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merge develop into vkd#400

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langevin-usgs merged 202 commits intoMODFLOW-USGS:vkdMODFLOW-USGS/modflow6:vkdfrom langevin-usgs:vkdlangevin-usgs/modflow6:vkdCopy head branch name to clipboardApr 14, 2020

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Commits on Aug 27, 2018

• Initial changes to address MODFLOW-USGS#36. Still need to test and perform clean up.

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Commits on Aug 28, 2018

• Updates to OBS to deallocate internal members with gfortran-8. Clean

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• Cleanup of variable definitions. Still more cleaning required.

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Commits on Aug 29, 2018

• Fixed compile issue with mf5to6...added contiguous to vectors/arrays

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• Proposed fix for denormal results occurring with gfortran-8 and

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• Proposed fix for denormal results occurring with gfortran-8 and

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• Additional cleanup of variable definitions. Modified .travis.yml to

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Commits on Aug 30, 2018

• docs(ReleaseNotes): Updated release notes

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• docs: updates and additions

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Commits on Sep 18, 2018

• Merge branch 'develop' of github.com:MODFLOW-USGS/modflow6 into develop

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• fix(ArrayReaders): Fix issue reading binary 2d arrays

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• Merge pull request MODFLOW-USGS#41 from jdhughes-usgs/develop

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Commits on Sep 20, 2018

• test(test_gwf_binaryinput01): write discretization top to binary file and read binary file with open/close statement

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• docs(gwf-sfr.dfn): corrected typo

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Commits on Sep 25, 2018

• docs(gwf-lak.dfn): fixed error in description of rough

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Commits on Sep 27, 2018

• feat(tdis): error check for invalid time step lengths

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Commits on Oct 1, 2018

• test:(test_gwf_utl) : renamed two of the autotests

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Commits on Oct 3, 2018

• docs(readme): fix directory name

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• Merge pull request MODFLOW-USGS#44 from visr/patch-1

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Commits on Oct 12, 2018

• fix(GwfModule): fix to apply ptc to problems with the STO package

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Commits on Oct 14, 2018

• refactor(pre-commit.py): use OrderdedDict to load and write code.json

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Oct 15, 2018

• refactor(InputOutputModule): refactor dclosetest (MODFLOW-USGS#49)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• refactor(pre-commit.py): use OrderdedDict to load and write code.json (MODFLOW-USGS#50)

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Commits on Oct 16, 2018

• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Oct 30, 2018

• perf(GwfModule): improvements to ptc (MODFLOW-USGS#53)

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• fix(GwfGwfExchangeModule): specific discharge not updated correctly for LGR

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• fix(GwfGwfExchangeModule): specific discharge not updated correctly for LGR

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Commits on Oct 31, 2018

• fix(ObsModule): implemented non-advancing output (MODFLOW-USGS#55)

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• Merge commit 'cfe6e02f35876961c68a88e00f07565002be2317' into develop

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• fix(GwfGwfExchangeModule): correct specific discharge calculation for LGR (MODFLOW-USGS#56)

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Commits on Nov 9, 2018

• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• docs(dfn): fix 3 dfn typos (MODFLOW-USGS#59)

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Commits on Nov 10, 2018

• docs(mf6ivar): readme.md needed a description of the valid keyword

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• docs(mf6ivar): readme.md updated to include valid keyword (MODFLOW-USGS#60)

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Commits on Dec 10, 2018

• Corrected misspelling of execution in the release notes.

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• docs(releasenotes): corrected spelling error in release notes (MODFLOW-USGS#64)

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Commits on Dec 23, 2018

• Merge remote-tracking branch 'upstream/develop' into develop

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Commits on Dec 28, 2018

• fix(docs): maximum_iterations in gwf-sfr.dfn should be of type integer (MODFLOW-USGS#71)

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• fix(inputoutput): columns and width were not be checked properly for the print_format (MODFLOW-USGS#72)

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• Merge remote-tracking branch 'upstream/develop' into develop

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Commits on Jan 7, 2019

• test(test000_setup): download a zip file of modflow executables for testing purposes (MODFLOW-USGS#75)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• docs(hooks): update pre-commit hook (MODFLOW-USGS#76)

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Commits on Jan 8, 2019

• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Jan 31, 2019

• fix(typos): fixed a variety of typos throughout project (MODFLOW-USGS#82)

  

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 7, 2019

• feat(maw): program head limit and rate scaling to work for injection wells

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 11, 2019

• fix(src_cc): Add SFR convergence check (MODFLOW-USGS#85)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• refactor(mover): refactor and clean up water mover for possible BOUNDNAME support (MODFLOW-USGS#86)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 13, 2019

