refactor(sfr): use read_value_or_time_series_adv() for timeseries #424
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langevin-usgs
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May 8, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * Add option to save density to binary file Add new multi-species variable-density buoyancy test * Minor buy cleanup * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]>
langevin-usgs
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May 14, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) * refactor(uzf): use read_value_or_time_series_adv() for timeseries (#429) * docs(gwf-uzf.dfn): fix typo (#431) * refactor(maw): use read_value_or_time_series_adv() for timeseries (#430) * refactor(Memory): remove unused MemoryTSType (#434) * fix(sfr): fix error in upstream factor check with diversions (#435) Initialize diversion flow (divflow) to zero in the event that they are not defined in the first stress period. * fix(uzf): fix memory leak in UzfCellGroup (#437) close #436 * initialized a few variables to make Travis happy Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]>
langevin-usgs
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May 16, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) * refactor(uzf): use read_value_or_time_series_adv() for timeseries (#429) * docs(gwf-uzf.dfn): fix typo (#431) * refactor(maw): use read_value_or_time_series_adv() for timeseries (#430) * refactor(Memory): remove unused MemoryTSType (#434) * fix(sfr): fix error in upstream factor check with diversions (#435) Initialize diversion flow (divflow) to zero in the event that they are not defined in the first stress period. * fix(uzf): fix memory leak in UzfCellGroup (#437) close #436 * refactor(lak/sfr): changes for future support of density variations (#441) * feat(sfr): Add picard iteration loop in sfr_fc() (#440) Also cleanup sparse and remove as a sfrtype variables. * docs(gwf-drn.dfn): fix typo (#439) * refactor(csub): use read_value_or_time_series_adv() for timeseries (#442) Also error message cleanup. Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]>
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Jun 3, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) * refactor(uzf): use read_value_or_time_series_adv() for timeseries (#429) * docs(gwf-uzf.dfn): fix typo (#431) * refactor(maw): use read_value_or_time_series_adv() for timeseries (#430) * refactor(Memory): remove unused MemoryTSType (#434) * fix(sfr): fix error in upstream factor check with diversions (#435) Initialize diversion flow (divflow) to zero in the event that they are not defined in the first stress period. * fix(uzf): fix memory leak in UzfCellGroup (#437) close #436 * refactor(lak/sfr): changes for future support of density variations (#441) * feat(sfr): Add picard iteration loop in sfr_fc() (#440) Also cleanup sparse and remove as a sfrtype variables. * docs(gwf-drn.dfn): fix typo (#439) * refactor(csub): use read_value_or_time_series_adv() for timeseries (#442) Also error message cleanup. * docs(gwf-drn.dfn): offer clarification to AUXDEPTHNAME definition (#443) * refactor(mvr): implement provider mapping array for mvr budget (#450) * mvr budget now contains lake number instead of outlet number when lake is a provider * added first cut of maw density routine * fix(maw): fixed storage bug in maw * refactor(bmi): clean up modflow 6 code structure to refine bmi implementation (#454) - add do_timestep() to the ami - remove prepareIteration(), moved logic to *_rp() - remove subtiming - removed kpicard from sln_ca and further subroutines (*_ad()) - Additional refactoring and cleaning of the code structure * refactor(MemoryManager): Add specified length sting and string array (#449) Remove TdisModule dependency in table object. Revise memory manager output to use table object. Add table source files to mf5to6 converter `extrafiles.txt`. Use table object to print lake stages. Add logical size to kind (LGP) for future use. * fix(maw): initialize xsto and add test (#456) * fix(NumericalSolution): add counter for time step iteration total (#457) Refactor iteration total for time step and simulation to clarify data stored in these variables. Updated test_gwf_npf03_sfr.py and test_gwf_ts_sfr01.py to output inner and outer iteration convergence information to listing and csv files for evaluation of proper output. Also evaluated results for test_gwf_npf02_rewet.py autotest since it has more than 1 time step. Closes #410 * add maw density test * updated buy maw test * clean up targets.py * refactoring transport to work with latest develop changes * Changes to get transport working again * docs: fix typo in developer guide (#464) * refactor(model_ad): revert the model advance back to numerical model (#462) * allocate auxname to size 0 and then reallocate when auxiliary detected * Further refactoring BMI for upcoming release (#465) * - finished refactoring *_ad back to sln_ca in the shape of a prepareSolve call (c.f. #462) - changed prepare_iteration to prepare_solve, etc. - style change in ami functions, e.g. perform_time_step instead of perform_timestep * - add safety check: multiple solution groups are not supported for use with BMI. Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: Hofer Julian <[email protected]>
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this pull request
Jun 4, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) * refactor(uzf): use read_value_or_time_series_adv() for timeseries (#429) * docs(gwf-uzf.dfn): fix typo (#431) * refactor(maw): use read_value_or_time_series_adv() for timeseries (#430) * refactor(Memory): remove unused MemoryTSType (#434) * fix(sfr): fix error in upstream factor check with diversions (#435) Initialize diversion flow (divflow) to zero in the event that they are not defined in the first stress period. * fix(uzf): fix memory leak in UzfCellGroup (#437) close #436 * refactor(lak/sfr): changes for future support of density variations (#441) * feat(sfr): Add picard iteration loop in sfr_fc() (#440) Also cleanup sparse and remove as a sfrtype variables. * docs(gwf-drn.dfn): fix typo (#439) * refactor(csub): use read_value_or_time_series_adv() for timeseries (#442) Also error message cleanup. * docs(gwf-drn.dfn): offer clarification to AUXDEPTHNAME definition (#443) * refactor(mvr): implement provider mapping array for mvr budget (#450) * mvr budget now contains lake number instead of outlet number when lake is a provider * added first cut of maw density routine * refactor(bmi): clean up modflow 6 code structure to refine bmi implementation (#454) - add do_timestep() to the ami - remove prepareIteration(), moved logic to *_rp() - remove subtiming - removed kpicard from sln_ca and further subroutines (*_ad()) - Additional refactoring and cleaning of the code structure * refactor(MemoryManager): Add specified length sting and string array (#449) Remove TdisModule dependency in table object. Revise memory manager output to use table object. Add table source files to mf5to6 converter `extrafiles.txt`. Use table object to print lake stages. Add logical size to kind (LGP) for future use. * fix(maw): initialize xsto and add test (#456) * fix(NumericalSolution): add counter for time step iteration total (#457) Refactor iteration total for time step and simulation to clarify data stored in these variables. Updated test_gwf_npf03_sfr.py and test_gwf_ts_sfr01.py to output inner and outer iteration convergence information to listing and csv files for evaluation of proper output. Also evaluated results for test_gwf_npf02_rewet.py autotest since it has more than 1 time step. Closes #410 * feat(validate): validate MODFLOW 6 simulation mode. * docs: fix typo in developer guide (#464) * refactor(model_ad): revert the model advance back to numerical model (#462) * allocate auxname to size 0 and then reallocate when auxiliary detected * Further refactoring BMI for upcoming release (#465) * - finished refactoring *_ad back to sln_ca in the shape of a prepareSolve call (c.f. #462) - changed prepare_iteration to prepare_solve, etc. - style change in ami functions, e.g. perform_time_step instead of perform_timestep * - add safety check: multiple solution groups are not supported for use with BMI. * refactor(bmi): refactor grid routines (#460) * refactor(bmi): refactor grid routines Previously we used the 'save' attribute to allocate the memory and persist over the call to the routine. This is not fool proof (multiple calls before using the results will mess things up). After this commit, the caller has to allocate the appropriate memory, similar to get_var_shape. * refactor(bmi): change i6 to i0 * feat(maw): add defined flow correction option (#463) * feat(maw): add defined flow correction option * feat(validate): validate MODFLOW 6 simulation mode. * feat(validate): validate MODFLOW 6 simulation mode. * feat(validate): validate MODFLOW 6 simulation mode. * ci(bmi): update rch02 autotest and add sto01 autotest Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: Hofer Julian <[email protected]>
langevin-usgs
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Jun 17, 2020
