On 12. May 2022, at 18:27, Pham, Vuong Van
<[email protected]<mailto:[email protected]>> wrote:
Hi Timo,
I appreciate your swift response. Thanks for your support, I am now capable of
setting up my own DuMux model using the resources you suggested.
Regarding the recent recommendation you mentioned in your previous email, I
went through most of them as you directed. Some additional concerns I have are
detailed as below:
1. In the biomineralization example, there exists “new” solid & fluid
system(s) in the system as I could not find these systems in my DuMux
installation folders. In specific, I refer to these files:
*
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/solidsystems/biominsolids.hh
(solid system)
*
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh
(complex brine)
*
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh
2. Also in the biomineralization example, there exists these files that I am
not certain about:
*
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/components/biofilm.hh
*
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/components/suspendedbiomass.hh
Hi Vuong,
the idea is that you write these files yourself for your specific problem and
then “inject” them by setting the corresponding property (e.g. FluidSystem) to
your custom implementation.
So the example gives you an idea how to write such custom solid/fluidsystems
and components. The same goes for the Problem and SpatialParams classes that
are always case-specific and therefore custom implementations (usually based on
some default implementation)
and set via the property system. (Almost every test folder contains a
“problem.hh”, “spatialparams.hh” and “properties.hh”.)
*
Taking a look at these files, my conclusion is that, these files are
problem-specific and are coded inherited on the “base” files or “available”
files provided in DuMux installation files. So, is there a guideline to code
such new files (if the system model requires) in order to be compliant with the
current DuMux installation files? Are there any structures that the new files
shall follow in order to be compatible with the DuMux installation files?
I agree that this can be a bit tricky. Essentially, in order to find the
minimal set of interface functions you need to implement you could start from
(talking about fluid system as an example) an empty class and then add the
functions that the compiler complains about missing. In practice it’s easier to
start from a given implementation that you expect to be close to your use case.
If you are unsure if you really need to implement a certain interface function
(e.g. fugacityCoefficient) for your model, you can just delete it and see if
the program still compiles. (The files that come with Dumux are often more
general so that they can be used by many different models and therefore may
have more functions implemented than needed by a specific model). The compiler
will complain when a necessary function is missing.
Sometimes, there is a base class that all implementation inherit from which
make it possible to only implement a subset of the interface required by Dumux
(e.g. for the fluid system).
I recommend looking at the tests/examples/lecture/course and try to use these
implementations as inspiration.
Best wishes
Timo
I hope my question is not that awkward and at least you may give me certain
instructions. For my recent research needs, DuMux is the most feasible option
to use.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: [email protected]<mailto:[email protected]>
Phone: +1-(785)-979-2664
From: Timo Koch <[email protected]<mailto:[email protected]>>
Sent: 12 Tháng Năm 2022 10:28 SA
To: DuMuX User Forum
<[email protected]<mailto:[email protected]>>
Cc: Pham, Vuong Van <[email protected]<mailto:[email protected]>>
Subject: Re: [DuMux] hydrogen injection setup
Hi Vuong,
first of all a brief answer:
yes, you can definitely do these things with Dumux,
and no, there is most likely not going to be a ready executable that will
exactly solve your specific problem.
Did you try the suggestions A) and B) of the answer to your last post? The
dumux course material should hopefully make it more clear how to setup your own
model in Dumux.
This is also what the user did whose presentation you linked from the User
Meeting 2015.
You would usually try to find the model that is closest to your used case, as
described in the answer to your last post.
As an example:
Let’s say you are going to have hydrogen and water in an aquifer, you will most
likely have a two-phase two-component system where the components can be
miscible.
So you could start from a 2p2c test (all tests are located in the “test” folder
sorted by model type). The test might use water and air instead of water and
hydrogen. So you have to exchange the constitutive relations in the fluid
system to your needs (described in the dumux-course).
You might have to increase the number of components so you could have a look at
a 2pnc (n components) test or at the documented biomineralization example
(https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/tree/master/examples/biomineralization<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Ftree%2Fmaster%2Fexamples%2Fbiomineralization&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RpoeTpnYfky5p7ld0t0uuJAeZpcOXSFi9iTDqe62FDY%3D&reserved=0>).
Descriptions of different models can be found in the code documentation (e.g.
here
https://dumux.org/docs/doxygen/master/a01603.html<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdumux.org%2Fdocs%2Fdoxygen%2Fmaster%2Fa01603.html&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2wZuE2r3hNmp0yPQ9sxSOckestTXO9f3arefZAIiQZk%3D&reserved=0>),
or for 2p2c specifically here
https://dumux.org/docs/doxygen/master/a18478.html<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdumux.org%2Fdocs%2Fdoxygen%2Fmaster%2Fa18478.html&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=zWrvmZK7fEQy93VuYiXY6XTi%2FL4MYCFC5RpP%2BhwZVWE%3D&reserved=0>
Best wishes
Timo
On 11. May 2022, at 18:28, Pham, Vuong Van
<[email protected]<mailto:[email protected]>> wrote:
Hi Timo,
I hope this email finds you well. I write this email to concern about the
capability of DuMux in:
1. Simulating hydrogen injection into a reservoir
2. Hydrodynamic and biochemical effects are included in the simulation task
(similarly described in this link that I found in DuMux
material:https://dumux.org/docs/usermeeting2015/hagemann_dumux.pdf<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdumux.org%2Fdocs%2Fusermeeting2015%2Fhagemann_dumux.pdf&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZRF%2Fh91Kk1WWZXCV2y3eI6y8jXXAjpuSv%2BbeyJqduqI%3D&reserved=0>)
Since I spent time searching for the necessary .hh files in DuMux GitLab, but I
could not find any relevant .hh files to serve the simulation purpose mentioned
as above. Therefore, I hope that you may give me some advice.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: [email protected]<mailto:[email protected]>
Phone: +1-(785)-979-2664
From: Timo Koch <[email protected]<mailto:[email protected]>>
Sent: 28 Tháng Ba 2022 6:12 SA
To: DuMuX User Forum
<[email protected]<mailto:[email protected]>>
Cc: Pham, Vuong Van <[email protected]<mailto:[email protected]>>
Subject: [DuMux] hydrogen injection setup
Hi Vuong,
in short, yes, this is something that Dumux should be good for.
As you didn’t succeed with the help of the examples and tests so far I would
first recommend two other resources:
A) Try to complete the Dumux course material
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux-course&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C9zD0%2BInRp5ruXSqpZEPJ91M3HV3vbtNtIr1rOJDSXo%3D&reserved=0>
In particular it discusses the basics of using Dumux. And it has an exercise
and some explanations regarding 2-phase immiscible and compositional models
(which directly apply to your use case).
More over there are exercises on how to change the fluid system (which you need
for your hydrogen + water fluid system).
B) There is also some lecture material for 2-phase models here:
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-lecture/-/tree/master/lecture/efm<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux-lecture%2F-%2Ftree%2Fmaster%2Flecture%2Fefm&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Xdsg3nvs8NkU1HCQpVt4dRX2MLs5mUTxwN1GxneREh4%3D&reserved=0>
In case I have misunderstood your setup and you have a three phase system
(water, oil, gas) you need to use the 3p (immiscible) or 3p3c (compositional)
model.
But the resources will still be helpful.
If you know the basics, you need to know which equations you are trying to
solve and what software components are required for your specific setup.
Some short answers for your point
1. Define grid by Grid.LowerLeft/UpperRight/Cells in the input file (using
YaspGrid)
2. Implement the well as a source term in the “problem” class (functions
“source” (interface for volumetric source terms) or “pointSource” (interface
for points sources at specified location))
3. Implement a fluid system class with your given properties (inspired by some
of the existing fluid systems)
For the rest I can’t answer anything right now. You would need to be more
specific about what mathematical model you are using and which physical
processes you want to consider.
After having worked with resources A) and B), I would suggest you to start with
one of the 2p2c/3p3c tests that seem closest to your setup and modify from
these.
Best wishes
Timo
On 26. Mar 2022, at 03:12, Pham, Vuong Van
<[email protected]<mailto:[email protected]>> wrote:
Dear Timo,
My name is Vuong Van Pham, and I am a graduate research assistant who is
interested in using DuMuX for academic use. I believe that DuMux allows me to
build a model as follow:
1. 3D box-shape reservoir
2. One single well for injection of hydrogen gas into the reservoir
3. Reservoir has 2-phases:
a. A petroleum fluid with pre-defined properties (i.e, viscosity,
temperature, etc)
b. Water
4. The property to be observed is the dispersion of hydrogen gas inside the
reservoir over time
However, I got lost in understanding DuMux’s file inheritance system, therefore
I am unable to know which header files (i.e, .hh files) are needed to build the
model I described as above. Please, if possible, give me a starting guideline
to build it. I readily tried to read the examples/tests from DuMux’s gitlab,
however they are not quite helpful for me to apply for my model building case.
I look forward to hearing from you.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: [email protected]<mailto:[email protected]>
Phone: +1-(785)-979-2664
From: Timo Koch <[email protected]<mailto:[email protected]>>
Sent: 08 Tháng Ba 2022 3:52 CH
To: DuMuX User Forum
<[email protected]<mailto:[email protected]>>
Cc: Pham, Vuong Van <[email protected]<mailto:[email protected]>>
Subject: Re: [DuMux] Installation issues
Dear Vuong,
please subscribe to the dumux mailing list
(https://listserv.uni-stuttgart.de/mailman/listinfo/dumux<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flistserv.uni-stuttgart.de%2Fmailman%2Flistinfo%2Fdumux&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bNIU%2B92as%2Fz48yEPtck%2BP1K519mAq87UVqttakPRBzg%3D&reserved=0>),
so you can see the answers to your post. Two people already posted answers to
your question.
Best
Timo
On 7. Mar 2022, at 04:56, Pham, Vuong Van
<[email protected]<mailto:[email protected]>> wrote:
To someone who may concern,
My name is Vuong Van Pham, and I am a graduate research assistant who is
interested in using DuMuX for academic use. While tempting to install DuMuX
following the guideline, I scoped with the issue (detailed in the attached
file).
Please respond to this email with further instruction to resolve this issue.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: [email protected]<mailto:[email protected]>
Phone: +1-(785)-979-2664
From: Pham, Vuong Van
Sent: 23 Tháng Hai 2022 4:11 CH
To: [email protected]<mailto:[email protected]>
Subject: Installation issues
To someone who may concern,
My name is Vuong Van Pham, and I am a graduate research assistant who is
interested in using DuMuX for academic use. While tempting to install DuMuX
following the guideline, I scoped with the issue (detailed in the attached
file).
Please respond to this email with further instruction to resolve this issue.
Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: [email protected]<mailto:[email protected]>
Phone: +1-(785)-979-2664
<installdumux.log>_______________________________________________
DuMux mailing list
[email protected]<mailto:[email protected]>
https://listserv.uni-stuttgart.de/mailman/listinfo/dumux<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flistserv.uni-stuttgart.de%2Fmailman%2Flistinfo%2Fdumux&data=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bNIU%2B92as%2Fz48yEPtck%2BP1K519mAq87UVqttakPRBzg%3D&reserved=0>
_______________________________________________
DuMux mailing list
[email protected]
https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
