esbmtk 0.0.0__tar.gz

esbmtk-0.0.0/.gitattributes

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+./esbmtk/_version.py export-subst

esbmtk-0.0.0/.gitignore

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+# gitignore file for ESS345 Computational Geology.
+
+# The goal is to only push files which make sense to the students
+# so we exclude everything but the Jupyter Notebooks files
+# and image files
+
+# exclude everything
+
+# but add these 2 files
+# none at the moment
+
+# but allow the following directories
+
+# within this directory, allow for the following file types
+!LICENSE
+!README.md
+!*.png
+!*.jpg
+!*.ipynb
+!*.py
+!*.xlsx
+!*.csv
+!*.txt
+!*.md
+!*.org
+!*.pdf
+!*.html
+!*
+
+# last but not least, make sure the above rules are applied
+# to all subdirs as well
+!*/
+/build/
+/.directory
+/.mypy_cache/
+/Documentation/.directory
+/Documentation/*.tex
+*.log
+*.tex
+/esbmtk/*.py#
+./directory
+/esbmtk/__pycache__/
+/auto/
+/dist/
+/tests/__pycache__/
+examples/
+tests/
+/package.sh
+/esbmtk/.directory
+/esbmtk.egg-info/PKG-INFO
+/tests/.coverage
+/tests/TAGS
+/tests/foo.py
+/tests/.coverage
+/esbmtk/.esbmtk.py.~undo-tree~
+*.~undo-tree~
+Notes.org
+/docs/ltximg/
+docs/_minted-*
+
+/notes.org
+
+/.sourcery.yaml
+/Documentation/_minted-*
+/#%2Aediff-merge%2A#a5u92t#
+/#Release_History.org#
+/#README.org#
+/esbmtk/esbmtk.egg-info/
+__pycache__

esbmtk-0.0.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at uli.wortmann@utoronto.ca. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

esbmtk-0.0.0/Documentation/ESBMTK-Tutorial.org

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+#+TITLE: ESBMTK Tutorial 
+#+AUTHOR:Ulrich G Wortmann
+#+OX-IPYNB-LANGUAGE: ipython
+#+BIND: org-export-use-babel nil
+#+STARTUP: showall 
+#+STARTUP: latexpreview
+#+OPTIONS: todo:nil tasks:nil tags:nil toc:nil
+#+PROPERTY: header-args :eval never-export
+#+EXCLUDE_TAGS: noexport
+#+LATEX_HEADER: \usepackage{breakurl}
+#+LATEX_HEADER: \usepackage{newuli}
+#+LATEX_HEADER: \usepackage{uli-german-paragraphs}
+\maketitle
+
+#+TOC: headlines
+
+* A simple example
+
+A simple model of the marine P-cycle would consider the delivery of P from weathering, the burial of P in the sediments, the thermohaline transport of dissolved PO_4 as well as the export of P in form of sinking organic matter (POP). The concentration in the respective surface an deep water boxes is then sum of the respective fluxes (see Fig.\space{}ref:pcycle). The model parameters are taken from Glover 2011, Modeling Methods in the Marine Sciences.
+#+attr_org: :width 300
+#+attr_latex: :width 0.5\textwidth
+#+name: pcycle
+#+caption: A two-box model of the marine P-cycle. F_w = weathering
+#+caption: F_u = upwelling, F_d = downwelling, F_{POP} = particulate 
+#+caption: organic phosphor, F_b = burial.
+[[/home/uliw/user/python-scripts/esbmtk/Documentation/mpc.png]]
+
+If we define equations that control the export of particulate P (F_{POP}) as a fraction of the upwelling P (F_u), and the burial of P (F_b) as fraction of (F_{POP}), we express this model as coupled ordinary differential equations (ODE, or initial value problem):
+
+\begin{equation}\label{}
+\frac{d[PO_{4}]_{S}}{dt} = \frac{F_w + F_u - F_d - F_{POP}}{V_S}
+\end{equation}
+
+and for the deep ocean, 
+
+\begin{equation}\label{}
+\frac{d[PO_{4}]_{D}}{dt}= \frac{F_{POP} + F_d - F_u - F_b}{V_D}
+\end{equation}
+
+
+which is easily encoded as a python function
+#+BEGIN_SRC ipython
+def dCdt(t, C_0, V, F_w, thx):
+    """Calculate the change in concentration as
+    a function of time. After Glover 2011, Modeling
+    Methods for Marine Science.
+
+    :param C: list of initial concentrations mol/m*3
+    :param time: array of time points
+    :params V: lits of surface and deep ocean volume [m^3]
+    :param F_w: River (weathering) flux of PO4 mol/s
+    :param thx: thermohaline circulation in m*3/s
+    :returns dCdt: list of concentration changes mol/s
+    """
+
+    C_S = C_0[0]  # surface
+    C_D = C_0[1]  # deep
+    F_d = C_S * thx  # downwelling
+    F_u = C_D * thx  # upwelling
+    tau = 100 # residence time of P in surface waters [yrs]
+    F_POP = C_S * V[0] / tau  # export production
+    F_b = F_POP / 100  # burial
+
+    dCdt[0] = (F_w + F_u - F_d - F_POP) / V[0]
+    dCdt[1] = (F_d + F_POP - F_u - F_b) / V[1]
+
+    return dCdt
+#+END_SRC
+
+** Implementing the P-cycle with ESBMTK
+While ESBMTK provides abstractions to efficiently define complex models, the following section will use the basic ESBMTK classes to define the above model. While quite verbose, it demonstrates the design philosophy behind ESBMTK. More complex approaches are described further down. 
+
+Currently ESBMTK is only available via pip install as
+#+BEGIN_SRC ipython
+import sys
+!{sys.executable} -m pip install esbmtk
+#+END_SRC
+
+
+
+*** Defining the model geometry and initial conditions
+In a first step one needs to define a model object that describes fundamental model parameters. The following code first loads the various esbmtk classes that will help with model construction, and then defines the model object. Note that units are automatically translated into model units. While convenient, there are some import caveats: 
+Internally, the model uses 'year' as the time unit, mol as the mass unit, and liter as the volume unit. You can change this by setting these values to e.g., 'mol' and 'kg', however, some functions assume that their input values are in 'mol/l' rather than mol/m**3 or 'kg/s'. Ideally this would be caught by ESBMTK, but at present, this not guaranteed. So your mileage may vary, if you fiddle with these settings.  Note: Using mol/kg e.g., for seawater, will be discussed below.
+#+BEGIN_SRC ipython :tangle po4_1.py
+# import classes from the esbmtk library
+from esbmtk import (
+    Model,  # the model class
+    Reservoir,  # the reservoir class
+    Connection,  # the connection class
+    Source,  # the source class
+    Sink,  # sink class
+    Q_,  # Quantity operator
+)
+
+# define the basic model parameters
+M = Model(
+    name="M",  # model name
+    stop="3 Myr",  # end time of model
+    timestep="1 kyr",  # upper limit of time step
+    element=["Phosphor"],  # list of element definitions
+)
+#+END_SRC
+
+Next, we need to declare some boundary conditions. Most ESBMTK classes will be able to accept input in the form of strings that also contain units (e.g., ="30 Gmol/a"= ). Internally these strings are parsed and converted into the model base units. This works most of the time, but not always. In the below example, we the residence time \tau.  This variable is then used as input to calculate the scale for the primary production as =M.sb.volume / tau= which must fail since =M.sb.volume= is a numeric value and =tau= is a string. 
+#+BEGIN_SRC ipython
+# try the following
+tau = "100 years"
+tau * 12
+#+END_SRC
+
+To avoid this we have to manually parse the string into a quantity. This is done with the quantity operator =Q_= Note that =Q_= is not part of ESBMTk but imported from the =pint= library. 
+#+BEGIN_SRC ipython
+# now try this
+from esbmtk import Q_
+tau = Q_("100 years")
+tau * 12
+#+END_SRC
+
+Most ESBMTK classes accept quantities, strings that represent quantities as well as numerical values. Weathering and burial fluxes are often defined in =mol/year=, whereas ocean models use =kg/year=. ESBMTK provides a method (=set_flux()= )  that will automatically convert the input into the correct units. In this example it is not necessary since the flux and the model both use =mol= . It is however good practice to to relay on the automatic conversion. Note that it makes a difference for the mole to kilogram conversion whether ones uses =M.P= or =M.PO4= as the reference species!
+#+BEGIN_SRC ipython :tangle po4_1.py
+# boundary conditions
+F_w =  M.set_flux("45 Gmol", "year", M.P) # P @280 ppm (Filipelli 2002)
+tau = Q_("100 year")  # PO4 residence time in surface box
+F_b = 0.01  # About 1% of the exported P is buried in the deep ocean
+thc = "20*Sv"  # Thermohaline circulation in Sverdrup
+#+END_SRC
+
+To set up the model geometry, we first  use the =Source= and  =Reservoir= classes  to create a source for the weathering flux, a sink for the burial flux, and instances of the surface and deep oceans boxes. Since we loaded the element definitions for phosphor in the model definition above, we can directly refer to the "PO4" species in the reservoir definition. 
+#+BEGIN_SRC ipython :tangle po4_1.py
+# Source definitions
+Source(
+    name="weathering",
+    species=M.PO4,
+    register=M,  # i.e., the instance will be available as M.weathering
+)
+Sink(
+    name="burial",
+    species=M.PO4,
+    register=M,  #
+)
+
+# reservoir definitions
+Reservoir(
+    name="sb",  # box name
+    species=M.PO4,  # species in box
+    register=M,  # this box will be available as M.sb
+    volume="3E16 m**3",  # surface box volume
+    concentration="0 umol/l",  # initial concentration
+)
+Reservoir(
+    name="db",  # box name
+    species=M.PO4,  # species in box
+    register=M,  # this box will be available M.db
+    volume="100E16 m**3",  # deeb box volume
+    concentration="0 umol/l",  # initial concentration
+)
+#+END_SRC
+
+
+
+*** Model processes
+For many models, processes can mapped as the transfer of mass from one box to the next. Within the ESBMTK framework this is accomplished through the =Connection= class. To connect the a weathering flux from the source object (M.w) to the surface ocean (M.sb) we declare a connection instance describing this relationship as follows:
+#+BEGIN_SRC ipython :tangle po4_1.py
+Connection(
+    source=M.weathering,  # source of flux
+    sink=M.sb,  # target of flux
+    rate=F_w,  # rate of flux
+    id="river",  # connection id
+)
+#+END_SRC
+Unless the=register= keyword is given, connections will be automatically registered withe the parent of the source, i.e., the model =M=. Unless explicitly given through the =name= keyword, connection names will be automatically constructed from the names of the source and sink instances. However, it is a good habit to provide the =id= keyword to keep connections separate in cases where two reservoir instances share more than one connection. The list of all connection instances can be obtained from the model object (see below).
+
+To map the process of thermohaline circulation, we connect the surface and deep ocean boxes  using a connection type that scales the mass transfer as a function of the concentration in a given reservoir (=ctype ="scale_with_concentration"= ) . The concentration data is taken from the reference reservoir which defaults to the source reservoir. As such, in most cases the =ref_reservoirs= keyword can be omitted. The =scale= keyword can be a string, or a numerical value. If its provided as a string ESBMTK will map the value into model units. Note that the connection class does not require the =name= keyword. Rather the name is derived from the source and sink reservoir instances. Since reservoir instances can have more than one connection (i.e., surface to deep via downwelling, and surface to deep via primary production), it is required to set the =id= keyword.
+#+BEGIN_SRC ipython :tangle po4_1.py
+Connection(  # thermohaline downwelling
+    source=M.sb,  # source of flux
+    sink=M.db,  # target of flux
+    ctype="scale_with_concentration",
+    scale=thc,
+    id="downwelling_PO4",
+    # ref_reservoirs=M.sb, defaults to the source instance
+)
+Connection(  # thermohaline upwelling
+    source=M.db,  # source of flux
+    sink=M.sb,  # target of flux
+    ctype="scale_with_concentration",
+    scale=thc,
+    id="upwelling_PO4",
+)
+#+END_SRC
+
+There are several ways to define the biological export production, e.g., as  function of the upwelling PO_4, or as function of the residence time of PO_4 in surface ocean. Here we follow Glover (2011), and use the residence time \tau = 100 years.
+#+BEGIN_SRC ipython :tangle po4_1.py
+Connection(  #
+    source=M.sb,  # source of flux
+    sink=M.db,  # target of flux
+    ctype="scale_with_concentration",
+    scale=M.sb.volume / tau,
+    id="primary_production",
+)
+#+END_SRC
+
+We require one more connection to describe the burial of P in the sediment. We describe this flux as a fraction of the primary export productivity. To create the connection we can either recalculate the export productivity, or use the previously calculated flux. We can query the export productivity using the =id_string= of the above connection with the =flux_summary()= method of the model instance:
+#+BEGIN_SRC ipython
+M.flux_summary(filter_by="primary_production", return_list=True)[0]
+#+END_SRC
+The =flux_summary()= method will return a list of matching fluxes but since there is only one match, we can simply use  the first result, and use it to define the phosphor burial as a consequence of export production in the following way:
+#+BEGIN_SRC ipython :tangle po4_1.py
+Connection(  #
+    source=M.db,  # source of flux
+    sink=M.burial,  # target of flux
+    ctype="scale_with_flux",
+    ref_flux=M.flux_summary(filter_by="primary_production", return_list=True)[0],
+    scale=F_b,
+    id="burial",
+)
+#+END_SRC
+
+
+** Running the model, visualizing and saving the results
+
+#+BEGIN_SRC ipython :tangle po4_1.py
+M.run()
+M.plot([M.sb, M.db])
+#+END_SRC
+
+

