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: [email protected]<mailto:[email protected]> Phone: +1-(785)-979-2664 From: Timo Koch <[email protected]> Sent: 12 Tháng Năm 2022 11:44 SA To: DuMuX User Forum <[email protected]> Cc: Pham, Vuong Van <[email protected]> Subject: Re: [DuMux] hydrogen injection setup 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<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&data=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=K6BnOkY20O38ldFG1pgF3dKj8OH2X3qdp5ETYJ%2BLLe8%3D&reserved=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&data=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I770Aw4uvozhmikZ37JCB1B47BuMn%2B5WuvIGgZFi%2Boc%3D&reserved=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&data=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xBhl7creQKx2AvFRf6hZxHG6DEow6eoKFhMmvptycgE%3D&reserved=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&data=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=E7qDf3s%2FBdDnUZw%2BgDA%2Be9q3ge5iBFxIWusZnqC3lLs%3D&reserved=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.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fblob%2Fmaster%2Fexamples%2Fbiomineralization%2Fmaterial%2Fcomponents%2Fsuspendedbiomass.hh&data=05%7C01%7Cvuongvanpham%40ku.edu%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=d%2FavzScQ83YhSjDMwmUluYks%2BR5Bjyyl%2BgsqRShcIgc%3D&reserved=0> 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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2BYYVY0dc%2FdjenoTjs2lL%2BwEBPgfjqqJIrp%2F1gzDW18%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2B1jUTMvo63NiWn7wg9OMSSoTp53fy8HGyp38BBrciY4%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XtOPmQ8h0br252FdmlQ2rRHm7dDi%2Fefk5whjmbLkYu0%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iI5b%2Fc8slXHU4L8105JGnbnSd5l7IBErrn628iwThFY%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LyzYeoocmeijShJjgkCvAv9q%2FzAEsI6E0q78B%2Fk11uE%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VD3ZAw3B2pIDdzLTs7FNZkfLjguRgXPSpdUfyK0x2Kg%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WP2%2B05XBsbt7ltis9xFdoHH0I%2B57SrDBfEbeeMBXG58%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%7C50d987070a914c509af408da34369623%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637879707086768684%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WP2%2B05XBsbt7ltis9xFdoHH0I%2B57SrDBfEbeeMBXG58%3D&reserved=0>
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