diff --git a/.github/workflows/expreccs.yml b/.github/workflows/CI.yml similarity index 100% rename from .github/workflows/expreccs.yml rename to .github/workflows/CI.yml diff --git a/README.md b/README.md index ab44486..9302850 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://github.com/daavid00/expreccs/actions/workflows/expreccs.yml/badge.svg)](https://github.com/daavid00/expreccs/actions/workflows/expreccs.yml) +[![Build Status](https://github.com/daavid00/expreccs/actions/workflows/CI.yml/badge.svg)](https://github.com/daavid00/expreccs/actions/workflows/CI.yml) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) @@ -14,11 +14,11 @@ for CO2 storage using the [_OPM-Flow_](https://opm-project.org/?page_id=19) simu You will first need to install * Flow (https://opm-project.org) -There are active pull requests to the master branches of OPM to update the boundary conditions -in the schedule section. Then, for now you need to build OPM from source and clone the branches -bc_schedule. To build dune and the corresponding OPM branches from source, you can run the script -`./build_dune_and_opm-flow.bash`, which in turn should build flow in the folder -./build/opm-simulators/bin/flow. +For now you need to build OPM from source using the master branch (this since there have been updates for +the boundary conditions (BC) keywords, which will be available in the next OPM stable release 2023.10). +You can run the script `./build_dune_and_opm-flow.bash`, which in turn should build flow in the folder +./build/opm-simulators/bin/flow (this builds OPM without mpi support [for macOS users]; changue +the mpi cmake flags accordingly for mpi support). You can install the Python requirements in a virtual environment with the following commands: @@ -33,8 +33,10 @@ python3 -m venv vexpreccs source vexpreccs/bin/activate # Upgrade pip, setuptools, and wheel pip install --upgrade pip setuptools wheel -# Install the expreccs package -pip install . +# Install the expreccs package (in editable mode for contributions/modifications; otherwise, pip install .) +pip install -e . +# For contributions/testing/linting, install the dev-requirements +pip install -r dev-requirements.txt ``` ## Running expreccs diff --git a/build_dune_and_opm-flow.bash b/build_dune_and_opm-flow.bash index b724978..201decc 100755 --- a/build_dune_and_opm-flow.bash +++ b/build_dune_and_opm-flow.bash @@ -12,7 +12,7 @@ done # OPM modules for repo in common grid models simulators do - git clone https://github.com/daavid00/opm-$repo.git --branch bc_schedule + git clone https://github.com/OPM/opm-$repo.git done mkdir build diff --git a/docs/_static/_sphinx_javascript_frameworks_compat.js b/docs/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/docs/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + 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index 7577acb..cfc60b8 100644 --- a/docs/_static/basic.css +++ b/docs/_static/basic.css @@ -670,6 +670,16 @@ dd { margin-left: 30px; } +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + dl > dd:last-child, dl > dd:last-child > :last-child { margin-bottom: 0; @@ -738,6 +748,14 @@ abbr, acronym { cursor: help; } +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + /* -- code displays --------------------------------------------------------- */ pre { diff --git a/docs/_static/css/theme.css b/docs/_static/css/theme.css index c03c88f..19a446a 100644 --- a/docs/_static/css/theme.css +++ b/docs/_static/css/theme.css @@ -1,4 +1,4 @@ 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"expreccs.visualization.plotting.difference"]], "expreccs.visualization.plotting": [[13, "module-expreccs.visualization.plotting"]], "final_time_maps() (in module expreccs.visualization.plotting)": [[13, "expreccs.visualization.plotting.final_time_maps"]], "main() (in module expreccs.visualization.plotting)": [[13, "expreccs.visualization.plotting.main"]], "over_time_distance() (in module expreccs.visualization.plotting)": [[13, "expreccs.visualization.plotting.over_time_distance"]], "over_time_max_difference() (in module expreccs.visualization.plotting)": [[13, "expreccs.visualization.plotting.over_time_max_difference"]]}}) \ No newline at end of file diff --git a/src/expreccs/core/expreccs.py b/src/expreccs/core/expreccs.py index 90e6cde..23c791e 100644 --- a/src/expreccs/core/expreccs.py +++ b/src/expreccs/core/expreccs.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """Main script""" import os import time diff --git a/src/expreccs/templates/co2/reference.mako b/src/expreccs/templates/co2/reference.mako index deb495d..7054bad 100644 --- a/src/expreccs/templates/co2/reference.mako +++ b/src/expreccs/templates/co2/reference.mako @@ -1,3 +1,4 @@ +-- Copyright (C) 2023 NORCE ---------------------------------------------------------------------------- RUNSPEC ---------------------------------------------------------------------------- @@ -206,7 +207,7 @@ WCONINJE %endif % endfor / -BC +BCPROP 1 FREE / 2 FREE / 3 FREE / diff --git a/src/expreccs/templates/co2/regional.mako b/src/expreccs/templates/co2/regional.mako index 8750c65..138d9f0 100644 --- a/src/expreccs/templates/co2/regional.mako +++ b/src/expreccs/templates/co2/regional.mako @@ -1,3 +1,4 @@ +-- Copyright (C) 2023 NORCE ---------------------------------------------------------------------------- RUNSPEC ---------------------------------------------------------------------------- @@ -190,7 +191,7 @@ WCONINJE %endif % endfor / -BC +BCPROP 1 FREE / 2 FREE / 3 FREE / diff --git a/src/expreccs/templates/co2/site.mako b/src/expreccs/templates/co2/site.mako index 94c9766..4296e08 100644 --- a/src/expreccs/templates/co2/site.mako +++ b/src/expreccs/templates/co2/site.mako @@ -1,3 +1,4 @@ +-- Copyright (C) 2023 NORCE ---------------------------------------------------------------------------- RUNSPEC ---------------------------------------------------------------------------- @@ -244,7 +245,7 @@ ${i+1+len(dic['AQUFLUX_left'][0][0])+len(dic['AQUFLUX_right'][0][0])+len(dic['AQ % endif % endfor / -BC +BCPROP ${1+len(dic['AQUFLUX_left'][0][0])+len(dic['AQUFLUX_right'][0][0])+len(dic['AQUFLUX_bottom'][0][0])+len(dic['AQUFLUX_top'][0][0])} DIRICHLET OIL 1* ${dic['PRESSURE_bottom'][j+1][0][0]} / / TSTEP diff --git a/src/expreccs/templates/co2/site_openboundaries.mako b/src/expreccs/templates/co2/site_openboundaries.mako index 05d3c95..f49f98a 100644 --- a/src/expreccs/templates/co2/site_openboundaries.mako +++ b/src/expreccs/templates/co2/site_openboundaries.mako @@ -1,3 +1,4 @@ +-- Copyright (C) 2023 NORCE ---------------------------------------------------------------------------- RUNSPEC ---------------------------------------------------------------------------- @@ -189,7 +190,7 @@ WCONINJE %endif % endfor / -BC +BCPROP 1 FREE / 2 FREE / 3 FREE / diff --git a/src/expreccs/templates/common/grid.mako b/src/expreccs/templates/common/grid.mako index 00831b8..799a53f 100644 --- a/src/expreccs/templates/common/grid.mako +++ b/src/expreccs/templates/common/grid.mako @@ -1,3 +1,4 @@ +-- Copyright (C) 2023 NORCE SPECGRID ${dic['site_noCells'][0]} ${dic['site_noCells'][1]} ${dic['site_noCells'][2]} 1 F / diff --git a/src/expreccs/templates/common/plotting.mako b/src/expreccs/templates/common/plotting.mako deleted file mode 100644 index d7a1443..0000000 --- a/src/expreccs/templates/common/plotting.mako +++ /dev/null @@ -1,119 +0,0 @@ -"""" -Script to plot the top surface for a CO2 model -""" - -from datetime import timedelta -import numpy as np -import matplotlib.pyplot as plt -from mpl_toolkits.axes_grid1 import make_axes_locatable -from ecl.summary import EclSum -from ecl.eclfile import EclFile -from ecl.grid import EclGrid - - -def main(): - """Postprocessing""" - path = "${dic["exe"]}/${dic["fol"]}/output/" - dic = {"xcor": [], "ycor": []} - dic["xmx"] = np.linspace(0, ${dic["site_dims"][0]}, ${dic["site_noCells"][0]} + 1) - dic["ymy"] = np.linspace(0, ${dic["site_dims"][1]}, ${dic["site_noCells"][0]} + 1) - dic["xcor"], dic["ycor"] = np.meshgrid(dic["xmx"], dic["ymy"][::-1]) - dic["saturation"] = np.zeros([len(dic["xmx"]) - 1, len(dic["ymy"]) - 1]) - dic["pressure"] = np.zeros([len(dic["xmx"]) - 1, len(dic["ymy"]) - 1]) - dic["mass"] = np.zeros([len(dic["xmx"]) - 1, len(dic["ymy"]) - 1]) - case = path + "SITE" - dic["rst"] = EclFile(case + ".UNRST") - dic["ini"] = EclFile(case + ".INIT") - dic["grid"] = EclGrid(case + ".EGRID") - dic["smsp"] = EclSum(case + ".SMSPEC") - dic["sgas"] = dic["rst"].iget_kw("SGAS") - dic["pres"] = dic["rst"].iget_kw("PRESSURE") - dic["phiv"] = dic["ini"].iget_kw("PORV") - dic["rhog"] = dic["rst"].iget_kw("GAS_DEN") - dic["rhog_ref"] = 1.86843 - - m_m = dic["sgas"][-1] * dic["rhog"][-1] * dic["phiv"][0] - p_p = dic["pres"][-1] - s_s = dic["sgas"][-1] - - for i in np.arange(0, len(dic["ymy"]) - 1): - dic["saturation"][i, :] = s_s[ - i * (len(dic["xmx"]) - 1) : (i + 1) * (len(dic["xmx"]) - 1) - ] - dic["mass"][i, :] = m_m[ - i * (len(dic["xmx"]) - 1) : (i + 1) * (len(dic["xmx"]) - 1) - ] - dic["pressure"][i, :] = p_p[ - i * (len(dic["xmx"]) - 1) : (i + 1) * (len(dic["xmx"]) - 1) - ] - totalMass = sum(m_m) - dic["mass"] /= totalMass - - for names in ["saturation", "mass", "pressure"]: - fig, axis = plt.subplots() - imag = axis.pcolormesh( - dic["xcor"], dic["ycor"], dic[names], shading="flat", cmap="jet" - ) - axis.axis("scaled") - if names == "mass": - axis.set_title(f"normalized {names} (Total mass: {sum(m_m) : .2E} [kg])") - elif names == "pressure": - axis.set_title(f"{names} [bar]") - else: - axis.set_title(f"{names}") - divider = make_axes_locatable(axis) - cax = divider.append_axes("right", size="5%", pad=0.05) - vect = np.linspace(dic[names].min(), dic[names].max(), 5, endpoint=True) - fig.colorbar( - imag, - cax=cax, - orientation="vertical", - ticks=vect, - format=lambda x, _: f"{x:.2f}", - ) - imag.set_clim(dic[names].min(), dic[names].max()) - fig.savefig(f"{names}.png", bbox_inches="tight") - - print(f"Total simulation time: {timedelta(seconds=${'{0:.2f}'.format(time)})}") - - case = path + 'REFERENCE' - dic["rst"] = EclFile(case + ".UNRST") - dic["ini"] = EclFile(case + ".INIT") - dic["grid"] = EclGrid(case + ".EGRID") - dic["smsp"] = EclSum(case + ".SMSPEC") - dic["sgas"] = dic["rst"].iget_kw("SGAS") - dic["pres"] = dic["rst"].iget_kw("PRESSURE") - dic["phiv"] = dic["ini"].iget_kw("PORV") - dic["fipn"] = dic["ini"].iget_kw("FIPNUM") - dic["rhog"] = dic["rst"].iget_kw("GAS_DEN") - - inx = 0 - for cell in dic["grid"].cells(): - if dic["fipn"][0][cell.global_index] == 1: - m_m[inx] -= dic['sgas'][-1][cell.global_index]*dic['rhog'][-1][cell.global_index]*dic["phiv"][0][cell.global_index] - inx += 1 - - for i in np.arange(0, len(dic["ymy"]) - 1): - dic["mass"][i, :] = m_m[i * (len(dic["xmx"]) - 1) : (i + 1) * (len(dic["xmx"]) - 1)] - dic["mass"] /= totalMass - for names in ['mass']: - fig, ax = plt.subplots() - imag = ax.pcolormesh(dic['xcor'], dic['ycor'], dic[names], shading="flat", cmap="jet") - ax.axis([dic['xcor'].min(), dic['xcor'].max(), dic['ycor'].min(), dic['ycor'].max()]) - ax.axis("scaled") - if names == 'mass': - ax.set_title(f"sum abs(massSite-massReference) ({abs(dic['mass']).sum() : .2E})") - else: - ax.set_title(f"{names}") - divider = make_axes_locatable(ax) - cax = divider.append_axes("right", size="5%", pad=1e-3) - vect = np.linspace(dic[names].min(), dic[names].max(), 5, endpoint=True) - fig.colorbar( - imag, cax=cax, orientation="vertical", ticks=vect, format=lambda x, _: f"{x:.3f}" - ) - imag.set_clim(dic[names].min(), dic[names].max()) - fig.savefig("difference.png", bbox_inches="tight") - - -if __name__ == "__main__": - main() diff --git a/src/expreccs/templates/common/safu_eval.mako b/src/expreccs/templates/common/safu_eval.mako index b6c57de..d6566da 100644 --- a/src/expreccs/templates/common/safu_eval.mako +++ b/src/expreccs/templates/common/safu_eval.mako @@ -1,3 +1,5 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 #!/usr/bin/env python """" diff --git a/src/expreccs/utils/inputvalues.py b/src/expreccs/utils/inputvalues.py index 8dbe85f..a540032 100644 --- a/src/expreccs/utils/inputvalues.py +++ b/src/expreccs/utils/inputvalues.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """ Utiliy functions to set the requiried input values by expreccs. """ diff --git a/src/expreccs/utils/mapproperties.py b/src/expreccs/utils/mapproperties.py index 2939f06..cd6faa0 100644 --- a/src/expreccs/utils/mapproperties.py +++ b/src/expreccs/utils/mapproperties.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """ Utiliy function for finding the well i,j, and k ids. """ diff --git a/src/expreccs/utils/runs.py b/src/expreccs/utils/runs.py index f41e79c..13b8541 100644 --- a/src/expreccs/utils/runs.py +++ b/src/expreccs/utils/runs.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """ Utiliy functions to run the studies. """ diff --git a/src/expreccs/utils/writefile.py b/src/expreccs/utils/writefile.py index 4207207..d10e0fc 100644 --- a/src/expreccs/utils/writefile.py +++ b/src/expreccs/utils/writefile.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """ Utiliy functions for necessary files and variables to run OPM Flow. """ diff --git a/src/expreccs/visualization/plotting.py b/src/expreccs/visualization/plotting.py index 3327a5b..70f778e 100644 --- a/src/expreccs/visualization/plotting.py +++ b/src/expreccs/visualization/plotting.py @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2023 NORCE +# SPDX-License-Identifier: GPL-3.0 + """" Script to plot the top surface for the reference, regionla, and site reservoirs. """