Re: [DuMux] hydrogen injection setup

[Timo Koch]

On 18. May 2022, at 11:30, Pham, Vuong Van 
mailto:vuongvanp...@ku.edu>> wrote:

Hi Timo,
I hope this email finds you well, and I appreciate your support by far in the 
usage of DuMuX. Continuing from the previous emails I sent, I write this email 
to clarify a few terminologies used in DuMuX files:

  1.  What are the so-call “flux variables” in DuMuX (i.e., the files as 
fluxvariables.hh)?

Hi Vuong,

The finite volume scheme concept is explained in the Dumux paper: 
https://dumux.org/docs/#paper.

FluxVariables (probably a slight misnomer) are the variables need to compute 
fluxes across control volume boundaries (finite volume scheme). But they also 
have interface functions to compute the flux.
It’s a helper class in the local residual used because computing fluxes and 
reconstructing gradients is different for every finite volume discretisation 
scheme.

  1.
  2.   What are the so-call “volume variables” in DuMuX (i.e., the files as 
volumevariables.hh)?

VolumeVariables (same misnomer here) are the variables of a (sub) control 
volume. They also compute secondary variables from primary variables and store 
both.
During setup they usually interact with the FluidSystem for example.

  1.
  2.  What are the so-call “local residuals” in DuMuX (i.e., the files as 
localresiduals.hh)?


LocalResiduals are the element-local residuals of the discrete balance 
equations. That is basically your PDE that has to be fulfilled (equal to zero). 
Since it is not necessarily zero before the solution has been found (e.g. with 
the Newton scheme) there is a non-zero residual when all parts of the equations 
are added up.
This is the main class used by the assembly to assemble the system matrix. The 
residual for all models has the from dS/dt + div(F) - Q = 0 with storage, flux, 
and source terms (see Dumux papers: https://dumux.org/docs/#paper)


  1.

Within the context of these 3 questions:

  1.  In case of a custom fluid system, shall those three flux-variables, 
volume-variables, and local-residuals, need to be changed (i.e., in the .hh 
files, as custom .hh files as well)?

That will depend on your model. If you only change e.g. from Air to Hydrogen, 
then you don’t need to change any of these classes. If you change the number of 
phases or component, you might have to choose a different model (3p3c, 2pnc) 
which will automatically choose different volume variables.
FluxVariables and local residual rarely need to be changed. Only if you have 
flux or source term which cannot be modelled with any of the existing models.

All classes can be customised and “injected”/set via the property system.
If you really need full customisation, you can compute any secondary variables 
from primary variables and expose them via an interface in custom volume 
variables and then use these variables in the storage/flux/source functions of 
a custom LocalResidual class.
FluxVariables also have smaller customization points with the flux classes. For 
example DarcysLaw computes a flux according to Darcy’s law with is usually used 
for the advective flux term in porous medium flow problems. The property 
AdvectionType allows you to customise that.
It’s important to stress that this is rarely needed.

Timo


  1.
  2.  Please give me examples, if possible, to better understand the relevant 
concepts.

I have not found anything from DuMuX website, or GitLab documentation, however, 
please remind me whether I may miss anything relevant there.

Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664




From: Timo Koch mailto:timok...@math.uio.no>>
Sent: 12 Tháng Năm 2022 11:44 SA
To: DuMuX User Forum 
mailto:dumux@listserv.uni-stuttgart.de>>
Cc: Pham, Vuong Van mailto:vuongvanp...@ku.edu>>
Subject: Re: [DuMux] hydrogen injection setup




On 12. May 2022, at 18:27, Pham, Vuong Van 
mailto:vuongvanp...@ku.edu>> 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<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Fsolidsystems%2Fbiominsolids.hh=05%7C01%7Cvuongvanpham%

Re: [DuMux] hydrogen injection setup

[Pham, Vuong Van]

Hi Timo,
I hope this email finds you well, and I appreciate your support by far in the 
usage of DuMuX. Continuing from the previous emails I sent, I write this email 
to clarify a few terminologies used in DuMuX files:

  1.  What are the so-call “flux variables” in DuMuX (i.e., the files as 
fluxvariables.hh)?
  2.   What are the so-call “volume variables” in DuMuX (i.e., the files as 
volumevariables.hh)?
  3.  What are the so-call “local residuals” in DuMuX (i.e., the files as 
localresiduals.hh)?
Within the context of these 3 questions:

  1.  In case of a custom fluid system, shall those three flux-variables, 
volume-variables, and local-residuals, need to be changed (i.e., in the .hh 
files, as custom .hh files as well)?
  2.  Please give me examples, if possible, to better understand the relevant 
concepts.
I have not found anything from DuMuX website, or GitLab documentation, however, 
please remind me whether I may miss anything relevant there.

Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664




From: Timo Koch 
Sent: 12 Tháng Năm 2022 11:44 SA
To: DuMuX User Forum 
Cc: Pham, Vuong Van 
Subject: Re: [DuMux] hydrogen injection setup




On 12. May 2022, at 18:27, Pham, Vuong Van 
mailto:vuongvanp...@ku.edu>> 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<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Fsolidsystems%2Fbiominsolids.hh=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=K6BnOkY20O38ldFG1pgF3dKj8OH2X3qdp5ETYJ%2BLLe8%3D=0>
 (solid system)
 *   
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/fluidsystems/icpcomplexsalinitybrine.hh<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Ffluidsystems%2Ficpcomplexsalinitybrine.hh=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=I770Aw4uvozhmikZ37JCB1B47BuMn%2B5WuvIGgZFi%2Boc%3D=0>
 (complex brine)
 *   
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/fluidsystems/biominsimplechemistry.hh<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Ffluidsystems%2Fbiominsimplechemistry.hh=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=xBhl7creQKx2AvFRf6hZxHG6DEow6eoKFhMmvptycgE%3D=0>