esbmtk-0.0.0/Documentation/po4_1.py

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+# import classes from the esbmtk library
+from esbmtk import (
+    Model,  # the model class
+    Reservoir,  # the reservoir class
+    Connection,  # the connection class
+    Source,  # the source class
+    Sink,  # sink class
+    Q_,  # Quantity operator
+)
+
+# define the basic model parameters
+M = Model(
+    name="M",  # model name
+    stop="3 Myr",  # end time of model
+    timestep="1 kyr",  # upper limit of time step
+    element=["Phosphor"],  # list of element definitions
+)
+
+# boundary conditions
+F_w =  M.set_flux("45 Gmol", "year", M.P) # P @280 ppm (Filipelli 2002)
+tau = Q_("100 year")  # PO4 residence time in surface box
+F_b = 0.01  # About 1% of the exported P is buried in the deep ocean
+thc = "20*Sv"  # Thermohaline circulation in Sverdrup
+
+# Source definitions
+Source(
+    name="weathering",
+    species=M.PO4,
+    register=M,  # i.e., the instance will be available as M.weathering
+)
+Sink(
+    name="burial",
+    species=M.PO4,
+    register=M,  #
+)
+
+# reservoir definitions
+Reservoir(
+    name="sb",  # box name
+    species=M.PO4,  # species in box
+    register=M,  # this box will be available as M.sb
+    volume="3E16 m**3",  # surface box volume
+    concentration="0 umol/l",  # initial concentration
+)
+Reservoir(
+    name="db",  # box name
+    species=M.PO4,  # species in box
+    register=M,  # this box will be available M.db
+    volume="100E16 m**3",  # deeb box volume
+    concentration="0 umol/l",  # initial concentration
+)
+
+Connection(
+    source=M.weathering,  # source of flux
+    sink=M.sb,  # target of flux
+    rate=F_w,  # rate of flux
+    id="river",  # connection id
+)
+
+Connection(  # thermohaline downwelling
+    source=M.sb,  # source of flux
+    sink=M.db,  # target of flux
+    ctype="scale_with_concentration",
+    scale=thc,
+    id="downwelling_PO4",
+    # ref_reservoirs=M.sb, defaults to the source instance
+)
+Connection(  # thermohaline upwelling
+    source=M.db,  # source of flux
+    sink=M.sb,  # target of flux
+    ctype="scale_with_concentration",
+    scale=thc,
+    id="upwelling_PO4",
+)
+
+Connection(  #
+    source=M.sb,  # source of flux
+    sink=M.db,  # target of flux
+    ctype="scale_with_concentration",
+    scale=M.sb.volume / tau,
+    id="primary_production",
+)
+
+Connection(  #
+    source=M.db,  # source of flux
+    sink=M.burial,  # target of flux
+    ctype="scale_with_flux",
+    ref_flux=M.flux_summary(filter_by="primary_production", return_list=True)[0],
+    scale=F_b,
+    id="burial",
+)
+
+M.run()
+M.plot([M.sb, M.db])

esbmtk-0.0.0/LICENSE.md

@@ -0,0 +1,157 @@
+# GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+This version of the GNU Lesser General Public License incorporates the
+terms and conditions of version 3 of the GNU General Public License,
+supplemented by the additional permissions listed below.
+
+## 0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the
+GNU General Public License.
+
+"The Library" refers to a covered work governed by this License, other
+than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
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+A "Combined Work" is a work produced by combining or linking an
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+## 1. Exception to Section 3 of the GNU GPL.
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+You may convey a covered work under sections 3 and 4 of this License
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+## 2. Conveying Modified Versions.
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+    based on the Library, uncombined with any other library
+    facilities, conveyed under the terms of this License.
+-   b) Give prominent notice with the combined library that part of it
+    is a work based on the Library, and explaining where to find the
+    accompanying uncombined form of the same work.
+
+## 6. Revised Versions of the GNU Lesser General Public License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+as you received it specifies that a certain numbered version of the
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+it, you have the option of following the terms and conditions either
+of that published version or of any later version published by the
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+specify a version number of the GNU Lesser General Public License, you
+may choose any version of the GNU Lesser General Public License ever
+published by the Free Software Foundation.
+
+If the Library as you received it specifies that a proxy can decide
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