* fix(uzf): fix indexing error in UZF (#274) * Error introduced as part of recent UZF refactoring * Closes #273 * fix(memory): some variables not deallocated (#278) Implemented new check in develop mode so code bombs with error if memory manager variable not deallocated * refactor(budobj): new budget object for advanced packages (#279) * single code base for writing binary budget files for advanced packages * single code base for creating and writing budget tables to list file for advanced packages * implemented for MAW, UZF, LAK, SFR, and MVR * closes #277 * update mf6exes from 2.0 to 3.0 * will allow generalized transport calculations for advanced packages * refactor(advanced packages): read static data as part of df() (#281) * refactor(advanced packages): modify advanced packages to read all static data as part of df() * modify setup_budobj to include the connectivity so that it is available to other models * fix(budterm): initialize nlist to zero (#283) * initialize nlist to zero (#284) * fix(lak): initialize chdratin and chdratout to zero (#286) * fix(lak): added sign checks for user specified lak flow terms (#288) * User-specified values for RAINFALL, EVAPORATION, RUNOFF, INFLOW, and WITHDRAWAL must be positive. The program worked if these values were negative, but that doesn't necessarily make sense and is probably an input error. * Updated definition file to reflect these changes * Corrected minor typo in lake definition file * Updated release notes to reflect this change * Close #287 * feat(sfr): add storage term to sfr budget (#293) * Also includes a reach volume term written as an aux variable. This is needed for transport. * initialize str so non-ascii characters don't show up in output files * updated notes for these changes * * fix(csub): Fix CSUB binary budget data saved as IMETH=6 datatype closes #290 * refactor(sfr): Refactor SFR Package to remove use of Geometry objects (#296) * refactor(sfr): Refactor SFR Package to remove use of Geometry objects * doc(pak-ts): update description of package timeseries variables. * ci(yml): update yml to clone shallow copy of flopy and pymake repos * doc(release): Update release notes * Closes #276, and #289 * refactor(xt3d): accumulate flowja instead of set (#306) This change is required for transport, which accumulates terms in flowja * fix(dis): corrected connection vector error in DIS package (#308) Code was incorrectly calculating cell center elevations when nozee was .false. This error would have affected XT3D simulations with unconfined flow and non-zero values specified for ANGLE2 in the NPF Package. It also would affect dispersive transport with XT3D for unconfined conditions. * Update sln-ims-example.dat * refactor(maw): refactor MAW conductance calculation for issue 305 (#310) Add traps to catch 1) skin factors that are <= 0 when using the SKIN conductance equation and 2) and negative saturated conductances values. Closes #305 * feat(tableobj): Add a generic table object for lst file output (#303) Full implementation for SFR package. Partial implementation for LAK, MAW, and UZF packages. * feat(tableobj): update MAW package to use tableobj for data output (#315) Also fix some budget reporting issues in the MAW package * fix(auxmult): auxmult fix when auxmult and bound are in time series (#316) * change order of time series interpolation so aux is done first in case it is an auxmult column * partially addresses #314 * updated release notes * refactor(BoundaryPackage): Add use of TableObject for print_flows option (#317) * feat(lnf): update n-point geometry package data * Revert "feat(lnf): update n-point geometry package data" This reverts commit 3460cfb. * fix(lak): revise the way outlet to-mvr flows are stored in budobj (#321) * fix(lak): revise the way outlet to-mvr flows are stored in budobj * updated release notes * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file (#329) * refactor(lak/maw/sfr): for CONSTANT features write fixed value instead of DHNOFLO to binary file * update release notes * fix(maw): new headtable corrected to have mawwells rows instead of maxbound (#332) * fix(sfr): Remove upstream_fraction check from PACKAGEDATA block (#334) closes #324 * feat(transport): update develop with some general routines needed for transport (#339) * feat(transport): update develop with some general routines needed for transport * fix(mover): correct typo in error message * closes #336 * refactor(disu): correct type in disu error message * closes #635 * fix(csub): Allow interbed observations when no interbeds specified (#338) DNODATA values reported if 1) delay interbed observations are specified and no delay interbeds are specified and 2) interbed observations are specified