtuzt.py.  Variable was in pre-release versions of MT3D-USGS, but didn't make the final cut and was never removed from flopy until now.  Fixes and closes issue #423

* Indexes needed adjusting after removing un-used variable from Item 2 in UZT input file.

* Fixing another index issue brought about by the removal of MXUZCON

* test(t012_test.py): Account for UZT -> UZT2 input file changes

With the release of MT3D-USGS 1.0.1, required UZT input was reduced

#466 and #482

* test(t012_test.py): Adapt flopy src to new UZT2 input requirements

These changes required witth the release of MT3D-USGS 1.0.1

#466 and #482

* docs(releasenotes): update releasenotes with UZT2 fix
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