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v 3.3.1 release PR (#926)

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jdhughes-usgs 2020-06-26 12:21:05 -04:00 committed by GitHub
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5
.flake8
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@ -3,7 +3,9 @@ exclude =
.git,
__pycache__,
build,
dist
dist,
examples,
autotest
ignore =
# https://flake8.pycqa.org/en/latest/user/error-codes.html
F401, # 'module' imported but unused
@ -20,6 +22,7 @@ ignore =
E241, # multiple spaces after ','
E402, # module level import not at top of file
E501, # line too long (> 79 characters)
E502, # backslash is redundant between brackets
E722, # do not use bare 'except'
W291, # trailing whitespace
W292, # no newline at end of file

18
.gitattributes vendored Normal file
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@ -0,0 +1,18 @@
###############################################################################
# Set default behavior to automatically normalize line endings.
###############################################################################
* text=auto
###############################################################################
# Set the merge driver for windows files
#
*.bat text eol=crlf
# Denote all files that are truly binary and should not be modified.
*.png binary
*.jpg binary
*.pdf binary
# Do not modify the model data in various directories
examples/data/** binary
examples/groundwater_paper/uspb/** binary

2
.travis.yml
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@ -29,8 +29,6 @@ addons:
sources:
- ubuntu-toolchain-r-test
packages:
- gfortran-8
- g++-8
- libhdf5-serial-dev
- netcdf-bin
- libnetcdf-dev

17
CONTRIBUTING.md
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@ -4,7 +4,6 @@ Contributing
Contributions to FloPy are welcome from the community. As a contributor, here are the guidelines we would like you to follow:
- [Code of Conduct](#coc)
- [Question or Problem?](#question)
- [Issues and Bugs](#issue)
- [Feature Requests](#feature)
- [Submission Guidelines](#submit)
@ -14,18 +13,6 @@ Contributions to FloPy are welcome from the community. As a contributor, here ar
## <a name="coc"></a> Code of Conduct
Help us keep FloPy open and inclusive. Please read and follow our [Code of Conduct][coc].
## <a name="question"></a> Got a Question or Problem?
Do not open issues for general support questions as we want to keep GitHub issues for bug reports and feature requests. You've got much better chances of getting your question answered on [Stack Overflow](https://stackoverflow.com/questions/tagged/flopy) where the questions should be tagged with tag `flopy`.
Stack Overflow is a much better place to ask questions since:
- there are thousands of people willing to help on Stack Overflow
- questions and answers stay available for public viewing so your question / answer might help someone else
- Stack Overflow's voting system assures that the best answers are prominently visible.
To save your and our time, we will systematically close all issues that are requests for general support and redirect people to Stack Overflow.
## <a name="issue"></a> Found a Bug?
If you find a bug in the source code, you can help us by
[submitting an issue](#submit-issue) to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#submit-pr) with a fix.
@ -73,9 +60,9 @@ Before you submit your Pull Request (PR) consider the following guidelines:
```shell
cd autotest
nosetests -v build_exes.py
nosetests -v t*_test.py
nosetests -v
```
Note: the FloPy test suite requires the [nosetests](https://pypi.org/project/nose/) and [pymake](https://github.com/modflowpy/pymake) python packages.
Note: the FloPy test suite requires the [nosetests](https://pypi.org/project/nose/) and [pymake](https://github.com/modflowpy/pymake) python packages. All the FloPy dependencies must also be installed for the tests to pass.
1. Commit your changes using a descriptive commit message that follows our
[commit message conventions](#commit). Adherence to these conventions

174
README.md
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@ -1,11 +1,13 @@
<img src="https://raw.githubusercontent.com/modflowpy/flopy/master/examples/images/flopy3.png" alt="flopy3" style="width:50;height:20">
### Version 3.3.0
### Version 3.3.1
[![Build Status](https://travis-ci.org/modflowpy/flopy.svg?branch=master)](https://travis-ci.org/modflowpy/flopy)
[![PyPI Version](https://img.shields.io/pypi/v/flopy.png)](https://pypi.python.org/pypi/flopy)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/b23a5edd021b4aa19e947545ab49e577)](https://www.codacy.com/manual/jdhughes-usgs/flopy?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=modflowpy/flopy&amp;utm_campaign=Badge_Grade)
[![Coverage Status](https://coveralls.io/repos/github/modflowpy/flopy/badge.svg?branch=master)](https://coveralls.io/github/modflowpy/flopy?branch=master)
[![Codacy Badge](https://api.codacy.com/project/badge/Grade/b23a5edd021b4aa19e947545ab49e577)](https://www.codacy.com/app/jdhughes-usgs/flopy?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=modflowpy/flopy&amp;utm_campaign=Badge_Grade)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/flopy/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
[![Anaconda-Server Badge](https://anaconda.org/conda-forge/flopy/badges/version.svg)](https://anaconda.org/conda-forge/flopy)
[![PyPI Version](https://img.shields.io/pypi/v/flopy.png)](https://pypi.python.org/pypi/flopy)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/modflowpy/flopy.git/master)
Introduction
@ -16,10 +18,21 @@ FloPy includes support for [MODFLOW 6](docs/mf6.md), MODFLOW-2005, MODFLOW-NWT,
For general modeling issues, please consult a modeling forum, such as the [MODFLOW Users Group](https://groups.google.com/forum/#!forum/modflow). Other MODFLOW resources are listed in the [MODFLOW Resources](https://github.com/modflowpy/flopy#modflow-resources) section.
Contributing
------------------------------------------------
Installation
-----------------------------------------------
Bug reports, code contributions, or improvements to the documentation are welcome from the community. Prior to contributing, please read up on our guidelines for [contributing](CONTRIBUTING.md) and then check out one of our issues in the [hotlist: community-help](https://github.com/modflowpy/flopy/labels/hotlist%3A%20community%20help).
FloPy requires **Python** 3.5 (or higher) and **NumPy** 1.9 (or higher). Dependencies for optional FloPy methods are summarized [here](docs/flopy_method_dependencies.md).
To install FloPy type:
conda install -c conda-forge flopy
or
pip install flopy
The release candidate version can also be installed from the git repository using the instructions provided [below](#relcand).
Documentation
@ -32,6 +45,7 @@ Getting Started
-----------------------------------------------
### MODFLOW 6 Quick Start
```python
import os
import flopy
@ -66,157 +80,61 @@ pmv.plot_specific_discharge(spdis, color='white')
```
<img src="examples/images/quickstart.png" alt="plot" style="width:30;height:30">
### [Frequently asked questions](docs/flopyFAQ.md)
### [Tutorials](http://modflowpy.github.io/flopydoc/tutorials.html)
Additional FloPy Resources
------------------------------------------------
### [Additional jupyter Notebook Examples](docs/notebook_examples.md)
- [Tutorials](http://modflowpy.github.io/flopydoc/tutorials.html) demonstrating basic FloPy use.
### [Python Script Examples](docs/script_examples.md)
- [Jupyter notebooks](docs/notebook_examples.md) demonstrating the use of FloPy pre- and post-processing capabilities with a variety of MODFLOW-based models.
- [Scripts](docs/script_examples.md) demonstrating the use of FloPy for running and post-processing MODFLOW-based models.
If You Get Stuck
-----------------------------------------------
- A list of supported packages in FloPy is available in [docs/supported_packages.md](docs/supported_packages.md) on the github repo.
- A table of the supported and proposed model checks implemented in FloPy is available in [docs/model_checks.md](docs/model_checks.md) on the github repo.
- A summary of changes in each FloPy version is available in [docs/version_changes.md](docs/version_changes.md) on the github repo.
Questions
------------------------------------------------
FloPy usage has been growing rapidly, and as the number of users has increased, so has the number of questions about how to use FloPy. We ask our users to carefully consider the nature of their problem and seek help in the appropriate manner.
### Questions
Do not open issues for general support questions as we want to keep GitHub issues for bug reports and feature requests. You've got much better chances of getting your question answered on [Stack Overflow](https://stackoverflow.com/questions/tagged/flopy) where the questions should be tagged with tag `flopy` or the [MODFLOW google group](https://groups.google.com/forum/#!forum/modflow).
For questions related to how to do something with FloPy, we ask our users to submit the question to [Stack Overflow](https://stackoverflow.com) and assign the [flopy](https://stackoverflow.com/questions/tagged/flopy) tag. Many of our recent questions have been related to MODFLOW or Python, and the Flopy developers cannot always respond to these inquiries.
Stack Overflow is a much better place to ask questions since:
### Bugs
- there are thousands of people willing to help on Stack Overflow and the MODFLOW google group
- questions and answers stay available for public viewing so your question / answer might help someone else
- Stack Overflow's voting system assures that the best answers are prominently visible.
If you think you have discovered a bug in FloPy in which you feel that the program does not work as intended, then we ask you to submit a [Github issue](https://github.com/modflowpy/flopy/labels/bug).
To save your and our time, **we will systematically close all issues that are requests for general support and redirect people to Stack Overflow or the MODFLOW google group**.
FloPy Supported Packages
-----------------------------------------------
Contributing
------------------------------------------------
A list of supported packages in FloPy is available in [docs/supported_packages.md](docs/supported_packages.md) on the github repo.
Bug reports, code contributions, or improvements to the documentation are welcome from the community. Prior to contributing, please read up on our guidelines for [contributing](CONTRIBUTING.md) and then check out one of our issues in the [hotlist: community-help](https://github.com/modflowpy/flopy/labels/hotlist%3A%20community%20help).
FloPy Model Checks
-----------------------------------------------
<a name="relcand"></a>Installing the latest FloPy release candidate
------------------------------------------------
A table of the supported and proposed model checks implemented in FloPy is available in [docs/model_checks.md](docs/model_checks.md) on the github repo.
FloPy Changes
-----------------------------------------------
A summary of changes in each FloPy version is available in [docs/version_changes.md](docs/version_changes.md) on the github repo.
Installation
-----------------------------------------------
**Python versions:**
FloPy requires **Python** 3.5 (or higher).
**Dependencies:**
FloPy requires **NumPy** 1.9 (or higher).
**For base and Anaconda Python distributions:**
To install FloPy type:
pip install flopy
or
conda install -c conda-forge flopy
To update FloPy type:
pip install flopy --upgrade
or
conda update -c conda-forge flopy
To uninstall FloPy type:
pip uninstall flopy
or
conda uninstall flopy
**Installing from the git repository:**
***Current Version of FloPy:***
To install the current version of FloPy from the git repository type:
pip install https://github.com/modflowpy/flopy/zipball/master
To update your version of FloPy with the current version from the git repository type:
pip install https://github.com/modflowpy/flopy/zipball/master --upgrade
***Development version of FloPy:***
To install the latest development version of FloPy from the git repository type:
To install the latest release candidate type:
pip install https://github.com/modflowpy/flopy/zipball/develop
To update your version of FloPy with the latest development version from the git repository type:
pip install https://github.com/modflowpy/flopy/zipball/develop --upgrade
***Optional Method Dependencies:***
Additional dependencies to use optional FloPy helper methods are listed below.
| Method | Python Package |
| ------------------------------------------------------------------------------------ | -------------------------------------------------- |
| `.PlotMapView()` in `flopy.plot` | **matplotlib** >= 1.4 |
| `.PlotCrossSection()` in `flopy.plot` | **matplotlib** >= 1.4 |
| `.plot()` | **matplotlib** >= 1.4 |
| `.plot_shapefile()` | **matplotlib** >= 1.4 and **Pyshp** >= 1.2 |
| `.to_shapefile()` | **Pyshp** >= 1.2 |
| `.export(*.shp)` | **Pyshp** >= 1.2 |
| `.export(*.nc)` | **netcdf4** >= 1.1 and **python-dateutil** >= 2.4 |
| `.export(*.tif)` | **rasterio** |
| `.export(*.asc)` in `flopy.utils.reference` `SpatialReference` class | **scipy.ndimage** |
| `.interpolate()` in `flopy.utils.reference` `SpatialReference` class | **scipy.interpolate** |
| `.interpolate()` in `flopy.mf6.utils.reference` `StructuredSpatialReference` class | **scipy.interpolate** |
| `.get_dataframes()` in `flopy.utils.mflistfile` `ListBudget` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.observationfile` `ObsFiles` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.sfroutputfile` `ModflowSfr2` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.util_list` `MfList` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.zonebud` `ZoneBudget` class | **pandas** >= 0.15 |
| `.pivot_keyarray()` in `flopy.mf6.utils.arrayutils` `AdvancedPackageUtil` class | **pandas** >= 0.15 |
| `._get_vertices()` in `flopy.mf6.utils.binaryfile_utils` `MFOutputRequester` class | **pandas** >= 0.15 |
| `.get_dataframe()` in `flopy.mf6.utils.mfobservation` `Observations` class | **pandas** >= 0.15 |
| `.df()` in `flopy.modflow.mfsfr2` `SfrFile` class | **pandas** >= 0.15 |
| `.time_coverage()` in `flopy.export.metadata` `acc` class - ***used if available*** | **pandas** >= 0.15 |
| `.loadtxt()` in `flopy.utils.flopyio` - ***used if available*** | **pandas** >= 0.15 |
| `.generate_classes()` in `flopy.mf6.utils` | [**pymake**](https://github.com/modflowpy/pymake) |
| `.intersect()` in `flopy.discretization.VertexGrid` | **matplotlib** >= 1.4 |
| `GridIntersect()` in `flopy.utils.gridintersect` | **shapely** |
| `GridIntersect().plot_polygon()` in `flopy.utils.gridintersect` | **shapely** and **descartes** |
| `Raster()` in `flopy.utils.Raster` | **rasterio**, **affine**, and **scipy** |
| `Raster().sample_polygon()` in `flopy.utils.Raster` | **shapely** |
| `Raster().crop()` in `flopy.utils.Raster` | **shapely** |
How to Cite
-----------------------------------------------
##### ***Citation for FloPy:***
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
##### ***Software/Code citation for FloPy:***
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0: U.S. Geological Survey Software Release, 14 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2020, FloPy v3.3.1: U.S. Geological Survey Software Release, 26 June 2020, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
MODFLOW Resources

375
autotest/build_exes.py
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@ -1,375 +0,0 @@
# Build the executables that are used in the flopy autotests
import os
import sys
import shutil
try:
import pymake
except:
print('pymake is not installed...will not build executables')
pymake = None
os.environ["TRAVIS"] = "1"
download_version = '3.0'
# path where downloaded executables will be extracted
exe_pth = 'exe_download'
# make the directory if it does not exist
if not os.path.isdir(exe_pth):
os.makedirs(exe_pth)
# determine if running on Travis
is_travis = 'TRAVIS' in os.environ
bindir = '.'
dotlocal = False
if is_travis:
dotlocal = True
if not dotlocal:
for idx, arg in enumerate(sys.argv):
if '--travis' in arg.lower():
dotlocal = True
break
if dotlocal:
bindir = os.path.join(os.path.expanduser('~'), '.local', 'bin')
bindir = os.path.abspath(bindir)
# write where the executables will be downloaded
print('modflow executables will be downloaded to:\n\n "{}"'.format(bindir))
build_from_source = False
if not build_from_source:
for idx, arg in enumerate(sys.argv):
if '--build' in arg.lower():
build_from_source = True
break
# write if the executables will be built from source
msg = 'build all executables from source code: {}\n'.format(build_from_source)
print(msg)
def get_targets():
targets = pymake.usgs_program_data.get_keys(current=True)
targets.sort()
targets.remove('vs2dt')
return targets
def build_target(target):
if pymake is not None:
pymake.build_apps(targets=target)
return
def which(program):
"""
Test to make sure that the program is executable
"""
import os
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
def get_modflow_exes(pth='.', version='', platform=None):
"""
Get the latest MODFLOW binary executables from a github site
(https://github.com/MODFLOW-USGS/executables) for the specified
operating system and put them in the specified path.
Parameters
----------
pth : str
Location to put the executables (default is current working directory)
version : str
Version of the MODFLOW-USGS/executables release to use.
platform : str
Platform that will run the executables. Valid values include mac,
linux, win32 and win64. If platform is None, then routine will
download the latest asset from the github reposity.
"""
# Determine the platform in order to construct the zip file name
if platform is None:
if sys.platform.lower() == 'darwin':
platform = 'mac'
elif sys.platform.lower().startswith('linux'):
platform = 'linux'
elif 'win' in sys.platform.lower():
is_64bits = sys.maxsize > 2 ** 32
if is_64bits:
platform = 'win64'
else:
platform = 'win32'
else:
errmsg = ('Could not determine platform'
'. sys.platform is {}'.format(sys.platform))
raise Exception(errmsg)
else:
assert platform in ['mac', 'linux', 'win32', 'win64']
zipname = '{}.zip'.format(platform)
# Determine path for file download and then download and unzip
url = ('https://github.com/MODFLOW-USGS/executables/'
'releases/download/{}/'.format(version))
assets = {p: url + p for p in ['mac.zip', 'linux.zip',
'win32.zip', 'win64.zip']}
download_url = assets[zipname]
pymake.download_and_unzip(download_url, pth)
return
def get_exes_list():
temp = os.listdir(exe_pth)
avail_targets = pymake.usgs_program_data.get_keys(current=True)
targets = []
for target in avail_targets:
for tt in temp:
if target in tt:
targets.append(tt)
# write summary of available download executables
msg = 'executables that are available from the download:\n'
for idx, target in enumerate(targets):
msg += ' {:>2d}: {}\n'.format(idx + 1, target)
print('{}\n'.format(msg))
return targets
def is_executable(f):
# write message
msg = 'testing if {} is executable.'.format(f)
print(msg)
fname = os.path.join(exe_pth, f)
errmsg = '{} not executable'.format(fname)
assert which(fname) is not None, errmsg
return
def get_code_json():
jpth = 'code.json'
json_dict = None
if jpth in os.listdir(exe_pth):
fpth = os.path.join(exe_pth, jpth)
json_dict = pymake.usgs_program_data.load_json(fpth)
return json_dict
def evaluate_versions(target, src):
# get code.json dictionary
json_dict = get_code_json()
# get current modflow program dictionary
prog_dict = pymake.usgs_program_data.get_program_dict()
if json_dict is not None:
# extract the json keys
json_keys = list(json_dict.keys())
# evaluate if the target is in the json keys
if target in json_keys:
source_version = prog_dict[target].version
git_version = json_dict[target].version
# write a message
msg = 'Source code version of {} '.format(target) + \
'is "{}"'.format(source_version)
print(4 * ' ' + msg)
msg = 'Download code version of {} '.format(target) + \
'is "{}"\n'.format(git_version)
print(4 * ' ' + msg)
prog_version = source_version.split('.')
json_version = git_version.split('.')
# evaluate major, minor, etc. version numbers
for sp, sj in zip(prog_version, json_version):
if int(sp) > int(sj):
src = None
break
return src
def copy_target(target, src):
srcpth = os.path.join(exe_pth, src)
dstpth = os.path.join(bindir, src)
# write message showing copy src and dst
msg = 'copying {} -> {}'.format(srcpth, dstpth)
print(msg)
# copy the target
shutil.copy(srcpth, dstpth)
# determine if json file in directory with downloaded files
json_file = None
for f in os.listdir(exe_pth):
if f.lower().endswith('.json'):
json_file = f
break
# update code.json with data from from the json file in exe_pth
if json_file is not None:
fpth = os.path.join(bindir, json_file)
# set default program dictionary
usgs_dict = pymake.usgs_program_data.get_program_dict()
target_dict = {target: usgs_dict[target]}
# process the json
download_dict = pymake.usgs_program_data.load_json(fpth)
if download_dict is not None:
if target in list(download_dict.keys()):
target_dict = {target: download_dict[target]}
# update the json
pymake.usgs_program_data.update_json(fpth=fpth,
temp_dict=target_dict)
return
def list_json():
# build list_json command
fpth = os.path.join(bindir, 'code.json')
ljson = 'pymake.usgs_program_data.list_json(fpth="{}")'.format(fpth)
# build full command
cmd = "python -c 'from __future__ import print_function; " + \
"import pymake; {}'".format(ljson)
# run command
os.system(cmd)
return
def cleanup():
if os.path.isdir(exe_pth):
shutil.rmtree(exe_pth)
return
def main():
get_modflow_exes(exe_pth, download_version)
etargets = get_exes_list()
for f in etargets:
is_executable(f)
# build each target
targets = get_targets()
for etarget in etargets:
src = None
for target in targets:
if target in etarget:
src = etarget
break
# evaluate if the usgs source files and newer versions than
# downloaded executables...if so build the target from source code
if src is not None:
src = evaluate_versions(target, src)
# reset source if code should be rebuilt from source
if build_from_source:
src = None
# copy the downloaded executable
if src is not None:
copy_target(target, src)
# build the target from source code
else:
msg = 'building {}'.format(target)
print(msg)
build_target(target)
# # build all targets (until github gfortran-8 exes are available)
# build_target(target)
# list the created json file
list_json()
# clean up the download directory
cleanup()
def test_download_and_unzip():
yield get_modflow_exes, exe_pth, download_version
etargets = get_exes_list()
for f in etargets:
yield is_executable, f
return
def test_build_all_apps():
# get list of downloaded targets
etargets = get_exes_list()
# build each target
targets = get_targets()
for etarget in etargets:
src = None
for target in targets:
if target in etarget:
src = etarget
break
# evaluate if the usgs source files and newer versions than
# downloaded executables...if so build the target from source code
if src is not None:
src = evaluate_versions(target, src)
# reset source if code should be rebuilt from source
if build_from_source:
src = None
# copy the downloaded executable
if src is not None:
yield copy_target, target, src
# build the target
else:
msg = 'building {}'.format(target)
print(msg)
yield build_target, target
# # build all targets (until github gfortran-8 exes are available)
# yield build_target, target
return
def test_list_json():
list_json()
return
def test_cleanup():
cleanup()
if __name__ == '__main__':
main()

88
autotest/get_exes.py Normal file
View File

@ -0,0 +1,88 @@
# Build the executables that are used in the flopy autotests
import os
import sys
import shutil
try:
import pymake
except:
print('pymake is not installed...will not build executables')
pymake = None
os.environ["TRAVIS"] = "1"
# path where downloaded executables will be extracted
exe_pth = 'exe_download'
# make the directory if it does not exist
if not os.path.isdir(exe_pth):
os.makedirs(exe_pth)
# determine if running on Travis
is_travis = 'TRAVIS' in os.environ
bindir = '.'
dotlocal = False
if is_travis:
dotlocal = True
if not dotlocal:
for idx, arg in enumerate(sys.argv):
if '--travis' in arg.lower():
dotlocal = True
break
if dotlocal:
bindir = os.path.join(os.path.expanduser('~'), '.local', 'bin')
bindir = os.path.abspath(bindir)
if not os.path.isdir(bindir):
os.makedirs(bindir)
# write where the executables will be downloaded
print('modflow executables will be downloaded to:\n\n "{}"'.format(bindir))
def cleanup():
if os.path.isdir(exe_pth):
shutil.rmtree(exe_pth)
return
def list_exes():
cmd = 'ls -l {}'.format(bindir)
os.system(cmd)
return
def test_download_and_unzip():
pymake.getmfexes(exe_pth)
# move the exes from exe_pth to bindir
files = os.listdir(exe_pth)
for file in files:
if file.startswith('__'):
continue
src = os.path.join(exe_pth, file)
dst = os.path.join(bindir, file)
print('moving {} -> {}'.format(src, dst))
os.replace(src, dst)
def test_cleanup():
cleanup()
def test_list_download():
list_exes()
def main():
test_download_and_unzip()
# clean up the download directory
cleanup()
# list executables
list_exes()
if __name__ == '__main__':
main()

8
autotest/runtests.bat
View File

@ -1,4 +1,4 @@
rmdir /S /Q __pycache__
nosetests -v
rmdir /S /Q __pycache__
pause
rmdir /S /Q __pycache__
nosetests -v
rmdir /S /Q __pycache__
pause

2
autotest/t006_test.py
View File

@ -24,6 +24,7 @@ def test_binaryfile_reference():
if matplotlib is not None:
assert isinstance(h.plot(), matplotlib.axes.Axes)
matplotlib.pyplot.close()
return
@ -36,6 +37,7 @@ def test_formattedfile_reference():
if matplotlib is not None:
assert isinstance(h.plot(masked_values=[6999.000]), matplotlib.axes.Axes)
matplotlib.pyplot.close()
return

274
autotest/t007_test.py
View File

@ -163,6 +163,19 @@ def export_shapefile_modelgrid_override(namfile):
raise Exception(msg)
def test_output_helper_shapefile_export():
ws = os.path.join('..', 'examples', 'data', 'freyberg_multilayer_transient')
name = 'freyberg.nam'
ml = flopy.modflow.Modflow.load(name, model_ws=ws)
head = flopy.utils.HeadFile(os.path.join(ws, 'freyberg.hds'))
cbc = flopy.utils.CellBudgetFile(os.path.join(ws, "freyberg.cbc"))
flopy.export.utils.output_helper(os.path.join('temp', 'test.shp'), ml,
{'HDS': head, 'cbc': cbc},
mflay=1, kper=10)
def test_freyberg_export():
from flopy.discretization import StructuredGrid
namfile = 'freyberg.nam'
@ -874,6 +887,17 @@ def test_read_usgs_model_reference():
model_ws = os.path.join('temp', 't007')
mrf = os.path.join(model_ws, 'usgs.model.reference')
shutil.copy('../examples/data/usgs.model.reference', mrf)
xul, yul = 0, 0
with open(mrf) as foo:
for line in foo:
if 'xul' in line.lower():
xul = float(line.strip().split()[1])
elif "yul" in line.lower():
yul = float(line.strip().split()[1])
else:
continue
fm = flopy.modflow
m = fm.Modflow(modelname='junk', model_ws=model_ws)
# feet and days
@ -888,6 +912,11 @@ def test_read_usgs_model_reference():
mg.read_usgs_model_reference_file(mrf)
m2.modelgrid = mg
if abs(mg.xvertices[0, 0] - xul) > 0.01:
raise AssertionError()
if abs(mg.yvertices[0, 0] - yul) > 0.01:
raise AssertionError
assert m2.modelgrid.xoffset == mg.xoffset
assert m2.modelgrid.yoffset == mg.yoffset
assert m2.modelgrid.angrot == mg.angrot
@ -1119,10 +1148,179 @@ def test_modelgrid_with_PlotMapView():
plt.close()
def test_mapview_plot_bc():
from matplotlib.collections import QuadMesh, PatchCollection
import matplotlib.pyplot as plt
sim_name = 'mfsim.nam'
sim_path = os.path.join("..", "examples", "data", "mf6",
"test003_gwfs_disv")
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("gwf_1")
ml6.modelgrid.set_coord_info(angrot=-14)
mapview = flopy.plot.PlotMapView(model=ml6)
mapview.plot_bc('CHD')
ax = mapview.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, PatchCollection):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6', 'test045_lake2tr')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("lakeex2a")
mapview = flopy.plot.PlotMapView(model=ml6)
mapview.plot_bc('LAK')
mapview.plot_bc("SFR")
ax = mapview.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, QuadMesh):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6',
'test006_2models_mvr')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("parent")
ml6c = sim.get_model('child')
ml6c.modelgrid.set_coord_info(xoff=700, yoff=0, angrot=0)
mapview = flopy.plot.PlotMapView(model=ml6)
mapview.plot_bc("MAW")
mapview2 = flopy.plot.PlotMapView(model=ml6c, ax=mapview.ax)
mapview2.plot_bc("MAW")
ax = mapview2.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, QuadMesh):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6',
'test001e_UZF_3lay')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("gwf_1")
mapview = flopy.plot.PlotMapView(model=ml6)
mapview.plot_bc("UZF")
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, QuadMesh):
raise AssertionError("Unexpected collection type")
plt.close()
def test_crosssection_plot_bc():
from matplotlib.collections import PatchCollection
import matplotlib.pyplot as plt
sim_name = 'mfsim.nam'
sim_path = os.path.join("..", "examples", "data", "mf6",
"test003_gwfs_disv")
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("gwf_1")
xc = flopy.plot.PlotCrossSection(ml6, line={'line': ([0, 5.5],
[10, 5.5])})
xc.plot_bc('CHD')
ax = xc.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, PatchCollection):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6', 'test045_lake2tr')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("lakeex2a")
xc = flopy.plot.PlotCrossSection(ml6, line={'row': 10})
xc.plot_bc('LAK')
xc.plot_bc("SFR")
ax = xc.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, PatchCollection):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6',
'test006_2models_mvr')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("parent")
xc = flopy.plot.PlotCrossSection(ml6, line={'column': 1})
xc.plot_bc("MAW")
ax = xc.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, PatchCollection):
raise AssertionError("Unexpected collection type")
plt.close()
sim_name = 'mfsim.nam'
sim_path = os.path.join('..', 'examples', 'data', 'mf6',
'test001e_UZF_3lay')
sim = flopy.mf6.MFSimulation.load(sim_name=sim_name,
sim_ws=sim_path)
ml6 = sim.get_model("gwf_1")
xc = flopy.plot.PlotCrossSection(ml6, line={"row": 0})
xc.plot_bc("UZF")
ax = xc.ax
if len(ax.collections) == 0:
raise AssertionError("Boundary condition was not drawn")
for col in ax.collections:
if not isinstance(col, PatchCollection):
raise AssertionError("Unexpected collection type")
plt.close()
def test_tricontour_NaN():
from flopy.plot import PlotMapView
import numpy as np
from flopy.discretization import StructuredGrid
import matplotlib.pyplot as plt
arr = np.random.rand(10, 10) * 100
arr[-1, :] = np.nan
@ -1154,6 +1352,8 @@ def test_tricontour_NaN():
if not np.allclose(lev, levels[ix]):
raise AssertionError("TriContour NaN catch Failed")
plt.close()
def test_get_vertices():
from flopy.utils.reference import SpatialReference
@ -1183,7 +1383,21 @@ def test_get_vertices():
assert np.array_equal(a1, a2)
def test_get_lrc_get_node():
node = 50
ml = flopy.modflow.Modflow()
dis = flopy.modflow.ModflowDis(ml, nlay=1, nrow=1, ncol=201, delr=10,
delc=1, top=50, botm=0)
lrc = dis.get_lrc([node, ])
if lrc[0] != (0, 0, 50):
raise AssertionError("get_lrc() is not returning zero based (k, i, j)")
nodes = dis.get_node(lrc)
if nodes[0] != node:
raise AssertionError('get_node() is not returning zero based node')
def test_vertex_model_dot_plot():
import matplotlib.pyplot as plt
# load up the vertex example problem
sim_name = "mfsim.nam"
sim_path = "../examples/data/mf6/test003_gwftri_disv"
@ -1193,13 +1407,16 @@ def test_vertex_model_dot_plot():
disv_ml = disv_sim.get_model('gwf_1')
ax = disv_ml.plot()
assert ax
plt.close('all')
def test_model_dot_plot():
import matplotlib.pyplot as plt
loadpth = os.path.join('..', 'examples', 'data', 'secp')
ml = flopy.modflow.Modflow.load('secp.nam', model_ws=loadpth)
ax = ml.plot()
assert ax
plt.close('all')
def test_get_rc_from_node_coordinates():
@ -1258,43 +1475,6 @@ def test_netcdf_classmethods():
assert len(diff) == 0, str(diff)
# def test_netcdf_overloads():
# import os
# import flopy
# nam_file = "freyberg.nam"
# model_ws = os.path.join('..', 'examples', 'data', 'freyberg_multilayer_transient')
# ml = flopy.modflow.Modflow.load(nam_file,model_ws=model_ws,check=False,
# verbose=False,load_only=[])
#
# f = ml.export(os.path.join("temp","freyberg.nc"))
# fzero = flopy.export.NetCdf.zeros_like(f)
# assert fzero.nc.variables["model_top"][:].sum() == 0
# print(f.nc.variables["model_top"][0,:])
# fplus1 = f + 1
# assert fplus1.nc.variables["model_top"][0,0] == f.nc.variables["model_top"][0,0] + 1
# assert (f + fplus1).nc.variables["model_top"][0,0] ==\
# f.nc.variables["model_top"][0,0] + \
# fplus1.nc.variables["model_top"][0,0]
#
# fminus1 = f - 1
# assert fminus1.nc.variables["model_top"][0,0] == f.nc.variables["model_top"][0,0] - 1
# assert (f - fminus1).nc.variables["model_top"][0,0]==\
# f.nc.variables["model_top"][0,0] - \
# fminus1.nc.variables["model_top"][0,0]
#
# ftimes2 = f * 2
# assert ftimes2.nc.variables["model_top"][0,0] == f.nc.variables["model_top"][0,0] * 2
# assert (f * ftimes2).nc.variables["model_top"][0,0] ==\
# f.nc.variables["model_top"][0,0] * \
# ftimes2.nc.variables["model_top"][0,0]
#
# fdiv2 = f / 2
# assert fdiv2.nc.variables["model_top"][0,0] == f.nc.variables["model_top"][0,0] / 2
# assert (f / fdiv2).nc.variables["model_top"][0,0] == \
# f.nc.variables["model_top"][0,0] / \
# fdiv2.nc.variables["model_top"][0,0]
#
# assert f.nc.variables["ibound"][0,0,0] == 1
def test_wkt_parse():
"""Test parsing of Coordinate Reference System parameters
from well-known-text in .prj files."""
@ -1453,20 +1633,20 @@ def test_export_contourf():
cs = plt.contourf(a)
export_contourf(filename, cs)
assert os.path.isfile(filename), 'did not create contourf shapefile'
plt.close()
return
def main():
# test_shapefile()
# test_shapefile_ibound()
# test_netcdf_classmethods()
test_netcdf_classmethods()
# for namfile in namfiles:
# export_mf2005_netcdf(namfile)
# export_shapefile(namfile)
for namfile in namfiles:
export_mf2005_netcdf(namfile)
export_shapefile(namfile)
for namfile in namfiles[0:2]:
export_shapefile_modelgrid_override(namfile)
# for namfile in namfiles[0:2]:
# export_shapefile_modelgrid_override(namfile)
# test_netcdf_overloads()
# test_netcdf_classmethods()
@ -1480,7 +1660,7 @@ def main():
# test_vertex_model_dot_plot()
# test_sr_with_Map()
# test_modelgrid_with_PlotMapView()
test_epsgs()
# test_epsgs()
# test_sr_scaling()
# test_read_usgs_model_reference()
# test_dynamic_xll_yll()
@ -1500,7 +1680,9 @@ def main():
# test_export_contourf()
# test_sr()
# test_shapefile_polygon_closed()
test_mapview_plot_bc()
test_crosssection_plot_bc()
test_output_helper_shapefile_export()
if __name__ == '__main__':

