Merge pull request #41 from jdhughes-usgs/develop

fix(ArrayReaders): Fix issue reading binary 2d arrays
MODFLOW-USGS · Sep 18, 2018 · 9bcd7c4 · 9bcd7c4
2 parents 868fb81 + 447b97c
commit 9bcd7c4
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diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 ## Automated Testing Status on Travis-CI
 
-### Version 6.0.3 develop &mdash; build 13
+### Version 6.0.3 develop &mdash; build 18
 [![Build Status](https://travis-ci.org/MODFLOW-USGS/modflow6.svg?branch=develop)](https://travis-ci.org/MODFLOW-USGS/modflow6)
 
 ## Introduction
@@ -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 &mdash; develop: U.S. Geological Survey Software Release, 30 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 &mdash; develop: U.S. Geological Survey Software Release, 17 September 2018, https://doi.org/10.5066/F76Q1VQV](https://doi.org/10.5066/F76Q1VQV)
 
 
 ## Instructions for building definition files for new packages

diff --git a/autotest/test_gwf_binaryinput01.py b/autotest/test_gwf_binaryinput01.py
@@ -74,32 +74,126 @@ def get_model(idx, dir):
  relaxation_factor=relax)
  sim.register_ims_package(ims, [gwf.name])
 
+ # discretization
+ # write botarr to binary file
+ if idx == 0:
+ botarr = []
+ for k in range(nlay):
+ text = 'BOTM_L{}'.format(k+1)
+ fname = 'botm.l{:02d}.bin'.format(k+1)
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
+ header = flopy.utils.BinaryHeader.create(bintype='HEAD',
+ precision='double',
+ text=text,
+ nrow=nrow,
+ ncol=ncol,
+ ilay=k+1, pertim=1.0,
+ totim=1.0, kstp=1,
+ kper=1)
+ flopy.utils.Util2d.write_bin((nrow, ncol), f,
+ np.ones((nrow, ncol),
+ dtype=np.float64) * botm[k],
+ header_data=header)
+ f.close()
+ botarr.append({'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1})
+ elif idx == 1:
+ fname = 'botm.bin'
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
+ tarr = np.ones((nlay, nrow, ncol), dtype=np.float64)
+ for k in range(nlay):
+ tarr[k, :, :] = botm[k]
+ tarr = tarr.flatten()
+ header = flopy.utils.BinaryHeader.create(bintype='HEAD',
+ precision='double',
+ text='BOTM', nrow=1,
+ ncol=ncol*nrow*nlay,
+ ilay=1, pertim=1.0,
+ totim=1.0, kstp=1, kper=1)
+ flopy.utils.Util2d.write_bin((nrow, ncol), f,
+ tarr,
+ header_data=header)
+ f.close()
+ botarr = {'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1}
+
+ # write idomain to binary file
+ if idx == 0:
+ idomain = []
+ for k in range(nlay):
+ text = 'IDOMAIN_L{}'.format(k+1)
+ fname = 'idomain.l{:02d}.bin'.format(k+1)
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
+ header = flopy.utils.BinaryHeader.create(bintype='HEAD',
+ precision='double',
+ text=text,
+ nrow=nrow,
+ ncol=ncol,
+ ilay=k+1, pertim=1.0,
+ totim=1.0, kstp=1,
+ kper=1)
+ flopy.utils.Util2d.write_bin((nrow, ncol), f,
+ np.ones((nrow, ncol),
+ dtype=np.int32),
+ header_data=header)
+ f.close()
+ idomain.append({'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1})
+ elif idx == 1:
+ fname = 'idomain.bin'
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
+ header = flopy.utils.BinaryHeader.create(bintype='HEAD',
+ precision='double',
+ text='IDOMAIN', nrow=1,
+ ncol=ncol*nrow*nlay,
+ ilay=1, pertim=1.0,
+ totim=1.0, kstp=1, kper=1)
+ flopy.utils.Util2d.write_bin((nrow, ncol), f,
+ np.ones((nrow*ncol*nlay),
+ dtype=np.int32),
+ header_data=header)
+ f.close()
+ idomain = {'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1}
+
  dis = flopy.mf6.ModflowGwfdis(gwf, nlay=nlay, nrow=nrow, ncol=ncol,
  delr=delr, delc=delc,
- top=0., botm=botm,
- idomain=1,
+ top=0., botm=botarr,
+ idomain=idomain,
  fname='{}.dis'.format(name))
 
  # initial conditions
  # write initial heads to binary file
- fname = 'ic.strt.bin'
- pth = os.path.join(exdirs[idx], fname)
- f = open(pth, 'wb')
  if idx == 0:
+ strt = []
  for k in range(nlay):
+ text = 'IC_L{}'.format(k+1)
+ fname = 'ic.strt_l{:02d}.bin'.format(k+1)
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
  header = flopy.utils.BinaryHeader.create(bintype='HEAD',
  precision='double',
- text='HEAD',
+ text=text,
  nrow=nrow,
  ncol=ncol,
  ilay=k+1, pertim=1.0,
  totim=1.0, kstp=1,
  kper=1)
  flopy.utils.Util2d.write_bin((nrow, ncol), f,
  np.ones((nrow, ncol),
- dtype=np.float),
+ dtype=np.float64),
  header_data=header)
+ f.close()
+ strt.append({'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1})
  elif idx == 1:
+ fname = 'ic.strt.bin'
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
  header = flopy.utils.BinaryHeader.create(bintype='HEAD',
  precision='double',
  text='HEAD', nrow=1,
@@ -108,21 +202,23 @@ def get_model(idx, dir):
  totim=1.0, kstp=1, kper=1)
  flopy.utils.Util2d.write_bin((nrow, ncol), f,
  np.ones((nrow*ncol*nlay),
- dtype=np.float),
+ dtype=np.float64),
  header_data=header)
- f.close()
- strt = {'factor': 1., 'filename': fname,
- 'data': None, 'binary': True, 'iprn': 1}
+ f.close()
+ strt = {'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1}
+
  ic = flopy.mf6.ModflowGwfic(gwf, strt=strt,
  fname='{}.ic'.format(name))
 