and the number of interbeds is zero. Added test of all observation types to test_gwf_csub_sk01.py which has no interbeds. closes #298 * ci(travis): update travis.yml to install miniconda instead of apt python (#346) * refactor(mf6): standardize output to STDOUT to use istdout variable * refactor(mf6): standardize output to STDOUT to use istdout variable Modify mf5to6 to use standard SimVariables.f90 in mf6 src and add ListType variables in original mf5to6 SimVariables.f90 file to SimListVariables.f90 and update use statements. * feat(npf): add save saturation option to NPF (#351) * changed some things to public in lak, uzf, sfr * fixed minor bug in uzf * updated release notes and dfn files * modified lak to store hlak and clak in the bound array * refactor(sim_message): Refactor to have independent sim_message (#353) * bug(csub): Write better cellid format to strain csv files (#355) Write integer cellids to csv files instead of string. Add method to discretization classes to return array of user indices. Refactored table output to use table object instead of UWWORD. closes #299 * fix(csub): Add additional inelastic- and elastic-compaction-cell obs. (#356) Closes #302 * fix(csub): Report NODATA for CSUB observ. not calculated in steady-state (#359) CSUB source has been modified to report NODATA values for observations that are not calculated during steady-state stress periods. Observations that are not calculated for steady-state stress periods include SKE, SK, SKE-CELL, SK-CELL, DELAY-HEAD, DELAY-PRECONSTRESS, DELAY-GSTRESS, DELAY-ESTRESS, PRECONSTRESS-CELL. Update mfio to reflect these changes. Also modified CSUB observations so that thick-cell observation is correctly calculated during steady-state stress periods. Closes #300 * Merge refactor-src into develop (#361) * refactor(ListReader): Refactor ListReader to use table object (#362) * fix(npf): remove isavsat hardwire (#364) * refactor(src): remove unused variables (#366) * update mkdist.py to copy additional MSVS solutions and projects * refactor(uzf): refactor uzf to use table object instead of UWWORD (#367) * refactor(uzf): refactor uzf to use table object instead of UWWORD Also simplify table object to write tables of unknown length. * refactor(uzf): refactor uzf to use table object instead of UWWORD Simplify table object to write tables of unknown length. Update observations to use table object when PRINT_INPUT (iprpak=1) is specified to write input observation data. * fix(uzf): flowjaface is not ordered for uzf (#372) * fix(bnd_cf): make another call to bnd_cf routines in gwf bnd_bd (#378) * boundary budgets were being calculated using hcof and rhs values from the previous iteration. This could cause drain flows to be into the aquifer, for example. This fix recalculates the package hcof and rhs values in bd using the final head solution. * update release notes to reflect this change * docs(sfr/lak): couple minor doc changes (#380) * refactor(src): remove unused variables * update mkdist.py to copy additional MSVS solutions and projects * docs(sfr/lak): couple minor doc changes * feature(ims): add additional solver output (#375) Closes #375 * refactor(lak package dfn - perioddata): combined all perioddata into one recarray (#381) * refactor(lak package dfn - perioddata): combined lakeperioddata and outletperioddata into perioddata * refactor(lak stress period data): updated dfn * feature(ims): refactor package convergence check (#382) * Introduce end-of-line normalization (#386) * refactor(xt3d): update develop with minor changes needed for transport (#388) * feature(ims): update inner iteration summary (#389) * refactor(NumericalSolution): refactor csv output (#395) * refactor(NumericalSolution): refactor csv output Refactor csv output to save at the end of the each outer iteration. Add options to save separate outer and inner iteration data. closes #172 * refactor(NumericalSolution): refactor *_cc() methods (#396) Refactor *_cc() methods to pass package integer (ipak) location information and the total number of inner iterations. The ipak variable simplifies construction of the solution outer iteration information for the csv file. The total number of inner iterations makes package convergence csv files consistent with the outer iteration csv file. Update the release notes to reflect recent changes to csv convergence output. Also moved changes for previous versions to release notes appendix (Appendix A). * refactor(Sim): Add MessageModule to containerize message functionality (#399) Add generic message functionality (in Message.f90) to standardize messages (errors, warnings, notes) written