26
autotest/t009_test.py
View File

@ -166,6 +166,7 @@ def test_sfr():
if matplotlib is not None:
assert isinstance(sfr.plot()[0],
matplotlib.axes.Axes) # test the plot() method
matplotlib.pyplot.close()
# trout lake example (only sfr file is included)
# can add tests for sfr connection with lak package
@ -183,6 +184,8 @@ def test_sfr():
/ sfr.reach_data.rchlen[reach_inds]
chk = sfr.check()
assert sfr.reach_data.slope.min() < 0.0001 and 'minimum slope' in chk.warnings
# negative segments for lakes shouldn't be included in segment numbering order check
assert 'segment numbering order' not in chk.warnings
sfr.reach_data.slope[0] = 1.1
chk.slope(maximum_slope=1.0)
assert 'maximum slope' in chk.warnings
@ -552,6 +555,22 @@ def test_SfrFile():
assert df.gradient.values[-1] == 5.502E-02
assert df.shape == (1080, 20)
ml = flopy.modflow.Modflow.load('test1tr.nam',
model_ws=path, exe_name='mf2005')
ml.change_model_ws(outpath)
ml.write_input()
ml.run_model()
sfrout = SfrFile(os.path.join(outpath, 'test1tr.flw'))
assert sfrout.ncol == 16, sfrout.ncol
assert sfrout.names == common_names + ['gradient'], sfrout.names
expected_times = [
(0, 0), (4, 0), (9, 0), (12, 0), (14, 0), (19, 0), (24, 0), (29, 0),
(32, 0), (34, 0), (39, 0), (44, 0), (49, 0), (0, 1), (4, 1), (9, 1),
(12, 1), (14, 1), (19, 1), (24, 1), (29, 1), (32, 1), (34, 1), (39, 1),
(44, 1), (45, 1), (46, 1), (47, 1), (48, 1), (49, 1)]
assert sfrout.times == expected_times, sfrout.times
def test_sfr_plot():
#m = flopy.modflow.Modflow.load('test1ss.nam', model_ws=path, verbose=False)
@ -559,19 +578,20 @@ def test_sfr_plot():
#sfr.plot(key='strtop')
#plt.show()
#assert True
#plt.close()
pass
if __name__ == '__main__':
# test_sfr()
test_sfr()
# test_ds_6d_6e_disordered()
test_disordered_reachdata_fields()
# test_disordered_reachdata_fields()
# test_sfr_renumbering()
# test_example()
# test_export()
# test_transient_example()
# mtest_sfr_plot()
# test_assign_layers()
# test_SfrFile()
#test_SfrFile()
# test_const()
pass

17
autotest/t011_test.py
View File

@ -68,6 +68,22 @@ def test_mflist_reducedpumping():
return
def test_mf6listfile():
pth = os.path.join('..', 'examples', 'data', 'mf6', 'test005_advgw_tidal',
'expected_output')
list_file = os.path.join(pth, 'AdvGW_tidal.gitlist')
assert os.path.exists(list_file)
mflist = flopy.utils.Mf6ListBudget(list_file)
names = mflist.get_record_names()
for item in ['RCH_IN', 'RCH2_IN', 'RCH3_IN', 'RCH_OUT', 'RCH2_OUT',
'RCH3_OUT']:
assert item in names, '{} not found in names'.format(item)
assert len(names) == 25
inc = mflist.get_incremental()
return
@raises(AssertionError)
def test_mflist_reducedpumping_fail():
'''
@ -89,3 +105,4 @@ if __name__ == '__main__':
test_mflistfile()
test_mflist_reducedpumping()
test_mflist_reducedpumping_fail()
test_mf6listfile()

2
autotest/t012_test.py
View File

@ -61,7 +61,7 @@ def test_mf2000_p07():
pth = os.path.join(pth2000, 'P07')
namfile = 'p7mf2k.nam'
mf = flopy.modflow.Modflow.load(namfile, model_ws=pth,
version='mf2k', verbose=True,
verbose=True,
exe_name=mf2k_exe)
cpth = os.path.join(newpth, 'P07_2K')

116
autotest/t015_test.py
View File

@ -1,15 +1,30 @@
__author__ = 'aleaf'
import os
try:
import matplotlib
# if os.getenv('TRAVIS'): # are we running https://travis-ci.org/ automated tests ?
# matplotlib.use('Agg') # Force matplotlib not to use any Xwindows backend
except:
matplotlib = None
import flopy
try:
import pymake
except:
pymake = None
tpth = os.path.abspath(os.path.join('temp', 't015'))
# make the directory if it does not exist
if not os.path.isdir(tpth):
os.makedirs(tpth)
mfexe = 'mf2005'
v = flopy.which(mfexe)
run = True
if v is None:
run = False
print(os.getcwd())
if os.path.split(os.getcwd())[-1] == 'flopy3':
@ -21,12 +36,107 @@ str_items = {0: {'mfnam': 'str.nam',
'sfrfile': 'str.str'}}
def test_str_free():
m = flopy.modflow.Modflow.load(str_items[0]['mfnam'], exe_name=mfexe,
model_ws=path, verbose=False, check=False)
ws = tpth
m.change_model_ws(ws)
# get pointer to str package
str = m.str
str.istcb2 = -1
# add aux variables to str
aux_names = ['aux iface', 'aux xyz']
names = ['iface', 'xyz']
current, current_seg = flopy.modflow.ModflowStr.get_empty(23, 7,
aux_names=names)
# copy data from existing stress period data
for name in str.stress_period_data[0].dtype.names:
current[:][name] = str.stress_period_data[0][:][name]
# fill aux variable data
for idx, c in enumerate(str.stress_period_data[0]):
for jdx, name in enumerate(names):
current[idx][name] = idx + jdx * 10
# replace str data with updated str data
str = flopy.modflow.ModflowStr(m, mxacts=str.mxacts, nss=str.nss,
ntrib=str.ntrib, ndiv=str.ndiv,
icalc=str.icalc, const=str.const,
ipakcb=str.ipakcb, istcb2=str.istcb2,
iptflg=str.iptflg, irdflg=str.irdflg,
stress_period_data={0: current},
segment_data=str.segment_data,
options=aux_names)
# add head output to oc file
oclst = ['PRINT HEAD', 'PRINT BUDGET', 'SAVE HEAD', 'SAVE BUDGET']
spd = {(0, 0): oclst, (0, 1): oclst, (0, 2): oclst}
oc = flopy.modflow.ModflowOc(m, stress_period_data=spd)
oc.reset_budgetunit()
# reset ipakcb for str package to get ascii output in lst file
str.ipakcb = -1
m.write_input()
if run:
try:
success, buff = m.run_model()
except:
success = False
assert success, 'base model run did not terminate successfully'
# load the fixed format model with aux variables
try:
m2 = flopy.modflow.Modflow.load(str_items[0]['mfnam'], exe_name=mfexe,
model_ws=ws, verbose=False, check=False)
except:
m2 = None
msg = 'could not load the fixed format model with aux variables'
assert m2 is not None, msg
ws = os.path.join(tpth, 'mf2005')
m.change_model_ws(ws)
m.set_ifrefm()
m.write_input()
if run:
try:
success, buff = m.run_model()
except:
success = False
assert success, 'free format model run did not terminate successfully'
# load the free format model
try:
m2 = flopy.modflow.Modflow.load(str_items[0]['mfnam'], exe_name=mfexe,
model_ws=ws, verbose=False, check=False)
except:
m2 = None
msg = 'could not load the free format model with aux variables'
assert m2 is not None, msg
# compare the fixed and free format head files
if run:
if pymake is not None:
fn1 = os.path.join(tpth, 'str.nam')
fn2 = os.path.join(ws, 'str.nam')
success = pymake.autotest.compare_heads(fn1, fn2, verbose=True)
msg = 'fixed and free format input output head files are different'
assert success, msg
def test_str_plot():
m = flopy.modflow.Modflow.load(str_items[0]['mfnam'], model_ws=path,
verbose=True)
verbose=True, check=False)
if matplotlib is not None:
assert isinstance(m.str.plot()[0], matplotlib.axes.Axes)
matplotlib.pyplot.close()
if __name__ == '__main__':
test_str_free()
test_str_plot()

52
autotest/t016_test.py
View File

@ -2,6 +2,20 @@ import os
import flopy
import numpy as np
tpth = os.path.abspath(os.path.join('temp', 't016'))
if not os.path.isdir(tpth):
os.makedirs(tpth)
exe_name = 'mfusg'
v = flopy.which(exe_name)
run = True
if v is None:
run = False
def test_usg_disu_load():
pthusgtest = os.path.join('..', 'examples', 'data', 'mfusg_test',
@ -17,7 +31,7 @@ def test_usg_disu_load():
assert isinstance(disu, flopy.modflow.ModflowDisU)
# Change where model files are written
model_ws = os.path.join('temp', 't016')
model_ws = tpth
m.model_ws = model_ws
# Write the disu file
@ -37,6 +51,7 @@ def test_usg_disu_load():
return
def test_usg_sms_load():
pthusgtest = os.path.join('..', 'examples', 'data', 'mfusg_test',
@ -52,7 +67,7 @@ def test_usg_sms_load():
assert isinstance(sms, flopy.modflow.ModflowSms)
# Change where model files are written
model_ws = os.path.join('temp', 't016')
model_ws = tpth
m.model_ws = model_ws
# Write the sms file
@ -69,6 +84,39 @@ def test_usg_sms_load():
return
def test_usg_model():
mf = flopy.modflow.Modflow(version='mfusg', structured=True,
model_ws=tpth, modelname='simple',
exe_name=v)
dis = flopy.modflow.ModflowDis(mf, nlay=1, nrow=11, ncol=11)
bas = flopy.modflow.ModflowBas(mf)
lpf = flopy.modflow.ModflowLpf(mf)
wel = flopy.modflow.ModflowWel(mf, stress_period_data={0: [[0, 5, 5, -1.]]})
ghb = flopy.modflow.ModflowGhb(mf,
stress_period_data={
0: [[0, 0, 0, 1.0, 1000.],
[0, 9, 9, 0.0, 1000.], ]})
oc = flopy.modflow.ModflowOc(mf)
sms = flopy.modflow.ModflowSms(mf, options='complex')
# run with defaults
mf.write_input()
if run:
success, buff = mf.run_model()
assert success
# try different complexity options; all should run successfully
for complexity in ['simple', 'moderate', 'complex']:
print('testing MFUSG with sms complexity: ' + complexity)
sms = flopy.modflow.ModflowSms(mf, options=complexity)
sms.write_file()
if run:
success, buff = mf.run_model()
assert success
if __name__ == '__main__':
test_usg_disu_load()
test_usg_sms_load()
test_usg_model()

1
autotest/t024_test.py
View File

@ -40,6 +40,7 @@ def test_bcs_check():
ibound[1, 1, 1] = 1 # fully isolated cell
ibound[0:2, 4, 4] = 1 # cell connected vertically to one other cell
bas = flopy.modflow.ModflowBas(mf, ibound=ibound)
mf._mg_resync = True
chk = bas.check()
assert chk.summary_array['desc'][0] == 'isolated cells in ibound array'
assert chk.summary_array.i[0] == 1 and chk.summary_array.i[0] == 1 and \

139
autotest/t039_test.py
View File

@ -232,6 +232,143 @@ def test_get_model_shape():
return
def test_zonebudget_output_to_netcdf():
from flopy.utils import HeadFile, ZoneBudgetOutput
from flopy.modflow import Modflow
from flopy.mf6 import MFSimulation
from flopy.export.utils import output_helper
model_ws = os.path.join("..", "examples", "data",
"freyberg_multilayer_transient")
zb_ws = os.path.join("..", "examples", "data", "zonbud_examples")
hds = "freyberg.hds"
nam = "freyberg.nam"
zon = "zonef_mlt.zbr"
hds = HeadFile(os.path.join(model_ws, hds))
ml = Modflow.load(nam, model_ws=model_ws)
zone_array = read_zbarray(os.path.join(zb_ws, zon))
# test with standard zonebudget output
zbout = "freyberg_mlt.txt"
ncf_name = zbout + ".nc"
zb = ZoneBudgetOutput(os.path.join(zb_ws, zbout), ml.dis, zone_array)
vdf = zb.volumetric_flux()
netobj = zb.dataframe_to_netcdf_fmt(vdf, flux=False)
export_dict = {"hds": hds,
"zonebud": netobj}
output_helper(os.path.join(outpth, ncf_name), ml, export_dict)
# test with zonebudget csv 1 output
zbout = "freyberg_mlt.1.csv"
ncf_name = zbout + ".nc"
zb = ZoneBudgetOutput(os.path.join(zb_ws, zbout), ml.dis, zone_array)
netobj = zb.dataframe_to_netcdf_fmt(zb.dataframe)
export_dict = {"hds": hds,
"zonebud": netobj}
output_helper(os.path.join(outpth, ncf_name), ml, export_dict)
# test with zonebudget csv 2 output
zbout = "freyberg_mlt.2.csv"
ncf_name = zbout + ".nc"
zb = ZoneBudgetOutput(os.path.join(zb_ws, zbout), ml.dis, zone_array)
vdf = zb.volumetric_flux(extrapolate_kper=True)
netobj = zb.dataframe_to_netcdf_fmt(vdf, flux=False)
export_dict = {"hds": hds,
"zonebud": netobj}
output_helper(os.path.join(outpth, ncf_name), ml, export_dict)
# test built in export function
zbout = "freyberg_mlt.2.csv"
ncf_name = zbout + ".bi1" + ".nc"
zb = ZoneBudgetOutput(os.path.join(zb_ws, zbout), ml.dis, zone_array)
zb.export(os.path.join(outpth, ncf_name), ml)
# test built in export function with NetCdf output object
zbout = "freyberg_mlt.2.csv"
ncf_name = zbout + ".bi2" + ".nc"
zb = ZoneBudgetOutput(os.path.join(zb_ws, zbout), ml.dis, zone_array)
export_dict = {"hds": hds}
ncfobj = output_helper(os.path.join(outpth, ncf_name), ml, export_dict)
zb.export(ncfobj, ml)
# test with modflow6/zonebudget6
sim_ws = os.path.join("..", "examples", 'data',
'mf6', 'test005_advgw_tidal')
hds = "advgw_tidal.hds"
nam = "mfsim"
zon = "zonebudget6.csv"
ncf_name = zon + ".nc"
zone_array = np.ones((3, 15, 10), dtype=int)
zone_array = np.add.accumulate(zone_array, axis=0)
sim = MFSimulation.load(nam, sim_ws=sim_ws, exe_name='mf6')
sim.set_sim_path(outpth)
sim.write_simulation()
sim.run_simulation()
hds = HeadFile(os.path.join(outpth, hds))
ml = sim.get_model("gwf_1")
zb = ZoneBudgetOutput(os.path.join(zb_ws, zon), sim.tdis, zone_array)
vdf = zb.volumetric_flux()
netobj = zb.dataframe_to_netcdf_fmt(vdf, flux=False)
export_dict = {"hds": hds,
"zbud": netobj}
output_helper(os.path.join(outpth, ncf_name), ml, export_dict)
def test_zonbud_active_areas_zone_zero(rtol=1e-2):
try:
import pandas as pd
except ImportError:
'Pandas is not available'
# Read ZoneBudget executable output and reformat
zbud_f = os.path.join(loadpth, 'zonef_mlt_active_zone_0.2.csv')
zbud = pd.read_csv(zbud_f)
zbud.columns = [c.strip() for c in zbud.columns]
zbud.columns = ['_'.join(c.split()) for c in zbud.columns]
zbud.index = pd.Index(['ZONE_{}'.format(z) for z in zbud.ZONE.values],
name='name')
cols = [c for c in zbud.columns if 'ZONE_' in c]
zbud = zbud[cols]
# Run ZoneBudget utility and reformat output
zon_f = os.path.join(loadpth, 'zonef_mlt_active_zone_0.zbr')
zon = read_zbarray(zon_f)
zb = ZoneBudget(cbc_f, zon, kstpkper=(0, 1096))
fpbud = zb.get_dataframes().reset_index()
fpbud = fpbud[['name'] + [c for c in fpbud.columns if 'ZONE' in c]]
fpbud = fpbud.set_index('name').T
fpbud = fpbud[[c for c in fpbud.columns if 'ZONE' in c]]
fpbud = fpbud.loc[['ZONE_{}'.format(z) for z in range(1, 4)]]
# Test for equality
allclose = np.allclose(zbud, fpbud, rtol)
s = 'Zonebudget arrays do not match.'
assert allclose, s
return
if __name__ == '__main__':
# test_compare2mflist_mlt()
test_compare2zonebudget()
@ -244,3 +381,5 @@ if __name__ == '__main__':
test_dataframes()
test_get_budget()
test_get_model_shape()
test_zonebudget_output_to_netcdf()
test_zonbud_active_areas_zone_zero()

1
autotest/t042_test.py
View File

@ -82,6 +82,7 @@ def test_get_sat_thickness_gradients():
m = mf.Modflow('junk', version='mfnwt', model_ws='temp')
dis = mf.ModflowDis(m, nlay=nl, nrow=nr, ncol=nc, botm=botm, top=top)
lpf = mf.ModflowLpf(m, laytyp=np.ones(nl))
grad = get_gradients(hds, m, nodata=nodata)
dh = np.diff(hds[:, 1, 1])

803
autotest/t050_test.py
View File

@ -1,116 +1,214 @@
import shutil
import os
import numpy as np
import os
import flopy
from flopy.export import vtk
# Test vtk export
# Note: initially thought about asserting that exported file size in bytes is
# unchanged, but this seems to be sensitive to the running environment.
# Thus, only asserting that the number of lines is unchanged.
# Still keeping the file size check commented for development purposes.
# create output directory
cpth = os.path.join('temp', 't050')
if os.path.isdir(cpth):
shutil.rmtree(cpth)
os.makedirs(cpth)
# binary output directory
binot = os.path.join(cpth, 'bin')
if os.path.isdir(binot):
shutil.rmtree(binot)
os.makedirs(binot)
def count_lines_in_file(filepath, binary=False):
if binary:
f = open(filepath, 'rb')
else:
f = open(filepath, 'r')
# note this does not mean much for a binary file but still allows for check
n = len(f.readlines())
f.close()
return n
def test_vtk_export_array2d():
"""Export 2d array"""
# test mf 2005 freyberg
mpath = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False)
m.dis.top.export(os.path.join(cpth, 'array_2d_test'), fmt='vtk')
# with smoothing
m.dis.top.export(os.path.join(cpth, 'array_2d_test'), fmt='vtk',
name='top_smooth', smooth=True)
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6'])
output_dir = os.path.join(cpth, 'array_2d_test')
# export and check
m.dis.top.export(output_dir, name='top', fmt='vtk')
filetocheck = os.path.join(output_dir, 'top.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==351846)
nlines = count_lines_in_file(filetocheck)
assert(nlines==2846)
# with smoothing
m.dis.top.export(output_dir, fmt='vtk', name='top_smooth', smooth=True)
filetocheck = os.path.join(output_dir, 'top_smooth.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==351715)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==2846)
return
def test_vtk_export_array3d():
"""Vtk export 3d array"""
# test mf 2005 freyberg
mpath = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False)
m.upw.hk.export(os.path.join(cpth, 'array_3d_test'), fmt='vtk')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6', 'upw'])
output_dir = os.path.join(cpth, 'array_3d_test')
# export and check
m.upw.hk.export(output_dir, fmt='vtk', name='hk')
filetocheck = os.path.join(output_dir, 'hk.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==992036)
nlines = count_lines_in_file(filetocheck)
assert(nlines==8486)
# with point scalars
m.upw.hk.export(os.path.join(cpth, 'array_3d_test'), fmt='vtk',
name='hk_points', point_scalars=True)
# binary test
m.upw.hk.export(os.path.join(binot, 'array_3d_test'), fmt='vtk',
name='hk_points', point_scalars=True, binary=True)
m.upw.hk.export(output_dir, fmt='vtk', name='hk_points',
point_scalars=True)
filetocheck = os.path.join(output_dir, 'hk_points.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==1320666)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==10605)
# with point scalars and binary
m.upw.hk.export(output_dir, fmt='vtk', name='hk_points_bin',
point_scalars=True, binary=True)
filetocheck = os.path.join(output_dir, 'hk_points_bin.vtu')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==629401)
# nlines2 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines2==2105)
assert(os.path.exists(filetocheck))
return
def test_vtk_transient_array_2d():
"""VTK export transient 2d array"""
# test mf 2005 freyberg
mpath = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False)
m.rch.rech.export(os.path.join(cpth, 'transient_2d_test'), fmt='vtk')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6', 'rch'])
output_dir = os.path.join(cpth, 'transient_2d_test')
output_dir_bin = os.path.join(cpth, 'transient_2d_test_bin')
kpers = [0, 1, 1096]
# binary test
m.rch.rech.export(os.path.join(binot, 'transient_2d_test'), fmt='vtk',
binary=True)
# export and check
m.rch.rech.export(output_dir, fmt='vtk', kpers=kpers)
filetocheck = os.path.join(output_dir, 'rech_01.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==355144)
nlines = count_lines_in_file(filetocheck)
assert(nlines==2851)
filetocheck = os.path.join(output_dir, 'rech_01097.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==354442)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==2851)
# with binary
m.rch.rech.export(output_dir_bin, fmt='vtk', binary=True, kpers=kpers)
filetocheck = os.path.join(output_dir_bin, 'rech_01.vtu')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==168339)
# nlines2 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines2==846)
assert(os.path.exists(filetocheck))
filetocheck = os.path.join(output_dir_bin, 'rech_01097.vtu')
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==168339)
# nlines3 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines3==846)
assert(os.path.exists(filetocheck))
return
def test_vtk_export_packages():
"""testing vtk package export"""
# test mf 2005 freyberg
mpath = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False)
# test dis export
m.dis.export(os.path.join(cpth, 'DIS'), fmt='vtk')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6', 'upw', 'DRN'])
# dis export and check
output_dir = os.path.join(cpth, 'DIS')
m.dis.export(output_dir, fmt='vtk')
filetocheck = os.path.join(output_dir, 'DIS.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==1019857)
nlines = count_lines_in_file(filetocheck)
assert(nlines==8496)
# upw with point scalar output
m.upw.export(os.path.join(cpth, 'UPW'), fmt='vtk', point_scalars=True)
output_dir = os.path.join(cpth, 'UPW')
m.upw.export(output_dir, fmt='vtk', point_scalars=True)
filetocheck = os.path.join(output_dir, 'UPW.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==2559173)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==21215)
# bas with smoothing on
m.bas6.export(os.path.join(cpth, 'BAS'), fmt='vtk', smooth=True)
output_dir = os.path.join(cpth, 'BAS')
m.bas6.export(output_dir, fmt='vtk', smooth=True)
filetocheck = os.path.join(output_dir, 'BAS6.vtu')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==1001580)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==8491)
# transient package drain
m.drn.export(os.path.join(cpth, 'DRN'), fmt='vtk')
# binary test
m.dis.export(os.path.join(binot, 'DIS'), fmt='vtk', binary=True)
# upw with point scalar output
m.upw.export(os.path.join(binot, 'UPW'), fmt='vtk', point_scalars=True,
binary=True)
kpers = [0, 1, 1096]
output_dir = os.path.join(cpth, 'DRN')
m.drn.export(output_dir, fmt='vtk', kpers=kpers)
filetocheck = os.path.join(output_dir, 'DRN_01.vtu')
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==20670)
nlines3 = count_lines_in_file(filetocheck)
assert(nlines3==191)
filetocheck = os.path.join(output_dir, 'DRN_01097.vtu')
# totalbytes4 = os.path.getsize(filetocheck)
# assert(totalbytes4==20670)
nlines4 = count_lines_in_file(filetocheck)
assert(nlines4==191)
# dis with binary
output_dir = os.path.join(cpth, 'DIS_bin')
m.dis.export(output_dir, fmt='vtk', binary=True)
filetocheck = os.path.join(output_dir, 'DIS.vtu')
# totalbytes5 = os.path.getsize(filetocheck)
# assert(totalbytes5==519516)
# nlines5 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines5==1797)
assert(os.path.exists(filetocheck))
# upw with point scalars and binary
output_dir = os.path.join(cpth, 'UPW_bin')
m.upw.export(output_dir, fmt='vtk', point_scalars=True, binary=True)
filetocheck = os.path.join(output_dir, 'UPW.vtu')
# totalbytes6 = os.path.getsize(filetocheck)
# assert(totalbytes6==1349801)
# nlines6 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines6==4240)
assert(os.path.exists(filetocheck))
return
# add mf2005 model exports
def test_export_mf2005_vtk():
"""test vtk model export mf2005"""
pth = os.path.join('..', 'examples', 'data', 'mf2005_test')
namfiles = [namfile for namfile in os.listdir(pth) if
namfile.endswith('.nam')]
skip = ['bcf2ss.nam']
for namfile in namfiles:
if namfile in skip:
continue
print('testing namefile', namfile)
m = flopy.modflow.Modflow.load(namfile, model_ws=pth, verbose=False)
m.export(os.path.join(cpth, m.name), fmt='vtk')
# binary test
m.export(os.path.join(binot, m.name), fmt='vtk', binary=True)
return
def test_vtk_mf6():
# test mf6
mf6expth = os.path.join('..', 'examples', 'data', 'mf6')
# test vtk mf6 export
mf6sims = ['test045_lake1ss_table',
'test036_twrihfb', 'test045_lake2tr', 'test006_2models_mvr']
# mf6sims = ['test005_advgw_tidal']
# mf6sims = ['test036_twrihfb']
mf6sims = ['test045_lake1ss_table', 'test036_twrihfb', 'test045_lake2tr',
'test006_2models_mvr']
for simnm in mf6sims:
print(simnm)
@ -124,91 +222,596 @@ def test_vtk_mf6():
m = loaded_sim.get_model(mname)
m.export(os.path.join(cpth, m.name), fmt='vtk')
# check one
filetocheck = os.path.join(cpth, 'twrihfb2015', 'npf.vtr')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==21609)
nlines = count_lines_in_file(filetocheck)
assert(nlines==76)
return
def test_vtk_binary_head_export():
# test mf 2005 freyberg
mpth = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
hdsfile = os.path.join(mpth, 'freyberg.hds')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpth, verbose=False,
load_only=['dis', 'bas6'])
filenametocheck = 'freyberg_head_KPER455_KSTP1.vtu'
"""test vet export of heads"""
freyberg_pth = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
hdsfile = os.path.join(freyberg_pth, 'freyberg.hds')
m = flopy.modflow.Modflow.load('freyberg.nam', model_ws=freyberg_pth,
verbose=False)
# export and check
otfolder = os.path.join(cpth, 'heads_test')
vtk.export_heads(m, hdsfile, otfolder, nanval=-999.99, kstpkper=[(0, 0),
(0, 199),
(0, 354),
(0, 454),
(0,
1089)])
# test with points
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==993215)
nlines = count_lines_in_file(filetocheck)
assert(nlines==8486)
# with point scalars
otfolder = os.path.join(cpth, 'heads_test_1')
vtk.export_heads(m, hdsfile, otfolder,
kstpkper=[(0, 0), (0, 199), (0, 354), (0, 454), (0,
1089)],
point_scalars=True, nanval=-999.99)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==1331858)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==10605)
# test vtk export heads with smoothing and no point scalars
# with smoothing
otfolder = os.path.join(cpth, 'heads_test_2')
vtk.export_heads(m, hdsfile, otfolder,
kstpkper=[(0, 0), (0, 199), (0, 354), (0, 454), (0,
1089)],
point_scalars=False, smooth=True, nanval=-999.99)
smooth=True, nanval=-999.99)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==993077)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==8486)
# test binary output
# with smoothing and binary
otfolder = os.path.join(cpth, 'heads_test_3')
vtk.export_heads(m, hdsfile, otfolder,
kstpkper=[(0, 0), (0, 199), (0, 354), (0, 454), (0,
1089)],
point_scalars=False, smooth=True, binary=True,
nanval=-999.99)
smooth=True, binary=True, nanval=-999.99)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==493853)
# nlines3 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines3==1781)
assert(os.path.exists(filetocheck))
# with smoothing and binary, single time
otfolder = os.path.join(cpth, 'heads_test_4')
vtk.export_heads(m, hdsfile, otfolder, kstpkper=(0, 0),
point_scalars=False,
smooth=True, binary=True, nanval=-999.99)
point_scalars=False, smooth=True, binary=True,
nanval=-999.99)
filetocheck = os.path.join(otfolder, 'freyberg_head_KPER1_KSTP1.vtu')
# totalbytes4 = os.path.getsize(filetocheck)
# assert(totalbytes4==493853)
# nlines4 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines4==1787)
assert(os.path.exists(filetocheck))
return
def test_vtk_cbc():
# test mf 2005 freyberg
freyberg_cbc = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient',
'freyberg.cbc')
mpth = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
cbcfile = os.path.join(mpth, 'freyberg.cbc')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpth, verbose=False,
load_only=['dis', 'bas6'])
filenametocheck = 'freyberg_CBC_KPER1_KSTP1.vtu'
freyberg_mpth = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
m = flopy.modflow.Modflow.load('freyberg.nam', model_ws=freyberg_mpth,
verbose=False)
vtk.export_cbc(m, freyberg_cbc, os.path.join(cpth, 'freyberg_CBCTEST'),
# export and check with point scalar
otfolder = os.path.join(cpth, 'freyberg_CBCTEST')
vtk.export_cbc(m, cbcfile, otfolder,
kstpkper=[(0, 0), (0, 1), (0, 2)], point_scalars=True)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==2630875)
nlines = count_lines_in_file(filetocheck)
assert(nlines==19093)
vtk.export_cbc(m, freyberg_cbc, os.path.join(cpth, 'freyberg_CBCTEST_bin'),
# with point scalars and binary
otfolder = os.path.join(cpth, 'freyberg_CBCTEST_bin')
vtk.export_cbc(m, cbcfile, otfolder,
kstpkper=[(0, 0), (0, 1), (0, 2)], point_scalars=True,
binary=True)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==1205818)
# nlines1 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines1==3088)
assert(os.path.exists(filetocheck))
vtk.export_cbc(m, freyberg_cbc, os.path.join(cpth,
'freyberg_CBCTEST_bin2'),
# with point scalars and binary, only one budget component
otfolder = os.path.join(cpth, 'freyberg_CBCTEST_bin2')
vtk.export_cbc(m, cbcfile, otfolder,
kstpkper=(0, 0), text='CONSTANT HEAD',
point_scalars=True, binary=True)
filetocheck = os.path.join(otfolder, filenametocheck)
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==10142)
# nlines2 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines2==66)
assert(os.path.exists(filetocheck))
return
def test_vtk_vector():
from flopy.utils import postprocessing as pp
# test mf 2005 freyberg
mpth = os.path.join('..', 'examples', 'data',
'freyberg_multilayer_transient')
namfile = 'freyberg.nam'
cbcfile = os.path.join(mpth, 'freyberg.cbc')
hdsfile = os.path.join(mpth, 'freyberg.hds')
m = flopy.modflow.Modflow.load(namfile, model_ws=mpth, verbose=False,
load_only=['dis', 'bas6', 'upw'])
q = pp.get_specific_discharge(m, cbcfile=cbcfile)
output_dir = os.path.join(cpth, 'freyberg_vector')
filenametocheck = 'discharge.vtu'
# export and check with point scalar
vtk.export_vector(m, q, output_dir, 'discharge', point_scalars=True)
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==2247857)
nlines = count_lines_in_file(filetocheck)
assert(nlines==10605)
# with point scalars and binary
vtk.export_vector(m, q, output_dir + '_bin', 'discharge',
point_scalars=True, binary=True)
filetocheck = os.path.join(output_dir + '_bin', filenametocheck)
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==942413)
# nlines1 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines1==3824)
assert(os.path.exists(filetocheck))
# with values directly given at vertices
q = pp.get_specific_discharge(m, cbcfile=cbcfile, hdsfile=hdsfile,
position='vertices')
nancount = np.count_nonzero(np.isnan(q[0]))
assert(nancount==308)
overall = np.nansum(q[0]) + np.nansum(q[1]) + np.nansum(q[2])
assert np.allclose(overall, -15.467904755216372)
output_dir = os.path.join(cpth, 'freyberg_vector')
filenametocheck = 'discharge_verts.vtu'
vtk.export_vector(m, q, output_dir, 'discharge_verts')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==1990047)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==10598)
# with values directly given at vertices and binary
vtk.export_vector(m, q, output_dir + '_bin', 'discharge_verts',
binary=True)
filetocheck = os.path.join(output_dir + '_bin', filenametocheck)
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==891486)
# nlines3 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines3==3012)
assert(os.path.exists(filetocheck))
return
def test_vtk_vti():
# create model with regular and equal grid spacing in x, y and z directions
name = 'test_vti'
m = flopy.modflow.Modflow(name)
nlay, nrow, ncol = 2, 3, 4
delr = np.ones(ncol)
delc = np.ones(nrow)
top = 2. * np.ones((nrow, ncol))
botm1 = np.ones((1, nrow, ncol))
botm2 = np.zeros((1, nrow, ncol))
botm = np.concatenate((botm1, botm2))
dis = flopy.modflow.ModflowDis(m, nlay, nrow, ncol, delr=delr, delc=delc,
top=top, botm=botm)
output_dir = os.path.join(cpth, m.name)
filenametocheck = 'DIS.vti'
# export and check
dis.export(output_dir, fmt='vtk')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==1075)
nlines = count_lines_in_file(filetocheck)
assert(nlines==21)
# with point scalar
dis.export(output_dir + '_points', fmt='vtk', point_scalars=True)
filetocheck = os.path.join(output_dir + '_points', filenametocheck)
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==2474)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==38)
# with binary
dis.export(output_dir + '_bin', fmt='vtk', binary=True)
filetocheck = os.path.join(output_dir + '_bin', filenametocheck)
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==1144)
# nlines2 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines2==18)
assert(os.path.exists(filetocheck))
# force .vtr
filenametocheck = 'DIS.vtr'
dis.export(output_dir, fmt='vtk', vtk_grid_type='RectilinearGrid')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==1606)
nlines3 = count_lines_in_file(filetocheck)
assert(nlines3==41)
# force .vtu
filenametocheck = 'DIS.vtu'
dis.export(output_dir, fmt='vtk', vtk_grid_type='UnstructuredGrid')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes4 = os.path.getsize(filetocheck)
# assert(totalbytes4==5723)
nlines4 = count_lines_in_file(filetocheck)
assert(nlines4==129)
# vector
filenametocheck = 'vect.vti'
ones_array = np.ones(m.modelgrid.shape)
v = (ones_array, 2.*ones_array, 3.*ones_array)
vtk.export_vector(m, v, output_dir, 'vect', point_scalars=True)
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes5 = os.path.getsize(filetocheck)
# assert(totalbytes5==1578)
nlines5 = count_lines_in_file(filetocheck)
assert(nlines5==20)
# vector with point scalars and binary
vtk.export_vector(m, v, output_dir + '_bin', 'vect', point_scalars=True,
binary=True)
filetocheck = os.path.join(output_dir + '_bin', filenametocheck)
# totalbytes6 = os.path.getsize(filetocheck)
# assert(totalbytes6==2666)
# nlines6 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines6==18)
assert(os.path.exists(filetocheck))
return
def test_vtk_vtr():
# test mf 2005 l1a2k
mpth = os.path.join('..', 'examples', 'data', 'mf2005_test')
namfile = 'l1a2k.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpth, verbose=False)
output_dir = os.path.join(cpth, m.name)
filenametocheck = 'EVT_01.vtr'
# export and check
m.export(output_dir, fmt='vtk')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==79953)
nlines = count_lines_in_file(filetocheck)
assert(nlines==87)
# with point scalar
m.export(output_dir + '_points', fmt='vtk', point_scalars=True)
filetocheck = os.path.join(output_dir + '_points', filenametocheck)
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==182168)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==121)
# with binary
m.export(output_dir + '_bin', fmt='vtk', binary=True)
filetocheck = os.path.join(output_dir + '_bin', filenametocheck)
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==47874)
# nlines2 = count_lines_in_file(filetocheck, binary=True)
# assert(nlines2==28)
assert(os.path.exists(filetocheck))
# force .vtu
filenametocheck = 'EVT_01.vtu'
m.export(output_dir, fmt='vtk', vtk_grid_type='UnstructuredGrid')
filetocheck = os.path.join(output_dir, filenametocheck)
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==78762)
nlines3 = count_lines_in_file(filetocheck)
assert(nlines3==1105)
return
def test_vtk_export_true2d_regular():
mpath = os.path.join('..', 'examples', 'data', 'mf2005_test')
output_dir = os.path.join(cpth, 'true2d_regular')
# test mf 2005 test1ss, which has one layer with non-constant elevations
namfile = 'test1ss.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6'])
# export and check (.vti, with point scalars)
m.dis.botm.export(output_dir, name='test1ss_botm', fmt='vtk',
point_scalars=True, true2d=True)
filetocheck = os.path.join(output_dir, 'test1ss_botm.vti')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==3371)
nlines = count_lines_in_file(filetocheck)
assert(nlines==32)
# vector (.vti, with point scalars)
vect = (m.dis.botm.array, m.dis.botm.array)
vtk.export_vector(m, vect, output_dir, 'test1ss_botm_vect',
point_scalars=True, true2d=True)
filetocheck = os.path.join(output_dir, 'test1ss_botm_vect.vti')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==6022)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==32)
# vector directly at vertices (.vti)
vect = [m.dis.botm.array, m.dis.botm.array]
for i, vcomp in enumerate(vect):
vect[i] = m.modelgrid.array_at_verts(vcomp)
vtk.export_vector(m, vect, output_dir, 'test1ss_botm_vectv', true2d=True)
filetocheck = os.path.join(output_dir, 'test1ss_botm_vectv.vti')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==3496)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==27)
# export and check (force .vtu, with point scalars)
m.dis.botm.export(output_dir, name='test1ss_botm', fmt='vtk',
point_scalars=True, vtk_grid_type='UnstructuredGrid',
true2d=True)
filetocheck = os.path.join(output_dir, 'test1ss_botm.vtu')
# totalbytes3 = os.path.getsize(filetocheck)
# assert(totalbytes3==23827)
nlines3 = count_lines_in_file(filetocheck)
assert(nlines3==608)
# test mf 2005 swiex3, which has one row
namfile = 'swiex3.nam'
m = flopy.modflow.Modflow.load(namfile, model_ws=mpath, verbose=False,
load_only=['dis', 'bas6'])
# export and check (.vtr)
m.dis.botm.export(output_dir, name='swiex3_botm', fmt='vtk', true2d=True)
filetocheck = os.path.join(output_dir, 'swiex3_botm.vtr')
# totalbytes4 = os.path.getsize(filetocheck)
# assert(totalbytes4==8022)
nlines4 = count_lines_in_file(filetocheck)
assert(nlines4==229)
# export and check (force .vtu)
m.dis.botm.export(output_dir, name='swiex3_botm', fmt='vtk',
vtk_grid_type='UnstructuredGrid', true2d=True)
filetocheck = os.path.join(output_dir, 'swiex3_botm.vtu')
# totalbytes5 = os.path.getsize(filetocheck)
# assert(totalbytes5==85446)
nlines5 = count_lines_in_file(filetocheck)
assert(nlines5==2426)
return
def test_vtk_export_true2d_nonregxy():
import flopy.utils.binaryfile as bf
from flopy.utils import postprocessing as pp
output_dir = os.path.join(cpth, 'true2d_nonregxy')
cbc_unit_nb = 53
# model with one layer, non-regular grid in x and y
name = 'nonregxy'
m = flopy.modflow.Modflow(name, model_ws=output_dir, exe_name='mf2005')
nlay, nrow, ncol = 1, 10, 10
delr = np.concatenate((np.ones((5,)), 2.*np.ones((5,))))
delc = delr
top = 50.
botm = 0.
dis = flopy.modflow.ModflowDis(m, nlay, nrow, ncol, delr=delr, delc=delc,
top=top, botm=botm)
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
ibound[:, :, 0] = -1
ibound[:, :, -1] = -1
strt = np.linspace(1., 0., ncol).reshape(1, 1, ncol)
strt = strt * np.ones((nlay, nrow, ncol))
bas = flopy.modflow.ModflowBas(m, ibound=ibound, strt=strt)
lpf = flopy.modflow.ModflowLpf(m, hk=1., vka=1., ipakcb=cbc_unit_nb)
spd = {(0, 0): ['print head', 'print budget', 'save head', 'save budget']}
oc = flopy.modflow.ModflowOc(m, stress_period_data=spd, compact=True)
pcg = flopy.modflow.ModflowPcg(m)
m.write_input()
m.run_model(silent=True)
# export and check head with point scalar
hdsfile = os.path.join(output_dir, name + '.hds')
hds = bf.HeadFile(hdsfile)
head = hds.get_data()
vtk.export_array(m, head, output_dir, name + '_head', point_scalars=True,
true2d=True)
filetocheck = os.path.join(output_dir, name + '_head.vtr')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==4997)
nlines = count_lines_in_file(filetocheck)
assert(nlines==59)
# export and check specific discharge given at vertices
cbcfile = os.path.join(output_dir, name + '.cbc')
q = pp.get_specific_discharge(m, cbcfile, position='vertices')
vtk.export_vector(m, q, output_dir, name + '_q', point_scalars=True,
true2d=True)
filetocheck = os.path.join(output_dir, name + '_q.vtr')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==5772)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==54)
return
def test_vtk_export_true2d_nonregxz():
import flopy.utils.binaryfile as bf
from flopy.utils import postprocessing as pp
output_dir = os.path.join(cpth, 'true2d_nonregxz')
cbc_unit_nb = 53
# model with one row, non-regular grid in x and stepwise z
name = 'nonregxz'
m = flopy.modflow.Modflow(name, model_ws=output_dir, exe_name='mf2005')
nlay, nrow, ncol = 2, 1, 10
delr = np.concatenate((np.ones((5,)), 2.*np.ones((5,))))
delc = 1.
top = np.linspace(2., 3., ncol).reshape((1, 1, ncol))
botm1 = np.linspace(1., 2.5, ncol).reshape((1, 1, ncol))
botm2 = np.linspace(0., 0.5, ncol).reshape((1, 1, ncol))
botm = np.concatenate((botm1, botm2))
dis = flopy.modflow.ModflowDis(m, nlay, nrow, ncol, delr=delr, delc=delc,
top=top, botm=botm)
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
ibound[:, :, 0] = -1
ibound[:, :, -1] = -1
strt = np.linspace(0., 1., ncol).reshape(1, 1, ncol)
strt = strt * np.ones((nlay, nrow, ncol))
bas = flopy.modflow.ModflowBas(m, ibound=ibound, strt=strt)
lpf = flopy.modflow.ModflowLpf(m, hk=1., vka=1., ipakcb=cbc_unit_nb)
spd = {(0, 0): ['print head', 'print budget', 'save head', 'save budget']}
oc = flopy.modflow.ModflowOc(m, stress_period_data=spd, compact=True)
pcg = flopy.modflow.ModflowPcg(m)
m.write_input()
m.run_model(silent=True)
# export and check head
hdsfile = os.path.join(output_dir, name + '.hds')
hds = bf.HeadFile(hdsfile)
head = hds.get_data()
vtk.export_array(m, head, output_dir, name + '_head', true2d=True)
filetocheck = os.path.join(output_dir, name + '_head.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==4217)
nlines = count_lines_in_file(filetocheck)
assert(nlines==105)
# export and check head with point scalar
hdsfile = os.path.join(output_dir, name + '.hds')
hds = bf.HeadFile(hdsfile)
head = hds.get_data()
vtk.export_array(m, head, output_dir, name + '_head_points',
point_scalars=True, true2d=True)
filetocheck = os.path.join(output_dir, name + '_head_points.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==6155)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==129)
# export and check specific discharge given at vertices
cbcfile = os.path.join(output_dir, name + '.cbc')
q = pp.get_specific_discharge(m, cbcfile, position='vertices')
vtk.export_vector(m, q, output_dir, name + '_q', point_scalars=True,
true2d=True)
filetocheck = os.path.join(output_dir, name + '_q.vtu')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==7036)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==123)
return
def test_vtk_export_true2d_nonregyz():
import flopy.utils.binaryfile as bf
from flopy.utils import postprocessing as pp
output_dir = os.path.join(cpth, 'true2d_nonregyz')
cbc_unit_nb = 53
# model with one col, non-regular grid in y and stepwise z
name = 'nonregyz'
m = flopy.modflow.Modflow(name, model_ws=output_dir, exe_name='mf2005')
nlay, nrow, ncol = 2, 10, 1
delr = 1.
delc = np.concatenate((2.*np.ones((5,)), np.ones((5,))))
top = np.linspace(3., 2., nrow).reshape((1, nrow, 1))
botm1 = np.linspace(2.5, 1., nrow).reshape((1, nrow, 1))
botm2 = np.linspace(0.5, 0., nrow).reshape((1, nrow, 1))
botm = np.concatenate((botm1, botm2))
dis = flopy.modflow.ModflowDis(m, nlay, nrow, ncol, delr=delr, delc=delc,
top=top, botm=botm)
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
ibound[:, 0, :] = -1
ibound[:, -1, :] = -1
strt = np.linspace(1., 0., nrow).reshape(1, nrow, 1)
strt = strt * np.ones((nlay, nrow, ncol))
bas = flopy.modflow.ModflowBas(m, ibound=ibound, strt=strt)
lpf = flopy.modflow.ModflowLpf(m, hk=1., vka=1., ipakcb=cbc_unit_nb)
spd = {(0, 0): ['print head', 'print budget', 'save head', 'save budget']}
oc = flopy.modflow.ModflowOc(m, stress_period_data=spd, compact=True)
pcg = flopy.modflow.ModflowPcg(m)
m.write_input()
m.run_model(silent=True)
# export and check head
hdsfile = os.path.join(output_dir, name + '.hds')
hds = bf.HeadFile(hdsfile)
head = hds.get_data()
vtk.export_array(m, head, output_dir, name + '_head', true2d=True)
filetocheck = os.path.join(output_dir, name + '_head.vtu')
# totalbytes = os.path.getsize(filetocheck)
# assert(totalbytes==4217)
nlines = count_lines_in_file(filetocheck)
assert(nlines==105)
# export and check head with point scalar
hdsfile = os.path.join(output_dir, name + '.hds')
hds = bf.HeadFile(hdsfile)
head = hds.get_data()
vtk.export_array(m, head, output_dir, name + '_head_points',
point_scalars=True, true2d=True)
filetocheck = os.path.join(output_dir, name + '_head_points.vtu')
# totalbytes1 = os.path.getsize(filetocheck)
# assert(totalbytes1==6155)
nlines1 = count_lines_in_file(filetocheck)
assert(nlines1==129)
# export and check specific discharge given at vertices
cbcfile = os.path.join(output_dir, name + '.cbc')
q = pp.get_specific_discharge(m, cbcfile, position='vertices')
vtk.export_vector(m, q, output_dir, name + '_q', point_scalars=True,
true2d=True)
filetocheck = os.path.join(output_dir, name + '_q.vtu')
# totalbytes2 = os.path.getsize(filetocheck)
# assert(totalbytes2==7032)
nlines2 = count_lines_in_file(filetocheck)
assert(nlines2==123)
return
if __name__ == '__main__':
test_vtk_export_array2d()
test_vtk_export_array3d()
test_vtk_transient_array_2d()
test_vtk_export_packages()
test_export_mf2005_vtk()
test_vtk_mf6()
test_vtk_binary_head_export()
test_vtk_cbc()
test_vtk_vector()
test_vtk_vti()
test_vtk_vtr()
test_vtk_export_true2d_regular()
test_vtk_export_true2d_nonregxy()
test_vtk_export_true2d_nonregxz()
test_vtk_export_true2d_nonregyz()