• docs(uzf): clarified dfn descriptions for nuzfcells and ivertcon (MODFLOW-USGS#90)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• docs(dfn): improve description of ANGLDEGX and CDIST (MODFLOW-USGS#91)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 14, 2019

• refactor(autotest): refactor nightly build autotest scripts (MODFLOW-USGS#89)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 15, 2019

• refactor(MemoryManager): add mem_reassignptr functions and clean up (MODFLOW-USGS#92)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• refactor(BndType): Generalized BndType pointer to NPF ICELLTYPE to be model agnostic (MODFLOW-USGS#93)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• docs(dfn): update information on when vertices and cell2d information is required (MODFLOW-USGS#94)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 16, 2019

• refactor(Xt3dAlgorithmModule): reformatted source to look like MF6 source (MODFLOW-USGS#95)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 20, 2019

• fix(gwf3): correct error message to mention DISV6 (MODFLOW-USGS#97)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 21, 2019

• fix(listreader): corrected two typos to the word exist, which was spelled as exit (MODFLOW-USGS#98)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Feb 27, 2019

• docs(releasenotes): minor changes for release (MODFLOW-USGS#99)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• fix(comarg): exe cannot be in file path with a space (MODFLOW-USGS#101)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Mar 1, 2019

• fix(comarg): restored cexe to be executable basename instead of full exe path (MODFLOW-USGS#103)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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Commits on Mar 7, 2019

• fix(disu): fixed error message for disu connectiondata block (MODFLOW-USGS#104)

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• Merge branch 'develop' of https://github.com/MODFLOW-USGS/modflow6 into develop

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• feat(compile): added gfortran compile flags to bomb if source code isn't clean

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• Updated MODFLOW-USG download link

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• removed the character-truncation flag. Not clear how to get this to work for the fpp file.

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• Reverting the size of words in namefile

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• Had to turn off extra code error checking; was getting an error on linux that couldn't be resolved.

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• small latex change

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• feat(compile): added gfortran compile flags to bomb if source code isn't clean (MODFLOW-USGS#105)

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Commits on Mar 13, 2019

• Release 6.0.4.

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• Fixed small bug in numericalsolution.f90. Rereleasing this as version 6.0.4.

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• small change to distribution script

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• feat(release): updated develop with master

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• fix(ci): fix to pre-commit when working on a fork

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Commits on Mar 18, 2019

• fix(update_flopy): there is a new flopy.dfn file that cannot be removed (MODFLOW-USGS#112)

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Commits on Mar 19, 2019

• refactor(tests): to work with recent flopy changes (MODFLOW-USGS#113)

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Commits on Mar 20, 2019

• fix(disvdfn): corrected top shape to (ncpl) (MODFLOW-USGS#115)

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• refactor(test000_setup.py): cleaning up the build process using new pymake functionality (MODFLOW-USGS#117)

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Commits on Mar 30, 2019

• fix(dis/disv): terminate with error if all IDOMAIN values less than or equal to zero (MODFLOW-USGS#124)

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Commits on Apr 1, 2019

• refactor(make-release): refactor updates to version numbers (MODFLOW-USGS#126)

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Commits on Apr 4, 2019

• test(test000_setup): fallback for when os.path.relpath throws (MODFLOW-USGS#45)

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• test(idomain): add zero idomain autotest (MODFLOW-USGS#129)

  

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Commits on Apr 5, 2019

• fix(mover): added better error trapping for mover entries (MODFLOW-USGS#131)

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• test(returncodes): add mf6 return codes and command args autotest (MODFLOW-USGS#132)

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• feat(ims): Add no_ptc_option FIRST and ALL to no_ptc options keyword (MODFLOW-USGS#134)

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Commits on Apr 8, 2019

• docs(gwf.tex): minor fix (MODFLOW-USGS#135)

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• ci(z01/z02): minor change to look for examples with .git extension (MODFLOW-USGS#136)

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• fix(z02): correcting mistake from last commit (MODFLOW-USGS#139)

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Commits on Apr 23, 2019

• ci(slack): add slack notifications

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Commits on May 2, 2019

• fix(auxiliary): corrected advanced package auxiliary variables (MODFLOW-USGS#146)

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Commits on May 7, 2019

• fix(ims): Allow for optional nonlinear and linear block (MODFLOW-USGS#147)

  

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Commits on May 17, 2019

• ci(travis): Add simple test of Newton-Raphson with known solution (MODFLOW-USGS#149)

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Commits on May 21, 2019

• fix(oc): error message causing runtime error (MODFLOW-USGS#152)

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Commits on May 29, 2019

• Update gwf-dis.dfn

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Commits on Jun 10, 2019

• fix(mkdist): error output problem in the make distribution script (MODFLOW-USGS#162)

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Commits on Jun 17, 2019

• docs(disu.dfn): small typo fix

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Commits on Jun 18, 2019

• fix(evt): fixed error in evapotranspiration rate calculation (MODFLOW-USGS#169)

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Commits on Aug 12, 2019

• refact(sync dfns): Disu dfn synced with flopy. (MODFLOW-USGS#188)

  

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Commits on Sep 9, 2019

• refactor(sfr): move SfrDataType members into flat arrays (MODFLOW-USGS#194)

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Commits on Sep 30, 2019

• refactor(gwf): cleaning up call statements and arguments(MODFLOW-USGS#202)

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Commits on Oct 1, 2019

• refactor(griddata): refactor grid data to isolate read and constructor (MODFLOW-USGS#197)

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Commits on Oct 10, 2019

• fix(gwf3lak8): error trap for outlet lakein incorrectly compared against noutlet instead of nlak (MODFLOW-USGS#214)

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• fix(npf): reset lastedge to zero (MODFLOW-USGS#217)

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• fix(ListReaderType): initialize attributes in declaration (MODFLOW-USGS#220)

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• feat(maxerrors): limit the number of errors stored to maxerrors (MODFLOW-USGS#221)

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• test(gwf_errors): new test to make sure mf6 is failing correctly (MODFLOW-USGS#222)

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Commits on Oct 14, 2019

• feat(cmask): add mask for calculation of amat terms (MODFLOW-USGS#215)

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• ci(.travis.yml)

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• ci(.travis.yml): add back conda update conda

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Commits on Oct 16, 2019

• ci(.travis.yml): upgrade to xenial, replace miniconda with apt-get (MODFLOW-USGS#226)

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• feat(disu): ensure cell elevations decrease with depth (MODFLOW-USGS#224)

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• docs(mf6io/ReleaseNotes): updates to describe changes for next release (MODFLOW-USGS#227)

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Commits on Oct 17, 2019

• feat(dis): add get_cellxy procedure to DisBaseType MODFLOW-USGS#204 (MODFLOW-USGS#228)

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• fix(dis): cellxy in DIS (MODFLOW-USGS#239)

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• ci(.travis.yml): use change branch of modflow6-examples (MODFLOW-USGS#242)

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Commits on Nov 6, 2019

• refactor(fortran): turned on gfortran flags for better error checking (MODFLOW-USGS#246)

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• fix(fortran): turn on gfortran 2008 standard check (MODFLOW-USGS#248)

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• test(rch): add test for reported issue MODFLOW-USGS#181 (MODFLOW-USGS#249)

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Commits on Nov 7, 2019

• feat(anistropy): add anisotropy input option for NPF (MODFLOW-USGS#253)

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• fix(getblock): many of the parser%getblock calls did not have supportopenclose=.true. (MODFLOW-USGS#254)

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• fix(mf5to6): fix converter for multiple mnw2 wells (MODFLOW-USGS#256)

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• refactor(dfn): turn off default for maxerrors (MODFLOW-USGS#257)

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• feat(disu idomain): add support for disu idomain (MODFLOW-USGS#261)

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• docs(version): update doc information and version (MODFLOW-USGS#264)

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• feat(csub): Add csub package to develop (MODFLOW-USGS#262)

  

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• refactor(uzf): converting to large vector storage (MODFLOW-USGS#265)

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• docs(release notes): few small changes to get ready for release (MODFLOW-USGS#266)

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• ci(mkdist): getting 6.1 distribution ready (MODFLOW-USGS#267)

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Commits on Dec 12, 2019

• docs(csub): corrected a few typos and updated date (MODFLOW-USGS#270)

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• 6.1.0 release

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• merge master into develop and update version to 6.1.1

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Commits on Dec 17, 2019

• fix(uzf): fix indexing error in UZF (MODFLOW-USGS#274)

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Commits on Dec 31, 2019

• fix(memory): some variables not deallocated (MODFLOW-USGS#278)

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• refactor(budobj): new budget object for advanced packages (MODFLOW-USGS#279)

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Commits on Jan 3, 2020

• refactor(advanced packages): read static data as part of df() (MODFLOW-USGS#281)

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Commits on Jan 6, 2020

• fix(budterm): initialize nlist to zero (MODFLOW-USGS#283)

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• initialize nlist to zero (MODFLOW-USGS#284)

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Commits on Jan 8, 2020

• fix(lak): initialize chdratin and chdratout to zero (MODFLOW-USGS#286)