at the end of the simulation. Added initial warning messages in mf6. Warning messages and notes are not written if the 'SUMMARY' level command line switch is specified. Refactor IMS package to replace outer_hclose and inner_hclose with outer_dvclose and inner_dvclose. Using outer_hclose and inner_hclose will return warning messages. Added error messages for outer_rclosebnd and csv_output. * docs(gwf-mvr.dfn): clarify mvrtype definition (#408) Closes #393 * refactor(misc): bringing in changes made on transport branch (#409) * implemented table writer for mvr flows * turned on fpp preprocessing in vfproj for compilerversion.fpp * modifed obs table header in tex file * minor changes to budget and budgetobject to support transport * Output in bmi - writing stdout to file or screen is now configurable through bmi (cherry picked from commit ba98a37) * Cleaning up the bmi a bit... (cherry picked from commit 798afe9) * Introduced option to update storage (sc2) for each timestep (cherry picked from commit 93b5cc9) * and also update flag for sc1 now (cherry picked from commit c4ff085) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 (#413) * refactor(misc): add deprecated tag to dfn, refactor budget.f90 * updated mf6ivar readme.md to included deprecated description * fix for maw02 failure resulting from flopy updates * feat(DRN): add option for scaling drainage discharge * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn02) that compares cubic scaled drain discharge to groundwater seepage calculated by the UZF package. * feat(DRN): add option for scaling drainage discharge Add autotest (test_gwf_drn_ddrn01) that compares scaled drain discharge to calculated values. Update release notes with scaled drainage discharge option. * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * feat(sim): add standard subroutine for deprecation warnings Modify get_filename() subroutine to trim filename path based on OS. * BMI work: writing bmi messages through generic utils * sorry, forgot width specifier... * docs(gwf-sfr.dfn): clarify 2nd idv definition (#418) Close #417 * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): update to travis yml - patterned after flopy * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): rework travis.yml * ci(update): cleanup * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(advanced packages): minor changes to support buoyancy package (#422) * refactor(advanced packages): add minor changes to support buoyancy package * add change to boundarypackage.f90 to support the noupdateauxvar variable * fix for latests flopy changes * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() * refactor(lak): refactor timeseries to use read_value_or_time_series() Fixed issue in HashTable when key does not exist and return from function with uninitialized indx. With gfortran indx was initialized by default to a value greater than 0. * refactor(lak): refactor timeseries to use read_value_or_time_series() Cleanup of error messages. * fix(exg-mvr): dis object not associated for binary save flows (#425) * refactoring of the budget object resulted in an unassociated dis object when writing flows for exchange water mover * dis is no longer optional for mvr_cr() * closes #423 * refactor(sfr): use read_value_or_time_series_adv() for timeseries (#424) * refactor(uzf): use read_value_or_time_series_adv() for timeseries (#429) * docs(gwf-uzf.dfn): fix typo (#431) * refactor(maw): use read_value_or_time_series_adv() for timeseries (#430) * refactor(Memory): remove unused MemoryTSType (#434) * fix(sfr): fix error in upstream factor check with diversions (#435) Initialize diversion flow (divflow) to zero in the event that they are not defined in the first stress period. * fix(uzf): fix memory leak in UzfCellGroup (#437) close #436 * refactor(lak/sfr): changes for future support of density variations (#441) * feat(sfr): Add picard iteration loop in sfr_fc() (#440) Also cleanup sparse and remove as a sfrtype variables. * docs(gwf-drn.dfn): fix typo (#439) * refactor(csub): use read_value_or_time_series_adv() for timeseries (#442) Also error message cleanup. * docs(gwf-drn.dfn): offer clarification to AUXDEPTHNAME definition (#443) * refactor(mvr): implement provider mapping array for mvr budget (#450) * mvr budget now contains lake number instead of outlet number when lake is a provider * added first cut of maw density routine * refactor(bmi): clean up modflow 6 code structure to refine bmi implementation (#454) - add do_timestep() to the ami - remove prepareIteration(), moved logic to *_rp() - remove subtiming - removed kpicard from sln_ca and further