71
autotest/t060_test_lkt.py
View File

@ -9,7 +9,7 @@ import numpy as np
import flopy
# make the working directory
tpth = os.path.join('temp', 't057')
tpth = os.path.join('temp', 't060')
if not os.path.isdir(tpth):
os.makedirs(tpth)
@ -25,7 +25,8 @@ def test_lkt_with_multispecies():
mtexe = 'mt3dusgs'
# Instantiate MODFLOW object in flopy
mf = flopy.modflow.Modflow(modelname=modelname, exe_name=mfexe, model_ws=modelpth, version='mfnwt')
mf = flopy.modflow.Modflow(modelname=modelname, exe_name=mfexe,
model_ws=modelpth, version='mfnwt')
Lx = 27500.0
Ly = 22000.0
@ -58,8 +59,10 @@ def test_lkt_with_multispecies():
iprnwt = 1
ibotav = 1
nwt = flopy.modflow.ModflowNwt(mf, headtol=headtol, fluxtol=fluxtol, maxiterout=maxiterout,
thickfact=thickfact, linmeth=linmeth, iprnwt=iprnwt, ibotav=ibotav,
nwt = flopy.modflow.ModflowNwt(mf, headtol=headtol,
fluxtol=fluxtol, maxiterout=maxiterout,
thickfact=thickfact, linmeth=linmeth,
iprnwt=iprnwt, ibotav=ibotav,
options='SIMPLE')
## Instantiate discretization (DIS) package for MODFLOW-NWT
@ -124,16 +127,17 @@ def test_lkt_with_multispecies():
# Create the discretization object
# itmuni = 4 (days); lenuni = 2 (meters)
dis = flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, nper=1, delr=delr, delc=delc,
top=top1, botm=botm, laycbd=0, itmuni=4, lenuni=2,
steady=Steady, nstp=nstp, tsmult=tsmult, perlen=perlen)
dis = flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, nper=1,
delr=delr, delc=delc,
top=top1, botm=botm, laycbd=0,
itmuni=4, lenuni=2,
steady=Steady, nstp=nstp, tsmult=tsmult,
perlen=perlen)
## Instantiate upstream weighting (UPW) flow package for MODFLOW-NWT
# UPW parameters
# UPW must be instantiated after DIS. Otherwise, during the mf.write_input() procedures,
# flopy will crash.
# First line of UPW input is: IUPWCB HDRY NPUPW IPHDRY
hdry = -1.e+30
iphdry = 0
@ -141,7 +145,7 @@ def test_lkt_with_multispecies():
# Next variables are: LAYTYP, LAYAVG, CHANI, LAYVKA, LAYWET
laytyp = [1, 1, 1] # >0: convertible
layavg = 0 # 0: harmonic mean
chani = 1.0 # >0: CHANI is the horizontal anisotropy for the entire layer
chani = 1.0 # >0: CHANI is the horizontal anis for entire layer
layvka = 0 # =0: indicates VKA is vertical hydraulic conductivity
laywet = 0 # Always set equal to zero in UPW package
hk = 3.172E-03
@ -150,8 +154,10 @@ def test_lkt_with_multispecies():
ss = 0.00001
sy = 0.30
upw = flopy.modflow.ModflowUpw(mf, laytyp=laytyp, layavg=layavg, chani=chani, layvka=layvka,
laywet=laywet, ipakcb=53, hdry=hdry, iphdry=iphdry, hk=hk,
upw = flopy.modflow.ModflowUpw(mf, laytyp=laytyp, layavg=layavg,
chani=chani, layvka=layvka,
laywet=laywet, ipakcb=53, hdry=hdry,
iphdry=iphdry, hk=hk,
vka=vka, ss=ss, sy=sy)
## Instantiate basic (BAS or BA6) package for MODFLOW-NWT
@ -482,21 +488,30 @@ def test_lkt_with_multispecies():
[0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0]]}
lak = flopy.modflow.ModflowLak(mf, nlakes=nlakes, ipakcb=ipakcb, theta=theta,
nssitr=nssitr, sscncr=sscncr, surfdep=surfdep,
stages=stages, stage_range=stage_range, lakarr=lkarr,
bdlknc=bdlknc, flux_data=flux_data, unit_number=16)
lak = flopy.modflow.ModflowLak(mf, nlakes=nlakes, ipakcb=ipakcb,
theta=theta,
nssitr=nssitr, sscncr=sscncr,
surfdep=surfdep,
stages=stages, stage_range=stage_range,
lakarr=lkarr,
bdlknc=bdlknc, flux_data=flux_data,
unit_number=16)
## Instantiate linkage with mass transport routing (LMT) package for MODFLOW-NWT (generates linker file)
## Instantiate linkage with mass transport routing (LMT) package
# for MODFLOW-NWT (generates linker file)
lmt = flopy.modflow.ModflowLmt(mf, output_file_name='lkttest.ftl', output_file_header='extended',
output_file_format='formatted', package_flows = ['lak'])
lmt = flopy.modflow.ModflowLmt(mf, output_file_name='lkttest.ftl',
output_file_header='extended',
output_file_format='formatted',
package_flows = ['lak'])
## Now work on MT3D-USGS file creation
mt = flopy.mt3d.Mt3dms(modflowmodel=mf, modelname=modelname, model_ws=modelpth,
version='mt3d-usgs', namefile_ext='mtnam', exe_name=mtexe,
mt = flopy.mt3d.Mt3dms(modflowmodel=mf, modelname=modelname,
model_ws=modelpth,
version='mt3d-usgs', namefile_ext='mtnam',
exe_name=mtexe,
ftlfilename='lkttest.ftl', ftlfree=True)
## Instantiate basic transport (BTN) package for MT3D-USGS
@ -523,8 +538,10 @@ def test_lkt_with_multispecies():
btn = flopy.mt3d.Mt3dBtn(mt, lunit=lunit, ncomp=ncomp, mcomp=mcomp,
sconc=sconc, prsity=prsity, cinact=cinact,
laycon=laycon, thkmin=thkmin, nprs=nprs, nprobs=nprobs,
chkmas=True,nprmas=nprmas, perlen=perlen, dt0=dt0,
laycon=laycon, thkmin=thkmin, nprs=nprs,
nprobs=nprobs,
chkmas=True,nprmas=nprmas, perlen=perlen,
dt0=dt0,
nstp=nstp, tsmult=tsmult, mxstrn=mxstrn,
ttsmult=ttsmult, ttsmax=ttsmax, sconc2=sconc2)
@ -538,7 +555,8 @@ def test_lkt_with_multispecies():
adv = flopy.mt3d.Mt3dAdv(mt, mixelm=mixelm, percel=percel, mxpart=mxpart,
nadvfd=nadvfd)
## Instantiate generalized conjugate gradient solver (GCG) package for MT3D-USGS
## Instantiate generalized conjugate gradient solver (GCG)
# package for MT3D-USGS
mxiter = 1
iter1 = 50
@ -572,7 +590,8 @@ def test_lkt_with_multispecies():
lkt = flopy.mt3d.Mt3dLkt(mt, nlkinit=nlkinit, mxlkbc=mxlkbc, icbclk=icbclk,
ietlak=ietlak, coldlak=coldlak,
lk_stress_period_data=lkt_flux_data, coldlak2=coldlak2)
lk_stress_period_data=lkt_flux_data,
coldlak2=coldlak2)
mf.write_input()
mt.write_input()

327
autotest/t065_test_gridintersect.py
View File

@ -1,3 +1,5 @@
import sys
sys.path.insert(1, "..")
import flopy.discretization as fgrid
import flopy.plot as fplot
import matplotlib.pyplot as plt
@ -11,20 +13,36 @@ except Exception as e:
print("Shapely not installed, tests cannot be run.")
from flopy.utils.gridintersect import GridIntersect
triangle_exe = None
def get_tri_grid(angrot=0., xyoffset=0., triangle_exe=None):
if not triangle_exe:
return -1
maximum_area = 50.
x0, x1, y0, y1 = (0.0, 20.0, 0.0, 20.0)
domainpoly = [(x0, y0), (x0, y1), (x1, y1), (x1, y0)]
tri = Triangle(maximum_area=maximum_area, angle=45, model_ws=".",
exe_name=triangle_exe)
tri.add_polygon(domainpoly)
tri.build(verbose=False)
cell2d = tri.get_cell2d()
vertices = tri.get_vertices()
cell2d = [[0, 16.666666666666668, 13.333333333333334, 3, 4, 2, 7],
[1, 3.3333333333333335, 6.666666666666667, 3, 4, 0, 5],
[2, 6.666666666666667, 16.666666666666668, 3, 1, 8, 4],
[3, 3.3333333333333335, 13.333333333333334, 3, 5, 1, 4],
[4, 6.666666666666667, 3.3333333333333335, 3, 6, 0, 4],
[5, 13.333333333333334, 3.3333333333333335, 3, 4, 3, 6],
[6, 16.666666666666668, 6.666666666666667, 3, 7, 3, 4],
[7, 13.333333333333334, 16.666666666666668, 3, 8, 2, 4]]
vertices = [[0, 0.0, 0.0],
[1, 0.0, 20.0],
[2, 20.0, 20.0],
[3, 20.0, 0.0],
[4, 10.0, 10.0],
[5, 0.0, 10.0],
[6, 10.0, 0.0],
[7, 20.0, 10.0],
[8, 10.0, 20.0]]
else:
maximum_area = 50.
x0, x1, y0, y1 = (0.0, 20.0, 0.0, 20.0)
domainpoly = [(x0, y0), (x0, y1), (x1, y1), (x1, y0)]
tri = Triangle(maximum_area=maximum_area, angle=45, model_ws=".",
exe_name=triangle_exe)
tri.add_polygon(domainpoly)
tri.build(verbose=False)
cell2d = tri.get_cell2d()
vertices = tri.get_vertices()
tgr = fgrid.VertexGrid(vertices, cell2d,
botm=np.atleast_2d(np.zeros(len(cell2d))),
top=np.ones(len(cell2d)), xoff=xyoffset,
@ -33,8 +51,8 @@ def get_tri_grid(angrot=0., xyoffset=0., triangle_exe=None):
def get_rect_grid(angrot=0., xyoffset=0.):
delc = 10*np.ones(2, dtype=np.float)
delr = 10*np.ones(2, dtype=np.float)
delc = 10 * np.ones(2, dtype=np.float)
delr = 10 * np.ones(2, dtype=np.float)
sgr = fgrid.StructuredGrid(
delc, delr, top=None, botm=None, xoff=xyoffset, yoff=xyoffset,
angrot=angrot)
@ -153,69 +171,69 @@ def test_rect_grid_multipoint_in_multiple_cells():
# %% test point shapely
def test_rect_grid_point_outside_shapely():
def test_rect_grid_point_outside_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_point(Point(25., 25.))
assert len(result) == 0
return result
def test_rect_grid_point_on_outer_boundary_shapely():
def test_rect_grid_point_on_outer_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_point(Point(20., 10.))
assert len(result) == 1
assert np.all(result.cellids[0] == (0, 1))
return result
def test_rect_grid_point_on_inner_boundary_shapely():
def test_rect_grid_point_on_inner_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_point(Point(10., 10.))
assert len(result) == 1
assert np.all(result.cellids[0] == (0, 0))
return result
def test_rect_grid_multipoint_in_one_cell_shapely():
def test_rect_grid_multipoint_in_one_cell_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_point(MultiPoint([Point(1., 1.), Point(2., 2.)]))
assert len(result) == 1
assert result.cellids[0] == (1, 0)
return result
def test_rect_grid_multipoint_in_multiple_cells_shapely():
def test_rect_grid_multipoint_in_multiple_cells_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_point(MultiPoint([Point(1., 1.), Point(12., 12.)]))
assert len(result) == 2
assert result.cellids[0] == (0, 1)
@ -223,79 +241,79 @@ def test_rect_grid_multipoint_in_multiple_cells_shapely():
return result
def test_tri_grid_point_outside():
def test_tri_grid_point_outside(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_point(Point(25., 25.))
assert len(result) == 0
return result
def test_tri_grid_point_on_outer_boundary():
def test_tri_grid_point_on_outer_boundary(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_point(Point(20., 10.))
assert len(result) == 1
assert np.all(result.cellids[0] == 0)
return result
def test_tri_grid_point_on_inner_boundary():
def test_tri_grid_point_on_inner_boundary(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_point(Point(10., 10.))
assert len(result) == 1
assert np.all(result.cellids[0] == 0)
return result
def test_tri_grid_multipoint_in_one_cell():
def test_tri_grid_multipoint_in_one_cell(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_point(MultiPoint([Point(1., 1.), Point(2., 2.)]))
assert len(result) == 1
assert result.cellids[0] == 1
return result
def test_tri_grid_multipoint_in_multiple_cells():
def test_tri_grid_multipoint_in_multiple_cells(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_point(MultiPoint([Point(1., 1.), Point(12., 12.)]))
assert len(result) == 2
assert result.cellids[0] == 0
@ -420,27 +438,27 @@ def test_rect_grid_linestring_in_and_out_of_cell2():
# %% test linestring shapely
def test_rect_grid_linestring_outside_shapely():
def test_rect_grid_linestring_outside_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(LineString([(25., 25.), (21., 5.)]))
assert len(result) == 0
return result
def test_rect_grid_linestring_in_2cells_shapely():
def test_rect_grid_linestring_in_2cells_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(LineString([(5., 5.), (15., 5.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -449,14 +467,14 @@ def test_rect_grid_linestring_in_2cells_shapely():
return result
def test_rect_grid_linestring_on_outer_boundary_shapely():
def test_rect_grid_linestring_on_outer_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(LineString([(15., 20.), (5., 20.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -465,14 +483,14 @@ def test_rect_grid_linestring_on_outer_boundary_shapely():
return result
def test_rect_grid_linestring_on_inner_boundary_shapely():
def test_rect_grid_linestring_on_inner_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(LineString([(5., 10.), (15., 10.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -481,14 +499,14 @@ def test_rect_grid_linestring_on_inner_boundary_shapely():
return result
def test_rect_grid_multilinestring_in_one_cell_shapely():
def test_rect_grid_multilinestring_in_one_cell_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(MultiLineString(
[LineString([(1., 1), (9., 1.)]), LineString([(1., 9.), (9., 9.)])]))
assert len(result) == 1
@ -497,14 +515,14 @@ def test_rect_grid_multilinestring_in_one_cell_shapely():
return result
def test_rect_grid_linestring_in_and_out_of_cell_shapely():
def test_rect_grid_linestring_in_and_out_of_cell_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_linestring(
LineString([(5., 9), (15., 5.), (5., 1.)]))
assert len(result) == 2
@ -514,31 +532,31 @@ def test_rect_grid_linestring_in_and_out_of_cell_shapely():
return result
def test_tri_grid_linestring_outside():
def test_tri_grid_linestring_outside(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_linestring(LineString([(25., 25.), (21., 5.)]))
assert len(result) == 0
return result
def test_tri_grid_linestring_in_2cells():
def test_tri_grid_linestring_in_2cells(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_linestring(LineString([(5., 5.), (5., 15.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -547,16 +565,16 @@ def test_tri_grid_linestring_in_2cells():
return result
def test_tri_grid_linestring_on_outer_boundary():
def test_tri_grid_linestring_on_outer_boundary(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_linestring(LineString([(15., 20.), (5., 20.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -565,16 +583,16 @@ def test_tri_grid_linestring_on_outer_boundary():
return result
def test_tri_grid_linestring_on_inner_boundary():
def test_tri_grid_linestring_on_inner_boundary(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_linestring(LineString([(5., 10.), (15., 10.)]))
assert len(result) == 2
assert result.lengths.sum() == 10.
@ -583,16 +601,16 @@ def test_tri_grid_linestring_on_inner_boundary():
return result
def test_tri_grid_multilinestring_in_one_cell():
def test_tri_grid_multilinestring_in_one_cell(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_linestring(MultiLineString(
[LineString([(1., 1), (9., 1.)]), LineString([(2., 2.), (9., 2.)])]))
assert len(result) == 1
@ -715,28 +733,28 @@ def test_rect_grid_polygon_with_hole():
# %% test polygon shapely
def test_rect_grid_polygon_outside_shapely():
def test_rect_grid_polygon_outside_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_polygon(
Polygon([(21., 11.), (23., 17.), (25., 11.)]))
assert len(result) == 0
return result
def test_rect_grid_polygon_in_2cells_shapely():
def test_rect_grid_polygon_in_2cells_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_polygon(
Polygon([(2.5, 5.0), (7.5, 5.0), (7.5, 15.), (2.5, 15.)]))
assert len(result) == 2
@ -744,28 +762,28 @@ def test_rect_grid_polygon_in_2cells_shapely():
return result
def test_rect_grid_polygon_on_outer_boundary_shapely():
def test_rect_grid_polygon_on_outer_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_polygon(
Polygon([(20., 5.0), (25., 5.0), (25., 15.), (20., 15.)]))
assert len(result) == 0
return result
def test_rect_grid_polygon_on_inner_boundary_shapely():
def test_rect_grid_polygon_on_inner_boundary_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
result = ix.intersect_polygon(
Polygon([(5., 10.0), (15., 10.0), (15., 5.), (5., 5.)]))
assert len(result) == 2
@ -773,14 +791,14 @@ def test_rect_grid_polygon_on_inner_boundary_shapely():
return result
def test_rect_grid_multipolygon_in_one_cell_shapely():
def test_rect_grid_multipolygon_in_one_cell_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
p1 = Polygon([(1., 1.), (8., 1.), (8., 3.), (1., 3.)])
p2 = Polygon([(1., 9.), (8., 9.), (8., 7.), (1., 7.)])
p = MultiPolygon([p1, p2])
@ -790,14 +808,14 @@ def test_rect_grid_multipolygon_in_one_cell_shapely():
return result
def test_rect_grid_multipolygon_in_multiple_cells_shapely():
def test_rect_grid_multipolygon_in_multiple_cells_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
p1 = Polygon([(1., 1.), (19., 1.), (19., 3.), (1., 3.)])
p2 = Polygon([(1., 9.), (19., 9.), (19., 7.), (1., 7.)])
p = MultiPolygon([p1, p2])
@ -807,14 +825,14 @@ def test_rect_grid_multipolygon_in_multiple_cells_shapely():
return result
def test_rect_grid_polygon_with_hole_shapely():
def test_rect_grid_polygon_with_hole_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_rect_grid()
ix = GridIntersect(gr)
ix = GridIntersect(gr, method='vertex', rtree=rtree)
p = Polygon([(5., 5.), (5., 15.), (25., 15.), (25., -5.),
(5., -5.)], holes=[[(9., -1), (9, 11), (21, 11), (21, -1)]])
result = ix.intersect_polygon(p)
@ -823,32 +841,48 @@ def test_rect_grid_polygon_with_hole_shapely():
return result
def test_tri_grid_polygon_outside():
def test_rect_grid_polygon_in_edge_in_cell(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_rect_grid()
ix = GridIntersect(gr, method='vertex', rtree=rtree)
p = Polygon([(0., 5.), (3., 0.), (7., 0.),
(10., 5.), (10., -1.), (0., -1.)])
result = ix.intersect_polygon(p)
assert len(result) == 1
assert result.areas.sum() == 15.
return result
def test_tri_grid_polygon_outside(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_polygon(
Polygon([(21., 11.), (23., 17.), (25., 11.)]))
assert len(result) == 0
return result
def test_tri_grid_polygon_in_2cells():
def test_tri_grid_polygon_in_2cells(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_polygon(
Polygon([(2.5, 5.0), (5.0, 5.0), (5.0, 15.), (2.5, 15.)]))
assert len(result) == 2
@ -856,27 +890,27 @@ def test_tri_grid_polygon_in_2cells():
return result
def test_tri_grid_polygon_on_outer_boundary():
def test_tri_grid_polygon_on_outer_boundary(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_polygon(
Polygon([(20., 5.0), (25., 5.0), (25., 15.), (20., 15.)]))
assert len(result) == 0
return result
def test_tri_grid_polygon_on_inner_boundary():
gr = get_tri_grid(triangle_exe=triangle_exe)
def test_tri_grid_polygon_on_inner_boundary(rtree=True):
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
result = ix.intersect_polygon(
Polygon([(5., 10.0), (15., 10.0), (15., 5.), (5., 5.)]))
assert len(result) == 4
@ -884,16 +918,16 @@ def test_tri_grid_polygon_on_inner_boundary():
return result
def test_tri_grid_multipolygon_in_one_cell():
def test_tri_grid_multipolygon_in_one_cell(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
p1 = Polygon([(1., 1.), (8., 1.), (8., 3.), (3., 3.)])
p2 = Polygon([(5., 5.), (8., 5.), (8., 8.)])
p = MultiPolygon([p1, p2])
@ -903,16 +937,16 @@ def test_tri_grid_multipolygon_in_one_cell():
return result
def test_tri_grid_multipolygon_in_multiple_cells():
def test_tri_grid_multipolygon_in_multiple_cells(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
p1 = Polygon([(1., 1.), (19., 1.), (19., 3.), (1., 3.)])
p2 = Polygon([(1., 9.), (19., 9.), (19., 7.), (1., 7.)])
p = MultiPolygon([p1, p2])
@ -922,16 +956,16 @@ def test_tri_grid_multipolygon_in_multiple_cells():
return result
def test_tri_grid_polygon_with_hole():
def test_tri_grid_polygon_with_hole(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
gr = get_tri_grid(triangle_exe=triangle_exe)
gr = get_tri_grid()
if gr == -1:
return
ix = GridIntersect(gr)
ix = GridIntersect(gr, rtree=rtree)
p = Polygon([(5., 5.), (5., 15.), (25., 15.), (25., -5.),
(5., -5.)], holes=[[(9., -1), (9, 11), (21, 11), (21, -1)]])
result = ix.intersect_polygon(p)
@ -978,15 +1012,17 @@ def test_polygon_offset_rot_structured_grid():
except:
return
sgr = get_rect_grid(angrot=45., xyoffset=10.)
p = Polygon([(5, 10. + np.sqrt(200.)), (15, 10. + np.sqrt(200.)),
(15, 10. + 1.5*np.sqrt(200.)), (5, 10. + 1.5*np.sqrt(200.))])
p = Polygon([(5, 10. + np.sqrt(200.)),
(15, 10. + np.sqrt(200.)),
(15, 10. + 1.5 * np.sqrt(200.)),
(5, 10. + 1.5 * np.sqrt(200.))])
ix = GridIntersect(sgr, method="structured")
result = ix.intersect_polygon(p)
# assert len(result) == 3.
return result
def test_point_offset_rot_structured_grid_shapely():
def test_point_offset_rot_structured_grid_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
@ -994,13 +1030,13 @@ def test_point_offset_rot_structured_grid_shapely():
return
sgr = get_rect_grid(angrot=45., xyoffset=10.)
p = Point(10., 10 + np.sqrt(200.))
ix = GridIntersect(sgr, method="strtree")
ix = GridIntersect(sgr, method="vertex", rtree=rtree)
result = ix.intersect_point(p)
# assert len(result) == 1.
return result
def test_linestring_offset_rot_structured_grid_shapely():
def test_linestring_offset_rot_structured_grid_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
@ -1008,26 +1044,91 @@ def test_linestring_offset_rot_structured_grid_shapely():
return
sgr = get_rect_grid(angrot=45., xyoffset=10.)
ls = LineString([(5, 10. + np.sqrt(200.)), (15, 10. + np.sqrt(200.))])
ix = GridIntersect(sgr, method="strtree")
ix = GridIntersect(sgr, method="vertex", rtree=rtree)
result = ix.intersect_linestring(ls)
# assert len(result) == 2.
return result
def test_polygon_offset_rot_structured_grid_shapely():
def test_polygon_offset_rot_structured_grid_shapely(rtree=True):
# avoid test fail when shapely not available
try:
import shapely
except:
return
sgr = get_rect_grid(angrot=45., xyoffset=10.)
p = Polygon([(5, 10. + np.sqrt(200.)), (15, 10. + np.sqrt(200.)),
(15, 10. + 1.5*np.sqrt(200.)), (5, 10. + 1.5*np.sqrt(200.))])
ix = GridIntersect(sgr, method="strtree")
p = Polygon([(5, 10. + np.sqrt(200.)),
(15, 10. + np.sqrt(200.)),
(15, 10. + 1.5 * np.sqrt(200.)),
(5, 10. + 1.5 * np.sqrt(200.))])
ix = GridIntersect(sgr, method="vertex", rtree=rtree)
result = ix.intersect_polygon(p)
# assert len(result) == 3.
return result
# %% test non strtree shapely intersect
def test_all_intersections_shapely_no_strtree():
"""avoid adding separate tests for rtree=False"""
# Points
# regular grid
test_rect_grid_point_on_inner_boundary_shapely(rtree=False)
test_rect_grid_point_on_outer_boundary_shapely(rtree=False)
test_rect_grid_point_outside_shapely(rtree=False)
test_rect_grid_multipoint_in_one_cell_shapely(rtree=False)
test_rect_grid_multipoint_in_multiple_cells_shapely(rtree=False)
# vertex grid
test_tri_grid_point_on_inner_boundary(rtree=False)
test_tri_grid_point_on_outer_boundary(rtree=False)
test_tri_grid_point_outside(rtree=False)
test_tri_grid_multipoint_in_multiple_cells(rtree=False)
test_tri_grid_multipoint_in_one_cell(rtree=False)
# LineStrings
# regular grid
test_rect_grid_linestring_on_inner_boundary_shapely(rtree=False)
test_rect_grid_linestring_on_outer_boundary_shapely(rtree=False)
test_rect_grid_linestring_outside_shapely(rtree=False)
test_rect_grid_linestring_in_2cells_shapely(rtree=False)
test_rect_grid_linestring_in_and_out_of_cell_shapely(rtree=False)
test_rect_grid_multilinestring_in_one_cell_shapely(rtree=False)
# vertex grid
test_tri_grid_linestring_on_inner_boundary(rtree=False)
test_tri_grid_linestring_on_outer_boundary(rtree=False)
test_tri_grid_linestring_outside(rtree=False)
test_tri_grid_linestring_in_2cells(rtree=False)
test_tri_grid_multilinestring_in_one_cell(rtree=False)
# Polygons
# regular grid
test_rect_grid_polygon_on_inner_boundary_shapely(rtree=False)
test_rect_grid_polygon_on_outer_boundary_shapely(rtree=False)
test_rect_grid_polygon_outside_shapely(rtree=False)
test_rect_grid_polygon_in_2cells_shapely(rtree=False)
test_rect_grid_polygon_with_hole_shapely(rtree=False)
test_rect_grid_multipolygon_in_one_cell_shapely(rtree=False)
test_rect_grid_multipolygon_in_multiple_cells_shapely(rtree=False)
# vertex grid
test_tri_grid_polygon_on_inner_boundary(rtree=False)
test_tri_grid_polygon_on_outer_boundary(rtree=False)
test_tri_grid_polygon_outside(rtree=False)
test_tri_grid_polygon_in_2cells(rtree=False)
test_tri_grid_polygon_with_hole(rtree=False)
test_tri_grid_multipolygon_in_multiple_cells(rtree=False)
test_tri_grid_multipolygon_in_one_cell(rtree=False)
# offset and rotated grids
test_point_offset_rot_structured_grid_shapely(rtree=False)
test_linestring_offset_rot_structured_grid_shapely(rtree=False)
ix = test_polygon_offset_rot_structured_grid_shapely(rtree=False)
return ix
# %% test rasters
def test_rasters():
from flopy.utils import Raster
import os
@ -1038,7 +1139,7 @@ def test_rasters():
try:
rio = Raster.load(os.path.join(ws, "dem", raster_name))
except ImportError:
except:
return
ml = fp.modflow.Modflow.load("sagehen.nam", version="mfnwt",
@ -1090,7 +1191,3 @@ def test_rasters():
raise AssertionError
del rio
if __name__ == "__main__":
test_rasters()