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Commits on Jan 10, 2020

• fix(lak): added sign checks for user specified lak flow terms (MODFLOW-USGS#288)

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Commits on Jan 27, 2020

• feat(sfr): add storage term to sfr budget (MODFLOW-USGS#293)

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Commits on Jan 29, 2020

• * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype

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Commits on Jan 30, 2020

• refactor(sfr): Refactor SFR Package to remove use of Geometry objects (MODFLOW-USGS#296)

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Commits on Feb 12, 2020

• refactor(xt3d): accumulate flowja instead of set (MODFLOW-USGS#306)

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Commits on Feb 13, 2020

• fix(dis): corrected connection vector error in DIS package (MODFLOW-USGS#308)

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• Update sln-ims-example.dat

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• refactor(maw): refactor MAW conductance calculation for issue 305 (MODFLOW-USGS#310)

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• feat(tableobj): Add a generic table object for lst file output (MODFLOW-USGS#303)

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• feat(tableobj): update MAW package to use tableobj for data output (MODFLOW-USGS#315)

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• fix(auxmult): auxmult fix when auxmult and bound are in time series (MODFLOW-USGS#316)

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• refactor(BoundaryPackage): Add use of TableObject for print_flows option (MODFLOW-USGS#317)

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Commits on Feb 26, 2020

• feat(lnf): update n-point geometry package data

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• Revert "feat(lnf): update n-point geometry package data"

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Commits on Feb 27, 2020

• fix(lak): revise the way outlet to-mvr flows are stored in budobj (MODFLOW-USGS#321)

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• refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (MODFLOW-USGS#329)

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• fix(maw): new headtable corrected to have mawwells rows instead of maxbound (MODFLOW-USGS#332)

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• fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (MODFLOW-USGS#334)

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Commits on Mar 10, 2020

• feat(transport): update develop with some general routines needed for transport (MODFLOW-USGS#339)

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• fix(csub): Allow interbed observations when no interbeds specified (MODFLOW-USGS#338)

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• ci(travis): update travis.yml to install miniconda instead of apt python (MODFLOW-USGS#346)

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Commits on Mar 14, 2020

• refactor(mf6): standardize output to STDOUT to use istdout variable

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• refactor(mf6): standardize output to STDOUT to use istdout variable

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• refactor(mf6): standardize output to STDOUT to use istdout variable (MODFLOW-USGS#348)

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Commits on Mar 18, 2020

• feat(npf): add save saturation option to NPF (MODFLOW-USGS#351)

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• refactor(sim_message): Refactor to have independent sim_message (MODFLOW-USGS#353)

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Commits on Mar 20, 2020

• bug(csub): Write better cellid format to strain csv files (MODFLOW-USGS#355)

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Commits on Mar 21, 2020

• fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (MODFLOW-USGS#356)

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Commits on Mar 24, 2020

• fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (MODFLOW-USGS#359)

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Commits on Mar 25, 2020

• Merge refactor-src into develop (MODFLOW-USGS#361)

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• refactor(ListReader): Refactor ListReader to use table object (MODFLOW-USGS#362)

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Commits on Mar 26, 2020

• fix(npf): remove isavsat hardwire (MODFLOW-USGS#364)

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Commits on Mar 27, 2020

• refactor(src): remove unused variables (MODFLOW-USGS#366)

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• refactor(uzf): refactor uzf to use table object instead of UWWORD (MODFLOW-USGS#367)

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• fix(uzf): flowjaface is not ordered for uzf (MODFLOW-USGS#372)

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Commits on Apr 6, 2020

• fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (MODFLOW-USGS#378)

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Commits on Apr 7, 2020

• docs(sfr/lak): couple minor doc changes (MODFLOW-USGS#380)

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• feature(ims): add additional solver output (MODFLOW-USGS#375)

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• refactor(lak package dfn - perioddata): combined all perioddata into one recarray (MODFLOW-USGS#381)

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Commits on Apr 8, 2020

• feature(ims): refactor package convergence check (MODFLOW-USGS#382)

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• Introduce end-of-line normalization (MODFLOW-USGS#386)

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• refactor(xt3d): update develop with minor changes needed for transport (MODFLOW-USGS#388)

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• feature(ims): update inner iteration summary (MODFLOW-USGS#389)

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Commits on Apr 10, 2020

• refactor(NumericalSolution): refactor csv output (MODFLOW-USGS#395)

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Commits on Apr 11, 2020

• refactor(NumericalSolution): refactor *_cc() methods (MODFLOW-USGS#396)

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• Merge branch 'develop' into vkd

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