subroutines (*_ad()) - Additional refactoring and cleaning of the code structure * refactor(MemoryManager): Add specified length sting and string array (#449) Remove TdisModule dependency in table object. Revise memory manager output to use table object. Add table source files to mf5to6 converter `extrafiles.txt`. Use table object to print lake stages. Add logical size to kind (LGP) for future use. * fix(maw): initialize xsto and add test (#456) * fix(NumericalSolution): add counter for time step iteration total (#457) Refactor iteration total for time step and simulation to clarify data stored in these variables. Updated test_gwf_npf03_sfr.py and test_gwf_ts_sfr01.py to output inner and outer iteration convergence information to listing and csv files for evaluation of proper output. Also evaluated results for test_gwf_npf02_rewet.py autotest since it has more than 1 time step. Closes #410 * feat(validate): validate MODFLOW 6 simulation mode. * docs: fix typo in developer guide (#464) * refactor(model_ad): revert the model advance back to numerical model (#462) * allocate auxname to size 0 and then reallocate when auxiliary detected * Further refactoring BMI for upcoming release (#465) * - finished refactoring *_ad back to sln_ca in the shape of a prepareSolve call (c.f. #462) - changed prepare_iteration to prepare_solve, etc. - style change in ami functions, e.g. perform_time_step instead of perform_timestep * - add safety check: multiple solution groups are not supported for use with BMI. * refactor(bmi): refactor grid routines (#460) * refactor(bmi): refactor grid routines Previously we used the 'save' attribute to allocate the memory and persist over the call to the routine. This is not fool proof (multiple calls before using the results will mess things up). After this commit, the caller has to allocate the appropriate memory, similar to get_var_shape. * refactor(bmi): change i6 to i0 * feat(maw): add defined flow correction option (#463) * feat(maw): add defined flow correction option * feat(validate): validate MODFLOW 6 simulation mode. * feat(validate): validate MODFLOW 6 simulation mode. * feat(validate): validate MODFLOW 6 simulation mode. * ci(bmi): update rch02 autotest and add sto01 autotest * fix(NumericalSolution): remove unused advanceSolution method (#470) * ci(bmi): add evt-well autotest and recharge estimation autotest * ci(bmi): add evt-well autotest and recharge estimation autotest * docs(releasenotes): cleanup for 6.1.1 distribution (#472) * docs(releasenotes): cleanup for 6.1.1 distribution * removed print_list_entry from discretizationbase * docs(releasenotes): update to include supplemental technical information document (#473) * refactor(MemoryManager): memory usage units function of allocated size (#474) Add subroutine definitions to all routines and standardize dummy variable names for scalars, integer arrays, and real arrays. Fix simulation script when comparison is mf6. * fix(drn): fix issue with drainage depth option when mover is on (#475) * fix(BndType): fix issue with boundary rates when mvr package in use (#476) Since tomvr flows are lagged by one non-linear iteration it is possible for tomvr to be numerically greater than the calculated boundary discharge. This can result in small positive values in the lst budget when there should not be (for example, with the drn package). Add check for tomvr/rrate ratio > 1. In this case, set rrate to 0 so that the budget error is correctly accounted for the the lst budget. * refactor(distribution): modify distribution scripts to use a definition file for examples (#477) * docs(mf6io): removed mention of point in time obs * docs(converter/zbud): revise history sections * docs(gwf-lak.dfn): removed ambiguous CTABNAME variable reference in tab6_filename definition (#479) * docs(gwf-drn.dfn): offer clarification to AUXDEPTHNAME definition * docs(gwf-lak.dfn): replace undefined CTABNAME variable name from tab6_filename definition fixes 384 * docs(gwf-lak.dfn): latex requires underscores be preceded by backslash * doc(release): address review comments for version 6.1.1 (#480) * fix(MSVS): fix MSVS fortran projects for zbud6 and mf5to6 (#481) * fix(build): fix issue with linux build (#482) * Commit files for 6.1.1 release * ci(develop): reset develop files for next release (#483) Co-authored-by: Hughes, J.D <[email protected]> Co-authored-by: spaulins-usgs <[email protected]> Co-authored-by: Eric Morway <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: mjr-deltares <[email protected]> Co-authored-by: Hofer Julian <[email protected]>
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