139
autotest/t068_test_ssm.py
View File

@ -3,37 +3,45 @@ Test MT3D model creation and file writing
"""
import os
import warnings
import flopy
import numpy as np
mf_exe_name = 'mf2005'
mt_exe_name = 'mt3dms'
v1 = flopy.which(mf_exe_name)
v2 = flopy.which(mt_exe_name)
run = True
if v1 is None or v2 is None:
run = False
def test_mt3d_ssm_with_nodata_in_1st_sp():
model_ws = os.path.join('.', 'temp', 't068')
nlay, nrow, ncol = 10, 10, 10
nlay, nrow, ncol = 3, 5, 5
perlen = np.zeros((10), dtype=np.float) + 10
nper = len(perlen)
ibound = np.ones((nlay,nrow,ncol), dtype=np.int)
botm = np.arange(-1,-11,-1)
botm = np.arange(-1,-4,-1)
top = 0.
# creating MODFLOW model
model_ws = 'data'
modelname = 'ssm_ex2'
model_ws = os.path.join('.', 'temp', 't068a')
modelname = 'model_mf'
mf = flopy.modflow.Modflow(modelname, model_ws=model_ws, version='mfnwt')
mf = flopy.modflow.Modflow(modelname, model_ws=model_ws,
exe_name=mf_exe_name)
dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,
perlen=perlen, nper=nper, botm=botm, top=top,
steady=False)
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=top)
upw = flopy.modflow.ModflowUpw(mf, hk=100, vka=100, ss=0.00001, sy=0.1)
lpf = flopy.modflow.ModflowLpf(mf, hk=100, vka=100, ss=0.00001, sy=0.1)
oc = flopy.modflow.ModflowOc(mf)
nwt = flopy.modflow.ModflowNwt(mf)
pcg = flopy.modflow.ModflowPcg(mf)
lmt = flopy.modflow.ModflowLmt(mf)
# recharge
rchrate = {}
@ -51,18 +59,18 @@ def test_mt3d_ssm_with_nodata_in_1st_sp():
# after the first stress period (this was crashing flopy
# version 3.2.13
ghb_data = {}
ghb_data[2] = [(4, 4, 4, 0.1, 1.5)]
ssm_data[2] = [(4, 4, 4, 1.0, itype['GHB'], 1.0, 100.0)]
ghb_data[5] = [(4, 4, 4, 0.25, 1.5)]
ssm_data[5] = [(4, 4, 4, 0.5, itype['GHB'], 0.5, 200.0)]
ssm_data[2] = [(nlay - 1, 4, 4, 1.0, itype['GHB'], 1.0, 100.0)]
ghb_data[2] = [(nlay - 1, 4, 4, 0.1, 1.5)]
ghb_data[5] = [(nlay - 1, 4, 4, 0.25, 1.5)]
ssm_data[5] = [(nlay - 1, 4, 4, 0.5, itype['GHB'], 0.5, 200.0)]
for k in range(nlay):
for i in range(nrow):
ghb_data[2].append((k, i, 0, 0.0, 100.0))
ssm_data[2].append((k, i, 0, 0.0, itype['GHB'], 0.0, 0.0))
ghb_data[5] = [(4, 4, 4, 0.25, 1.5)]
ssm_data[5] = [(4, 4, 4, 0.5, itype['GHB'], 0.5, 200.0)]
ghb_data[5] = [(nlay - 1, 4, 4, 0.25, 1.5)]
ssm_data[5] = [(nlay - 1, 4, 4, 0.5, itype['GHB'], 0.5, 200.0)]
for k in range(nlay):
for i in range(nrow):
ghb_data[5].append((k, i, 0, -0.5, 100.0))
@ -72,7 +80,9 @@ def test_mt3d_ssm_with_nodata_in_1st_sp():
ghb = flopy.modflow.ModflowGhb(mf, stress_period_data=ghb_data)
# create MT3D-USGS model
mt = flopy.mt3d.Mt3dms(modflowmodel=mf, modelname=modelname, model_ws=model_ws)
modelname = 'model_mt'
mt = flopy.mt3d.Mt3dms(modflowmodel=mf, modelname=modelname,
model_ws=model_ws, exe_name='mt3dms')
btn = flopy.mt3d.Mt3dBtn(mt, sconc=0, ncomp=2, sconc2=50.0)
adv = flopy.mt3d.Mt3dAdv(mt)
ssm = flopy.mt3d.Mt3dSsm(mt, stress_period_data=ssm_data)
@ -81,17 +91,98 @@ def test_mt3d_ssm_with_nodata_in_1st_sp():
# Write the output
mf.write_input()
mt.write_input()
# confirm that MT3D files exist
assert os.path.isfile(os.path.join(model_ws, '{}.{}'.format(mt.name, btn.extension[0]))) is True
assert os.path.isfile(os.path.join(model_ws, '{}.{}'.format(mt.name, adv.extension[0]))) is True
assert os.path.isfile(os.path.join(model_ws, '{}.{}'.format(mt.name, ssm.extension[0]))) is True
assert os.path.isfile(os.path.join(model_ws, '{}.{}'.format(mt.name, gcg.extension[0]))) is True
# run the models
if run:
success, buff = mf.run_model(report=True)
assert success, 'MODFLOW did not run'
success, buff = mt.run_model(report=True, normal_msg='Program completed.')
assert success, 'MT3D did not run'
model_ws2 = os.path.join('.', 'temp', 't068b')
mf2 = flopy.modflow.Modflow.load('model_mf.nam', model_ws=model_ws,
exe_name='mf2005')
mf2.change_model_ws(model_ws2)
mt2 = flopy.mt3d.Mt3dms.load('model_mt.nam', model_ws=model_ws,
verbose=True, exe_name='mt3dms')
mt2.change_model_ws(model_ws2)
mf2.write_input()
mt2.write_input()
success, buff = mf2.run_model(report=True)
assert success, 'MODFLOW did not run'
success, buff = mt2.run_model(report=True, normal_msg='Program completed.')
assert success, 'MT3D did not run'
fname = os.path.join(model_ws, 'MT3D001.UCN')
ucnobj = flopy.utils.UcnFile(fname)
conca = ucnobj.get_alldata()
fname = os.path.join(model_ws2, 'MT3D001.UCN')
ucnobj = flopy.utils.UcnFile(fname)
concb = ucnobj.get_alldata()
assert np.allclose(conca, concb)
return
def test_none_spdtype():
# ensure that -1 and None work as valid list entries in the
# stress period dictionary
model_ws = os.path.join('.', 'temp', 't068c')
mf = flopy.modflow.Modflow(model_ws=model_ws, exe_name=mf_exe_name)
dis = flopy.modflow.ModflowDis(mf, nper=2)
bas = flopy.modflow.ModflowBas(mf)
lpf = flopy.modflow.ModflowLpf(mf)
spd = {0: -1, 1: None}
wel = flopy.modflow.ModflowWel(mf, stress_period_data=spd)
pcg = flopy.modflow.ModflowPcg(mf)
mf.write_input()
mf2 = flopy.modflow.Modflow.load('modflowtest.nam', model_ws=model_ws,
verbose=True)
if run:
success, buff = mf.run_model(report=True)
assert success
def test_ssm_readwrite():
# Instantiate MODFLOW model
mf = flopy.modflow.Modflow()
# These dimensions work for the SSM file to be loaded
dis = flopy.modflow.ModflowDis(mf, nlay=10, nrow=118, ncol=153,
nper=100, delr=100, delc=100, perlen=1)
bas = flopy.modflow.ModflowBas(mf)
# Instantiate MT3D model
mt = flopy.mt3d.Mt3dms(modflowmodel=mf, modelname='tran_v1',
version='mt3d-usgs')
btn = flopy.mt3d.Mt3dBtn(mt)
# Point to ssm file for test load and write
pth = os.path.join('..','examples','data','ssm_load_test')
fl = os.path.join(pth, 'tran_v1_b1.ssm')
# Check that example input file with no data specified for crch works
# (file comes from: https://github.com/modflowpy/flopy/issues/743)
ssm = flopy.mt3d.Mt3dSsm.load(fl, mt)
# Change to dedicated work directory
cwd = os.getcwd()
if not os.path.exists(os.path.join('temp','t068_ssm_write')):
os.makedirs(os.path.join('temp','t068_ssm_write'))
os.chdir(os.path.join('temp','t068_ssm_write'))
# Ensure file is writeable
ssm.write_file()
# Return to starting directory
os.chdir(cwd)
if __name__ == '__main__':
test_mt3d_ssm_with_nodata_in_1st_sp()
test_none_spdtype()
test_ssm_readwrite()

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"""
Test vtk export_model function without packages_names definition
"""
import os
import flopy
from flopy.export import vtk
mf_exe_name = 'mf6'
def test_vtk_export_model_without_packages_names():
ws = os.path.join('.', 'temp', 't069')
name = 'mymodel'
sim = flopy.mf6.MFSimulation(sim_name=name, sim_ws=ws, exe_name='mf6')
tdis = flopy.mf6.ModflowTdis(sim)
ims = flopy.mf6.ModflowIms(sim)
gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
dis = flopy.mf6.ModflowGwfdis(gwf, nrow=10, ncol=10)
ic = flopy.mf6.ModflowGwfic(gwf)
npf = flopy.mf6.ModflowGwfnpf(gwf, save_specific_discharge=True)
chd = flopy.mf6.ModflowGwfchd(gwf, stress_period_data=[[(0, 0, 0), 1.],
[(0, 9, 9), 0.]])
# Export model without specifying packages_names parameter
vtk.export_model(sim.get_model(), ws)
# If the function executes without error then test was successful
assert True
if __name__ == '__main__':
test_vtk_export_model_without_packages_names()

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# -*- coding: utf-8 -*-
"""
Created on Mon Feb 17 12:29:35 2020
@author: Artesia
"""
import os
import numpy as np
import flopy
import matplotlib.pyplot as plt
def test_plotting_with_quasi3d_layers():
modelname = 'model_mf'
model_ws = os.path.join('.', 'temp', 't069a')
exe_name = 'mf2005'
mf = flopy.modflow.Modflow(modelname, model_ws=model_ws, exe_name=exe_name)
# Model domain and grid definition
Lx = 1000.
Ly = 1000.
ztop = 0.
zbot = -30.
nlay = 3
nrow = 10
ncol = 10
delr = Lx / ncol
delc = Ly / nrow
laycbd = [0]*(nlay)
laycbd[0] = 1
botm = np.linspace(ztop, zbot, nlay + np.sum(laycbd) + 1)[1:]
# Create the discretization object
flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, delr=delr, delc=delc,
top=ztop, botm=botm, laycbd=laycbd)
# Variables for the BAS package
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
ibound[:, :, 0] = -1
ibound[:, :, -1] = -1
strt = np.ones((nlay, nrow, ncol), dtype=np.float32)
strt[:, :, 0] = 10.
strt[:, :, -1] = 0.
flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)
# Add LPF package to the MODFLOW model
flopy.modflow.ModflowLpf(mf, hk=10., vka=10., ipakcb=53, vkcb=10)
# add a well
row = int((nrow-1)/2)
col = int((ncol-1)/2)
spd = {0:[[1, row, col, -1000]]}
flopy.modflow.ModflowWel(mf, stress_period_data=spd)
# Add OC package to the MODFLOW model
spd = {(0, 0): ['save head', 'save budget']}
flopy.modflow.ModflowOc(mf, stress_period_data=spd, compact=True)
# Add PCG package to the MODFLOW model
flopy.modflow.ModflowPcg(mf)
# Write the MODFLOW model input files
mf.write_input()
# Run the MODFLOW model
success, buff = mf.run_model()
# read output
hf = flopy.utils.HeadFile(os.path.join(mf.model_ws,'{}.hds'.format(mf.name)))
head = hf.get_data(totim=1.0)
cbb = flopy.utils.CellBudgetFile(os.path.join(mf.model_ws,'{}.cbc'.format(mf.name)))
frf = cbb.get_data(text='FLOW RIGHT FACE', totim=1.0)[0]
fff = cbb.get_data(text='FLOW FRONT FACE', totim=1.0)[0]
flf = cbb.get_data(text='FLOW LOWER FACE', totim=1.0)[0]
# plot a map
plt.figure()
mv = flopy.plot.PlotMapView(model=mf,layer=1)
mv.plot_grid()
mv.plot_array(head)
mv.contour_array(head)
mv.plot_ibound()
mv.plot_bc('wel')
mv.plot_discharge(frf,fff, head=head)
plt.close()
# plot a cross-section
plt.figure()
cs = flopy.plot.PlotCrossSection(model=mf, line={'row':int((nrow-1)/2)})
cs.plot_grid()
cs.plot_array(head)
cs.contour_array(head)
cs.plot_ibound()
cs.plot_bc('wel')
cs.plot_discharge(frf, fff, flf, head=head)
plt.close()

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# Test postprocessing and plotting functions related to specific discharge:
# - get_extended_budget()
# - get_specific_discharge()
# - PlotMapView.plot_vector()
# - PlotCrossSection.plot_vector()
# More precisely:
# - two models are created: one for mf005 and one for mf6
# - the two models are virtually identical; in fact, the options are such that
# the calculated heads are indeed exactly the same (which is, by the way,
# quite remarkable!)
# - the model is a very small synthetic test case that just contains enough
# things to allow for the functions to be thoroughly tested
import flopy
import os
import numpy as np
import flopy.utils.binaryfile as bf
# model names, file names and locations
modelname_mf2005 = 't070_mf2005'
modelname_mf6 = 't070_mf6'
postproc_test_ws = os.path.join('.', 'temp', 't070')
modelws_mf2005 = os.path.join(postproc_test_ws, modelname_mf2005)
modelws_mf6 = os.path.join(postproc_test_ws, modelname_mf6)
cbcfile_mf2005 = os.path.join(modelws_mf2005, modelname_mf2005 + '.cbc')
cbcfile_mf6 = os.path.join(modelws_mf6, modelname_mf6 + '.cbc')
hdsfile_mf2005 = os.path.join(modelws_mf2005, modelname_mf2005 + '.hds')
hdsfile_mf6 = os.path.join(modelws_mf6, modelname_mf6 + '.hds')
namfile_mf2005 = os.path.join(modelws_mf2005, modelname_mf2005 + '.nam')
namfile_mf6 = os.path.join(modelws_mf6, modelname_mf6 + '.nam')
# model domain, grid definition and properties
Lx = 100.
Ly = 100.
ztop = 0.
zbot = -100.
nlay = 4
nrow = 4
ncol = 4
delr = Lx/ncol
delc = Ly/nrow
delv = (ztop - zbot) / nlay
botm = np.linspace(ztop, zbot, nlay + 1)
hk=1.
rchrate = 0.1
lay_to_plot = 1
# variables for the BAS (mf2005) or DIS (mf6) package
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
ibound[1, 0, 1] = 0 # set a no-flow cell
strt = np.ones((nlay, nrow, ncol), dtype=np.float32)
# add inflow through west boundary using WEL package
Q = 100.
wel_list = []
wel_list_iface = []
for k in range(nlay):
for i in range(nrow):
wel_list.append([k, i, 0, Q])
wel_list_iface.append(wel_list[-1] + [1])
# allow flow through north, south, and bottom boundaries using GHB package
ghb_head = -30. # low enough to have dry cells in first layer
ghb_cond = hk * delr * delv / (0.5 * delc)
ghb_list = []
ghb_list_iface = []
for k in range(1, nlay):
for j in range(ncol):
if not (k==1 and j==1): # skip no-flow cell
ghb_list.append([k, 0, j, ghb_head, ghb_cond])
ghb_list_iface.append(ghb_list[-1] + [4])
ghb_list.append([k, nrow-1, j, ghb_head, ghb_cond])
ghb_list_iface.append(ghb_list[-1] + [3])
for i in range(nrow):
for j in range(ncol):
ghb_list.append([nlay-1, i, j, ghb_head, ghb_cond])
ghb_list_iface.append(ghb_list[-1] + [5])
# river in the eastern part
riv_stage = -30.
riv_cond = hk * delr * delc / (0.5 * delv)
riv_rbot = riv_stage - 5.
riv_list = []
for i in range(nrow):
riv_list.append([1, i, ncol-1, riv_stage, riv_cond, riv_rbot])
# drain in the south part
drn_stage = -30.
drn_cond = hk * delc * delv / (0.5 * delr)
drn_list = []
for j in range(ncol):
drn_list.append([1, i, nrow-1, drn_stage, drn_cond])
boundary_ifaces = {'WELLS': wel_list_iface,
'HEAD DEP BOUNDS': ghb_list_iface,
'RIVER LEAKAGE': 2,
'DRAIN': 3,
'RECHARGE': 6}
def build_model_mf2005():
# create folders
if not os.path.isdir(modelws_mf2005):
os.makedirs(modelws_mf2005)
# create modflow model
mf = flopy.modflow.Modflow(modelname_mf2005, model_ws=modelws_mf2005,
exe_name='mf2005')
# cell by cell flow file unit number
cbc_unit_nb = 53
# create DIS package
dis = flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, delr=delr, delc=delc,
top=ztop, botm=botm[1:])
# create BAS package
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)
# create LPF package
laytyp = np.zeros(nlay)
laytyp[0] = 1
laywet = np.zeros(nlay)
laywet[0] = 1
lpf = flopy.modflow.ModflowLpf(mf, hk=hk, ipakcb=cbc_unit_nb,
laytyp=laytyp, laywet=laywet, wetdry=-0.01)
# create WEL package
wel_dict = {0: wel_list}
wel = flopy.modflow.ModflowWel(mf, stress_period_data=wel_dict,
ipakcb=cbc_unit_nb)
# create GHB package
ghb_dict = {0: ghb_list}
ghb = flopy.modflow.ModflowGhb(mf, stress_period_data=ghb_dict,
ipakcb=cbc_unit_nb)
# create RIV package
riv_dict = {0: riv_list}
riv = flopy.modflow.ModflowRiv(mf, stress_period_data=riv_dict,
ipakcb=cbc_unit_nb)
# create DRN package
drn_dict = {0: drn_list}
drn = flopy.modflow.ModflowDrn(mf, stress_period_data=drn_dict,
ipakcb=cbc_unit_nb)
# create RCH package
rch = flopy.modflow.ModflowRch(mf, rech=rchrate, ipakcb=cbc_unit_nb)
# create OC package
spd = {(0, 0): ['print head', 'print budget', 'save head', 'save budget']}
oc = flopy.modflow.ModflowOc(mf, stress_period_data=spd, compact=True)
# create PCG package
pcg = flopy.modflow.ModflowPcg(mf)
# write the MODFLOW model input files
mf.write_input()
# run the MODFLOW model
success, buff = mf.run_model()
return
def build_model_mf6():
if not os.path.isdir(modelws_mf6):
os.makedirs(modelws_mf6)
# create simulation
simname = modelname_mf6
sim = flopy.mf6.MFSimulation(sim_name=simname, version='mf6',
exe_name='mf6', sim_ws=modelws_mf6)
# create tdis package
tdis_rc = [(1.0, 1, 1.0)]
tdis = flopy.mf6.ModflowTdis(sim, pname='tdis', time_units='DAYS',
perioddata=tdis_rc)
# create gwf model
gwf = flopy.mf6.ModflowGwf(sim, modelname=modelname_mf6,
model_nam_file='{}.nam'.format(modelname_mf6))
gwf.name_file.save_flows = True
# create iterative model solution and register the gwf model with it
rcloserecord = [1e-5, 'STRICT']
ims = flopy.mf6.ModflowIms(sim, pname='ims', print_option='SUMMARY',
complexity='SIMPLE', outer_hclose=1.e-5,
outer_maximum=50, under_relaxation='NONE',
inner_maximum=30, inner_hclose=1.e-5,
rcloserecord=rcloserecord,
linear_acceleration='CG',
scaling_method='NONE', reordering_method='NONE',
relaxation_factor=0.99)
sim.register_ims_package(ims, [gwf.name])
# create dis package
dis = flopy.mf6.ModflowGwfdis(gwf, nlay=nlay, nrow=nrow, ncol=ncol,
delr=delr, delc=delc,
top=ztop, botm=botm[1:], idomain=ibound)
# initial conditions
ic = flopy.mf6.ModflowGwfic(gwf, pname='ic', strt=strt)
# create node property flow package
rewet_record = [('WETFCT', 0.1, 'IWETIT', 1, 'IHDWET', 0)]
icelltype = np.zeros(ibound.shape)
icelltype[0, :, :] = 1
wetdry = np.zeros(ibound.shape)
wetdry[0, :, :] = -0.01
npf = flopy.mf6.ModflowGwfnpf(gwf,
icelltype=icelltype,
k=hk,
rewet_record=rewet_record,
wetdry=wetdry,
cvoptions=[()],
save_specific_discharge=True)
# create wel package
welspd = [[(wel_i[0], wel_i[1], wel_i[2]), wel_i[3]] for wel_i in wel_list]
wel = flopy.mf6.ModflowGwfwel(gwf, print_input=True,
stress_period_data=welspd)
# create ghb package
ghbspd = [[(ghb_i[0], ghb_i[1], ghb_i[2]), ghb_i[3], ghb_i[4]]
for ghb_i in ghb_list]
ghb = flopy.mf6.ModflowGwfghb(gwf, print_input=True,
stress_period_data=ghbspd)
# create riv package
rivspd = [[(riv_i[0], riv_i[1], riv_i[2]), riv_i[3], riv_i[4], riv_i[5]]
for riv_i in riv_list]
riv = flopy.mf6.ModflowGwfriv(gwf, stress_period_data=rivspd)
# create drn package
drnspd = [[(drn_i[0], drn_i[1], drn_i[2]), drn_i[3], drn_i[4]]
for drn_i in drn_list]
drn = flopy.mf6.ModflowGwfdrn(gwf, print_input=True,
stress_period_data=drnspd)
# create rch package
rch = flopy.mf6.ModflowGwfrcha(gwf, recharge=rchrate)
# output control
oc = flopy.mf6.ModflowGwfoc(gwf, pname='oc', budget_filerecord=
'{}.cbc'.format(modelname_mf6),
head_filerecord='{}.hds'.format(modelname_mf6),
headprintrecord=[('COLUMNS', 10, 'WIDTH', 15,
'DIGITS', 6, 'GENERAL')],
saverecord=[('HEAD', 'ALL'),
('BUDGET', 'ALL')],
printrecord=[('HEAD', 'ALL'),
('BUDGET', 'ALL')])
# write input files
sim.write_simulation()
# run simulation
sim.run_simulation()
return
def basic_check(Qx_ext, Qy_ext, Qz_ext):
# check shape
assert Qx_ext.shape == (nlay, nrow, ncol+1)
assert Qy_ext.shape == (nlay, nrow+1, ncol)
assert Qz_ext.shape == (nlay+1, nrow, ncol)
# check sign
assert Qx_ext[2, 1, 1] > 0
assert Qy_ext[2, 1, 1] > 0
assert Qz_ext[2, 1, 1] < 0
return
def local_balance_check(Qx_ext, Qy_ext, Qz_ext, hdsfile=None, model=None):
# calculate water blance at every cell
local_balance = Qx_ext[:, :, :-1] - Qx_ext[:, :, 1:] + \
Qy_ext[:, 1:, :] - Qy_ext[:, :-1, :] + \
Qz_ext[1:, :, :] - Qz_ext[:-1, :, :]
# calculate total flow through every cell
local_total = np.abs(Qx_ext[:, :, :-1]) + np.abs(Qx_ext[:, :, 1:]) + \
np.abs(Qy_ext[:, 1:, :]) + np.abs(Qy_ext[:, :-1, :]) + \
np.abs(Qz_ext[1:, :, :]) + np.abs(Qz_ext[:-1, :, :])
# we should disregard no-flow and dry cells
if hdsfile is not None and model is not None:
hds = bf.HeadFile(hdsfile, precision='single')
head = hds.get_data()
noflo_or_dry = np.logical_or(head==model.hnoflo, head==model.hdry)
local_balance[noflo_or_dry] = np.nan
# check water balance = 0 at every cell
rel_err = local_balance / local_total
max_rel_err = np.nanmax(rel_err)
assert np.allclose(max_rel_err + 1., 1.)
def test_extended_budget_default():
# build and run MODFLOW 2005 model
build_model_mf2005()
# load and postprocess
Qx_ext, Qy_ext, Qz_ext = \
flopy.utils.postprocessing.get_extended_budget(cbcfile_mf2005)
# basic check
basic_check(Qx_ext, Qy_ext, Qz_ext)
# overall check
overall = np.sum(Qx_ext) + np.sum(Qy_ext) + np.sum(Qz_ext)
assert np.allclose(overall, -1122.4931640625)
return
def test_extended_budget_comprehensive():
# load and postprocess
mf = flopy.modflow.Modflow.load(namfile_mf2005, check=False)
Qx_ext, Qy_ext, Qz_ext = \
flopy.utils.postprocessing.get_extended_budget(cbcfile_mf2005,
boundary_ifaces=boundary_ifaces,
hdsfile=hdsfile_mf2005, model=mf)
# basic check
basic_check(Qx_ext, Qy_ext, Qz_ext)
# local balance check
local_balance_check(Qx_ext, Qy_ext, Qz_ext, hdsfile_mf2005, mf)
# overall check
overall = np.sum(Qx_ext) + np.sum(Qy_ext) + np.sum(Qz_ext)
assert np.allclose(overall, -1110.646240234375)
return
def test_specific_discharge_default():
# load and postprocess
mf = flopy.modflow.Modflow.load(namfile_mf2005, check=False)
qx, qy, qz = flopy.utils.postprocessing.get_specific_discharge(mf,
cbcfile_mf2005)
# overall check
overall = np.sum(qx) + np.sum(qy) + np.sum(qz)
assert np.allclose(overall, -1.7959892749786377)
return
def test_specific_discharge_comprehensive():
import matplotlib.pyplot as plt
from matplotlib.quiver import Quiver
# load and postprocess
mf = flopy.modflow.Modflow.load(namfile_mf2005, check=False)
qx, qy, qz = flopy.utils.postprocessing.get_specific_discharge(mf,
cbcfile_mf2005,
boundary_ifaces=boundary_ifaces,
hdsfile=hdsfile_mf2005)
# check nan values
assert np.isnan(qx[0, 0, 2])
assert np.isnan(qx[1, 0, 1])
# overall check
overall = np.nansum(qx) + np.nansum(qy) + np.nansum(qz)
assert np.allclose(overall, -0.8558630187423599)
# plot discharge in map view
lay = 1
modelmap = flopy.plot.PlotMapView(model=mf, layer=lay)
quiver = modelmap.plot_vector(qx, qy, normalize=True,
masked_values=[qx[lay, 0, 0]],
color='orange')
# check plot
ax = modelmap.ax
if len(ax.collections) == 0:
raise AssertionError("Discharge vector was not drawn")
for col in ax.collections:
if not isinstance(col, Quiver):
raise AssertionError("Unexpected collection type")
assert np.sum(quiver.Umask) == 2
pos = np.sum(quiver.X) + np.sum(quiver.Y)
assert np.allclose(pos, 1600.)
val = np.sum(quiver.U) + np.sum(quiver.V)
assert np.allclose(val, 10.908548650065649)
# close figure
plt.close()
# plot discharge in cross-section view
hds = bf.HeadFile(hdsfile_mf2005, precision='single')
head = hds.get_data()
row = 0
xsect = flopy.plot.PlotCrossSection(model=mf, line={'row': row})
quiver = xsect.plot_vector(qx, qy, qz, head=head, normalize=True,
masked_values=qx[0, row, :2], color='orange')
# check plot
ax = xsect.ax
if len(ax.collections) == 0:
raise AssertionError("Discharge vector was not drawn")
for col in ax.collections:
if not isinstance(col, Quiver):
raise AssertionError("Unexpected collection type")
assert np.sum(quiver.Umask) == 5
X = np.ma.masked_where(quiver.Umask, quiver.X)
Y = np.ma.masked_where(quiver.Umask, quiver.Y)
pos = X.sum() + Y.sum()
assert np.allclose(pos, -153.8352064441874)
U = np.ma.masked_where(quiver.Umask, quiver.U)
V = np.ma.masked_where(quiver.Umask, quiver.V)
val = U.sum() + V.sum()
assert np.allclose(val, -3.25453417836753)
# close figure
plt.close()
return
def test_specific_discharge_mf6():
from flopy.mf6.modflow.mfsimulation import MFSimulation
import matplotlib.pyplot as plt
from matplotlib.quiver import Quiver
# build and run MODFLOW 6 model
build_model_mf6()
# load and postprocess
sim = MFSimulation.load(sim_name=modelname_mf6, sim_ws=modelws_mf6,
verbosity_level=0)
gwf = sim.get_model(modelname_mf6)
qx, qy, qz = flopy.utils.postprocessing.get_specific_discharge(gwf,
cbcfile_mf6, precision='double',
hdsfile=hdsfile_mf6)
# check nan values
assert np.isnan(qx[0, 0, 2])
assert np.isnan(qx[1, 0, 1])
# overall check
overall = np.nansum(qx) + np.nansum(qy) + np.nansum(qz)
assert np.allclose(overall, -2.5768726154495947)
# plot discharge in map view
lay = 1
modelmap = flopy.plot.PlotMapView(model=gwf, layer=lay)
quiver = modelmap.plot_vector(qx, qy, normalize=True)
# check plot
ax = modelmap.ax
if len(ax.collections) == 0:
raise AssertionError("Discharge vector was not drawn")
for col in ax.collections:
if not isinstance(col, Quiver):
raise AssertionError("Unexpected collection type")
assert np.sum(quiver.Umask) == 1
pos = np.sum(quiver.X) + np.sum(quiver.Y)
assert np.allclose(pos, 1600.)
val = np.sum(quiver.U) + np.sum(quiver.V)
assert np.allclose(val, 11.10085455942011)
# close figure
plt.close()
# plot discharge in cross-section view
hds = bf.HeadFile(hdsfile_mf6, precision='double')
head = hds.get_data()
row = 0
xsect = flopy.plot.PlotCrossSection(model=gwf, line={'row': row})
quiver = xsect.plot_vector(qx, qy, qz, head=head, normalize=True)
# check plot
ax = xsect.ax
if len(ax.collections) == 0:
raise AssertionError("Discharge vector was not drawn")
for col in ax.collections:
if not isinstance(col, Quiver):
raise AssertionError("Unexpected collection type")
assert np.sum(quiver.Umask) == 3
X = np.ma.masked_where(quiver.Umask, quiver.X)
Y = np.ma.masked_where(quiver.Umask, quiver.Y)
pos = X.sum() + Y.sum()
assert np.allclose(pos, -145.94665962387785)
U = np.ma.masked_where(quiver.Umask, quiver.U)
V = np.ma.masked_where(quiver.Umask, quiver.V)
val = U.sum() + V.sum()
assert np.allclose(val, -4.49596527119806)
# close figure
plt.close()
return
if __name__ == '__main__':
test_extended_budget_default()
test_extended_budget_comprehensive()
test_specific_discharge_default()
test_specific_discharge_comprehensive()
test_specific_discharge_mf6()

