PhreeqcMatlab

版本 0.1.0 (3.3 MB) 作者: Ehsan
Easily calling PhreeqcRM from Matlab
5.0
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121.0 次下载
更新时间 2021/9/17
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PhreeqcMatlab

Documents (work in progress)

Easily calling PhreeqcRM and IPhreeqc from Matlab

PhreeqcMatlab is a wrapper for the PhreeqcRM C interface and IPhreeqc. Most of the functions are wrapped, with the exception of MPI function (that I neither use nor know how to wrap). In general, the C++ interface of PhreeqcRM has more functionality and is easier to call. Therefore, I have implemented several classes and functions to make the usage of this package more convenient, similar to its c++ interface and better. All the original PhreeqcRM functions start with RM_. The additional utility functions that I have added do not have this extra RM_.

Installation

PhreeqcMatlab automatically downloads the latest compiled phreeqcRM .dll on Windows and .so on Linux machines, from this repository. I don't have access to macOS; hence, no library there and you'll have to compile PhreeqcRM yourself for mac. On Windows, you will need to have Visual C++ Redistributable for VC 2019 installed. All you need to do is to download or clone this repository and run the startup.m file. Before running the example, make sure that C/C++ compiler is already installed in your Matlab. Please let me know if you have any error messages when running the file.

Test cases

SimpleAdvect.m and Advect.m demonstrate advection simulation for Phreeqc reactive transport modeling software. It sets up initial conditions, defines boundary conditions, and runs a transient loop simulating advection. Species.m demonstrates species transport using PhreeqcRM. Gas_m.m demonstrates the equilibration of gas with an aqueous phase

You can run all tests by executing main.m.

Need more examples? Go to the examples folder and run the files.

Don't forget to run the startup file before running the examples.

Simple cases

Running a Phreeqc input file or string:

iph = IPhreeqc(); % load the library
iph = iph.CreateIPhreeqc(); % create an IPhreeqc instance
iph_string = ['SOLUTION 1 brine \n' ...
    'pH      7.0 \n' ...
    'temp    25.0 \n' ...
    'Na    1.0 \n' ...
    'Cl    1.0 \n' ...
    'END \n' ...
    'SELECTED_OUTPUT 1 \n'...
    '-reset false \n'...
    '-totals Na Cl \n'...
    'END']; % create the Phreeqc string
out_string = iph.RunPhreeqcString(iph_string, database_file('phreeqc.dat')); % Run the string
disp(out_string)       % display the results
iph.DestroyIPhreeqc(); % kill the phreeqc instance

Alternatively, you can save the string in a file and call it with RunPhreeqcFile function as shown here.

Sensitivity analysis

In this folder, there are a couple of examples that shows how to investigate the effect of temperature on the dissolution of anhydrite and gypsum. Save the following Phreeqc input in a file named ex2_input.pqc (example 2 of Phreeqc manual)

#TITLE Example 2.--Temperature dependence of solubility of gypsum and anhydrite
SOLUTION 1 Pure water
        pH      7.0
        temp    25.0                
EQUILIBRIUM_PHASES 1
        Gypsum          0.0     1.0
        Anhydrite       0.0     1.0
END

SELECTED_OUTPUT 1
        -reset false
        -si     Anhydrite  Gypsum
USER_PUNCH
        -headings equi_anhydrite
        10 PUNCH EQUI("Anhydrite")

END

and run the following script to calculate and plot the solubility in different temperatures:

phreeqc_rm = PhreeqcSingleCell('ex2_input.pqc', 'phreeqc.dat');
n_data = 51;
h_out = phreeqc_rm.GetSelectedOutputHeadings(1);
temperature = linspace(25.0, 75.0, n_data); % degree C
s_out = zeros(n_data, length(h_out));
for i = 1:length(temperature)
    phreeqc_rm.RM_SetTemperature(temperature(i));
    status = phreeqc_rm.RM_RunCells();
    c_out = phreeqc_rm.GetConcentrations();
    s_out(i, :) = phreeqc_rm.GetSelectedOutput(1);
end
plot(temperature, s_out, '-s');
legend(string(h_out));
xlabel('T (C)');
ylabel('SI');
status = phreeqc_rm.RM_Destroy();

And more

Look at the example folder for many more examples of batch and transport geochemical calculations.

Reactive transport

I'm writing several examples that calls this package from my finite volume package FVTool. You can help me by providing reactive transport cases with analytical solutions.

Other packages you might like

There are at least two more packages that have some of the functionalities of PhreeqcMatlab, and inspired me to write this package.

To do list

This package probably won't be broken by sudden changes. So you can start using it. Here's a list of near future activities. You contributions/suggestions are more than welcome :-)

  • Wrap IPhreeqc functions
  • More utility/helper functions
  • More tests
  • Documentation (please help)
  • New classes for solution, phases, surfaces, etc (in progress)
  • Utility functions for the IPhreeqc wrapper (in progress)
  • More examples for both IPhreeqc and PhreeqcRM (in progress)
  • More keywords in the new input file specific to PhreeqcMatlab
  • Simple GUI (in progress as part of a DOTC project)

Author

The original package was written by Ali A. Eftekhari in his free time. It is/will be used in some of the projects/publications at the Danish Offshore Technology Centre (DOTC) at the Technical University of Denmark. Some of the current development is done as part of an ongoing project at the DOTC.

Citation

Please cite as

Eftekhari, Ali A., and Behzad Hosseinzadeh. Simulkade/PhreeqcMatlab: Preliminary Release of PhreeqcMatlab. Zenodo, 2021, doi:10.5281/ZENODO.5513713.

引用格式

Eftekhari, Ali A., and Behzad Hosseinzadeh. Simulkade/PhreeqcMatlab: Preliminary Release of PhreeqcMatlab. Zenodo, 2021, doi:10.5281/ZENODO.5513713.

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创建方式 R2021a
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examples/IPhreeqc

examples/PhreeqcMatlabCases

examples/basetest

examples/batch

examples/benchmarks

examples/notebooks

examples/phreeqc

examples/transport

src/@Datafile

src/@Exchange

src/@Gas

src/@IPhreeqc

src/@IRM_RESULT

src/@Kinetics

src/@Phase

src/@PhaseResult

src/@PhreeqcRM

src/@SelectedOutput

src/@SingleCell

src/@SingleCellResult

src/@Solution

src/@SolutionResult

src/@Surface

src/@SurfaceResult

src/Advection1D

src/Bulk

src/FVTool

src/Tools

src/Transport1D

src/classes/@edl_layer

src/classes/@exchange_units

src/classes/@kinetics_units

src/classes/@phase_units

src/classes/@sites_units

src/classes/@solution_units

examples/PhreeqcMatlabCases

版本 已发布 发行说明
0.1.0

要查看或报告此来自 GitHub 的附加功能中的问题，请访问其 GitHub 仓库。
要查看或报告此来自 GitHub 的附加功能中的问题，请访问其 GitHub 仓库。