Initial commit

Disclaimer.md

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+# Disclaimer
+
+This software is preliminary or provisional and is subject to revision. It is 
+being provided to meet the need for timely best science. The software has not 
+received final approval by the U.S. Geological Survey (USGS). 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. The software is provided on the condition
+that neither the USGS nor the U.S. Government shall be held liable for any 
+damages resulting from the authorized or unauthorized use of the software.

LICENSE.md

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+# License
+
+Unless otherwise noted, This project is in the public domain in the United
+States because it contains materials that originally came from the United
+States Geological Survey, an agency of the United States Department of
+Interior. For more information, see the official USGS copyright policy at
+http:https://www.usgs.gov/visual-id/credit_usgs.html#copyright
+
+Additionally, we waive copyright and related rights in the work
+worldwide through the CC0 1.0 Universal public domain dedication.
+
+## CC0 1.0 Universal Summary
+
+This is a human-readable summary of the
+[Legal Code (read the full text)](https://creativecommons.org/publicdomain/zero/1.0/legalcode).
+
+### No Copyright
+
+The person who associated a work with this deed has dedicated the work to
+the public domain by waiving all of his or her rights to the work worldwide
+under copyright law, including all related and neighboring rights, to the
+extent allowed by law.
+
+You can copy, modify, distribute and perform the work, even for commercial
+purposes, all without asking permission.
+
+### Other Information
+
+In no way are the patent or trademark rights of any person affected by CC0,
+nor are the rights that other persons may have in the work or in how the
+work is used, such as publicity or privacy rights.
+
+Unless expressly stated otherwise, the person who associated a work with
+this deed makes no warranties about the work, and disclaims liability for
+all uses of the work, to the fullest extent permitted by applicable law.
+When using or citing the work, you should not imply endorsement by the
+author or the affirmer.

README.md

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-# heavy-review
+# Heavy
+A forward-gravity program for MODFLOW-2005 and MODFLOW-NWT
+
+![gravity calculation](./img/g_calculation.png)
+
+Heavy is a Fortran program for calculating the change in gravity caused by the change in groundwater storage as predicted by a MODFLOW groundwater-flow model.
+
+Gravity change is calculated relative to the initial time step at user-specified locations (e.g., measurement locations). At each location, the gravitational attraction is the sum of the attraction caused by storage change (confined or unconfined) within each model cell and layer. 
+
+Heavy is intended to be incorporated into workflows for parameter estimation such as [PEST++](https://www.usgs.gov/software/pest-parameter-estimation-code-optimized-large-environmental-models).
+
+## Running Heavy on Windows:
+```
+$> Heavy -q
+ Heavy debug routine
+ Forsberg gravity, single 100000 x 100000-m layer, 1.0-m thick prism, g = 41.927 uGal
+ Horizontal infinite slab (2*pi*G), g = 41.928 uGal
+ Forsberg gravity, single layer 10000 x 10000-m layer composed of 10x10x1-m prisms, g = 41.85 uGal
+
+ Gravitational attraction of a 20x20x20-m prism, 100 m deep, vs. an equivalent mass sphere:
+ Heavy point-mass gravity, g = 6.590618 uGal; Newton's Law (G*m/r^2) = 6.553962 uGal
+
+Process returned 0 (0x0) execution time : 0.585 s
+Press any key to continue.
+```
+(Copy /bin/Heavy.exe to /test/aac)
+```
+$> Heavy model1_hvy.nam
+
+ HEAVY-0.0.2 2021-09-10
+ U.S. GEOLOGICAL SURVEY MODELING TOOL FOR
+ THE FORWARD MODELING OF MICROGRAVITY WITH MODFLOW
+
+ Using NAME file: model1_hvy.nam
+ Run start date and time (yyyy/mm/dd hh:mm:ss): 2021/12/17 13:33:49
+
+ CALCULATING GRAVITY FOR ALL LAYERS
+ Single Precision Binary Head file
+ READ HEAD FOR PERIOD 1 STEP 1 PERTIM = 1.000000E+00 TOTIM = 1.000000E+00
+ READ HEAD FOR PERIOD 1 STEP 1 PERTIM = 1.000000E+00 TOTIM = 1.000000E+00
+...
+ READ HEAD FOR PERIOD 20 STEP 1 PERTIM = 1.000000E+00 TOTIM = 7.600000E+01
+ READ HEAD FOR PERIOD 21 STEP 1 PERTIM = 1.000000E+00 TOTIM = 7.700000E+01
+Elapsed Run Time: 6.859 seconds
+```
+
+**See /doc/User Guide.docx for information on running Heavy**
+
+## Compiling Heavy:
+
+**Windows**
+There is a compiled executable in the /bin/Release directory.
+
+Heavy has been compiled on Windows using the Code::Blocks IDE with the gfortran compiler, and using Visual Studio 2019 with the Intel oneAPI Fortran compiler. The latter is somewhat faster but more difficult to compile a standalone executable. 
+
+**Linux**
+1) Install pymake: ```pip install --user https://github.com/modflowpy/pymake/zipball/master```
+
+2) Compile: 
+```python -m pymake ./src ./bin/heavy -mc```
+
+This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). 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. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

autotest/make_gfortran.py

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+#! /usr/bin/env python
+try:
+ import pymake
+except:
+ msg = 'Error. Pymake package is not available.\n'
+ msg += 'Try installing using the following command:\n'
+ msg += ' pip install https://github.com/modflowpy/pymake/zipball/master'
+ print(msg)
+ raise Exception()
+import os
+import shutil
+import platform
+
+
+def copytree(src, dst, symlinks=False, ignore=None):
+ for item in os.listdir(src):
+ s = os.path.join(src, item)
+ d = os.path.join(dst, item)
+ if os.path.isdir(s):
+ shutil.copytree(s, d, symlinks, ignore)
+ else:
+ shutil.copy2(s, d)
+
+
+def cleanup(srcdir, tempdir):
+ """
+ Method to copy source code and cleanup the mfnwt code base
+ for gfortran compilation.
+ """
+ if os.path.isdir(tempdir):
+ shutil.rmtree(tempdir)
+ os.makedirs(tempdir)
+ copytree(srcdir, "./temp")
+# files = ["AACv4.hvy", "AACv4.lst", "AACv4.out", "Heavy.cbp",
+# "Heavy.depend", "Heavy.layout"]
+# for f in files:
+# os.remove(os.path.join(tempdir, f))
+ return tempdir
+
+
+if __name__ == "__main__":
+
+ args = pymake.parser()
+
+ srcdir = args.srcdir
+
+ srcdir = cleanup(srcdir, "./temp")
+
+ args.subdirs = False
+
+ args.makefile = False
+
+ #call main -- note that this form allows main to be called
+ #from python as a function.
+ try:
+ pymake.main(srcdir, args.target, args.fc, args.cc, args.makeclean,
+ args.expedite, args.dryrun, False, args.debug,
+ args.subdirs, "--static", arch=args.arch,
+ makefile=args.makefile)
+ except AttributeError:
+ pymake.main(srcdir, args.target, args.fc, args.cc, args.makeclean,
+ args.expedite, args.dryrun, False, args.debug,
+ args.subdirs, "--static", arch=args.arch,
+ makefile=args.makefile)
+
+ shutil.rmtree(srcdir)

autotest/make_linux_gfortran.sh

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+gfortran --version
+python make_gfortran.py -fc gfortran -ff='-std=legacy' -sd -mc ../src heavy

autotest/make_win_gfortran.bat

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+set PATH=%PATH%;C:\MinGW\bin
+gfortran --version
+python make_gfortran.py -fc gfortran -sd -mc ..\src heavy.exe 
+pause

autotest/test_000.py

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+# all test modules should be in a file that starts with the name test.
+import os
+import shutil
+import pandas
+import numpy as np
+
+def test_py():
+ cd = os.getcwd()
+ os.chdir(os.path.join('..','python'))
+ print("Heavy test: Python All American Canal model")
+ os.system('python model1_run.py')
+ os.chdir(cd)
+ assert True
+
+def test_aac_model():
+ cd = os.getcwd()
+ print("Heavy test: All American Canal model")
+ os.chdir(os.path.join('..','test','aac'))
+ os.system(r'..\..\autotest\heavy model1_hvy.nam')
+ os.chdir(cd)
+ assert True
+
+def test_py_vs_fortran():
+ cd = os.getcwd()
+ print("Heavy test: Comparing Python output to Fortran output")
+ os.chdir(os.path.join('..','test','aac'))
+ py_data = pandas.read_csv('sim_py.grav')
+ f_data = pandas.read_csv('model1.out', delim_whitespace=True, header=0, names=['Station','kper','kstp','totim','g','d2'])
+ for station in py_data['Station'].unique():
+ dp = py_data[py_data['Station'] == station]['g'].reset_index(drop=True)
+ df = f_data[f_data['Station'] == 'G' + station]['g'].reset_index(drop=True)
+ mse = np.sqrt(((df - dp) ** 2).mean())
+ print(f'mse, {station}: {mse:.3f}')
+ assert mse < 0.15
+ os.chdir(cd)
+
+def test_abq_model():
+ cd = os.getcwd()
+ print("Heavy test: Rio Grande Valley transient model")
+ os.chdir(os.path.join('..','test','abq','2013y_parent'))
+ os.system(r'..\..\..\autotest\heavy -g 6 tran_hvy.nam') 
+ os.chdir(cd)
+
+def test_truxton_model():
+ cd = os.getcwd()
+ print("Heavy test: Truxton Basin Hydrologic Model Xhigh Qhigh scenario")
+ os.chdir(os.path.join('..','test','truxton','tbhm_tr_Xhigh_Qhigh'))
+ os.system(r'..\..\..\autotest\heavy -g 6 tbhm_tr_Xhigh_Qhigh_hvy.nam') 
+ os.chdir(cd)
+
+def test_setup():
+ tempdir = os.path.join('.', 'temp')
+ if os.path.isdir(tempdir):
+ shutil.rmtree(tempdir)
+ os.mkdir(tempdir)
+ return
+
+
+if __name__ == "__main__":
+ test_setup()