82
autotest/t071_test_nwt_ag.py Normal file
View File

@ -0,0 +1,82 @@
import os
import flopy
import platform
import shutil
import numpy as np
mpth = os.path.join('..', 'examples', 'data', 'ag_test')
opth = os.path.join('temp', 't071')
if not os.path.exists(opth):
os.makedirs(opth)
def test_empty_ag_package():
ml = flopy.modflow.Modflow("agtest", version='mfnwt')
ag = flopy.modflow.ModflowAg(ml)
if not isinstance(ag, flopy.pakbase.Package):
raise Exception
def test_load_write_agwater():
agfile = "Agwater1.ag"
ml = flopy.modflow.Modflow("Agwater1", version='mfnwt')
ag1 = flopy.modflow.ModflowAg.load(os.path.join(mpth, agfile),
ml, nper=49, ext_unit_dict={})
loaded = False
for pak in ml.packagelist:
if isinstance(pak, flopy.modflow.ModflowAg):
loaded = True
break
if not loaded:
raise AssertionError("ModflowAg package not loaded")
ml.change_model_ws(opth)
ag1.write_file()
ml2 = flopy.modflow.Modflow("Agwater1", version='mfnwt', model_ws=opth)
ag2 = flopy.modflow.ModflowAg.load(os.path.join(opth, agfile),
ml2, nper=49)
if repr(ag1) != repr(ag2):
raise AssertionError("Ag package comparison failed")
def test_load_write_agwater_uzf():
uzffile = "Agwater1.uzf"
ml = flopy.modflow.Modflow("Agwater1", version='mfnwt')
dis = flopy.modflow.ModflowDis(ml, nlay=1, nrow=15, ncol=10, nper=49)
uzf1 = flopy.modflow.ModflowUzf1.load(os.path.join(mpth, uzffile), ml)
loaded = False
for pak in ml.packagelist:
if isinstance(pak, flopy.modflow.ModflowUzf1):
loaded = True
break
if not loaded:
raise AssertionError("ModflowUzf1 package not loaded")
ml.change_model_ws(opth)
uzf1.write_file()
ml2 = flopy.modflow.Modflow("Agwater1", version='mfnwt', model_ws=opth)
dis2 = flopy.modflow.ModflowDis(ml2, nlay=1, nrow=15, ncol=10, nper=49)
uzf2 = flopy.modflow.ModflowUzf1.load(os.path.join(opth, uzffile), ml2)
if not np.allclose(uzf1.air_entry.array, uzf2.air_entry.array):
raise AssertionError("Air entry pressure array comparison failed")
if not np.allclose(uzf1.hroot.array, uzf2.hroot.array):
raise AssertionError("root pressure array comparison failed")
if not np.allclose(uzf1.rootact.array, uzf2.rootact.array):
raise AssertionError("root activity array comparison failed")
if __name__ == "__main__":
test_empty_ag_package()
test_load_write_agwater()
test_load_write_agwater_uzf()

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4
code.json
View File

@ -29,9 +29,9 @@
"downloadURL": "https://code.usgs.gov/usgs/modflow/flopy/archive/master.zip",
"vcs": "git",
"laborHours": -1,
"version": "3.3.0",
"version": "3.3.1",
"date": {
"metadataLastUpdated": "2019-12-14"
"metadataLastUpdated": "2020-06-26"
},
"organization": "U.S. Geological Survey",
"permissions": {

25
docs/PyPi_release.md
View File

@ -6,10 +6,21 @@ FloPy includes support for MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, an
For general modeling issues, please consult a modeling forum, such as the [MODFLOW Users Group](https://groups.google.com/forum/#!forum/modflow). Other MODFLOW resources are listed in the [MODFLOW Resources](https://github.com/modflowpy/flopy#modflow-resources) section.
Contributing
------------------------------------------------
Installation
-----------------------------------------------
Bug reports, code contributions, or improvements to the documentation are welcome from the community. Prior to contributing, please read up on our guidelines for [contributing](CONTRIBUTING.md) and then check out one of our issues in the [hotlist: community-help](https://github.com/modflowpy/flopy/labels/hotlist%3A%20community%20help).
FloPy requires **Python** 3.5 (or higher) and **NumPy** 1.9 (or higher). Dependencies for optional FloPy methods are summarized [here](docs/flopy_method_dependencies.md).
To install FloPy type:
conda install -c conda-forge flopy
or
pip install flopy
The release candidate version can also be installed from the git repository using the instructions provided [below](#relcand).
Documentation
@ -23,11 +34,11 @@ How to Cite
*Citation for FloPy:*
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
*Software/Code citation for FloPy:*
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0: U.S. Geological Survey Software Release, 14 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2020, FloPy v3.3.1: U.S. Geological Survey Software Release, 26 June 2020, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
Disclaimer
@ -45,12 +56,12 @@ unauthorized use.
Installation
-----------------------------------------------
To install FloPy version 3.3.0:
To install FloPy version 3.3.1:
```
pip install flopy
```
To update to FloPy version 3.3.0:
To update to FloPy version 3.3.1:
```
pip install flopy --upgrade
```

35
docs/USGS_release.md
View File

@ -12,7 +12,7 @@ author:
- Michael W. Toews
- Eric D. Morway
- Jason C. Bellino
- Jeffrey J. Starn
- Jon J. Starn
- Michael N. Fienen
header-includes:
- \usepackage{fancyhdr}
@ -21,9 +21,9 @@ header-includes:
- \fancyhf{{}}
- \fancyhead[LE, LO, RE, RO]{}
- \fancyhead[CE, CO]{FloPy Release Notes}
- \fancyfoot[LE, RO]{FloPy version 3.3.0}
- \fancyfoot[LE, RO]{FloPy version 3.3.1}
- \fancyfoot[CO, CE]{\thepage\ of \pageref{LastPage}}
- \fancyfoot[RE, LO]{12/14/2019}
- \fancyfoot[RE, LO]{06/26/2020}
geometry: margin=0.75in
---
@ -35,10 +35,21 @@ FloPy includes support for MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, an
For general modeling issues, please consult a modeling forum, such as the [MODFLOW Users Group](https://groups.google.com/forum/#!forum/modflow). Other MODFLOW resources are listed in the [MODFLOW Resources](https://github.com/modflowpy/flopy#modflow-resources) section.
Contributing
------------------------------------------------
Installation
-----------------------------------------------
Bug reports, code contributions, or improvements to the documentation are welcome from the community. Prior to contributing, please read up on our guidelines for [contributing](CONTRIBUTING.md) and then check out one of our issues in the [hotlist: community-help](https://github.com/modflowpy/flopy/labels/hotlist%3A%20community%20help).
FloPy requires **Python** 3.5 (or higher) and **NumPy** 1.9 (or higher). Dependencies for optional FloPy methods are summarized [here](docs/flopy_method_dependencies.md).
To install FloPy type:
conda install -c conda-forge flopy
or
pip install flopy
The release candidate version can also be installed from the git repository using the instructions provided [below](#relcand).
Documentation
@ -52,11 +63,11 @@ How to Cite
##### ***Citation for FloPy:***
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, doi:10.1111/gwat.12413.](http://dx.doi.org/10.1111/gwat.12413)
##### ***Software/Code citation for FloPy:***
[Bakker, M., Post, V., Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2019, FloPy v3.3.0: U.S. Geological Survey Software Release, 14 December 2019, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
[Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Leaf, A. T., Paulinski, S. R., Larsen, J. D., Toews, M. W., Morway, E. D., Bellino, J. C., Starn, J. J., and Fienen, M. N., 2020, FloPy v3.3.1: U.S. Geological Survey Software Release, 26 June 2020, http://dx.doi.org/10.5066/F7BK19FH](http://dx.doi.org/10.5066/F7BK19FH)
Disclaimer
@ -74,12 +85,12 @@ unauthorized use.
Installation
-----------------------------------------------
To install FloPy version 3.3.0 from the USGS FloPy website:
To install FloPy version 3.3.1 from the USGS FloPy website:
```
pip install https://water.usgs.gov/ogw/flopy/flopy-3.3.0.zip
pip install https://water.usgs.gov/ogw/flopy/flopy-3.3.1.zip
```
To update to FloPy version 3.3.0 from the USGS FloPy website:
To update to FloPy version 3.3.1 from the USGS FloPy website:
```
pip install https://water.usgs.gov/ogw/flopy/flopy-3.3.0.zip --upgrade
pip install https://water.usgs.gov/ogw/flopy/flopy-3.3.1.zip --upgrade
```

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21
docs/flopyFAQ.md
View File

@ -1,21 +0,0 @@
Frequently Asked Questions
----------------------------------
#### Create a new model
#### Working with existing models
+ [How do I load an existing MODFLOW-2005 model](../examples/FAQ/load_existing_mf2005.ipynb)
+ [How do I load an existing MODFLOW model with auxiliary stress package data](../examples/FAQ/load_existing_model_wAUX.ipynb)
#### Running a MODFLOW model
+ [MODFLOW-2005 does not exist or is not executable](../examples/FAQ/mf2005_does_not_exist.ipynb)
#### Plotting model input and output
#### Exporting model input and output
#### Checking MODFLOW datasets
#### Advanced use of FloPy

35
docs/flopy_method_dependencies.md Normal file
View File

@ -0,0 +1,35 @@
Additional dependencies to use optional FloPy helper methods are listed below.
| Method | Python Package |
| ------------------------------------------------------------------------------------ | ------------------------------------------------------------------ |
| `.PlotMapView()` in `flopy.plot` | **matplotlib** >= 1.4 |
| `.PlotCrossSection()` in `flopy.plot` | **matplotlib** >= 1.4 |
| `.plot()` | **matplotlib** >= 1.4 |
| `.plot_shapefile()` | **matplotlib** >= 1.4 and **Pyshp** >= 1.2 |
| `.to_shapefile()` | **Pyshp** >= 1.2 |
| `.export(*.shp)` | **Pyshp** >= 1.2 |
| `.export(*.nc)` | **netcdf4** >= 1.1, and **python-dateutil** >= 2.4 |
| `.export(*.tif)` | **rasterio** |
| `.export(*.asc)` in `flopy.utils.reference` `SpatialReference` class | **scipy.ndimage** |
| `.interpolate()` in `flopy.utils.reference` `SpatialReference` class | **scipy.interpolate** |
| `.interpolate()` in `flopy.mf6.utils.reference` `StructuredSpatialReference` class | **scipy.interpolate** |
| `._parse_units_from_proj4()` in `flopy.utils.reference` `SpatialReference` class | **pyproj** |
| `.get_dataframes()` in `flopy.utils.mflistfile` `ListBudget` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.observationfile` `ObsFiles` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.sfroutputfile` `ModflowSfr2` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.util_list` `MfList` class | **pandas** >= 0.15 |
| `.get_dataframes()` in `flopy.utils.zonebud` `ZoneBudget` class | **pandas** >= 0.15 |
| `.pivot_keyarray()` in `flopy.mf6.utils.arrayutils` `AdvancedPackageUtil` class | **pandas** >= 0.15 |
| `._get_vertices()` in `flopy.mf6.utils.binaryfile_utils` `MFOutputRequester` class | **pandas** >= 0.15 |
| `.get_dataframe()` in `flopy.mf6.utils.mfobservation` `Observations` class | **pandas** >= 0.15 |
| `.df()` in `flopy.modflow.mfsfr2` `SfrFile` class | **pandas** >= 0.15 |
| `.time_coverage()` in `flopy.export.metadata` `acc` class - ***used if available*** | **pandas** >= 0.15 |
| `.loadtxt()` in `flopy.utils.flopyio` - ***used if available*** | **pandas** >= 0.15 |
| `.generate_classes()` in `flopy.mf6.utils` | [**pymake**](https://github.com/modflowpy/pymake) |
| `.intersect()` in `flopy.discretization.VertexGrid` | **matplotlib** >= 1.4 |
| `GridIntersect()` in `flopy.utils.gridintersect` | **shapely** |
| `GridIntersect().plot_polygon()` in `flopy.utils.gridintersect` | **shapely** and **descartes** |
| `Raster()` in `flopy.utils.Raster` | **rasterio**, **affine**, and **scipy** |
| `Raster().sample_polygon()` in `flopy.utils.Raster` | **shapely** |
| `Raster().crop()` in `flopy.utils.Raster` | **shapely** |
| `.array_at_verts()` in `flopy.discretization.structuredgrid` `StructuredGrid` class | **scipy.interpolate** |

10
docs/make_release.md
View File

@ -20,7 +20,7 @@ Instructions for making a FloPy release
## Update the Software/Code citation for FloPy
1. Update the `authors` list in `release/make-release.py` for the Software/Code citation for FloPy, if required.
1. Update the `author_dict` in `flopy/version.py` for the Software/Code citation for FloPy, if required.
## Build USGS release notes
@ -31,7 +31,13 @@ Instructions for making a FloPy release
python make-release.py
```
2. Run pandoc from the terminal in the root directory to create USGS release notes using:
2. Manually run `update-version_changes.py` in the `release/` directory to update version changes information using:
```
python update-version_changes.py
```
3. Run pandoc from the terminal in the root directory to create USGS release notes using:
```
pandoc -o ./docs/USGS_release.pdf ./docs/USGS_release.md ./docs/supported_packages.md ./docs/model_checks.md ./docs/version_changes.md

96
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View File

@ -1,48 +1,48 @@
Introduction
-----------------------------------------------
This file provides an overview of how FloPy for MODFLOW 6 (FPMF6) works under the hood and is intended for anyone who wants to add a new package, new model type, or new features to this library. FloPy library files that support MODFLOW 6 can be found in the flopy/mf6 folder and sub-folders.
Package Meta-Data and Package Files
-----------------------------------------------
FPMF6 uses meta-data files located in flopy/mf6/data/dfn to define the model and package types supported by MODFLOW 6. When additional model and package types are added to MODFLOW 6, additional meta-data files can be added to this folder and flopy/mf6/utils/createpackages.py can be run to add new packages to the FloPy library. createpackages.py uses flopy/mf6/data/mfstructure.py to read meta-data files (*.dfn) and use that meta-data to create the package files found in flopy/mf6/modflow (do not directly modify any of the files in this folder, they are all automatically generated). The automatically generated package files contain an interface for accessing package data and data documentation generated from the meta-data files. Additionally, meta-data describing package data types and shapes is stored in the dfn attribute. flopy/mf6/data/mfstructure.py can load structure information using the dfn attribute (instead of loading it from the meta-data files). This allows for flopy to be installed without the dfn files.
All meta-data can be accessed from the flopy.mf6.data.mfstructure.MFStructure class. This is a singleton class, meaning only one instance of this class can be created. The class contains a sim_struct attribute (which is a flopy.mf6.data.mfstructure.MFSimulationStructure object) which contains all of the meta-data for all package files. Meta-data is stored in a structured format. MFSimulationStructure contains MFModelStructure and MFInputFileStructure objects, which contain the meta-data for each model type and each "simulation-level" package (tdis, ims, ...). MFModelStructure contains model specific meta-data and a MFInputFileStructure object for each package in that model. MFInputFileStructure contains package specific meta-data and a MFBlockStructure object for each block contained in the package file. MFBlockStructure contains block specific meta-data and a MFDataStructure object for each data structure defined in the block, and MFDataStructure contains data structure specific meta-data and a MFDataItemStructure object for each data item contained in the data structure. Data structures define the structure of data that is naturally grouped together, for example, the data in a numpy recarray. Data item structures define the structure of specific pieces of data, for example, a single column of a numpy recarray. The meta-data defined in these classes provides all the information FloPy needs to read and write MODFLOW 6 package and name files, create the Flopy interface, and check the data for various constraints.
***
MFStructure --+ MFSimulationStructure --+ MFModelStructure --+ MFInputFileStructure --+ MFBlockStructure --+ MFDataStructure --+ MFDataItemStructure
Figure 1: FPMF6 generic data structure classes. Lines connecting classes show a relationship defined between the two connected classes. A "*" next to the class means that the class is a sub-class of the connected class. A "+" next to the class means that the class is contained within the connected class.
***
Package and Data Base Classes
-----------------------------------------------
The package and data classes are related as shown below in figure 2. On the top of the figure 2 is the MFPackage class, which is the base class for all packages. MFPackage contains generic methods for building data objects and reading and writing the package to a file. MFPackage contains a MFInputFileStructure object that defines how the data is structured in the package file. MFPackage also contains a dictionary of blocks (MFBlock). The MFBlock class is a generic class used to represent a block within a package. MFBlock contains a MFBlockStructure object that defines how the data in the block is structured. MFBlock also contains a dictionary of data objects (subclasses of MFData) contained in the block and a list of block headers (MFBlockHeader) for that block. Block headers contain the block's name and optionally data items (eg. iprn).
***
MFPackage --+ MFBlock --+ MFData
MFPackage --+ MFInputFileStructure
MFBlock --+ MFBlockStructure
MFData --+ MFDataStructure
MFData --* MFArray --* MFTransientArray
MFData --* MFList --* MFTransientList
MFData --* MFScalar --* MFTransientScalar
MFTransientData --* MFTransientArray, MFTransientList, MFTransientScalar
Figure 2: FPMF6 package and data classes. Lines connecting classes show a relationship defined between the two connected classes. A "*" next to the class means that the class is a sub-class of the connected class. A "+" next to the class means that the class is contained within the connected class.
***
There are three main types of data, MFList, MFArray, and MFScalar data. All three of these data types are derived from the MFData abstract base class. MFList data is the type of data stored in a spreadsheet with different column headings. For example, the data describing a flow barrier are of type MFList. MFList data is stored in numpy recarrays. MFArray data is data of a single type (eg. all integer values). For example, the model's HK values are of type MFArray. MFArrays are stored in numpy ndarrays. MFScalar data is a single data item. Most MFScalar data are options. All MFData subclasses contain an MFDataStructure object that defines the expected structure and types of the data.
Transient data, or data defined for each stress period (eg. data in the period blocks) is stored in MFTransientArray, MFTransientList, and MFTransientScalar. These classes are sub-classes of MFArray, MFList, and MFScalar, respectively. These classes are also subclasses of MFTransientData.
Introduction
-----------------------------------------------
This file provides an overview of how FloPy for MODFLOW 6 (FPMF6) works under the hood and is intended for anyone who wants to add a new package, new model type, or new features to this library. FloPy library files that support MODFLOW 6 can be found in the flopy/mf6 folder and sub-folders.
Package Meta-Data and Package Files
-----------------------------------------------
FPMF6 uses meta-data files located in flopy/mf6/data/dfn to define the model and package types supported by MODFLOW 6. When additional model and package types are added to MODFLOW 6, additional meta-data files can be added to this folder and flopy/mf6/utils/createpackages.py can be run to add new packages to the FloPy library. createpackages.py uses flopy/mf6/data/mfstructure.py to read meta-data files (*.dfn) and use that meta-data to create the package files found in flopy/mf6/modflow (do not directly modify any of the files in this folder, they are all automatically generated). The automatically generated package files contain an interface for accessing package data and data documentation generated from the meta-data files. Additionally, meta-data describing package data types and shapes is stored in the dfn attribute. flopy/mf6/data/mfstructure.py can load structure information using the dfn attribute (instead of loading it from the meta-data files). This allows for flopy to be installed without the dfn files.
All meta-data can be accessed from the flopy.mf6.data.mfstructure.MFStructure class. This is a singleton class, meaning only one instance of this class can be created. The class contains a sim_struct attribute (which is a flopy.mf6.data.mfstructure.MFSimulationStructure object) which contains all of the meta-data for all package files. Meta-data is stored in a structured format. MFSimulationStructure contains MFModelStructure and MFInputFileStructure objects, which contain the meta-data for each model type and each "simulation-level" package (tdis, ims, ...). MFModelStructure contains model specific meta-data and a MFInputFileStructure object for each package in that model. MFInputFileStructure contains package specific meta-data and a MFBlockStructure object for each block contained in the package file. MFBlockStructure contains block specific meta-data and a MFDataStructure object for each data structure defined in the block, and MFDataStructure contains data structure specific meta-data and a MFDataItemStructure object for each data item contained in the data structure. Data structures define the structure of data that is naturally grouped together, for example, the data in a numpy recarray. Data item structures define the structure of specific pieces of data, for example, a single column of a numpy recarray. The meta-data defined in these classes provides all the information FloPy needs to read and write MODFLOW 6 package and name files, create the Flopy interface, and check the data for various constraints.
***
MFStructure --+ MFSimulationStructure --+ MFModelStructure --+ MFInputFileStructure --+ MFBlockStructure --+ MFDataStructure --+ MFDataItemStructure
Figure 1: FPMF6 generic data structure classes. Lines connecting classes show a relationship defined between the two connected classes. A "*" next to the class means that the class is a sub-class of the connected class. A "+" next to the class means that the class is contained within the connected class.
***
Package and Data Base Classes
-----------------------------------------------
The package and data classes are related as shown below in figure 2. On the top of the figure 2 is the MFPackage class, which is the base class for all packages. MFPackage contains generic methods for building data objects and reading and writing the package to a file. MFPackage contains a MFInputFileStructure object that defines how the data is structured in the package file. MFPackage also contains a dictionary of blocks (MFBlock). The MFBlock class is a generic class used to represent a block within a package. MFBlock contains a MFBlockStructure object that defines how the data in the block is structured. MFBlock also contains a dictionary of data objects (subclasses of MFData) contained in the block and a list of block headers (MFBlockHeader) for that block. Block headers contain the block's name and optionally data items (eg. iprn).
***
MFPackage --+ MFBlock --+ MFData
MFPackage --+ MFInputFileStructure
MFBlock --+ MFBlockStructure
MFData --+ MFDataStructure
MFData --* MFArray --* MFTransientArray
MFData --* MFList --* MFTransientList
MFData --* MFScalar --* MFTransientScalar
MFTransientData --* MFTransientArray, MFTransientList, MFTransientScalar
Figure 2: FPMF6 package and data classes. Lines connecting classes show a relationship defined between the two connected classes. A "*" next to the class means that the class is a sub-class of the connected class. A "+" next to the class means that the class is contained within the connected class.
***
There are three main types of data, MFList, MFArray, and MFScalar data. All three of these data types are derived from the MFData abstract base class. MFList data is the type of data stored in a spreadsheet with different column headings. For example, the data describing a flow barrier are of type MFList. MFList data is stored in numpy recarrays. MFArray data is data of a single type (eg. all integer values). For example, the model's HK values are of type MFArray. MFArrays are stored in numpy ndarrays. MFScalar data is a single data item. Most MFScalar data are options. All MFData subclasses contain an MFDataStructure object that defines the expected structure and types of the data.
Transient data, or data defined for each stress period (eg. data in the period blocks) is stored in MFTransientArray, MFTransientList, and MFTransientScalar. These classes are sub-classes of MFArray, MFList, and MFScalar, respectively. These classes are also subclasses of MFTransientData.

70
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View File

@ -1,5 +1,75 @@
FloPy Changes
-----------------------------------------------
### Version 3.3.1
* New features:
* [feat(ModflowAg)](https://github.com/modflowpy/flopy/commit/c89b2d83a81125c986c05df57ffc980fe10fd663): Add the modflowag package for nwt (pull request #922). Committed by Joshua Larsen on 2020-06-25.
* [feat(GridIntersect)](https://github.com/modflowpy/flopy/commit/176c9b45eb158217b1aeb0657d60ed06739e53e6): #902 (#903). Committed by Davíd Brakenhoff on 2020-06-10.
* [feat(mbase)](https://github.com/modflowpy/flopy/commit/4fc61d573c108be7601a2e8479a86c35040998c2): Suppress duplicate package warning if verbose is false (#908). Committed by Hughes, J.D on 2020-06-09.
* [feat(ModflowSms)](https://github.com/modflowpy/flopy/commit/f539d072e20cb5654fab8826ac3bbaf7d1f8b52e): Add support for simple, moderate, complex (#906). Committed by langevin-usgs on 2020-06-09.
* [feat(str)](https://github.com/modflowpy/flopy/commit/3182f57479c1a45d614151867f419a0d35f7f2c2): Add irdflg and iptflg control to str (#905). Committed by Hughes, J.D on 2020-06-09.
* [feat(Mf6ListBudget)](https://github.com/modflowpy/flopy/commit/04b74bd8fb4ed71cf0ed07f721204296b9fd4388): Add support for mf6 budgets with multiple packages with same name (#900). Committed by langevin-usgs on 2020-06-02.
* [feat(mfchd.py)](https://github.com/modflowpy/flopy/commit/88fbd4ccdf837dd4b2a70795522fcaa0a2470dfe): Prevent write chk-file always (#869). Committed by Ralf Junghanns on 2020-05-08.
* [feat(set all data external)](https://github.com/modflowpy/flopy/commit/0336b5c4f6c62994a7ffea26318240fbaa0ca1fb): Set all data external for simulation (#846). Committed by spaulins-usgs on 2020-04-08.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/e43dccc29d87e182aaa82687968d98391fa78e5d): Improve export at vertices (#844). Committed by Etienne Bresciani on 2020-04-06.
* [feat(netcdf)](https://github.com/modflowpy/flopy/commit/fb942b4675c335247b81f9287bdb8cdb3bcf360b): Use modern features from pyproj>=2.2.0 (#840). Committed by Mike Taves on 2020-03-31.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/b975368a9c5a25df616b024a08450056e92b6426): Export vectors to vtk. Committed by Etienne Bresciani on 2020-03-31.
* [feat(vtk)](https://github.com/modflowpy/flopy/commit/13c1dd28b9c470c70aac624b70888f5f6badf795): Export in .vti and .vtr when possible. Committed by Etienne Bresciani on 2020-03-28.
* [feat(vectors)](https://github.com/modflowpy/flopy/commit/1284871e5b8ed26c9d925e28295c2098a76b1bc9): Vector plots when stresses applied along boundaries (#817). Committed by langevin-usgs on 2020-03-05.
* [feat(plot_bc)](https://github.com/modflowpy/flopy/commit/207cd1ee5dde116e5b8912232d9b94a9c9304161): Updated plot_bc for maw, uzf, sfr, and multiple bc packages (#808). Committed by Joshua Larsen on 2020-02-11.
* [feat(disl grids)](https://github.com/modflowpy/flopy/commit/469727bcb695ee42611f3df227830ef3b25853f6): Support for 1d vertex grids. fix for writing gridlines to shapefile (#799). Committed by spaulins-usgs on 2020-02-04.
* [feat(zb netcdf)](https://github.com/modflowpy/flopy/commit/491f4fe3923a942e9a0d535a7da54173c4df1204): Zonebudget netcdf export support added (#781). Committed by Joshua Larsen on 2020-01-17.
* [feat(mf6 checker)](https://github.com/modflowpy/flopy/commit/088f147f1d761875f3a1ffabdda82312c002305a): Input data check for mf6 (#779). Committed by spaulins-usgs on 2020-01-16.
* Bug fixes:
* [fix(#280, #835)](https://github.com/modflowpy/flopy/commit/6dae1b0ed5df6836ce6ea981de7050621a90477f): Set_all_data_external now includes constants, cellids in list data are checked (#920). Committed by spaulins-usgs on 2020-06-23.
* [fix(mfsfr2.check)](https://github.com/modflowpy/flopy/commit/796b7b15385de0181cabd33d3bc1915bfa76a83b): Negative segments for lakes no longer included in segment numbering order check (#915). Committed by aleaf on 2020-06-23.
* [fix(GridIntersect)](https://github.com/modflowpy/flopy/commit/d5672f585faa31ead48973834d9b30cf70512cba): Fixes #916 and #917 (#918). Committed by Davíd Brakenhoff on 2020-06-22.
* [fix(ZoneBudget)](https://github.com/modflowpy/flopy/commit/0207372769c5389835c555820c11fc377a4370c7): Fix faulty logic in ZoneBudget (#911). Committed by Jason Bellino on 2020-06-22.
* [fix(SwtListBudget)](https://github.com/modflowpy/flopy/commit/eed5afdd03917256b097a797ec1137c2b80fb8a1): Totim was not being read correctly for seawat list file (#910). Committed by langevin-usgs on 2020-06-10.
* [fix(Seawat.modelgrid)](https://github.com/modflowpy/flopy/commit/7a31a1d7a210894d9970e2e7a3a6a6453518289b): Pass lenuni from dis file into modelgrid instance (#901). Committed by Joshua Larsen on 2020-06-02.
* [fix(mfsimulation)](https://github.com/modflowpy/flopy/commit/0958b28added4b572b168c35657f1d5fd968e952): Repair change for case insensitive model names (#897). Committed by langevin-usgs on 2020-06-01.
* [fix(_plot_util3d_helper, export_array)](https://github.com/modflowpy/flopy/commit/617b98dd0f5750c7cf4d1a9e8376e00fdb4e94bf): (#895). Committed by Joshua Larsen on 2020-06-01.
* [fix()](https://github.com/modflowpy/flopy/commit/8e70c9284490b220ef6fe759b0fafbb5d252f1ae): fix building in clean env (#894). Committed by Ritchie Vink on 2020-05-28.
* [fix(setup.py)](https://github.com/modflowpy/flopy/commit/b80a89c18821fe1bc7375c15e4c03d1e0be70916): Read package name, version, etc. from version.py (#893). Committed by Hughes, J.D on 2020-05-26.
* [fix(MFSimulation)](https://github.com/modflowpy/flopy/commit/3cec7929f323e7753ef80e95b31a64a6105dce41): Remove case sensitivity from register_ims_package() (#890). Committed by Joshua Larsen on 2020-05-25.
* [fix(modelgrid)](https://github.com/modflowpy/flopy/commit/bb861ac2f05e7e8d38a832d03ae0a45a2249d10d): Fix offset for xul and yul in read_usgs_model_reference_file and attribs_from_namfile_header (#889). Committed by Joshua Larsen on 2020-05-19.
* [fix(#886)](https://github.com/modflowpy/flopy/commit/f4e5ed39c5316e9bd2b7941c31f1b91253cd51e5): Mfarray aux variable now always returned as an numpy.ndarray. fixed problem with pylistutil not fully supporting numpy.ndarray type. (#887). Committed by spaulins-usgs on 2020-05-19.
* [fix(CellBudgetFile)](https://github.com/modflowpy/flopy/commit/29d7f849f8d2f160a537494661bd096a9e1c1253): Update for auto precision with imeth = 5 or 6 (#876). Committed by Joshua Larsen on 2020-05-14.
* [fix(#870)](https://github.com/modflowpy/flopy/commit/cbf1f65a8f3389f55bb55249ce8c358ac06cf75c): Update ims name file record after removing ims package (#880). Committed by Joshua Larsen on 2020-05-14.
* [fix](https://github.com/modflowpy/flopy/commit/e3a6c26fe8ad39c69cd5fec78064f12d2edbb521): #868, #874, #879 (#881). Committed by spaulins-usgs on 2020-05-14.
* [fix(#867)](https://github.com/modflowpy/flopy/commit/265fc7c64956b9165b9be2607680de086a9cf973): Fixed minimum record entry count for lists to never include keywords in the count (#875). Committed by spaulins-usgs on 2020-05-11.
* [fix(SfrFile)](https://github.com/modflowpy/flopy/commit/4100de2b80cdb542e820f3b41a88eaf9865fa63d): Update sfrfile for streambed elevation when present (#866). Committed by Joshua Larsen on 2020-05-04.
* [fix(#831,#858)](https://github.com/modflowpy/flopy/commit/a177d59c691367e568de07b340d53e8b1f2322fb): Data length check and case-insensitive lookup (#864). Committed by spaulins-usgs on 2020-05-01.
* [fix(#856)](https://github.com/modflowpy/flopy/commit/c45a5e5f1fb2f8224d87307564b68dc1c30063d9): Specifying period data with value none now only removes data from that period. also, fixed an unrelated problem by updating the multi-package list. (#857). Committed by spaulins-usgs on 2020-04-22.
* [fix(plot_array)](https://github.com/modflowpy/flopy/commit/f6545ff28004f4f6573e07aab939d774230df0a6): Update plot_array method to mask using np.ma.masked_values (#851). Committed by Joshua Larsen on 2020-04-15.
* [fix(ModflowDis)](https://github.com/modflowpy/flopy/commit/52ecd98a11fc4f459c9bd0b59cb854ff402eeb08): Zero based get_node() and get_lrc()… (#847). Committed by Joshua Larsen on 2020-04-10.
* [fix(binaryfile_utils, CellbudgetFile)](https://github.com/modflowpy/flopy/commit/f514a22a38264dc81c0db6dae62db4beae8df227): Update for imeth == 6 (#823). Committed by Joshua Larsen on 2020-04-10.
* [fix(utils.gridintersect)](https://github.com/modflowpy/flopy/commit/14040ff605dfe496d8ec88ca8eeb3f73daeee06e): Bug in gridintersect for vertex grids (#845). Committed by Davíd Brakenhoff on 2020-04-06.
* [fix(mflmt.py)](https://github.com/modflowpy/flopy/commit/1f322f0ef50be9dfaa2252cacb091aded4159113): Clean up docstring for package_flows argument in lmt. Committed by emorway-usgs on 2020-03-31.
* [fix(str)](https://github.com/modflowpy/flopy/commit/59cac5c0466b497c36e833784b436d4a5e47fcd5): Add consistent fixed and free format approach (#838). Committed by Hughes, J.D on 2020-03-31.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/aa9f3148008dd4c23d86db4e4dae5bae8c8bc564): Issues related to nan and type cast. Committed by Etienne Bresciani on 2020-03-31.
* [fix(pyproj)](https://github.com/modflowpy/flopy/commit/9a1b9e344aefad4ed222bd8d10eb6b9000c9c7d0): Pyproj.proj's errcheck keyword option not reliable (#837). Committed by Mike Taves on 2020-03-29.
* [fix](https://github.com/modflowpy/flopy/commit/4bfab916592784180d57df59b78d190e28c9099b): (#830): handling 'none' cellids in sfr package (#834). Committed by spaulins-usgs on 2020-03-25.
* [fix()](https://github.com/modflowpy/flopy/commit/90a498ea2356e0eca7ddbf1c89a0f5f12f14b5a3): Fix quasi3d plotting (#819). Committed by Ruben Caljé on 2020-03-02.
* [fix(ModflowSfr2.export)](https://github.com/modflowpy/flopy/commit/b6c9a3a6668ee8a35fda785da3709bd4842b7ba9): Update modflowsfr2.export() to use grid instead of spatialreference (#820). Committed by Joshua Larsen on 2020-02-28.
* [fix(flopy3_MT3DMS_examples.ipynb)](https://github.com/modflowpy/flopy/commit/65e8adaeea55a14a3d61c125801741c5b9ceb699): Wrong indices were indexed (#815). Committed by Eric Morway on 2020-02-20.
* [fix(build_exes.py)](https://github.com/modflowpy/flopy/commit/f3136a233274baa63ace7555d862c43bc67894f5): Fix bugs for windows (#810) (#813). Committed by Etienne Bresciani on 2020-02-18.
* [fix(mflist)](https://github.com/modflowpy/flopy/commit/4a885a107ee5ead5a116f95bb1f7f60549cba295): Default value not working (#812). Committed by langevin-usgs on 2020-02-13.
* [fix(flopy3_MT3DMS_examples.ipynb)](https://github.com/modflowpy/flopy/commit/0d152513d4ecb84fd474cb0495dd0676f05d5b72): Match constant heads to original problem (#809). Committed by Eric Morway on 2020-02-11.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/ab8120bc3dc1214fef90077ade226471900b89d5): Change in export_cbc output file name (#795). Committed by rodrperezi on 2020-01-30.
* [fix(mf6)](https://github.com/modflowpy/flopy/commit/84ee8a72b00fbcd8e7f396af9b356170634cfda6): Update create packages to support additional models (#790). Committed by Hughes, J.D on 2020-01-24.
* [fix(remove_package)](https://github.com/modflowpy/flopy/commit/102d25b23dc0281cccf65eb0a9d3cc8b05755484): Fixed remove_package to rebuild namefile recarray correctly after removing package - issue #776 (#784). Committed by spaulins-usgs on 2020-01-17.
* [fix(gridgen)](https://github.com/modflowpy/flopy/commit/061c72771ae4bc023e970bf9048a4c53bba2ba80): X, y center was not correct for rotated grids (#783). Committed by langevin-usgs on 2020-01-16.
* [fix(mtssm.py)](https://github.com/modflowpy/flopy/commit/f7886e2762464f69ae6b1e3ef1124bbee017b8a8): Handle 1st stress period with incrch equal to -1 (#780). Committed by Eric Morway on 2020-01-16.
* [fix(vtk)](https://github.com/modflowpy/flopy/commit/73f70518238ff383628ba25066c41647e875dc2e): Change in export_model when packages_names is none (#770). Committed by rodrperezi on 2019-12-30.
* [fix()](https://github.com/modflowpy/flopy/commit/ec71e6ce2d2f4bc3d05e3172cccba6c42bf26b87): fix(repeating blocks) (#771). Committed by spaulins-usgs on 2019-12-30.
* [fix(replace package)](https://github.com/modflowpy/flopy/commit/cf3586f0602acd20c9c672b2c763f09c6a252e00): When a second package of the same type is added to a model, the model now checks to see if the package type supports multiple packages. if it does not it automatically removes the first package before adding the second (#767). (#768). Committed by spaulins-usgs on 2019-12-18.
* [fix(Mflist)](https://github.com/modflowpy/flopy/commit/51d80641e81f844490306d2cddefacb21bda8302): Allow none as a list entry (#765). Committed by langevin-usgs on 2019-12-16.
### Version 3.3.0
* Dropped support for python 2.7

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examples/Notebooks/flopy3.3_PlotCrossSection.ipynb
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examples/Notebooks/flopy3_LoadSWRBinaryData.ipynb
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@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.2.13\n"
"flopy version: 3.3.1\n"
]
}
],

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examples/Notebooks/flopy3_MT3D-USGS_example.ipynb
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examples/Notebooks/flopy3_MT3DMS_examples.ipynb
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examples/Notebooks/flopy3_ModelCheckerExample.ipynb
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@ -21,7 +21,7 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -169,8 +169,8 @@
" RCH package: Variable NRCHOP set to value other than 3\n",
"\n",
" Checks that passed:\n",
" Compatible solver package\n",
" Unit number conflicts\n",
" Compatible solver package\n",
" DIS package: zero or negative thickness\n",
" DIS package: thin cells (less than checker threshold of 1.0)\n",
" DIS package: nan values in top array\n",
@ -178,7 +178,6 @@
" BAS6 package: isolated cells in ibound array\n",
" BAS6 package: Not a number\n",
" LPF package: zero or negative horizontal hydraulic conductivity values\n",
" LPF package: zero or negative vertical hydraulic conductivity values\n",
" LPF package: negative horizontal anisotropy values\n",
" LPF package: vertical hydraulic conductivity values below checker threshold of 1e-11\n",
" LPF package: vertical hydraulic conductivity values above checker threshold of 100000.0\n",
@ -257,13 +256,16 @@
"\n",
"test1ss MODEL DATA VALIDATION SUMMARY:\n",
" 3 Warnings:\n",
" 1 instance of \r",
" OC package: action(s) defined in OC stress_period_data ignored as they are not part the stress periods defined by DIS\n",
" 1 instance of \r",
" RCH package: Mean R/T ratio < checker warning threshold of 2e-08 for 1 stress periods\n",
" 1 instance of \r",
" RCH package: Variable NRCHOP set to value other than 3\n",
"\n",
" Checks that passed:\n",
" Compatible solver package\n",
" Unit number conflicts\n",
" Compatible solver package\n",
" DIS package: zero or negative thickness\n",
" DIS package: thin cells (less than checker threshold of 1.0)\n",
" DIS package: nan values in top array\n",
@ -271,7 +273,6 @@
" BAS6 package: isolated cells in ibound array\n",
" BAS6 package: Not a number\n",
" LPF package: zero or negative horizontal hydraulic conductivity values\n",
" LPF package: zero or negative vertical hydraulic conductivity values\n",
" LPF package: negative horizontal anisotropy values\n",
" LPF package: vertical hydraulic conductivity values below checker threshold of 1e-11\n",
" LPF package: vertical hydraulic conductivity values above checker threshold of 100000.0\n",
@ -292,7 +293,7 @@
{
"data": {
"text/plain": [
"<flopy.utils.check.check at 0x1234fe7b8>"
"<flopy.utils.check.check at 0x11fbee400>"
]
},
"execution_count": 7,
@ -333,7 +334,7 @@
{
"data": {
"text/plain": [
"<flopy.utils.check.check at 0x1235208d0>"
"<flopy.utils.check.check at 0x11fbeeef0>"
]
},
"execution_count": 8,
@ -373,8 +374,8 @@
" see data/checksummary.csv for details.\n",
"\n",
" Checks that passed:\n",
" Compatible solver package\n",
" Unit number conflicts\n",
" Compatible solver package\n",
" DIS package: zero or negative thickness\n",
" DIS package: thin cells (less than checker threshold of 1.0)\n",
" DIS package: nan values in top array\n",
@ -382,7 +383,6 @@
" BAS6 package: isolated cells in ibound array\n",
" BAS6 package: Not a number\n",
" LPF package: zero or negative horizontal hydraulic conductivity values\n",
" LPF package: zero or negative vertical hydraulic conductivity values\n",
" LPF package: negative horizontal anisotropy values\n",
" LPF package: vertical hydraulic conductivity values below checker threshold of 1e-11\n",
" LPF package: vertical hydraulic conductivity values above checker threshold of 100000.0\n",
@ -398,7 +398,7 @@
{
"data": {
"text/plain": [
"<flopy.utils.check.check at 0x123523d68>"
"<flopy.utils.check.check at 0x11fc5a0f0>"
]
},
"execution_count": 9,

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examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb
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@ -21,7 +21,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -229,7 +229,7 @@
"output_type": "stream",
"text": [
"{'driver': 'GTiff', 'dtype': 'float32', 'nodata': 0.0, 'width': 25, 'height': 25, 'count': 1, 'crs': None, 'transform': Affine(400.0, 0.0, 0.0,\n",
" 0.0, -400.0, 0.0)}\n"
" 0.0, -400.0, 10000.0)}\n"
]
},
{

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examples/Notebooks/flopy3_PEST.ipynb
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@ -22,7 +22,7 @@
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

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examples/Notebooks/flopy3_PlotArrayExample.ipynb
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@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

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examples/Notebooks/flopy3_SEAWAT_henry_problem.ipynb
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@ -24,7 +24,7 @@
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -193,7 +193,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
" Elapsed run time: 8.450 Seconds\n",
" Elapsed run time: 9.030 Seconds\n",
"\n",
" Normal termination of SEAWAT\n"
]
@ -340,7 +340,7 @@
"output_type": "stream",
"text": [
"Util2d:hk layer 1: resetting 'how' to external\n",
" Elapsed run time: 8.282 Seconds\n",
" Elapsed run time: 9.038 Seconds\n",
"\n",
" Normal termination of SEAWAT\n"
]

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examples/Notebooks/flopy3_SFR2_load.ipynb
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@ -21,7 +21,7 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

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examples/Notebooks/flopy3_SpatialReference_demo.ipynb
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@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

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examples/Notebooks/flopy3_WatertableRecharge_example.ipynb
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@ -31,7 +31,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -208,16 +208,16 @@
" MODFLOW-NWT-SWR1 \n",
" U.S. GEOLOGICAL SURVEY MODULAR FINITE-DIFFERENCE GROUNDWATER-FLOW MODEL\n",
" WITH NEWTON FORMULATION\n",
" Version 1.1.4 4/01/2018 \n",
" Version 1.2.0 03/01/2020 \n",
" BASED ON MODFLOW-2005 Version 1.12.0 02/03/2017 \n",
"\n",
" SWR1 Version 1.04.0 09/15/2016 \n",
"\n",
" Using NAME file: watertable.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:05:28\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 10:14:25\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Groundwater-Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:05:28\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 10:14:25\n",
" Elapsed run time: 0.018 Seconds\n",
"\n",
" Normal termination of simulation\n"

8
examples/Notebooks/flopy3_Zaidel_example.ipynb
View File

@ -31,7 +31,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -145,11 +145,11 @@
" Version 1.5.00 02/27/2019 \n",
"\n",
" Using NAME file: zaidel.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:07:31\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 10:16:30\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Groundwater Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:07:31\n",
" Elapsed run time: 0.011 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 10:16:30\n",
" Elapsed run time: 0.012 Seconds\n",
"\n",
" Normal termination of simulation\n"
]

272
examples/Notebooks/flopy3_ZoneBudget_example.ipynb
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File diff suppressed because one or more lines are too long

20
examples/Notebooks/flopy3_array_outputformat_options.ipynb
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@ -30,7 +30,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -92,11 +92,11 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: freyberg.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Elapsed run time: 0.011 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
" Elapsed run time: 0.016 Seconds\n",
"\n",
" Normal termination of simulation\n",
"Output file located: freyberg.hds\n",
@ -221,11 +221,11 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: freyberg.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Elapsed run time: 0.011 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
" Elapsed run time: 0.016 Seconds\n",
"\n",
" Normal termination of simulation\n"
]
@ -333,11 +333,11 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: freyberg.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:21:38\n",
" Elapsed run time: 0.012 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:31:29\n",
" Elapsed run time: 0.014 Seconds\n",
"\n",
" Normal termination of simulation\n"
]

8
examples/Notebooks/flopy3_demo_of_modelgrid_classes.ipynb
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@ -23,7 +23,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -172,7 +172,7 @@
{
"data": {
"text/plain": [
"<matplotlib.collections.PathCollection at 0x11ff4ca90>"
"<matplotlib.collections.PathCollection at 0x12151cd30>"
]
},
"execution_count": 7,
@ -214,7 +214,7 @@
{
"data": {
"text/plain": [
"<matplotlib.collections.PathCollection at 0x11ffb7e80>"
"<matplotlib.collections.PathCollection at 0x1296376a0>"
]
},
"execution_count": 8,
@ -300,7 +300,7 @@
{
"data": {
"text/plain": [
"<matplotlib.collections.PathCollection at 0x12019f6d8>"
"<matplotlib.collections.PathCollection at 0x129827fd0>"
]
},
"execution_count": 11,

20
examples/Notebooks/flopy3_drain_return.ipynb
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@ -14,7 +14,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -82,16 +82,16 @@
" MODFLOW-NWT-SWR1 \n",
" U.S. GEOLOGICAL SURVEY MODULAR FINITE-DIFFERENCE GROUNDWATER-FLOW MODEL\n",
" WITH NEWTON FORMULATION\n",
" Version 1.1.4 4/01/2018 \n",
" Version 1.2.0 03/01/2020 \n",
" BASED ON MODFLOW-2005 Version 1.12.0 02/03/2017 \n",
"\n",
" SWR1 Version 1.04.0 09/15/2016 \n",
"\n",
" Using NAME file: drt_test.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:22:29\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:32:16\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Groundwater-Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:22:30\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:32:16\n",
" Elapsed run time: 0.011 Seconds\n",
"\n",
" Normal termination of simulation\n"
@ -122,7 +122,7 @@
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x10c9819b0>"
"<matplotlib.axes._subplots.AxesSubplot at 0x1240705f8>"
]
},
"execution_count": 5,
@ -176,17 +176,17 @@
" MODFLOW-NWT-SWR1 \n",
" U.S. GEOLOGICAL SURVEY MODULAR FINITE-DIFFERENCE GROUNDWATER-FLOW MODEL\n",
" WITH NEWTON FORMULATION\n",
" Version 1.1.4 4/01/2018 \n",
" Version 1.2.0 03/01/2020 \n",
" BASED ON MODFLOW-2005 Version 1.12.0 02/03/2017 \n",
"\n",
" SWR1 Version 1.04.0 09/15/2016 \n",
"\n",
" Using NAME file: drt_test.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:22:30\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:32:16\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Groundwater-Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 13:22:30\n",
" Elapsed run time: 0.005 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:32:16\n",
" Elapsed run time: 0.004 Seconds\n",
"\n",
" Normal termination of simulation\n"
]
@ -216,7 +216,7 @@
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x121545240>"
"<matplotlib.axes._subplots.AxesSubplot at 0x12415f390>"
]
},
"execution_count": 8,

845
examples/Notebooks/flopy3_export.ipynb
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@ -21,13 +21,14 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
"source": [
"import os\n",
"import sys\n",
"import datetime\n",
"\n",
"# run installed version of flopy or add local path\n",
"try:\n",
@ -175,17 +176,19 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n"
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n"
]
},
{
"data": {
"text/plain": [
"<flopy.export.netcdf.NetCdf at 0x122585208>"
"<flopy.export.netcdf.NetCdf at 0x11e6accc0>"
]
},
"execution_count": 8,
@ -216,8 +219,9 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"wrote data/netCDF_export/top.shp\n"
]
}
@ -273,8 +277,9 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"wrote data/netCDF_export/hk.shp\n"
]
}
@ -302,14 +307,15 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n"
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n"
]
},
{
"data": {
"text/plain": [
"<flopy.export.netcdf.NetCdf at 0x127732128>"
"<flopy.export.netcdf.NetCdf at 0x11e3255c0>"
]
},
"execution_count": 12,
@ -344,8 +350,9 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n"
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n"
]
},
{
@ -353,8 +360,8 @@
"text/plain": [
"<class 'netCDF4._netCDF4.Dataset'>\n",
"root group (NETCDF4 data model, file format HDF5):\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.0\n",
" date_created: 2019-12-14T12:23:00Z\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
" date_created: 2020-06-26T13:32:00Z\n",
" geospatial_vertical_positive: up\n",
" geospatial_vertical_min: -25.0\n",
" geospatial_vertical_max: 4.832500457763672\n",
@ -408,8 +415,9 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n"
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n"
]
},
{
@ -417,8 +425,8 @@
"text/plain": [
"<class 'netCDF4._netCDF4.Dataset'>\n",
"root group (NETCDF4 data model, file format HDF5):\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.0\n",
" date_created: 2019-12-14T12:23:00Z\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
" date_created: 2020-06-26T13:32:00Z\n",
" geospatial_vertical_positive: up\n",
" geospatial_vertical_min: -25.0\n",
" geospatial_vertical_max: 4.832500457763672\n",
@ -452,6 +460,801 @@
"fnc = ml.export(os.path.join(pth, 'model.nc'))\n",
"fnc.nc"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Export output to netcdf\n",
"\n",
"FloPy has utilities to export model outputs to a netcdf file. Valid output types for export are MODFLOW binary head files, formatted head files, cell budget files, seawat concentration files, and zonebudget output.\n",
"\n",
"Let's use output from the Freyberg model as an example of these functions"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
"error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
]
},
{
"data": {
"text/plain": [
"<class 'netCDF4._netCDF4.Dataset'>\n",
"root group (NETCDF4 data model, file format HDF5):\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
" date_created: 2020-06-26T13:33:00Z\n",
" geospatial_vertical_positive: up\n",
" geospatial_vertical_min: -25.0\n",
" geospatial_vertical_max: 4.832500457763672\n",
" geospatial_vertical_resolution: variable\n",
" featureType: Grid\n",
" namefile: freyberg.nam\n",
" model_ws: ../data/freyberg_multilayer_transient\n",
" exe_name: mf2005.exe\n",
" modflow_version: mfnwt\n",
" create_hostname: IGSAAAHMLT40179\n",
" create_platform: Darwin\n",
" create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
" solver_head_tolerance: -999\n",
" solver_flux_tolerance: -999\n",
" flopy_sr_xll: 123456.7\n",
" flopy_sr_yll: 765432.1\n",
" flopy_sr_rotation: 15.0\n",
" flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
" start_datetime: 7/4/1776\n",
" dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
" variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x)\n",
" groups: "
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# load binary head and cell budget files\n",
"fhead = os.path.join(model_ws, 'freyberg.hds')\n",
"fcbc = os.path.join(model_ws, 'freyberg.cbc')\n",
"\n",
"hds = flopy.utils.HeadFile(fhead)\n",
"cbc = flopy.utils.CellBudgetFile(fcbc)\n",
"\n",
"export_dict = {\"hds\": hds,\n",
" \"cbc\": cbc}\n",
"\n",
"# export head and cell budget outputs to netcdf\n",
"fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output.nc\"), ml, export_dict)\n",
"fnc.nc"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Exporting zonebudget output\n",
"\n",
"zonebudget output can be exported with other modflow outputs, and is placed in a seperate group which allows the user to post-process the zonebudget output before exporting.\n",
"\n",
"Here are two examples on how to export zonebudget output with a binary head and cell budget file\n",
"\n",
"__Example 1__: No postprocessing of the zonebudget output"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"ZoneBudgetOutput Class\n",
"----------------------\n",
"\n",
"Number of zones: 4\n",
"Unique zones: 0, 1, 2, 3\n",
"Number of buget records: 3291"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# load the zonebudget output file\n",
"zonbud_ws = os.path.join(\"..\", \"data\", \"zonbud_examples\")\n",
"fzonbud = os.path.join(zonbud_ws, \"freyberg_mlt.2.csv\")\n",
"zon_arrays = flopy.utils.zonbud.read_zbarray(os.path.join(zonbud_ws, \"zonef_mlt.zbr\"))\n",
"\n",
"zbout = flopy.utils.ZoneBudgetOutput(fzonbud, ml.dis, zon_arrays)\n",
"zbout"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
"error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
]
},
{
"data": {
"text/plain": [
"<class 'netCDF4._netCDF4.Dataset'>\n",
"root group (NETCDF4 data model, file format HDF5):\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
" date_created: 2020-06-26T13:33:00Z\n",
" geospatial_vertical_positive: up\n",
" geospatial_vertical_min: -25.0\n",
" geospatial_vertical_max: 4.832500457763672\n",
" geospatial_vertical_resolution: variable\n",
" featureType: Grid\n",
" namefile: freyberg.nam\n",
" model_ws: ../data/freyberg_multilayer_transient\n",
" exe_name: mf2005.exe\n",
" modflow_version: mfnwt\n",
" create_hostname: IGSAAAHMLT40179\n",
" create_platform: Darwin\n",
" create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
" solver_head_tolerance: -999\n",
" solver_flux_tolerance: -999\n",
" flopy_sr_xll: 123456.7\n",
" flopy_sr_yll: 765432.1\n",
" flopy_sr_rotation: 15.0\n",
" flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
" start_datetime: 7/4/1776\n",
" dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
" variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x), float32 budget_zones(time,layer,y,x)\n",
" groups: zonebudget"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"export_dict = {'hds': hds,\n",
" 'cbc': cbc}\n",
"\n",
"fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output_with_zonebudget.nc\"),\n",
" ml, export_dict)\n",
"\n",
"fnc = zbout.export(fnc, ml)\n",
"fnc.nc"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"A budget_zones variable has been added to the root group and a new zonebudget group has been added to the netcdf file which hosts all of the budget data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"__Example 2__: postprocessing zonebudget output then exporting"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>kper</th>\n",
" <th>kstp</th>\n",
" <th>zone</th>\n",
" <th>storage</th>\n",
" <th>constant head</th>\n",
" <th>other zones</th>\n",
" <th>total</th>\n",
" <th>zone 0</th>\n",
" <th>zone 1</th>\n",
" <th>zone 2</th>\n",
" <th>zone 3</th>\n",
" <th>tslen</th>\n",
" <th>totim</th>\n",
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" <tr>\n",
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" <td>-36.140</td>\n",
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" <td>0.0000</td>\n",
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" <td>1.0</td>\n",
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" <tr>\n",
" <th>3</th>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" <td>218.568500</td>\n",
" <td>-816.347300</td>\n",
" <td>-1173.221</td>\n",
" <td>-1770.999</td>\n",
" <td>0.0</td>\n",
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" <td>-38.2835</td>\n",
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" <tr>\n",
" <th>4</th>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>2</td>\n",
" <td>191.816342</td>\n",
" <td>-643.938700</td>\n",
" <td>433.628</td>\n",
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" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3286</th>\n",
" <td>1095</td>\n",
" <td>0</td>\n",
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" <td>0.000</td>\n",
" <td>-1375.6380</td>\n",
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" <tr>\n",
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" <td>-35.514</td>\n",
" <td>0.0</td>\n",
" <td>17.8163</td>\n",
" <td>1375.638</td>\n",
" <td>0.0000</td>\n",
" <td>1.0</td>\n",
" <td>1096.0</td>\n",
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" <tr>\n",
" <th>3288</th>\n",
" <td>1096</td>\n",
" <td>0</td>\n",
" <td>1</td>\n",
" <td>0.000000</td>\n",
" <td>-230.548300</td>\n",
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" <td>0.0</td>\n",
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" <td>-205.822</td>\n",
" <td>53.5856</td>\n",
" <td>1.0</td>\n",
" <td>1097.0</td>\n",
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" <tr>\n",
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" <td>1096</td>\n",
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" <td>-14.931</td>\n",
" <td>0.0</td>\n",
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" <td>-53.5856</td>\n",
" <td>236.617</td>\n",
" <td>0.0000</td>\n",
" <td>1.0</td>\n",
" <td>1097.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>3291 rows × 13 columns</p>\n",
"</div>"
],
"text/plain": [
" kper kstp zone storage constant head other zones total \\\n",
"0 0 0 1 0.000000 -821.281900 -1570.821 -2392.103 \n",
"1 0 0 2 0.000000 -648.804700 630.730 -18.075 \n",
"2 0 0 3 0.000000 -976.232200 940.092 -36.140 \n",
"3 1 0 1 218.568500 -816.347300 -1173.221 -1770.999 \n",
"4 1 0 2 191.816342 -643.938700 433.628 -18.493 \n",
"... ... ... ... ... ... ... ... \n",
"3286 1095 0 2 -626.408120 -505.116270 1113.766 -17.758 \n",
"3287 1095 0 3 -627.235750 -801.732376 1393.454 -35.514 \n",
"3288 1096 0 1 0.000000 -230.548300 -152.236 -382.784 \n",
"3289 1096 0 2 0.000000 15.864900 -30.796 -14.931 \n",
"3290 1096 0 3 0.000000 -212.896600 183.031 -29.865 \n",
"\n",
" zone 0 zone 1 zone 2 zone 3 tslen totim \n",
"0 0.0 0.0000 -1530.422 -40.3993 1.0 1.0 \n",
"1 0.0 1530.4220 0.000 -899.6920 1.0 1.0 \n",
"2 0.0 40.3993 899.692 0.0000 1.0 1.0 \n",
"3 0.0 0.0000 -1134.937 -38.2835 1.0 2.0 \n",
"4 0.0 1134.9370 0.000 -701.3090 1.0 2.0 \n",
"... ... ... ... ... ... ... \n",
"3286 0.0 2489.4040 0.000 -1375.6380 1.0 1096.0 \n",
"3287 0.0 17.8163 1375.638 0.0000 1.0 1096.0 \n",
"3288 0.0 0.0000 -205.822 53.5856 1.0 1097.0 \n",
"3289 0.0 205.8220 0.000 -236.6170 1.0 1097.0 \n",
"3290 0.0 -53.5856 236.617 0.0000 1.0 1097.0 \n",
"\n",
"[3291 rows x 13 columns]"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# load the zonebudget output and get the budget information\n",
"zbout = flopy.utils.ZoneBudgetOutput(fzonbud, ml.dis, zon_arrays)\n",
"df = zbout.dataframe\n",
"df"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's calculate a yearly volumetric budget from the zonebudget data"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"scrolled": false
},
"outputs": [
{
"data": {
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>year</th>\n",
" <th>zone</th>\n",
" <th>storage</th>\n",
" <th>constant head</th>\n",
" <th>other zones</th>\n",
" <th>zone 1</th>\n",
" <th>zone 2</th>\n",
" <th>zone 3</th>\n",
" <th>totim</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>1776</td>\n",
" <td>1</td>\n",
" <td>81203.267170</td>\n",
" <td>-134930.451200</td>\n",
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" <td>-4321.3803</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>1776</td>\n",
" <td>2</td>\n",
" <td>37268.485533</td>\n",
" <td>-102758.917473</td>\n",
" <td>62223.7540</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>1776</td>\n",
" <td>3</td>\n",
" <td>37296.183058</td>\n",
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" <tr>\n",
" <th>3</th>\n",
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" <td>-265545.355300</td>\n",
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" <td>-8512.4548</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>1777</td>\n",
" <td>2</td>\n",
" <td>42820.852999</td>\n",
" <td>-200142.961123</td>\n",
" <td>150829.2320</td>\n",
" <td>398769.3120</td>\n",
" <td>0.0000</td>\n",
" <td>-247940.0845</td>\n",
" <td>546.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>1777</td>\n",
" <td>3</td>\n",
" <td>42818.153555</td>\n",
" <td>-312276.958409</td>\n",
" <td>256452.5519</td>\n",
" <td>8512.4548</td>\n",
" <td>247940.0845</td>\n",
" <td>0.0000</td>\n",
" <td>546.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>1778</td>\n",
" <td>1</td>\n",
" <td>108226.799462</td>\n",
" <td>-255186.105500</td>\n",
" <td>-378440.1290</td>\n",
" <td>0.0000</td>\n",
" <td>-371720.4820</td>\n",
" <td>-6719.6672</td>\n",
" <td>911.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>1778</td>\n",
" <td>2</td>\n",
" <td>44930.564942</td>\n",
" <td>-188836.557151</td>\n",
" <td>137315.0100</td>\n",
" <td>371720.4820</td>\n",
" <td>0.0000</td>\n",
" <td>-234405.4742</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>1778</td>\n",
" <td>3</td>\n",
" <td>44936.970500</td>\n",
" <td>-299267.807443</td>\n",
" <td>241125.1428</td>\n",
" <td>6719.6672</td>\n",
" <td>234405.4742</td>\n",
" <td>0.0000</td>\n",
" <td>911.0</td>\n",
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" <tr>\n",
" <th>9</th>\n",
" <td>1779</td>\n",
" <td>1</td>\n",
" <td>5348.709896</td>\n",
" <td>-129448.085100</td>\n",
" <td>-231291.1680</td>\n",
" <td>0.0000</td>\n",
" <td>-227734.8190</td>\n",
" <td>-3556.3570</td>\n",
" <td>1097.0</td>\n",
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" <tr>\n",
" <th>10</th>\n",
" <td>1779</td>\n",
" <td>2</td>\n",
" <td>3241.895778</td>\n",
" <td>-95653.391040</td>\n",
" <td>88972.3010</td>\n",
" <td>227734.8190</td>\n",
" <td>0.0000</td>\n",
" <td>-138762.5241</td>\n",
" <td>1097.0</td>\n",
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" <tr>\n",
" <th>11</th>\n",
" <td>1779</td>\n",
" <td>3</td>\n",
" <td>3233.272516</td>\n",
" <td>-152427.866886</td>\n",
" <td>142318.8767</td>\n",
" <td>3556.3570</td>\n",
" <td>138762.5241</td>\n",
" <td>0.0000</td>\n",
" <td>1097.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" year zone storage constant head other zones zone 1 \\\n",
"0 1776 1 81203.267170 -134930.451200 -176631.7910 0.0000 \n",
"1 1776 2 37268.485533 -102758.917473 62223.7540 172310.4031 \n",
"2 1776 3 37296.183058 -158237.438437 114408.0385 4321.3803 \n",
"3 1777 1 91777.777222 -265545.355300 -407281.7640 0.0000 \n",
"4 1777 2 42820.852999 -200142.961123 150829.2320 398769.3120 \n",
"5 1777 3 42818.153555 -312276.958409 256452.5519 8512.4548 \n",
"6 1778 1 108226.799462 -255186.105500 -378440.1290 0.0000 \n",
"7 1778 2 44930.564942 -188836.557151 137315.0100 371720.4820 \n",
"8 1778 3 44936.970500 -299267.807443 241125.1428 6719.6672 \n",
"9 1779 1 5348.709896 -129448.085100 -231291.1680 0.0000 \n",
"10 1779 2 3241.895778 -95653.391040 88972.3010 227734.8190 \n",
"11 1779 3 3233.272516 -152427.866886 142318.8767 3556.3570 \n",
"\n",
" zone 2 zone 3 totim \n",
"0 -172310.4031 -4321.3803 181.0 \n",
"1 0.0000 -110086.6556 181.0 \n",
"2 110086.6556 0.0000 181.0 \n",
"3 -398769.3120 -8512.4548 546.0 \n",
"4 0.0000 -247940.0845 546.0 \n",
"5 247940.0845 0.0000 546.0 \n",
"6 -371720.4820 -6719.6672 911.0 \n",
"7 0.0000 -234405.4742 911.0 \n",
"8 234405.4742 0.0000 911.0 \n",
"9 -227734.8190 -3556.3570 1097.0 \n",
"10 0.0000 -138762.5241 1097.0 \n",
"11 138762.5241 0.0000 1097.0 "
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# get a dataframe of volumetric budget information\n",
"vol_df = zbout.volumetric_flux()\n",
"\n",
"# add a year field to the dataframe using datetime\n",
"start_date = ml.modeltime.start_datetime\n",
"start_date = datetime.datetime.strptime(start_date, \"%m/%d/%Y\")\n",
"nzones = len(zbout.zones) - 1\n",
"\n",
"year = [start_date.year] * nzones\n",
"for totim in vol_df.totim.values[:-nzones]:\n",
" t = start_date + datetime.timedelta(days=totim)\n",
" year.append(t.year)\n",
"\n",
"vol_df['year'] = year\n",
" \n",
"# calculate yearly volumetric change using pandas\n",
"totim_df = vol_df.groupby(['year', 'zone'], as_index=False)['totim'].max()\n",
"yearly = vol_df.groupby(['year', 'zone'], as_index=False)[['storage', 'constant head', 'other zones',\n",
" 'zone 1', 'zone 2', 'zone 3']].sum()\n",
"yearly['totim'] = totim_df['totim']\n",
"yearly"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"And finally, export the pandas dataframe to netcdf"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
"initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
"error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
]
},
{
"data": {
"text/plain": [
"<class 'netCDF4._netCDF4.Dataset'>\n",
"root group (NETCDF4 data model, file format HDF5):\n",
" Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
" date_created: 2020-06-26T13:33:00Z\n",
" geospatial_vertical_positive: up\n",
" geospatial_vertical_min: -25.0\n",
" geospatial_vertical_max: 4.832500457763672\n",
" geospatial_vertical_resolution: variable\n",
" featureType: Grid\n",
" namefile: freyberg.nam\n",
" model_ws: ../data/freyberg_multilayer_transient\n",
" exe_name: mf2005.exe\n",
" modflow_version: mfnwt\n",
" create_hostname: IGSAAAHMLT40179\n",
" create_platform: Darwin\n",
" create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
" solver_head_tolerance: -999\n",
" solver_flux_tolerance: -999\n",
" flopy_sr_xll: 123456.7\n",
" flopy_sr_yll: 765432.1\n",
" flopy_sr_rotation: 15.0\n",
" flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
" start_datetime: 7/4/1776\n",
" dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
" variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x), float32 budget_zones(time,layer,y,x)\n",
" groups: zonebudget"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# process the new dataframe into a format that is compatible with netcdf exporting\n",
"zbncf = zbout.dataframe_to_netcdf_fmt(yearly, flux=False)\n",
"\n",
"# export to netcdf\n",
"export_dict = {\"hds\": hds,\n",
" \"cbc\": cbc,\n",
" \"zbud\": zbncf}\n",
"\n",
"fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output_with_zonebudget.2.nc\"),\n",
" ml, export_dict)\n",
"fnc.nc"
]
}
],
"metadata": {