  1.  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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Fcomponents%2Fbiofilm.hh=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=E7qDf3s%2FBdDnUZw%2BgDA%2Be9q3ge5iBFxIWusZnqC3lLs%3D=0>
 *   
https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/examples/biomineralization/material/components/suspendedbiomass.hh<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.un

Re: [DuMux] hydrogen injection setup

[Timo Koch]

On 12. May 2022, at 18:27, Pham, Vuong Van 
mailto:vuongvanp...@ku.edu>> 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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664




From: Timo Koch mailto:timok...@math.uio.no>>
Sent: 12 Tháng Năm 2022 10:28 SA
To: DuMuX User Forum 
mailto:dumux@listserv.uni-stuttgart.de>>
Cc: Pham, Vuong Van mailto:vuongvanp...@ku.edu>>
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 ar

Re: [DuMux] hydrogen injection setup

[Pham, Vuong Van]

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
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 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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664




From: Timo Koch 
Sent: 12 Tháng Năm 2022 10:28 SA
To: DuMuX User Forum 
Cc: Pham, Vuong Van 
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=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=RpoeTpnYfky5p7ld0t0uuJAeZpcOXSFi9iTDqe62FDY%3D=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=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e3cfc04fc6cdec08da342bf385%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879662144831039%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=2wZuE2r3hNmp0yPQ9sxSOckestTXO9f3arefZAIiQZk%3D=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=05%7C01%7Cvuongvanpham%40ku.edu%7Cb22931e

Re: [DuMux] hydrogen injection setup

[Timo Koch]

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).

Descriptions of different models can be found in the code documentation (e.g. 
here https://dumux.org/docs/doxygen/master/a01603.html), or for 2p2c 
specifically here https://dumux.org/docs/doxygen/master/a18478.html

Best wishes
Timo


On 11. May 2022, at 18:28, Pham, Vuong Van 
mailto:vuongvanp...@ku.edu>> 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)

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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664



From: Timo Koch mailto:koch_t...@hotmail.com>>
Sent: 28 Tháng Ba 2022 6:12 SA
To: DuMuX User Forum 
mailto:dumux@listserv.uni-stuttgart.de>>
Cc: Pham, Vuong Van mailto:vuongvanp...@ku.edu>>
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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=VS2Y1u7oW7X2M6KLYF%2BklvgZgYHnVdNsD2fawfm3pjI%3D=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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=R6hwJLjfjLRSayJigGVy11nrpyvERuLmxH5a5MfKruM%3D=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 so

Re: [DuMux] hydrogen injection setup

[Pham, Vuong Van]

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)
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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664



From: Timo Koch 
Sent: 28 Tháng Ba 2022 6:12 SA
To: DuMuX User Forum 
Cc: Pham, Vuong Van 
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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=VS2Y1u7oW7X2M6KLYF%2BklvgZgYHnVdNsD2fawfm3pjI%3D=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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=R6hwJLjfjLRSayJigGVy11nrpyvERuLmxH5a5MfKruM%3D=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 
mailto:vuongvanp...@ku.edu>> 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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.ed

Re: [DuMux] hydrogen injection setup

[Pham, Vuong Van]

Dear Timo,
I appreciate your support. Please keep in touch as I shall need your expertise 
to help me build my model in DuMuX.

Best regards,
Vuong Van Pham
Graduate Research Assistant (GRA)
Department of Chemical and Petroleum Engineering (CPE), University of Kansas
Email: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664



From: Timo Koch 
Sent: Monday, March 28, 2022 6:12 AM
To: DuMuX User Forum 
Cc: Pham, Vuong Van 
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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=VS2Y1u7oW7X2M6KLYF%2BklvgZgYHnVdNsD2fawfm3pjI%3D=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=04%7C01%7Cvuongvanpham%40ku.edu%7C111446846f61468e3eb408da10abcfa3%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637840628194675624%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000=R6hwJLjfjLRSayJigGVy11nrpyvERuLmxH5a5MfKruM%3D=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 
mailto:vuongvanp...@ku.edu>> 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: vuongvanp...@ku.edu<mailto:vuongvanp...@ku.edu>
Phone: +1-(785)-979-2664



From: Timo Koch mailto:koch_t...@hotmail.com>>
Sent: 08 Tháng Ba 2022 3:52 CH
To: DuMuX User Forum 
mailto:dumux@listserv.uni-stuttgart.de>>
Cc: Pham, Vuong Van mailto:vuongvanp...@ku.edu>>
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/?ur

[DuMux] hydrogen injection setup

[Timo Koch]

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 

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
 


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  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:
> 3D box-shape reservoir
> One single well for injection of hydrogen gas into the reservoir
> Reservoir has 2-phases:
> A petroleum fluid with pre-defined properties (i.e, viscosity, temperature, 
> etc)
> Water
> 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: vuongvanp...@ku.edu 
> Phone: +1-(785)-979-2664
>  
>  
>  
> From: Timo Koch  
> Sent: 08 Tháng Ba 2022 3:52 CH
> To: DuMuX User Forum 
> Cc: Pham, Vuong Van 
> Subject: Re: [DuMux] Installation issues
>  
> Dear Vuong,
>  
> please subscribe to the dumux mailing list 
> (https://listserv.uni-stuttgart.de/mailman/listinfo/dumux 
> ),
>  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  > 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: vuongvanp...@ku.edu 
> Phone: +1-(785)-979-2664
>  
>  
>  
> From: Pham, Vuong Van 
> Sent: 23 Tháng Hai 2022 4:11 CH
> To: dumux@listserv.uni-stuttgart.de 
> Subject: