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fix(ArrayReaders): Fix issue reading binary 2d arrays #41

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merged 11 commits into from
Sep 18, 2018
Merged

fix(ArrayReaders): Fix issue reading binary 2d arrays #41

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57732dd
Initial changes to address #36. Still need to test and perform clean up.
jdhughes-usgs Aug 27, 2018
5d6a1c8
Updates to OBS to deallocate internal members with gfortran-8. Clean
jdhughes-usgs Aug 28, 2018
eb92fc0
Cleanup of variable definitions. Still more cleaning required.
jdhughes-usgs Aug 28, 2018
2b473cc
Fixed compile issue with mf5to6...added contiguous to vectors/arrays
jdhughes-usgs Aug 29, 2018
38f24a8
Proposed fix for denormal results occurring with gfortran-8 and
jdhughes-usgs Aug 29, 2018
76ae1b4
Proposed fix for denormal results occurring with gfortran-8 and
jdhughes-usgs Aug 29, 2018
8ec3f2e
Additional cleanup of variable definitions. Modified .travis.yml to
jdhughes-usgs Aug 29, 2018
5045800
docs(ReleaseNotes): Updated release notes
jdhughes-usgs Aug 30, 2018
2d81938
docs: updates and additions
jdhughes-usgs Aug 30, 2018
6cb6077
Merge branch 'develop' of github.com:MODFLOW-USGS/modflow6 into develop
jdhughes-usgs Sep 18, 2018
447b97c
fix(ArrayReaders): Fix issue reading binary 2d arrays
jdhughes-usgs Sep 18, 2018
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Fixed compile issue with mf5to6...added contiguous to vectors/arrays 
allocated using the memory manager. Also fixed issue with SEGFAULT in
mf5to6 that was related to a pointer in ChdPackageWriter that was not
pointed to null (=> null()) in definition.
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@jdhughes-usgs
jdhughes-usgs committed Aug 29, 2018
commit 2b473cc77462e6d120b04c85c10e66b0350cc66e
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -7,7 +7,7 @@

## Automated Testing Status on Travis-CI

### Version 6.0.3 develop — build 7
### Version 6.0.3 develop — build 8
[![Build Status](https://travis-ci.org/MODFLOW-USGS/modflow6.svg?branch=develop)](https://travis-ci.org/MODFLOW-USGS/modflow6)

## Introduction
Expand All @@ -31,7 +31,7 @@ MODFLOW 6 is the latest core version of MODFLOW. It synthesizes many of the capa

#### ***Software/Code citation for MODFLOW 6:***

[Langevin, C.D., Hughes, J.D., Banta, E.R., Provost, A.M., Niswonger, R.G., and Panday, Sorab, 2018, MODFLOW 6 Modular Hydrologic Model version 6.0.3 — develop: U.S. Geological Survey Software Release, 28 August 2018, https://doi.org/10.5066/F76Q1VQV](https://doi.org/10.5066/F76Q1VQV)
[Langevin, C.D., Hughes, J.D., Banta, E.R., Provost, A.M., Niswonger, R.G., and Panday, Sorab, 2018, MODFLOW 6 Modular Hydrologic Model version 6.0.3 — develop: U.S. Geological Survey Software Release, 29 August 2018, https://doi.org/10.5066/F76Q1VQV](https://doi.org/10.5066/F76Q1VQV)


## Instructions for building definition files for new packages
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18 changes: 9 additions & 9 deletions code.json
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@@ -1,26 +1,26 @@
[
{
"status": "Release Candidate",
"languages": [
"Fortran2008"
],
"downloadURL": "https://code.usgs.gov/usgs/modflow/modflow6/archive/master.zip",
"repositoryURL": "https://code.usgs.gov/usgs/modflow/modflow6.git",
"disclaimerURL": "https://code.usgs.gov/usgs/modflow/modflow6/blob/master/DISCLAIMER.md",
"tags": [
"MODFLOW",
"groundwater model"
],
"vcs": "git",
"name": "modflow6",
"downloadURL": "https://code.usgs.gov/usgs/modflow/modflow6/archive/master.zip",
"description": "MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions.",
"contact": {
"name": "Christian D. Langevin",
"email": "[email protected]"
},
"languages": [
"Fortran2008"
],
"vcs": "git",
"laborHours": -1,
"version": "6.0.3.7",
"version": "6.0.3.8",
"date": {
"metadataLastUpdated": "2018-08-28"
"metadataLastUpdated": "2018-08-29"
},
"organization": "U.S. Geological Survey",
"permissions": {
Expand All @@ -33,6 +33,6 @@
"usageType": "openSource"
},
"homepageURL": "https://code.usgs.gov/usgs/modflow/modflow6/",
"description": "MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an international standard for simulating and predicting groundwater conditions and groundwater/surface-water interactions."
"name": "modflow6"
}
]
4 changes: 2 additions & 2 deletions doc/version.tex
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@@ -1,3 +1,3 @@
\newcommand{\modflowversion}{mf6.0.3.7}
\newcommand{\modflowdate}{August 28, 2018}
\newcommand{\modflowversion}{mf6.0.3.8}
\newcommand{\modflowdate}{August 29, 2018}
\newcommand{\currentmodflowversion}{Version \modflowversion---\modflowdate}
2 changes: 1 addition & 1 deletion src/Utilities/version.f90
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Expand Up @@ -3,7 +3,7 @@ module VersionModule
public
! -- modflow 6 version
integer(I4B), parameter :: IDEVELOPMODE = 1
character(len=40), parameter :: VERSION = '6.0.3.7 08/28/2018'
character(len=40), parameter :: VERSION = '6.0.3.8 08/29/2018'
character(len=10), parameter :: MFVNAM = ' 6'
character(len=*), parameter :: MFTITLE = &
'U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL'
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14 changes: 7 additions & 7 deletions utils/mf5to6/src/ChdPackageWriter.f90
100755 → 100644
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Expand Up @@ -41,13 +41,13 @@ module ChdPackageWriterModule
integer :: kpercurrent
integer :: numtimeseries = 0
integer :: maxchds = 0
integer, dimension(:,:,:), pointer :: ibnd
integer, dimension(:,:,:), pointer :: ichdvar
double precision, dimension(:,:,:), pointer :: chdshead
double precision, dimension(:,:,:), pointer :: chdehead
type(ListType), pointer :: IbChdList => null() ! CHDs from IBOUND
type(ListType), pointer :: TvChdList => null() ! Time-variable CHDs from CHD package
type(ListType), pointer :: CnstChdList => null() ! Constant CHDs from CHD package
integer, dimension(:,:,:), pointer :: ibnd => null()
integer, dimension(:,:,:), pointer :: ichdvar => null()
double precision, dimension(:,:,:), pointer :: chdshead => null()
double precision, dimension(:,:,:), pointer :: chdehead => null()
type(ListType), pointer :: IbChdList => null() ! CHDs from IBOUND
type(ListType), pointer :: TvChdList => null() ! Time-variable CHDs from CHD package
type(ListType), pointer :: CnstChdList => null() ! Constant CHDs from CHD package
type(TimeSeriesFileType), pointer :: ChdTsGroup => null()
!type(ChdObsWriterType), pointer :: ChdObsWriter => null()
contains
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2 changes: 1 addition & 1 deletion utils/mf5to6/src/ChdType.f90
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Expand Up @@ -22,7 +22,7 @@ module ChdModule
character(len=MAXCHARLEN) :: tsfilename = ''
character(len=LENTIMESERIESNAME) :: AlternateTsName = ''
character(len=LENTIMESERIESNAME) :: OriginalTsName = ''
type(TimeSeriesType), pointer :: timeSeries
type(TimeSeriesType), pointer :: timeSeries => null()
contains
procedure :: CopyTo
end type ChdType
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14 changes: 7 additions & 7 deletions utils/mf5to6/src/Preproc/Discretization3D.f90
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Expand Up @@ -13,14 +13,14 @@ module DnmDis3dModule
public dis3d_cr, Dis3dType, CastAsDis3dType

type, extends(DisBaseType) :: Dis3dType
integer, pointer :: nlay !number of layers
integer, pointer :: nrow !number of rows
integer, pointer :: ncol !number of columns
integer, dimension(:), pointer :: nodereduced !(size:nodesuser) given user nodenumber provide the reduced nodenumber (size 0 if not reduced)
integer, dimension(:), pointer :: nodeuser !(size:nodes) given a reduced nodenumber, provide the user nodenumber (size 0 if not reduced)
integer, pointer :: nlay => null() !number of layers
integer, pointer :: nrow => null() !number of rows
integer, pointer :: ncol => null() !number of columns
integer, dimension(:), pointer, contiguous :: nodereduced => null() !(size:nodesuser) given user nodenumber provide the reduced nodenumber (size 0 if not reduced)
integer, dimension(:), pointer, contiguous :: nodeuser => null() !(size:nodes) given a reduced nodenumber, provide the user nodenumber (size 0 if not reduced)
! for PreHeadsMF
double precision :: gridXmax = DZERO
double precision :: gridYmin = DZERO
double precision :: gridXmax = DZERO
double precision :: gridYmin = DZERO
double precision, dimension(:), allocatable :: delr
double precision, dimension(:), allocatable :: delc
integer, dimension(:,:,:), allocatable :: idomain
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30 changes: 15 additions & 15 deletions utils/mf5to6/src/Preproc/DiscretizationBasePHMF.f90
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Expand Up @@ -11,21 +11,21 @@ module DnmDisBaseModule
public :: dis_cr

type :: DisBaseType
character(len=LENORIGIN), pointer :: origin => null() !origin name for mem allocation
character(len=LENMODELNAME), pointer :: name_model => null() !name of the model
integer, pointer :: inunit => null() !unit number for input file
integer, pointer :: iout => null() !unit number for output file
integer, pointer :: nodes => null() !number of nodes in solution
integer, pointer :: nodesuser => null() !number of user nodes (same as nodes for unstructured model)
integer, pointer :: ndim => null() !number of spatial model dimensions (1 for unstructured)
integer, pointer, dimension(:) :: mshape => null() !shape of the model; (nodes) for DisBaseType
integer, pointer :: nja => null() !number of connections plus number of nodes
integer, pointer :: njas => null() !(nja-nodes)/2
integer, pointer :: lenuni => null() !length unit
integer, pointer :: idsymrd => null() !indicates how symmetric arrays are read
double precision, dimension(:), pointer :: top => null() !(size:nodes) cell top elevation
double precision, dimension(:), pointer :: bot => null() !(size:nodes) cell bottom elevation
double precision, dimension(:), pointer :: area => null() !(size:nodes) cell area, in plan view
character(len=LENORIGIN), pointer :: origin => null() !origin name for mem allocation
character(len=LENMODELNAME), pointer :: name_model => null() !name of the model
integer, pointer :: inunit => null() !unit number for input file
integer, pointer :: iout => null() !unit number for output file
integer, pointer :: nodes => null() !number of nodes in solution
integer, pointer :: nodesuser => null() !number of user nodes (same as nodes for unstructured model)
integer, pointer :: ndim => null() !number of spatial model dimensions (1 for unstructured)
integer, pointer, dimension(:), contiguous :: mshape => null() !shape of the model; (nodes) for DisBaseType
integer, pointer :: nja => null() !number of connections plus number of nodes
integer, pointer :: njas => null() !(nja-nodes)/2
integer, pointer :: lenuni => null() !length unit
integer, pointer :: idsymrd => null() !indicates how symmetric arrays are read
double precision, dimension(:), pointer, contiguous :: top => null() !(size:nodes) cell top elevation
double precision, dimension(:), pointer, contiguous :: bot => null() !(size:nodes) cell bottom elevation
double precision, dimension(:), pointer, contiguous :: area => null() !(size:nodes) cell area, in plan view
! for PreHeadsMF
! For structured DIS, origin is outside corner of cell at row 1, column 1.
double precision :: Xorigin = DZERO ! X coordinate of grid origin
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116 changes: 64 additions & 52 deletions utils/mf5to6/src/Preproc/Global.f90
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Expand Up @@ -8,62 +8,74 @@ MODULE GLOBAL
double precision, save, pointer :: constantdelc
character(len=MAXCHARLEN), save, pointer :: cbcfilename
! arrays
INTEGER, SAVE, DIMENSION(:), POINTER :: IUNIT(:)
DOUBLE PRECISION, SAVE, DIMENSION(:,:,:), POINTER :: HNEW
INTEGER, SAVE, DIMENSION(:), POINTER :: LBOTM
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYCBD
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYHDT
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYHDS
double precision, SAVE, DIMENSION(:), POINTER :: PERLEN
INTEGER, SAVE, DIMENSION(:), POINTER :: NSTP
double precision, SAVE, DIMENSION(:), POINTER :: TSMULT
INTEGER, SAVE, DIMENSION(:), POINTER :: ISSFLG
double precision, SAVE, DIMENSION(:), POINTER :: DELR
double precision, SAVE, DIMENSION(:), POINTER :: DELC
double precision, SAVE, DIMENSION(:,:,:), POINTER :: BOTM
double precision, SAVE, DIMENSION(:,:,:), POINTER :: HOLD
INTEGER, SAVE, DIMENSION(:,:,:), POINTER :: IBOUND
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CR
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CC
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CV
double precision, SAVE, DIMENSION(:,:,:), POINTER :: HCOF
double precision, SAVE, DIMENSION(:,:,:), POINTER :: RHS
double precision, SAVE, DIMENSION(:,:,:), POINTER :: BUFF
double precision, SAVE, DIMENSION(:,:,:), POINTER :: STRT
double precision, SAVE, DIMENSION(:,:,:), POINTER :: DDREF
INTEGER, SAVE, DIMENSION(:), POINTER :: IUNIT(:) => null()
DOUBLE PRECISION, SAVE, DIMENSION(:,:,:), POINTER :: HNEW => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: LBOTM => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYCBD => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYHDT => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: LAYHDS => null()
double precision, SAVE, DIMENSION(:), POINTER :: PERLEN => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: NSTP => null()
double precision, SAVE, DIMENSION(:), POINTER :: TSMULT => null()
INTEGER, SAVE, DIMENSION(:), POINTER :: ISSFLG => null()
double precision, SAVE, DIMENSION(:), POINTER :: DELR => null()
double precision, SAVE, DIMENSION(:), POINTER :: DELC => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: BOTM => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: HOLD => null()
INTEGER, SAVE, DIMENSION(:,:,:), POINTER :: IBOUND => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CR => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CC => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: CV => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: HCOF => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: RHS => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: BUFF => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: STRT => null()
double precision, SAVE, DIMENSION(:,:,:), POINTER :: DDREF => null()

TYPE GLOBALTYPE
! scalars
INTEGER, POINTER :: NCOL,NROW,NLAY,NPER,NBOTM,NCNFBD
INTEGER, POINTER :: ITMUNI,LENUNI,IXSEC,ITRSS,INBAS
INTEGER, POINTER :: IFREFM,NODES,IOUT,MXITER
double precision, pointer :: constantdelr
double precision, pointer :: constantdelc
character(len=MAXCHARLEN), pointer :: cbcfilename
INTEGER, POINTER :: NCOL => null()
INTEGER, POINTER :: NROW => null()
INTEGER, POINTER :: NLAY => null()
INTEGER, POINTER :: NPER => null()
INTEGER, POINTER :: NBOTM => null()
INTEGER, POINTER :: NCNFBD => null()
INTEGER, POINTER :: ITMUNI => null()
INTEGER, POINTER :: LENUNI => null()
INTEGER, POINTER :: IXSEC => null()
INTEGER, POINTER :: ITRSS => null()
INTEGER, POINTER :: INBAS => null()
INTEGER, POINTER :: IFREFM => null()
INTEGER, POINTER :: NODES => null()
INTEGER, POINTER :: IOUT => null()
INTEGER, POINTER :: MXITER => null()
double precision, pointer :: constantdelr => null()
double precision, pointer :: constantdelc => null()
character(len=MAXCHARLEN), pointer :: cbcfilename => null()
! arrays
INTEGER, DIMENSION(:), POINTER ::IUNIT
DOUBLE PRECISION, DIMENSION(:,:,:), POINTER ::HNEW
INTEGER, DIMENSION(:), POINTER ::LBOTM
INTEGER, DIMENSION(:), POINTER ::LAYCBD
INTEGER, DIMENSION(:), POINTER ::LAYHDT
INTEGER, DIMENSION(:), POINTER ::LAYHDS
double precision, DIMENSION(:), POINTER ::PERLEN
INTEGER, DIMENSION(:), POINTER ::NSTP
double precision, DIMENSION(:), POINTER ::TSMULT
INTEGER, DIMENSION(:), POINTER ::ISSFLG
double precision, DIMENSION(:), POINTER ::DELR
double precision, DIMENSION(:), POINTER ::DELC
double precision, DIMENSION(:,:,:), POINTER ::BOTM
double precision, DIMENSION(:,:,:), POINTER ::HOLD
INTEGER, DIMENSION(:,:,:), POINTER ::IBOUND
double precision, DIMENSION(:,:,:), POINTER ::CR
double precision, DIMENSION(:,:,:), POINTER ::CC
double precision, DIMENSION(:,:,:), POINTER ::CV
double precision, DIMENSION(:,:,:), POINTER ::HCOF
double precision, DIMENSION(:,:,:), POINTER ::RHS
double precision, DIMENSION(:,:,:), POINTER ::BUFF
double precision, DIMENSION(:,:,:), POINTER ::STRT
double precision, DIMENSION(:,:,:), POINTER ::DDREF
INTEGER, DIMENSION(:), POINTER ::IUNIT => null()
DOUBLE PRECISION, DIMENSION(:,:,:), POINTER ::HNEW => null()
INTEGER, DIMENSION(:), POINTER ::LBOTM => null()
INTEGER, DIMENSION(:), POINTER ::LAYCBD => null()
INTEGER, DIMENSION(:), POINTER ::LAYHDT => null()
INTEGER, DIMENSION(:), POINTER ::LAYHDS => null()
double precision, DIMENSION(:), POINTER ::PERLEN => null()
INTEGER, DIMENSION(:), POINTER ::NSTP => null()
double precision, DIMENSION(:), POINTER ::TSMULT => null()
INTEGER, DIMENSION(:), POINTER ::ISSFLG => null()
double precision, DIMENSION(:), POINTER ::DELR => null()
double precision, DIMENSION(:), POINTER ::DELC => null()
double precision, DIMENSION(:,:,:), POINTER ::BOTM => null()
double precision, DIMENSION(:,:,:), POINTER ::HOLD => null()
INTEGER, DIMENSION(:,:,:), POINTER ::IBOUND => null()
double precision, DIMENSION(:,:,:), POINTER ::CR => null()
double precision, DIMENSION(:,:,:), POINTER ::CC => null()
double precision, DIMENSION(:,:,:), POINTER ::CV => null()
double precision, DIMENSION(:,:,:), POINTER ::HCOF => null()
double precision, DIMENSION(:,:,:), POINTER ::RHS => null()
double precision, DIMENSION(:,:,:), POINTER ::BUFF => null()
double precision, DIMENSION(:,:,:), POINTER ::STRT => null()
double precision, DIMENSION(:,:,:), POINTER ::DDREF => null()
END TYPE GLOBALTYPE

TYPE(GLOBALTYPE),SAVE ::GLOBALDAT(10)
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2 changes: 1 addition & 1 deletion utils/mf5to6/src/Preproc/SimVariables.f90
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Expand Up @@ -7,7 +7,7 @@ module SimVariablesModule
private
public :: ModelPacks, SimMovers, iout

type(ListType), pointer :: SimMovers
type(ListType), pointer :: SimMovers => null()
type(ListType) :: ModelPacks

end module SimVariablesModule
6 changes: 3 additions & 3 deletions utils/mf5to6/src/StoWriter.f90
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Expand Up @@ -16,9 +16,9 @@ module StoWriterModule
integer, pointer :: Nlaynew => null()
integer, dimension(:), pointer :: Layptr => null()
integer, pointer, dimension(:) :: Iconvert ! confined (0) or convertible (1), upstream (4)?
double precision, pointer, dimension(:,:,:) :: Ss ! specific storage (or storage coefficient)
double precision, pointer, dimension(:,:,:) :: Sy ! specific yield
logical, pointer, dimension(:) :: Transient
double precision, pointer, dimension(:,:,:) :: Ss => null() ! specific storage (or storage coefficient)
double precision, pointer, dimension(:,:,:) :: Sy => null() ! specific yield
logical, pointer, dimension(:) :: Transient => null()
logical :: Newton
contains
procedure :: AllocateArrays
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2 changes: 1 addition & 1 deletion utils/mf5to6/src/TdisWriter.f90
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Expand Up @@ -13,7 +13,7 @@ module TdisWriterModule
type, extends(FileWriterType) :: TdisWriterType
character(len=10), private :: TimeUnit = 'UNDEFINED'
integer, private :: Nper = -1
type(StressPeriodType), dimension(:), pointer :: StressPeriods
type(StressPeriodType), dimension(:), pointer :: StressPeriods => null()
contains
procedure, public :: InitializeFile => initialize_tdis
procedure, public :: Alloc
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2 changes: 1 addition & 1 deletion utils/mf5to6/src/mf5to6.f90
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Expand Up @@ -31,7 +31,7 @@ program mf5to6
type(ExchangeType), pointer :: exchange => null()
type(SimFileWriterType) :: SimFileWriter
type(SfrPackageWriterType), pointer :: SfrWriter => null()
class(*), pointer :: obj
class(*), pointer :: obj => null()
character(len=MAXCHARLEN) :: fname, namfil, basnam, basnamtemp, msg
logical :: WriteDisFile
! formats
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