115
examples/Notebooks/flopy3_external_file_handling.ipynb
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@ -22,7 +22,7 @@
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -712,7 +712,7 @@
{
"data": {
"text/plain": [
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.0.\\n',\n",
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.1.\\n',\n",
" '#xll:0.0; yll:0.0; rotation:0.0; units:meters; lenuni:2; start_datetime:1-1-1970\\n',\n",
" 'LIST 2 modflowtest.list\\n',\n",
" 'DIS 11 modflowtest.dis\\n',\n",
@ -791,73 +791,28 @@
"output_type": "stream",
"text": [
"Util2d:delr: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delr.ref\n",
"Util2d:delc: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delc.ref\n",
"Util2d:model_top: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/model_top.ref\n",
"Util2d:botm layer 1: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_1.ref\n",
"Util2d:botm layer 2: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_2.ref\n",
"Util2d:botm layer 3: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_3.ref\n",
"Util2d:botm layer 4: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_4.ref\n",
"Util2d:botm layer 5: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_5.ref\n",
"Util2d:botm layer 6: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_6.ref\n",
"Util2d:botm layer 7: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_7.ref\n",
"Util2d:botm layer 8: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_8.ref\n",
"Util2d:botm layer 9: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_9.ref\n",
"Util2d:botm layer 10: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_1.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka1.ref\n",
"Util2d:ss layer 1: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_1.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_2.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka2.ref\n",
"Util2d:ss layer 2: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_2.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_3.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka3.ref\n",
"Util2d:ss layer 3: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_3.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_4.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka4.ref\n",
"Util2d:ss layer 4: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_4.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_5.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka5.ref\n",
"Util2d:ss layer 5: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_5.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_6.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka6.ref\n",
"Util2d:ss layer 6: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_6.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_7.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka7.ref\n",
"Util2d:ss layer 7: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_7.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_8.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka8.ref\n",
"Util2d:ss layer 8: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_8.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_9.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka9.ref\n",
"Util2d:ss layer 9: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_9.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka10.ref\n",
"Util2d:ss layer 10: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/rech_0.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/important_recharge.ref\n"
"Util2d:ss layer 10: resetting 'how' to external\n"
]
}
],
@ -874,7 +829,7 @@
{
"data": {
"text/plain": [
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.0.\\n',\n",
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.1.\\n',\n",
" '#xll:0.0; yll:0.0; rotation:0.0; units:meters; lenuni:2; start_datetime:1-1-1970\\n',\n",
" 'LIST 2 modflowtest.list\\n',\n",
" 'DIS 11 modflowtest.dis\\n',\n",
@ -1018,31 +973,18 @@
"output_type": "stream",
"text": [
"Util2d:delr: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delr.ref\n",
"Util2d:delc: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delc.ref\n",
"Util2d:model_top: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/model_top.ref\n",
"Util2d:botm layer 1: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_1.ref\n",
"Util2d:botm layer 2: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_2.ref\n",
"Util2d:botm layer 3: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_3.ref\n",
"Util2d:botm layer 4: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_4.ref\n",
"Util2d:botm layer 5: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_5.ref\n",
"Util2d:botm layer 6: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_6.ref\n",
"Util2d:botm layer 7: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_7.ref\n",
"Util2d:botm layer 8: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_8.ref\n",
"Util2d:botm layer 9: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_9.ref\n",
"Util2d:botm layer 10: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_10.ref\n",
"\n",
" Util2d error: 'how' is openclose,but model doesn't support free fmt \n",
"\n"
@ -1105,72 +1047,27 @@
"output_type": "stream",
"text": [
"Util2d:delr: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delr.ref\n",
"Util2d:delc: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/delc.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/model_top.ref\n",
"Util2d:botm layer 1: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_1.ref\n",
"Util2d:botm layer 2: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_2.ref\n",
"Util2d:botm layer 3: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_3.ref\n",
"Util2d:botm layer 4: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_4.ref\n",
"Util2d:botm layer 5: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_5.ref\n",
"Util2d:botm layer 6: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_6.ref\n",
"Util2d:botm layer 7: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_7.ref\n",
"Util2d:botm layer 8: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_8.ref\n",
"Util2d:botm layer 9: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_9.ref\n",
"Util2d:botm layer 10: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/botm_layer_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_1.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka1.ref\n",
"Util2d:ss layer 1: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_1.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_2.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka2.ref\n",
"Util2d:ss layer 2: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_2.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_3.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka3.ref\n",
"Util2d:ss layer 3: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_3.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_4.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka4.ref\n",
"Util2d:ss layer 4: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_4.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_5.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka5.ref\n",
"Util2d:ss layer 5: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_5.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_6.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka6.ref\n",
"Util2d:ss layer 6: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_6.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_7.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka7.ref\n",
"Util2d:ss layer 7: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_7.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_8.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka8.ref\n",
"Util2d:ss layer 8: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_8.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_9.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka9.ref\n",
"Util2d:ss layer 9: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_9.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/hk_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/vka10.ref\n",
"Util2d:ss layer 10: resetting 'how' to external\n",
"BaseModel.add_external() warning: replacing existing filename ref/ss_layer_10.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/rech_0.ref\n",
"BaseModel.add_external() warning: replacing existing filename ref/important_recharge.ref\n"
"Util2d:ss layer 10: resetting 'how' to external\n"
]
}
],
@ -1279,7 +1176,7 @@
{
"data": {
"text/plain": [
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.0.\\n',\n",
"['# Name file for MODFLOW-2005, generated by Flopy version 3.3.1.\\n',\n",
" '#xll:0.0; yll:0.0; rotation:0.0; units:meters; lenuni:2; start_datetime:1-1-1970\\n',\n",
" 'LIST 2 modflowtest.list\\n',\n",
" 'DIS 11 modflowtest.dis\\n',\n",

4
examples/Notebooks/flopy3_get_transmissivities_example.ipynb
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@ -27,7 +27,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -208,7 +208,7 @@
{
"data": {
"text/plain": [
"<matplotlib.legend.Legend at 0x11af60908>"
"<matplotlib.legend.Legend at 0x128fd80b8>"
]
},
"execution_count": 6,

950
examples/Notebooks/flopy3_grid_intersection_demo.ipynb
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28
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8
examples/Notebooks/flopy3_lake_example.ipynb
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@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -173,11 +173,11 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: lake_example.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:19:30\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:36:05\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:19:30\n",
" Elapsed run time: 0.278 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:36:05\n",
" Elapsed run time: 0.305 Seconds\n",
"\n",
" Normal termination of simulation\n"
]

68
examples/Notebooks/flopy3_mf6_A_simple-model.ipynb
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examples/Notebooks/flopy3_mf6_B_complex-model.ipynb
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@ -32,7 +32,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -556,9 +556,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -573,386 +573,395 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:39:07\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:00\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Solving: Stress period: 2 Time step: 1\n",
" Solving: Stress period: 2 Time step: 2\n",
" Solving: Stress period: 2 Time step: 3\n",
" Solving: Stress period: 2 Time step: 4\n",
" Solving: Stress period: 2 Time step: 5\n",
" Solving: Stress period: 2 Time step: 6\n",
" Solving: Stress period: 2 Time step: 7\n",
" Solving: Stress period: 2 Time step: 8\n",
" Solving: Stress period: 2 Time step: 9\n",
" Solving: Stress period: 2 Time step: 10\n",
" Solving: Stress period: 2 Time step: 11\n",
" Solving: Stress period: 2 Time step: 12\n",
" Solving: Stress period: 2 Time step: 13\n",
" Solving: Stress period: 2 Time step: 14\n",
" Solving: Stress period: 2 Time step: 15\n",
" Solving: Stress period: 2 Time step: 16\n",
" Solving: Stress period: 2 Time step: 17\n",
" Solving: Stress period: 2 Time step: 18\n",
" Solving: Stress period: 2 Time step: 19\n",
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" Solving: Stress period: 2 Time step: 23\n",
" Solving: Stress period: 2 Time step: 24\n",
" Solving: Stress period: 2 Time step: 25\n",
" Solving: Stress period: 2 Time step: 26\n",
" Solving: Stress period: 2 Time step: 27\n",
" Solving: Stress period: 2 Time step: 28\n",
" Solving: Stress period: 2 Time step: 29\n",
" Solving: Stress period: 2 Time step: 30\n",
" Solving: Stress period: 2 Time step: 31\n",
" Solving: Stress period: 2 Time step: 32\n",
" Solving: Stress period: 2 Time step: 33\n",
" Solving: Stress period: 2 Time step: 34\n",
" Solving: Stress period: 2 Time step: 35\n",
" Solving: Stress period: 2 Time step: 36\n",
" Solving: Stress period: 2 Time step: 37\n",
" Solving: Stress period: 2 Time step: 38\n",
" Solving: Stress period: 2 Time step: 39\n",
" Solving: Stress period: 2 Time step: 40\n",
" Solving: Stress period: 2 Time step: 41\n",
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" Solving: Stress period: 2 Time step: 44\n",
" Solving: Stress period: 2 Time step: 45\n",
" Solving: Stress period: 2 Time step: 46\n",
" Solving: Stress period: 2 Time step: 47\n",
" Solving: Stress period: 2 Time step: 48\n",
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" Solving: Stress period: 2 Time step: 50\n",
" Solving: Stress period: 2 Time step: 51\n",
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" Solving: Stress period: 2 Time step: 58\n",
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" Solving: Stress period: 2 Time step: 83\n",
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" \n",
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" Solving: Stress period: 3 Time step: 1\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" Solving: Stress period: 3 Time step: 19\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" Solving: Stress period: 4 Time step: 59\n",
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" Solving: Stress period: 4 Time step: 120\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:39:09\n",
" Elapsed run time: 1.855 Seconds\n",
" Solving: Stress period: 4 Time step: 44\n",
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" Solving: Stress period: 4 Time step: 118\n",
" Solving: Stress period: 4 Time step: 119\n",
" Solving: Stress period: 4 Time step: 120\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:02\n",
" Elapsed run time: 1.932 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'advgw_tidal.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'advgw_tidal.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n",
"\n",
"Success is: True\n"
@ -1330,7 +1339,7 @@
{
"data": {
"text/plain": [
"<matplotlib.legend.Legend at 0x11dd444e0>"
"<matplotlib.legend.Legend at 0x122a8b080>"
]
},
"execution_count": 25,

7474
examples/Notebooks/flopy3_mf6_obs_ts_tas.ipynb
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74
examples/Notebooks/flopy3_mf6_tutorial.ipynb
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@ -44,7 +44,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -582,9 +582,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -599,19 +599,28 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:40:24\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:43\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Solving: Stress period: 2 Time step: 1\n",
" Solving: Stress period: 2 Time step: 2\n",
" Solving: Stress period: 2 Time step: 3\n",
" Solving: Stress period: 2 Time step: 4\n",
" Solving: Stress period: 2 Time step: 5\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:40:24\n",
" Elapsed run time: 0.040 Seconds\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" Solving: Stress period: 2 Time step: 1\n",
" Solving: Stress period: 2 Time step: 2\n",
" Solving: Stress period: 2 Time step: 3\n",
" Solving: Stress period: 2 Time step: 4\n",
" Solving: Stress period: 2 Time step: 5\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:43\n",
" Elapsed run time: 0.045 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'example_sim.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'example_sim.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
},
@ -658,8 +667,9 @@
"output_type": "stream",
"text": [
"initialize_geometry::proj4_str = epsg:4326\n",
"initialize_geometry::self.grid_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::nc_crs = Proj('+proj=longlat +datum=WGS84 +no_defs', preserve_units=True)\n",
"initialize_geometry::self.grid_crs = epsg:4326\n",
"initialize_geometry::nc_crs = epsg:4326\n",
"transforming coordinates using = proj=noop ellps=GRS80\n",
"wrote data/netCDF_export/botm.shp\n"
]
}
@ -714,7 +724,6 @@
" loading package oc...\n",
" loading package chd...\n",
" loading package rch...\n",
"WARNING: Block header for block \"continuous\" is not a unique block header ('example_model', 'rch', 'obs', 'continuous')\n",
" loading ims package example_model...\n"
]
}
@ -999,9 +1008,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -1016,19 +1025,28 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:40:25\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:43\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Solving: Stress period: 2 Time step: 1\n",
" Solving: Stress period: 2 Time step: 2\n",
" Solving: Stress period: 2 Time step: 3\n",
" Solving: Stress period: 2 Time step: 4\n",
" Solving: Stress period: 2 Time step: 5\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:40:25\n",
" Elapsed run time: 0.036 Seconds\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" Solving: Stress period: 2 Time step: 1\n",
" Solving: Stress period: 2 Time step: 2\n",
" Solving: Stress period: 2 Time step: 3\n",
" Solving: Stress period: 2 Time step: 4\n",
" Solving: Stress period: 2 Time step: 5\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:37:43\n",
" Elapsed run time: 0.045 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'example_sim.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'example_sim.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
},

43
examples/Notebooks/flopy3_mnw2package_example.ipynb
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@ -23,7 +23,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"pandas version: 0.25.2\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -721,17 +721,7 @@
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: unit 34 of package MNW2 already in use\n",
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfmnw2.ModflowMnw2'> <class 'flopy.modflow.mfmnw2.ModflowMnw2'>\n",
"replacing existing Package...\n"
]
}
],
"outputs": [],
"source": [
"tmp = flopy.modflow.ModflowMnw2(model=m,\n",
" itmp=[1, 1, -1], # reuse second per pumping for last stress period\n",
@ -793,8 +783,8 @@
{
"data": {
"text/plain": [
"{'well1': <flopy.modflow.mfmnw2.Mnw at 0x11deda668>,\n",
" 'well2': <flopy.modflow.mfmnw2.Mnw at 0x11de95518>}"
"{'well1': <flopy.modflow.mfmnw2.Mnw at 0x12650ca58>,\n",
" 'well2': <flopy.modflow.mfmnw2.Mnw at 0x1264db630>}"
]
},
"execution_count": 14,
@ -943,13 +933,13 @@
" gwt = False ('bool)\n",
" ipakcb = 0 ('int)\n",
" itmp (list, items = 3)\n",
" mnw = {'well1': <flopy.modflow.mfmnw2.Mnw object at 0x11deda668>, 'well2': <flopy.modflow.mfmnw2.Mnw object at 0x11de95518>} ('dict)\n",
" mnw = {'well1': <flopy.modflow.mfmnw2.Mnw object at 0x12650ca58>, 'well2': <flopy.modflow.mfmnw2.Mnw object at 0x1264db630>} ('dict)\n",
" mnwmax = 2 ('int)\n",
" mnwprnt = 0 ('int)\n",
" node_data (array, shape = 3,)\n",
" nodtot = 3 ('int)\n",
" nper = 3 ('int)\n",
" stress_period_data = <flopy.utils.util_list.MfList object at 0x11deda2e8> ('flopy.utils.util_list.MfList)\n",
" stress_period_data = <flopy.utils.util_list.MfList object at 0x12650c320> ('flopy.utils.util_list.MfList)\n",
" structured = True ('bool)\n",
" unit_number = 34, 'aux': [], 'wellid': 'well1', 'nnodes': -2, 'losstype': 'skin', 'pumploc': -1, 'qlimit': 0, 'ppflag': 0, 'pumpcap': 0, 'rw': [1.0,\n",
" 0.5], 'rskin': [2.0, 2.0], 'kskin': [5.0,\n",
@ -1226,17 +1216,7 @@
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: unit 34 of package MNW2 already in use\n",
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfmnw2.ModflowMnw2'> <class 'flopy.modflow.mfmnw2.ModflowMnw2'>\n",
"replacing existing Package...\n"
]
}
],
"outputs": [],
"source": [
"mnw2fromobj = flopy.modflow.ModflowMnw2(model=m, mnwmax=2,\n",
" mnw=mnw2.mnw,\n",
@ -1658,13 +1638,6 @@
"### Load some example MNW2 packages"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 25,
@ -1885,7 +1858,7 @@
{
"data": {
"text/plain": [
"{'well-a': <flopy.modflow.mfmnw2.Mnw at 0x11df21ba8>}"
"{'well-a': <flopy.modflow.mfmnw2.Mnw at 0x126573240>}"
]
},
"execution_count": 30,

8
examples/Notebooks/flopy3_modflow_boundaries.ipynb
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@ -34,7 +34,7 @@
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -609,9 +609,6 @@
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: unit 20 of package WEL already in use\n",
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfwel.ModflowWel'> <class 'flopy.modflow.mfwel.ModflowWel'>\n",
"replacing existing Package...\n",
"# WEL package for MODFLOW-2005, generated by Flopy.\r\n",
" 1 0 \r\n",
" 1 0 # stress period 1\r\n",
@ -648,9 +645,6 @@
"name": "stdout",
"output_type": "stream",
"text": [
"WARNING: unit 20 of package WEL already in use\n",
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfwel.ModflowWel'> <class 'flopy.modflow.mfwel.ModflowWel'>\n",
"replacing existing Package...\n",
"# WEL package for MODFLOW-2005, generated by Flopy.\r\n",
" 2 0 \r\n",
" 1 0 # stress period 1\r\n",

14
examples/Notebooks/flopy3_modpath6_example.ipynb
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@ -25,7 +25,7 @@
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"pandas version: 0.25.2\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -258,7 +258,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:525: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:553: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
" pa[list(idx[1:])] = 1\n"
]
},
@ -397,7 +397,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:525: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:553: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
" pa[list(idx[1:])] = 1\n"
]
},
@ -698,7 +698,7 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: Example_mnw.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:42:25\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:39:32\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 2 Time step: 1 Ground-Water Flow Eqn.\n",
@ -712,8 +712,8 @@
" Solving: Stress period: 2 Time step: 9 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 2 Time step: 10 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 3 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:42:25\n",
" Elapsed run time: 0.067 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:39:32\n",
" Elapsed run time: 0.074 Seconds\n",
"\n",
" Normal termination of simulation\n"
]
@ -818,7 +818,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:525: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
"/Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy/plot/map.py:553: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.\n",
" pa[list(idx[1:])] = 1\n"
]
},

29
examples/Notebooks/flopy3_modpath7_create_simulation.ipynb
View File

@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -145,9 +145,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -162,14 +162,23 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:42:51\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:39:48\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:42:51\n",
" Elapsed run time: 0.033 Seconds\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:39:48\n",
" Elapsed run time: 0.032 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'ex01_mf6.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'ex01_mf6.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
}
@ -285,7 +294,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Dec 13 2019 12:32:13 with IFORT compiler (ver. 19.0.5) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",
@ -352,7 +361,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Dec 13 2019 12:32:13 with IFORT compiler (ver. 19.0.5) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",

35
examples/Notebooks/flopy3_modpath7_structured_example.ipynb
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@ -23,7 +23,7 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.2.13\n"
"flopy version: 3.3.1\n"
]
}
],
@ -158,11 +158,11 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: ex01_mf2005.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/11/15 16:49:21\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:40:36\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/11/15 16:49:21\n",
" Elapsed run time: 0.014 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:40:36\n",
" Elapsed run time: 0.018 Seconds\n",
"\n",
" Normal termination of simulation\n"
]
@ -234,7 +234,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Mar 19 2019 16:49:28 with IFORT compiler (ver. 19.0.0) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",
@ -494,9 +494,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.0.4 03/13/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Mar 19 2019 16:46:21 with IFORT compiler (ver. 19.0.0)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -511,14 +511,23 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/11/15 16:49:44\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:41:00\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/11/15 16:49:44\n",
" Elapsed run time: 0.031 Seconds\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:41:00\n",
" Elapsed run time: 0.034 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'ex01_mf6.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'ex01_mf6.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
}
@ -615,7 +624,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Mar 19 2019 16:49:28 with IFORT compiler (ver. 19.0.0) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",

33
examples/Notebooks/flopy3_modpath7_unstructured_example.ipynb
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@ -30,7 +30,7 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -174,7 +174,7 @@
{
"data": {
"text/plain": [
"<matplotlib.collections.PatchCollection at 0x11d839da0>"
"<matplotlib.collections.PatchCollection at 0x127e64198>"
]
},
"execution_count": 7,
@ -221,7 +221,7 @@
{
"data": {
"text/plain": [
"<matplotlib.collections.PatchCollection at 0x11ddb0fd0>"
"<matplotlib.collections.PatchCollection at 0x1303df518>"
]
},
"execution_count": 9,
@ -402,9 +402,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -419,14 +419,23 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:47:12\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:41:45\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 15:47:12\n",
" Elapsed run time: 0.123 Seconds\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:41:45\n",
" Elapsed run time: 0.139 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'mp7p2.ims' WAS\n",
" DEPRECATED IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'mp7p2.ims' WAS DEPRECATED\n",
" IN VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
},
@ -730,7 +739,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Dec 13 2019 12:32:13 with IFORT compiler (ver. 19.0.5) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",
@ -871,7 +880,7 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mp7\n",
"\n",
"MODPATH Version 7.2.001 \n",
"Program compiled Dec 13 2019 12:32:13 with IFORT compiler (ver. 19.0.5) \n",
"Program compiled Jun 12 2020 12:05:21 with IFORT compiler (ver. 19.0.5) \n",
" \n",
" \n",
"Run particle tracking simulation ...\n",

14
examples/Notebooks/flopy3_mt3d-usgs_example_with_sft_lkt_uzt.ipynb
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@ -26,11 +26,11 @@
"output_type": "stream",
"text": [
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"3.7.7 (default, Mar 26 2020, 10:32:53) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"numpy version: 1.18.5\n",
"matplotlib version: 3.2.2\n",
"flopy version: 3.3.1\n"
]
}
],
@ -74,7 +74,7 @@
"metadata": {},
"outputs": [],
"source": [
"modelpth = os.path.join('no3')\n",
"modelpth = os.path.join('.', 'temp', 'no3')\n",
"modelname = 'no3'\n",
"mfexe = 'mfnwt'\n",
"mtexe = 'mt3dusgs'\n",
@ -85,7 +85,7 @@
"\n",
"# Make sure modelpth directory exists\n",
"if not os.path.exists(modelpth):\n",
" os.mkdir(modelpth)\n",
" os.makedirs(modelpth)\n",
"\n",
"# Instantiate MODFLOW object in flopy\n",
"mf = flopy.modflow.Modflow(modelname=modelname, exe_name=mfexe, model_ws=modelpth, version='mfnwt')"
@ -898,7 +898,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
"version": "3.7.7"
}
},
"nbformat": 4,

2
examples/Notebooks/flopy3_multi-component_SSM.ipynb
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@ -24,7 +24,7 @@
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

24
examples/Notebooks/flopy3_nwt_options.ipynb
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@ -23,7 +23,7 @@
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -52,7 +52,7 @@
"outputs": [],
"source": [
"load_ws = os.path.join(\"..\", \"data\", \"options\", \"sagehen\")\n",
"model_ws = os.path.join(load_ws, \"output\")"
"model_ws = os.path.join(\"temp\", \"nwt_options\", \"output\")"
]
},
{
@ -83,8 +83,11 @@
" loading finf array...\n",
"stress period 2:\n",
"\n",
"creating model workspace...\n",
" temp/nwt_options/output\n",
"\n",
"changing model workspace...\n",
" ../data/options/sagehen/output\n",
" temp/nwt_options/output\n",
"Something bad happened.\n"
]
}
@ -319,9 +322,7 @@
" loading thts array...\n",
"stress period 1:\n",
" loading finf array...\n",
"stress period 2:\n",
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfuzf1.ModflowUzf1'> <class 'flopy.modflow.mfuzf1.ModflowUzf1'>\n",
"replacing existing Package...\n"
"stress period 2:\n"
]
}
],
@ -602,16 +603,7 @@
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"****Warning -- two packages of the same type: <class 'flopy.modflow.mfwel.ModflowWel'> <class 'flopy.modflow.mfwel.ModflowWel'>\n",
"replacing existing Package...\n"
]
}
],
"outputs": [],
"source": [
"wel3 = flopy.modflow.ModflowWel(ml, stress_period_data=wel.stress_period_data,\n",
" options=options, unitnumber=99)\n",

20
examples/Notebooks/flopy3_raster_intersection.ipynb
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2
examples/Notebooks/flopy3_save_binary_data_file.ipynb
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@ -23,7 +23,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

32
examples/Notebooks/flopy3_sfrpackage_example.ipynb
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200
examples/Notebooks/flopy3_shapefile_export.ipynb
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12
examples/Notebooks/flopy3_shapefile_features.ipynb
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@ -24,12 +24,12 @@
"output_type": "stream",
"text": [
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"Resetting /Users/jdhughes/.flopy/epsgref.json\n",
"Resetting /Users/jdhughes/Library/Application Support/flopy/epsgref.json\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -307,8 +307,8 @@
{
"data": {
"text/plain": [
"rec.array([('Error', 'DIS', 1, 5, 5, -2.5, 'zero or negative thickness', <flopy.utils.geometry.Polygon object at 0x1286d64e0>),\n",
" ('Error', 'DIS', 1, 6, 6, -2.5, 'zero or negative thickness', <flopy.utils.geometry.Polygon object at 0x1286d6668>)],\n",
"rec.array([('Error', 'DIS', 1, 5, 5, -2.5, 'zero or negative thickness', <flopy.utils.geometry.Polygon object at 0x123b9d5f8>),\n",
" ('Error', 'DIS', 1, 6, 6, -2.5, 'zero or negative thickness', <flopy.utils.geometry.Polygon object at 0x123b73160>)],\n",
" dtype=[('type', 'O'), ('package', 'O'), ('k', '<i8'), ('i', '<i8'), ('j', '<i8'), ('value', '<f8'), ('desc', 'O'), ('geometry', 'O')])"
]
},
@ -527,7 +527,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Resetting /Users/jdhughes/.flopy/epsgref.json\n"
"Resetting /Users/jdhughes/Library/Application Support/flopy/epsgref.json\n"
]
}
],
@ -628,7 +628,7 @@
{
"data": {
"text/plain": [
"<flopy.utils.geometry.LineString at 0x12865a208>"
"<flopy.utils.geometry.LineString at 0x123cce860>"
]
},
"execution_count": 27,

2
examples/Notebooks/flopy3_swi2package_ex1.ipynb
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@ -37,7 +37,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

2
examples/Notebooks/flopy3_swi2package_ex4.ipynb
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@ -42,7 +42,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],

23
examples/Notebooks/flopy3_triangle.ipynb
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@ -25,7 +25,7 @@
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -495,9 +495,9 @@
"FloPy is using the following executable to run the model: /Users/jdhughes/.local/bin/mf6\n",
" MODFLOW 6\n",
" U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL\n",
" VERSION 6.1.0 12/12/2019\n",
" VERSION 6.1.1 06/12/2020\n",
"\n",
" MODFLOW 6 compiled Dec 13 2019 12:29:49 with IFORT compiler (ver. 19.0.5)\n",
" MODFLOW 6 compiled Jun 12 2020 12:02:16 with IFORT compiler (ver. 19.0.5)\n",
"\n",
"This software has been approved for release by the U.S. Geological \n",
"Survey (USGS). Although the software has been subjected to rigorous \n",
@ -512,14 +512,23 @@
"Resources Software User Rights Notice for complete use, copyright, \n",
"and distribution information.\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:02:04\n",
"\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:56:01\n",
" \n",
" Writing simulation list file: mfsim.lst\n",
" Using Simulation name file: mfsim.nam\n",
" Solving: Stress period: 1 Time step: 1\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:02:04\n",
" \n",
" Solving: Stress period: 1 Time step: 1\n",
" \n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:56:01\n",
" Elapsed run time: 0.021 Seconds\n",
" \n",
"\n",
"WARNING REPORT:\n",
"\n",
" 1. NONLINEAR BLOCK VARIABLE 'OUTER_HCLOSE' IN FILE 'mf.ims' WAS DEPRECATED\n",
" IN VERSION 6.1.1. SETTING OUTER_DVCLOSE TO OUTER_HCLOSE VALUE.\n",
" 2. LINEAR BLOCK VARIABLE 'INNER_HCLOSE' IN FILE 'mf.ims' WAS DEPRECATED IN\n",
" VERSION 6.1.1. SETTING INNER_DVCLOSE TO INNER_HCLOSE VALUE.\n",
" Normal termination of simulation.\n"
]
}

24
examples/Notebooks/flopy3_uzf_example.ipynb
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@ -36,7 +36,7 @@
"numpy version: 1.17.3\n",
"matplotlib version: 3.1.1\n",
"pandas version: 0.25.2\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -517,7 +517,7 @@
" Version 1.12.00 2/3/2017 \n",
"\n",
" Using NAME file: UZFtest2.nam \n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:02:31\n",
" Run start date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:56:23\n",
"\n",
" Solving: Stress period: 1 Time step: 1 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 2 Time step: 1 Ground-Water Flow Eqn.\n",
@ -619,16 +619,16 @@
" Solving: Stress period: 8 Time step: 7 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 8 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 9 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 10 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 11 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 12 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 13 Ground-Water Flow Eqn.\n"
" Solving: Stress period: 8 Time step: 10 Ground-Water Flow Eqn.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
" Solving: Stress period: 8 Time step: 11 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 12 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 13 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 14 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 8 Time step: 15 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 9 Time step: 1 Ground-Water Flow Eqn.\n",
@ -691,8 +691,8 @@
" Solving: Stress period: 12 Time step: 13 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 12 Time step: 14 Ground-Water Flow Eqn.\n",
" Solving: Stress period: 12 Time step: 15 Ground-Water Flow Eqn.\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2019/12/14 16:02:33\n",
" Elapsed run time: 2.432 Seconds\n",
" Run end date and time (yyyy/mm/dd hh:mm:ss): 2020/06/26 9:56:26\n",
" Elapsed run time: 2.891 Seconds\n",
"\n",
" Normal termination of simulation\n"
]
@ -861,13 +861,7 @@
"(5, 10, b' UZF RECHARGE', 10, 15, -1, 4, 121100.21, 504971.6, 24156966., b'', b'', b'', b'')\n",
"(5, 10, b' SURFACE LEAKAGE', 10, 15, -1, 4, 121100.21, 504971.6, 24156966., b'', b'', b'', b'')\n",
"(5, 10, b' HORT+DUNN', 10, 15, -1, 4, 121100.21, 504971.6, 24156966., b'', b'', b'', b'')\n",
"(5, 10, b' STORAGE CHANGE', 10, 15, -1, 4, 121100.21, 504971.6, 24156966., b'', b'', b'', b'')\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"(5, 10, b' STORAGE CHANGE', 10, 15, -1, 4, 121100.21, 504971.6, 24156966., b'', b'', b'', b'')\n",
"(10, 10, b' GW ET', 10, 15, -1, 4, 195033.11, 1318233.4, 24970228., b'', b'', b'', b'')\n",
"(10, 10, b' UZF RECHARGE', 10, 15, -1, 4, 195033.11, 1318233.4, 24970228., b'', b'', b'', b'')\n",
"(10, 10, b' SURFACE LEAKAGE', 10, 15, -1, 4, 195033.11, 1318233.4, 24970228., b'', b'', b'', b'')\n",

12
examples/Notebooks/flopy3_vtk_export.ipynb
View File

@ -21,9 +21,9 @@
"output_type": "stream",
"text": [
"flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
"3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 14:38:56) \n",
"3.7.7 (default, Mar 26 2020, 10:32:53) \n",
"[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
"flopy version: 3.3.0\n"
"flopy version: 3.3.1\n"
]
}
],
@ -67,9 +67,9 @@
"outputs": [],
"source": [
"# output folder to store the outputs from the notebook\n",
"workspace = os.path.join(\".\", \"VTK_EXAMPLE_OUTPUTS\")\n",
"workspace = os.path.join(\".\", \"temp\", \"VTK_EXAMPLE_OUTPUTS\")\n",
"if not os.path.exists(workspace):\n",
" os.mkdir(workspace)"
" os.makedirs(workspace)"
]
},
{
@ -248,7 +248,7 @@
{
"data": {
"text/plain": [
"'./VTK_EXAMPLE_OUTPUTS/model_output_test'"
"'./temp/VTK_EXAMPLE_OUTPUTS/model_output_test'"
]
},
"execution_count": 9,
@ -380,7 +380,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
"version": "3.7.7"
}
},
"nbformat": 4,