  # node property flow
  # write icelltype to binary file
- fname = 'npf.icelltype.bin'
- pth = os.path.join(exdirs[idx], fname)
- f = open(pth, 'wb')
  if idx == 0:
+ icelltype = []
  for k in range(nlay):
+ fname = 'npf.icelltype.l{}.bin'.format(k+1)
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
  header = flopy.utils.BinaryHeader.create(bintype='head',
  text='ICELLTYPE',
  precision='double',
@@ -136,7 +232,13 @@ def get_model(idx, dir):
  np.ones((nrow, ncol),
  dtype=np.int32),
  header_data=header)
+ f.close()
+ icelltype.append({'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1})
  elif idx == 1:
+ fname = 'npf.icelltype.bin'
+ pth = os.path.join(exdirs[idx], fname)
+ f = open(pth, 'wb')
  header = flopy.utils.BinaryHeader.create(bintype='head',
  text='ICELLTYPE',
  precision='double',
@@ -149,9 +251,11 @@ def get_model(idx, dir):
  np.ones((nrow*ncol*nlay),
  dtype=np.int32),
  header_data=header)
- f.close()
- icelltype = {'factor': 1., 'filename': fname,
- 'data': None, 'binary': True, 'iprn': 1}
+ icelltype = {'factor': 1., 'filename': fname,
+ 'data': None, 'binary': True, 'iprn': 1}
+
+ f.close()
+
  npf = flopy.mf6.ModflowGwfnpf(gwf, save_flows=True,
  icelltype=icelltype,
  k=hk,

diff --git a/code.json b/code.json
@@ -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": "6.0.3.13", 
+ "version": "6.0.3.18", 
  "date": {
- "metadataLastUpdated": "2018-08-30"
+ "metadataLastUpdated": "2018-09-17"
  }, 
  "organization": "U.S. Geological Survey", 
  "permissions": {
@@ -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"
  }
 ]
diff --git a/doc/version.tex b/doc/version.tex
@@ -1,3 +1,3 @@
-\newcommand{\modflowversion}{mf6.0.3.13}
-\newcommand{\modflowdate}{August 30, 2018}
+\newcommand{\modflowversion}{mf6.0.3.18}
+\newcommand{\modflowdate}{September 17, 2018}
 \newcommand{\currentmodflowversion}{Version \modflowversion---\modflowdate}
diff --git a/src/Utilities/ArrayReaders.f90 b/src/Utilities/ArrayReaders.f90
@@ -195,8 +195,8 @@ subroutine read_array_int2d(iu, iarr, aname, ndim, jj, ii, iout, k)
  else
  ! -- Read data as binary
  locat = -locat
+ call read_binary_header(locat, iout, aname, nval)
  do i=1,ii
- call read_binary_header(locat, iout, aname, nval)
  read(locat,iostat=istat,iomsg=ermsgr) (iarr(j,i),j=1,jj)
  if (istat /= 0) then
  arrname = adjustl(aname)
@@ -453,8 +453,8 @@ subroutine read_array_dbl2d(iu, darr, aname, ndim, jj, ii, iout, k)
  else
  ! -- Read data as binary
  locat = -locat
+ call read_binary_header(locat, iout, aname, nval)
  do i = 1, ii
- call read_binary_header(locat, iout, aname, nval)
  read(locat,iostat=istat,iomsg=ermsgr) (darr(j,i), j = 1, jj)
  if (istat /= 0) then
  arrname = adjustl(aname)

diff --git a/src/Utilities/version.f90 b/src/Utilities/version.f90
@@ -3,7 +3,7 @@ module VersionModule
  public
  ! -- modflow 6 version
  integer(I4B), parameter :: IDEVELOPMODE = 1
- character(len=40), parameter :: VERSION = '6.0.3.13 08/30/2018'
+ character(len=40), parameter :: VERSION = '6.0.3.18 09/17/2018'
  character(len=10), parameter :: MFVNAM = ' 6'
  character(len=*), parameter :: MFTITLE = &
  'U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL'

diff --git a/version.txt b/version.txt
@@ -1,12 +1,12 @@
 # MODFLOW 6 version file automatically created using...pre-commit.py
-# created on...August 30, 2018 13:49:52
+# created on...September 17, 2018 20:48:28
 
 # add some comments on how this version file
 # should be manually updated and used
 
 major = 6
 minor = 0
 micro = 3
-build = 13
-commit = 114
+build = 18
+commit = 119