233
examples/Notebooks/flopy3_working_stack_demo.ipynb
View File

File diff suppressed because one or more lines are too long

370
examples/Testing/flopy3_Oahu_02_02b.py
View File

@ -1,185 +1,185 @@
# OAHU island-wide GWRP model
# using retarded units (ft) and a coarse test grid
# simulating 1 short stress period (eventually steady-state)
# simulating 1 layer of volcanic rock referenced to sea level
# simulating 50% seawater salinity with SWI2
# uses GH relation for initial salinity conditions
# apply crude mask of Oahu coastline as ocean boundary
# uniform recharge, add 2 wells, and 1 horizontal flow barrier
# changed origin of grid in plot to upper left corner.
#
# uses FLOPY3, modified from FLOPY2 tutorial 2
#
# Kolja Rotzoll (kolja@usgs.gov), 1/15/2015
# ----------------------------------------------------
import os
import sys
import numpy as np
from pylab import *
from PIL import Image, ImageDraw
flopypath = os.path.join('..', '..')
if flopypath not in sys.path:
print('Adding to sys.path: ', flopypath)
sys.path.append(flopypath)
import flopy
workspace = os.path.join('data')
#make sure workspace directory exists
if not os.path.exists(workspace):
os.makedirs(workspace)
# flopy objects
modelname = 'Oahu_01'
mf = flopy.modflow.Modflow(modelname, exe_name='mf2005', model_ws=workspace)
# model domain and grid definition
ztop = 30. # top of layer (ft rel to msl)
botm = -1000. # bottom of layer (ft rel to msl)
nlay = 1 # number of layers (z)
nrow = 18 # number of rows (y)
ncol = 20 # number of columns (x)
delr = 16000 # row width of cell, in ft
delc = delr # column width of cell, in ft
Lx = delr * ncol # length of x model domain, in ft
Ly = delc * nrow # length of y model domain, in ft
# define the stress periods
nper = 1
ts = 1 # length of time step, in days
nstp = 1000 # number of time steps
perlen = nstp * ts # length of simulation, in days
steady = True # steady state or transient
dis = flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, delr=delr, delc=delc,
top=ztop, botm=botm, nper=nper,
perlen=perlen, nstp=nstp, steady=steady)
# hydraulic parameters (lpf or bcf)
hk = 1500. # horizontal K
sy = 0.05 # specific yield
ss = 1.e-5 # specific storage
layavg = 0 # 0 = harmonic mean, 1 = logarithmic mean,
# 2 = arithmetic mean of sat b and log-mean K
laytyp = 1 # 0 = confined, 1 = convertible
lpf = flopy.modflow.ModflowLpf(mf, hk=hk, sy=sy, ss=ss, laytyp=laytyp, layavg=layavg)
laycon = 2 # 0 = confined, 1 = unconfined T varies,
# 2 = convertible T const, 3 = convertible T varies
# water/land interface (now replaced with coarse Oahu coastline)
polyg = [(6, 13), (3, 6), (6, 6), (9, 3), (12, 8), (14, 9), (16, 13), (13, 14), (11, 13),
(6, 13)] # referenced to row/col
px, py = zip(*polyg)
colcell, rowcell = meshgrid(range(ncol), range(nrow))
mask = Image.new('L', (ncol, nrow), 0)
ImageDraw.Draw(mask).polygon(polyg, outline=1, fill=1)
index = np.array(mask)
# BAS package
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32) # active cells
h_start = np.zeros((nrow, ncol), dtype=float)
peak = 15 # maximum expected water level
h_start[:, :][index == 1] = peak # starting heads over land
h_start[:, :][index == 0] = 0 # starting heads over ocean
#print h_start
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=h_start)
# general head boundary
nghb = ncol * nrow - np.sum(index)
lrchc = np.zeros((nghb, 5))
lrchc[:, 0] = 0
lrchc[:, 1] = rowcell[index == 0]
lrchc[:, 2] = colcell[index == 0]
lrchc[:, 3] = 0.
lrchc[:, 4] = hk * 10
#print lrchc
ghb = flopy.modflow.ModflowGhb(mf, stress_period_data={0: lrchc})
# recharge & withdrawal
Recharge = 600 * 133680.56 # Total recharge over the island, in ft^3/d
nrech = np.sum(index)
lrcq = np.zeros((nrech, 4))
lrcq[:, 0] = 0
lrcq[:, 1] = rowcell[index == 1]
lrcq[:, 2] = colcell[index == 1]
lrcq[:, 3] = Recharge / nrech
lrcq = np.vstack((lrcq, [0, 8, 7, -90 * 133680], [0, 10, 9, -80 * 133680])) # add wells (row/col, zero-based)
#print lrcq
wel = flopy.modflow.ModflowWel(mf, stress_period_data={0: lrcq})
# horizontal flow barrier
nhfb = 12
lrcrch = np.zeros((nhfb, 6))
lrcrch[:, 0] = 0 # layer
lrcrch[:, 1] = arange(2, nhfb + 2) # row 1
lrcrch[:, 2] = ones(nhfb) * (ncol / 2 - 1) # col 1
lrcrch[:, 3] = arange(2, nhfb + 2) # row 2
lrcrch[:, 4] = ones(nhfb) * (ncol / 2) # col 2
lrcrch[:, 5] = 0.000001 # hydrologic characteristics
#print lrcrch
hfb = flopy.modflow.ModflowHfb(mf, hfb_data=lrcrch)
# SWI input
z1 = np.zeros((nrow, ncol))
z1[index == 1] = peak * (-40) # 50% salinity from starting head
z = array([z1]) # zeta interfaces
#print z
iso = np.zeros((nrow, ncol), dtype=np.int32) # water type of sinks and sources
iso[:, :][index == 1] = 1 # land
iso[:, :][index == 0] = -2 # ocean (ghb)
#print iso
swi = flopy.modflow.ModflowSwi2(mf, nsrf=1, istrat=1, toeslope=0.04, tipslope=0.04,
nu=[0, 0.025], zeta=z, ssz=0.05, isource=iso, nsolver=1)
# output control & solver
spd = {(0, 0): ['print head'],
(0, 1): [],
(0, 249): ['print head'],
(0, 250): [],
(0, 499): ['print head', 'save ibound'],
(0, 500): [],
(0, 749): ['print head', 'ddreference'],
(0, 750): [],
(0, 999): ['print head']}
#oc = flopy.modflow.ModflowOc(mf, stress_period_data=spd, cboufm='(20i5)')
oc = flopy.modflow.ModflowOc88(mf, save_head_every=100,
item2=[[0, 1, 0, 0]], item3=[[0, 1, 0, 0]])
pcg = flopy.modflow.ModflowPcg(mf, hclose=1.0e-4, rclose=5.0e-0) # pre-conjugate gradient solver
#de4 = flopy.modflow.ModflowDe4(mf, itmx=1, hclose=1e-5) # direct solver
# --------------------------------------------------------------------
# write the model input files
mf.write_input()
print('\n\nfinished write...\n')
m2 = flopy.modflow.Modflow.load(modelname, exe_name='mf2005', model_ws=workspace, verbose=True)
print('\nfinished read...\n')
oc2 = m2.get_package('OC')
#print(oc2.stress_period_data.keys())
oc2.write_file()
ax = m2.plot(colorbar=True)
print(len(ax))
plt.show()
#m2.dis.plot(colorbar=True)
#plt.show()
#m2.lpf.plot(colorbar=True)
#plt.show()
#m2.ghb.plot(key='cond', colorbar=True, masked_values=[0])
#plt.show()
#m2.ghb.plot()
#plt.show()
print('\nthis is the end...my friend\n')
# OAHU island-wide GWRP model
# using retarded units (ft) and a coarse test grid
# simulating 1 short stress period (eventually steady-state)
# simulating 1 layer of volcanic rock referenced to sea level
# simulating 50% seawater salinity with SWI2
# uses GH relation for initial salinity conditions
# apply crude mask of Oahu coastline as ocean boundary
# uniform recharge, add 2 wells, and 1 horizontal flow barrier
# changed origin of grid in plot to upper left corner.
#
# uses FLOPY3, modified from FLOPY2 tutorial 2
#
# Kolja Rotzoll (kolja@usgs.gov), 1/15/2015
# ----------------------------------------------------
import os
import sys
import numpy as np
from pylab import *
from PIL import Image, ImageDraw
flopypath = os.path.join('..', '..')
if flopypath not in sys.path:
print('Adding to sys.path: ', flopypath)
sys.path.append(flopypath)
import flopy
workspace = os.path.join('data')
#make sure workspace directory exists
if not os.path.exists(workspace):
os.makedirs(workspace)
# flopy objects
modelname = 'Oahu_01'
mf = flopy.modflow.Modflow(modelname, exe_name='mf2005', model_ws=workspace)
# model domain and grid definition
ztop = 30. # top of layer (ft rel to msl)
botm = -1000. # bottom of layer (ft rel to msl)
nlay = 1 # number of layers (z)
nrow = 18 # number of rows (y)
ncol = 20 # number of columns (x)
delr = 16000 # row width of cell, in ft
delc = delr # column width of cell, in ft
Lx = delr * ncol # length of x model domain, in ft
Ly = delc * nrow # length of y model domain, in ft
# define the stress periods
nper = 1
ts = 1 # length of time step, in days
nstp = 1000 # number of time steps
perlen = nstp * ts # length of simulation, in days
steady = True # steady state or transient
dis = flopy.modflow.ModflowDis(mf, nlay, nrow, ncol, delr=delr, delc=delc,
top=ztop, botm=botm, nper=nper,
perlen=perlen, nstp=nstp, steady=steady)
# hydraulic parameters (lpf or bcf)
hk = 1500. # horizontal K
sy = 0.05 # specific yield
ss = 1.e-5 # specific storage
layavg = 0 # 0 = harmonic mean, 1 = logarithmic mean,
# 2 = arithmetic mean of sat b and log-mean K
laytyp = 1 # 0 = confined, 1 = convertible
lpf = flopy.modflow.ModflowLpf(mf, hk=hk, sy=sy, ss=ss, laytyp=laytyp, layavg=layavg)
laycon = 2 # 0 = confined, 1 = unconfined T varies,
# 2 = convertible T const, 3 = convertible T varies
# water/land interface (now replaced with coarse Oahu coastline)
polyg = [(6, 13), (3, 6), (6, 6), (9, 3), (12, 8), (14, 9), (16, 13), (13, 14), (11, 13),
(6, 13)] # referenced to row/col
px, py = zip(*polyg)
colcell, rowcell = meshgrid(range(ncol), range(nrow))
mask = Image.new('L', (ncol, nrow), 0)
ImageDraw.Draw(mask).polygon(polyg, outline=1, fill=1)
index = np.array(mask)
# BAS package
ibound = np.ones((nlay, nrow, ncol), dtype=np.int32) # active cells
h_start = np.zeros((nrow, ncol), dtype=float)
peak = 15 # maximum expected water level
h_start[:, :][index == 1] = peak # starting heads over land
h_start[:, :][index == 0] = 0 # starting heads over ocean
#print h_start
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=h_start)
# general head boundary
nghb = ncol * nrow - np.sum(index)
lrchc = np.zeros((nghb, 5))
lrchc[:, 0] = 0
lrchc[:, 1] = rowcell[index == 0]
lrchc[:, 2] = colcell[index == 0]
lrchc[:, 3] = 0.
lrchc[:, 4] = hk * 10
#print lrchc
ghb = flopy.modflow.ModflowGhb(mf, stress_period_data={0: lrchc})
# recharge & withdrawal
Recharge = 600 * 133680.56 # Total recharge over the island, in ft^3/d
nrech = np.sum(index)
lrcq = np.zeros((nrech, 4))
lrcq[:, 0] = 0
lrcq[:, 1] = rowcell[index == 1]
lrcq[:, 2] = colcell[index == 1]
lrcq[:, 3] = Recharge / nrech
lrcq = np.vstack((lrcq, [0, 8, 7, -90 * 133680], [0, 10, 9, -80 * 133680])) # add wells (row/col, zero-based)
#print lrcq
wel = flopy.modflow.ModflowWel(mf, stress_period_data={0: lrcq})
# horizontal flow barrier
nhfb = 12
lrcrch = np.zeros((nhfb, 6))
lrcrch[:, 0] = 0 # layer
lrcrch[:, 1] = arange(2, nhfb + 2) # row 1
lrcrch[:, 2] = ones(nhfb) * (ncol / 2 - 1) # col 1
lrcrch[:, 3] = arange(2, nhfb + 2) # row 2
lrcrch[:, 4] = ones(nhfb) * (ncol / 2) # col 2
lrcrch[:, 5] = 0.000001 # hydrologic characteristics
#print lrcrch
hfb = flopy.modflow.ModflowHfb(mf, hfb_data=lrcrch)
# SWI input
z1 = np.zeros((nrow, ncol))
z1[index == 1] = peak * (-40) # 50% salinity from starting head
z = array([z1]) # zeta interfaces
#print z
iso = np.zeros((nrow, ncol), dtype=np.int32) # water type of sinks and sources
iso[:, :][index == 1] = 1 # land
iso[:, :][index == 0] = -2 # ocean (ghb)
#print iso
swi = flopy.modflow.ModflowSwi2(mf, nsrf=1, istrat=1, toeslope=0.04, tipslope=0.04,
nu=[0, 0.025], zeta=z, ssz=0.05, isource=iso, nsolver=1)
# output control & solver
spd = {(0, 0): ['print head'],
(0, 1): [],
(0, 249): ['print head'],
(0, 250): [],
(0, 499): ['print head', 'save ibound'],
(0, 500): [],
(0, 749): ['print head', 'ddreference'],
(0, 750): [],
(0, 999): ['print head']}
#oc = flopy.modflow.ModflowOc(mf, stress_period_data=spd, cboufm='(20i5)')
oc = flopy.modflow.ModflowOc88(mf, save_head_every=100,
item2=[[0, 1, 0, 0]], item3=[[0, 1, 0, 0]])
pcg = flopy.modflow.ModflowPcg(mf, hclose=1.0e-4, rclose=5.0e-0) # pre-conjugate gradient solver
#de4 = flopy.modflow.ModflowDe4(mf, itmx=1, hclose=1e-5) # direct solver
# --------------------------------------------------------------------
# write the model input files
mf.write_input()
print('\n\nfinished write...\n')
m2 = flopy.modflow.Modflow.load(modelname, exe_name='mf2005', model_ws=workspace, verbose=True)
print('\nfinished read...\n')
oc2 = m2.get_package('OC')
#print(oc2.stress_period_data.keys())
oc2.write_file()
ax = m2.plot(colorbar=True)
print(len(ax))
plt.show()
#m2.dis.plot(colorbar=True)
#plt.show()
#m2.lpf.plot(colorbar=True)
#plt.show()
#m2.ghb.plot(key='cond', colorbar=True, masked_values=[0])
#plt.show()
#m2.ghb.plot()
#plt.show()
print('\nthis is the end...my friend\n')

5
examples/Testing/testunitcbc.py
View File

@ -6,6 +6,7 @@ import flopy
# Assign name and create modflow model object
modelname = 'units'
mf = flopy.modflow.Modflow(modelname, exe_name='mf2005', model_ws=os.path.join('data'))
cbc_unit_nb = 1053
# Model domain and grid definition
Lx = 1000.
@ -34,10 +35,10 @@ strt[:, :, -1] = 0.
bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)
# Add LPF package to the MODFLOW model
lpf = flopy.modflow.ModflowLpf(mf, hk=10., vka=10.)
lpf = flopy.modflow.ModflowLpf(mf, hk=10., vka=10., ipakcb=cbc_unit_nb)
# add well
wel = flopy.modflow.ModflowWel(mf, ipakcb=1053, stress_period_data={0:[0, 4, 4, -100.]})
wel = flopy.modflow.ModflowWel(mf, ipakcb=cbc_unit_nb, stress_period_data={0:[0, 4, 4, -100.]})
# Add OC package to the MODFLOW model
spd = {(0, 0): ['print head', 'print budget', 'save head', 'save budget']}

567
examples/data/ag_test/Agwater1.ag Normal file
View File

@ -0,0 +1,567 @@
# AG options
options
etdemand
irrigation_diversion 1 6
supplemental_well 6 1
irrigation_well 6 1
maxwells 6
diversionlist -2
welllist -2
wellirrlist -2
diversionirrlist -2
timeseries_well
timeseries_diversion
timeseries_diversionet
end
# AG time series
time series
well 5 105
diversion 9 107
diversionet 9 108
end
# AG segment list
segment list
9
end
# AG well list
well list
1 6 4 -100.00
1 6 5 -100.00
1 7 4 -100.00
1 7 5 -100.00
1 8 4 -100.00
1 8 5 -100.00
end
# AG stress period
stress period 1
IRRdiversion
0
IRRWELL
0
SUPWELL
0
END
stress period 2
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 3
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 4
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 5
IRRdiversion
1 NUMIRRSEGSP
9 6 0.0 0.0 #SEGID NUMCELLSEG IRRPERIODSEG TRIGGERFACTSEG
6 4 0.0 0.16667 IRRROW IRRCOL EFF_FACT FIELD_FACT
6 5 0.0 0.16667
7 4 0.0 0.16667
7 5 0.0 0.16667
8 4 0.0 0.16667
8 5 0.0 0.16667
IRRWELL
6
1 1 0.0 0.0 #IRRWELLLID NUMCELLWELL IRRPERIODWELL TRIGGERPERIODWELL
6 4 0.0 1.0 IRRROW IRRCOL EFF_FACT FIELD_FACT
2 1
6 5 0.0 1.0
3 1
7 4 0.0 1.0
4 1
7 5 0.0 1.0
5 1
8 4 0.0 1.0
6 1
8 5 0.0 1.0
SUPWELL
6 NUMSUPWELLLSP
1 1 SUPWELLLNUM NUMSEGWELL
9 1.0 1.0 #SEGWELLID FACSUP FACSUPMAX
2 1
9 1.0 1.0
3 1
9 1.0 1.0
4 1
9 1.0 1.0
5 1
9 1.0 1.0
6 1
9 1.0 1.0
end
stress period 6
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 7
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 8
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 9
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 10
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 11
IRRdiversion
0
IRRWELL
0
SUPWELL
0
END
stress period 12
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 13
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 14
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 15
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 16
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 17
IRRdiversion
1 NUMIRRSEGSP
9 6 0.0 0.0 #SEGID NUMCELLSEG IRRPERIODSEG TRIGGERFACTSEG
6 4 0.0 0.16667 IRRROW IRRCOL EFF_FACT FIELD_FACT
6 5 0.0 0.16667
7 4 0.0 0.16667
7 5 0.0 0.16667
8 4 0.0 0.16667
8 5 0.0 0.16667
IRRWELL
6
1 1 0.0 0.0 #IRRWELLLID NUMCELLWELL IRRPERIODWELL TRIGGERPERIODWELL
6 4 0.0 1.0 IRRROW IRRCOL EFF_FACT FIELD_FACT
2 1
6 5 0.0 1.0
3 1
7 4 0.0 1.0
4 1
7 5 0.0 1.0
5 1
8 4 0.0 1.0
6 1
8 5 0.0 1.0
SUPWELL
6 NUMSUPWELLLSP
1 1 SUPWELLLNUM NUMSEGWELL
9 1.0 1.0 #SEGWELLID FACSUP FACSUPMAX
2 1
9 1.0 1.0
3 1
9 1.0 1.0
4 1
9 1.0 1.0
5 1
9 1.0 1.0
6 1
9 1.0 1.0
end
stress period 18
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 19
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 20
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 21
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 22
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 23
IRRdiversion
0
IRRWELL
0
SUPWELL
0
END
stress period 24
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 25
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 26
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 27
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 28
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 29
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 30
IRRdiversion
1 NUMIRRSEGSP
9 6 0.0 0.0 #SEGID NUMCELLSEG IRRPERIODSEG TRIGGERFACTSEG
6 4 0.0 0.16667 IRRROW IRRCOL EFF_FACT FIELD_FACT
6 5 0.0 0.16667
7 4 0.0 0.16667
7 5 0.0 0.16667
8 4 0.0 0.16667
8 5 0.0 0.16667
IRRWELL
6
1 1 0.0 0.0 #IRRWELLLID NUMCELLWELL IRRPERIODWELL TRIGGERPERIODWELL
6 4 0.0 1.0 IRRROW IRRCOL EFF_FACT FIELD_FACT
2 1
6 5 0.0 1.0
3 1
7 4 0.0 1.0
4 1
7 5 0.0 1.0
5 1
8 4 0.0 1.0
6 1
8 5 0.0 1.0
SUPWELL
6 NUMSUPWELLLSP
1 1 SUPWELLLNUM NUMSEGWELL
9 1.0 1.0 #SEGWELLID FACSUP FACSUPMAX
2 1
9 1.0 1.0
3 1
9 1.0 1.0
4 1
9 1.0 1.0
5 1
9 1.0 1.0
6 1
9 1.0 1.0
end
stress period 31
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 32
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 33
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 34
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 35
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 36
IRRdiversion
0
IRRWELL
0
SUPWELL
0
END
stress period 37
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 38
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 39
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 40
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 41
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 42
IRRdiversion
1 NUMIRRSEGSP
9 6 0.0 0.0 #SEGID NUMCELLSEG IRRPERIODSEG TRIGGERFACTSEG
6 4 0.0 0.16667 IRRROW IRRCOL EFF_FACT FIELD_FACT
6 5 0.0 0.16667
7 4 0.0 0.16667
7 5 0.0 0.16667
8 4 0.0 0.16667
8 5 0.0 0.16667
IRRWELL
6
1 1 0.0 0.0 #IRRWELLLID NUMCELLWELL IRRPERIODWELL TRIGGERPERIODWELL
6 4 0.0 1.0 IRRROW IRRCOL EFF_FACT FIELD_FACT
2 1
6 5 0.0 1.0
3 1
7 4 0.0 1.0
4 1
7 5 0.0 1.0
5 1
8 4 0.0 1.0
6 1
8 5 0.0 1.0
SUPWELL
6 NUMSUPWELLLSP
1 1 SUPWELLLNUM NUMSEGWELL
9 1.0 1.0 #SEGWELLID FACSUP FACSUPMAX
2 1
9 1.0 1.0
3 1
9 1.0 1.0
4 1
9 1.0 1.0
5 1
9 1.0 1.0
6 1
9 1.0 1.0
end
stress period 43
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 44
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 45
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 46
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 47
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 48
IRRdiversion
0
IRRWELL
0
SUPWELL
0
END
stress period 49
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 50
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END
stress period 51
IRRdiversion
-1
IRRWELL
-1
SUPWELL
-1
END

1286
examples/data/ag_test/Agwater1.uzf Normal file
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2
examples/data/mf6/create_tests/test028_sfr/sfr_rec.txt
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@ -1,5 +1,5 @@
1 1 1 1 4500. 12 8.6767896E-04 1093.048 3.0 0.00003 0.03 1 1.0 0
2 1 2 2 7000. 12 8.6767896E-04 1088.059 3.0 0.00003 0.03 2 1.0 0
2 None 7000. 12 8.6767896E-04 1088.059 3.0 0.00003 0.03 2 1.0 0
3 1 3 3 6000. 12 8.6767896E-04 1082.419 3.0 0.00003 0.03 2 1.0 0
4 1 3 4 5550. 12 8.6767896E-04 1077.408 3.0 0.00003 0.03 3 1.0 1
5 1 4 5 6500. 12 9.4339624E-04 1071.934 3.0 0.00003 0.03 2 1.0 0

3
examples/data/mf6/test001e_UZF_3lay/chd_spd.txt Normal file
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@ -0,0 +1,3 @@
# comment
3 1 1 -25.0000000
3 1 10 -25.0000000

3
examples/data/mf6/test001e_UZF_3lay/test001e_UZF_3lay.chd
View File

@ -9,6 +9,5 @@ BEGIN Dimensions
END Dimensions
BEGIN Period 1
3 1 1 -25.0000000
3 1 10 -25.0000000
OPEN/CLOSE 'chd_spd.txt'
END Period

1
examples/data/mf6/test001e_UZF_3lay/test001e_UZF_3lay.uzf
View File

@ -4,6 +4,7 @@ Begin options
boundnames
PRINT_FLOWS
OBS6 FILEIN test001e_UZF_3lay.obs
BUDGET FILEOUT test001e_UZF_3lay.uzf.cbc
SIMULATE_GWSEEP
SIMULATE_ET
LINEAR_GWET

BIN
examples/data/mf6/test003_gwfs_disv/test003_gwfs_disv.dbf
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BIN
examples/data/mf6/test003_gwfs_disv/test003_gwfs_disv.shp
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BIN
examples/data/mf6/test003_gwfs_disv/test003_gwfs_disv.shx
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296
examples/data/mf6/test005_advgw_tidal/expected_output/AdvGW_tidal.gitlist Normal file
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@ -0,0 +1,296 @@
MODFLOW 6
U.S. GEOLOGICAL SURVEY MODULAR HYDROLOGIC MODEL
GROUNDWATER FLOW MODEL (GWF)
VERSION 6.0.4 03/13/2019
MODFLOW 6 compiled Mar 14 2019 09:20:00 with GFORTRAN compiler (ver. 8.2.0)
This software has been approved for release by the U.S. Geological
Survey (USGS). Although the software has been subjected to rigorous
review, the USGS reserves the right to update the software as needed
pursuant to further analysis and review. No warranty, expressed or
implied, is made by the USGS or the U.S. Government as to the
functionality of the software and related material nor shall the
fact of release constitute any such warranty. Furthermore, the
software is released on condition that neither the USGS nor the U.S.
Government shall be held liable for any damages resulting from its
authorized or unauthorized use. Also refer to the USGS Water
Resources Software User Rights Notice for complete use, copyright,
and distribution information.
MODFLOW was compiled using uniform precision.
Precision of REAL variables: 15
OPENED AdvGW_tidal.ic
FILE TYPE:IC6 UNIT 1005 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.npf
FILE TYPE:NPF6 UNIT 1006 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.wel
FILE TYPE:WEL6 UNIT 1007 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.riv
FILE TYPE:RIV6 UNIT 1008 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal_1.rch
FILE TYPE:RCH6 UNIT 1009 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal_2.rch
FILE TYPE:RCH6 UNIT 1010 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal_3.rch
FILE TYPE:RCH6 UNIT 1011 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.oc
FILE TYPE:OC6 UNIT 1012 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.dis
FILE TYPE:DIS6 UNIT 1013 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.ghb
FILE TYPE:GHB6 UNIT 1014 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.sto
FILE TYPE:STO6 UNIT 1015 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.evt
FILE TYPE:EVT6 UNIT 1016 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
OPENED AdvGW_tidal.obs
FILE TYPE:OBS6 UNIT 1017 STATUS:OLD
FORMAT:FORMATTED ACCESS:SEQUENTIAL
ACTION:READ
VOLUME BUDGET FOR ENTIRE MODEL AT END OF TIME STEP 1, STRESS PERIOD 1
---------------------------------------------------------------------------------------------------
CUMULATIVE VOLUME L**3 RATES FOR THIS TIME STEP L**3/T PACKAGE NAME
------------------ ------------------------ ----------------
IN: IN:
--- ---
STO-SS = 0.0000 STO-SS = 0.0000 STORAGE
STO-SY = 0.0000 STO-SY = 0.0000 STORAGE
WEL = 0.0000 WEL = 0.0000 WEL
RIV = 19677.9327 RIV = 19677.9327 RIV
GHB = 0.0000 GHB = 0.0000 GHB-TIDAL
RCH = 30750.0000 RCH = 30750.0000 RCH-ZONE_1
RCH = 6800.0000 RCH = 6800.0000 RCH-ZONE_2
RCH = 24050.0000 RCH = 24050.0000 RCH-ZONE_3
EVT = 0.0000 EVT = 0.0000 EVT
TOTAL IN = 81277.9327 TOTAL IN = 81277.9327
OUT: OUT:
---- ----
STO-SS = 0.0000 STO-SS = 0.0000 STORAGE
STO-SY = 0.0000 STO-SY = 0.0000 STORAGE
WEL = 0.0000 WEL = 0.0000 WEL
RIV = 4891.5846 RIV = 4891.5846 RIV
GHB = 76116.3012 GHB = 76116.3012 GHB-TIDAL
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_1
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_2
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_3
EVT = 270.0459 EVT = 270.0459 EVT
TOTAL OUT = 81277.9317 TOTAL OUT = 81277.9317
IN - OUT = 1.0332E-03 IN - OUT = 1.0332E-03
PERCENT DISCREPANCY = 0.00 PERCENT DISCREPANCY = 0.00
TIME SUMMARY AT END OF TIME STEP 1 IN STRESS PERIOD 1
SECONDS MINUTES HOURS DAYS YEARS
-----------------------------------------------------------
TIME STEP LENGTH 86400. 1440.0 24.000 1.0000 2.73785E-03
STRESS PERIOD TIME 86400. 1440.0 24.000 1.0000 2.73785E-03
TOTAL TIME 86400. 1440.0 24.000 1.0000 2.73785E-03
VOLUME BUDGET FOR ENTIRE MODEL AT END OF TIME STEP 120, STRESS PERIOD 2
---------------------------------------------------------------------------------------------------
CUMULATIVE VOLUME L**3 RATES FOR THIS TIME STEP L**3/T PACKAGE NAME
------------------ ------------------------ ----------------
IN: IN:
--- ---
STO-SS = 45634.5133 STO-SS = 53.4129 STORAGE
STO-SY = 85658.9163 STO-SY = 8692.4699 STORAGE
WEL = 0.0000 WEL = 0.0000 WEL
RIV = 521527.7300 RIV = 28541.3439 RIV
GHB = 0.0000 GHB = 0.0000 GHB-TIDAL
RCH = 235750.0000 RCH = 20500.0000 RCH-ZONE_1
RCH = 80800.0000 RCH = 7598.3333 RCH-ZONE_2
RCH = 264550.0000 RCH = 22116.2500 RCH-ZONE_3
EVT = 0.0000 EVT = 0.0000 EVT
TOTAL IN = 1233921.1596 TOTAL IN = 87501.8100
OUT: OUT:
---- ----
STO-SS = 46352.6550 STO-SS = 14308.0596 STORAGE
STO-SY = 336599.3388 STO-SY = 10116.9414 STORAGE
WEL = 2500.0000 WEL = 250.0000 WEL
RIV = 6829.5406 RIV = 2028.7842 RIV
GHB = 838630.3721 GHB = 60521.4761 GHB-TIDAL
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_1
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_2
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_3
EVT = 3009.2429 EVT = 276.5487 EVT
TOTAL OUT = 1233921.1494 TOTAL OUT = 87501.8100
IN - OUT = 1.0215E-02 IN - OUT = 1.3167E-05
PERCENT DISCREPANCY = 0.00 PERCENT DISCREPANCY = 0.00
TIME SUMMARY AT END OF TIME STEP 120 IN STRESS PERIOD 2
SECONDS MINUTES HOURS DAYS YEARS
-----------------------------------------------------------
TIME STEP LENGTH 7200.0 120.00 2.0000 8.33333E-02 2.28154E-04
STRESS PERIOD TIME 8.64000E+05 14400. 240.00 10.000 2.73785E-02
TOTAL TIME 9.50400E+05 15840. 264.00 11.000 3.01164E-02
VOLUME BUDGET FOR ENTIRE MODEL AT END OF TIME STEP 120, STRESS PERIOD 3
---------------------------------------------------------------------------------------------------
CUMULATIVE VOLUME L**3 RATES FOR THIS TIME STEP L**3/T PACKAGE NAME
------------------ ------------------------ ----------------
IN: IN:
--- ---
STO-SS = 92326.1229 STO-SS = 13063.9452 STORAGE
STO-SY = 142015.7165 STO-SY = 8904.1423 STORAGE
WEL = 0.0000 WEL = 0.0000 WEL
RIV = 719514.5899 RIV = 19131.2997 RIV
GHB = 0.0000 GHB = 0.0000 GHB-TIDAL
RCH = 543250.0000 RCH = 30750.0000 RCH-ZONE_1
RCH = 150800.0000 RCH = 6405.0000 RCH-ZONE_2
RCH = 492050.0000 RCH = 23394.5833 RCH-ZONE_3
EVT = 0.0000 EVT = 0.0000 EVT
TOTAL IN = 2139956.4293 TOTAL IN = 101648.9705
OUT: OUT:
---- ----
STO-SS = 91010.2622 STO-SS = 16.2689 STORAGE
STO-SY = 368213.1394 STO-SY = 2025.1984 STORAGE
WEL = 25500.0000 WEL = 2300.0000 WEL
RIV = 53227.3651 RIV = 5928.1102 RIV
GHB = 1596232.3720 GHB = 91103.3212 GHB-TIDAL
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_1
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_2
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_3
EVT = 5773.2782 EVT = 276.0718 EVT
TOTAL OUT = 2139956.4170 TOTAL OUT = 101648.9705
IN - OUT = 1.2296E-02 IN - OUT = 6.8287E-05
PERCENT DISCREPANCY = 0.00 PERCENT DISCREPANCY = 0.00
TIME SUMMARY AT END OF TIME STEP 120 IN STRESS PERIOD 3
SECONDS MINUTES HOURS DAYS YEARS
-----------------------------------------------------------
TIME STEP LENGTH 7200.0 120.00 2.0000 8.33333E-02 2.28154E-04
STRESS PERIOD TIME 8.64000E+05 14400. 240.00 10.000 2.73785E-02
TOTAL TIME 1.81440E+06 30240. 504.00 21.000 5.74949E-02
VOLUME BUDGET FOR ENTIRE MODEL AT END OF TIME STEP 120, STRESS PERIOD 4
---------------------------------------------------------------------------------------------------
CUMULATIVE VOLUME L**3 RATES FOR THIS TIME STEP L**3/T PACKAGE NAME
------------------ ------------------------ ----------------
IN: IN:
--- ---
STO-SS = 136641.8243 STO-SS = 12.0295 STORAGE
STO-SY = 201207.5005 STO-SY = 6276.0852 STORAGE
WEL = 0.0000 WEL = 0.0000 WEL
RIV = 905396.1710 RIV = 18103.0142 RIV
GHB = 0.0000 GHB = 0.0000 GHB-TIDAL
RCH = 1055750.0000 RCH = 51250.0000 RCH-ZONE_1
RCH = 218800.0000 RCH = 7196.6667 RCH-ZONE_2
RCH = 739050.0000 RCH = 25989.1667 RCH-ZONE_3
EVT = 0.0000 EVT = 0.0000 EVT
TOTAL IN = 3256845.4958 TOTAL IN = 108826.9623
OUT: OUT:
---- ----
STO-SS = 137620.6061 STO-SS = 11424.0679 STORAGE
STO-SY = 593759.5707 STO-SY = 24995.5298 STORAGE
WEL = 32200.0000 WEL = 670.0000 WEL
RIV = 128064.8995 RIV = 8958.9833 RIV
GHB = 2356641.5987 GHB = 62497.5547 GHB-TIDAL
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_1
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_2
RCH = 0.0000 RCH = 0.0000 RCH-ZONE_3
EVT = 8558.8104 EVT = 280.8262 EVT
TOTAL OUT = 3256845.4854 TOTAL OUT = 108826.9618
IN - OUT = 1.0424E-02 IN - OUT = 4.9647E-04
PERCENT DISCREPANCY = 0.00 PERCENT DISCREPANCY = 0.00
TIME SUMMARY AT END OF TIME STEP 120 IN STRESS PERIOD 4
SECONDS MINUTES HOURS DAYS YEARS
-----------------------------------------------------------
TIME STEP LENGTH 7200.0 120.00 2.0000 8.33333E-02 2.28154E-04
STRESS PERIOD TIME 8.64000E+05 14400. 240.00 10.000 2.73785E-02
TOTAL TIME 2.67840E+06 44640. 744.00 31.000 8.48734E-02

20948
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examples/data/zonbud_examples/freyberg_mlt.1.csv Normal file
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