Fortran Interface on initializing with calculated flow field with multifab.

[paradoxknight1]

Dear Amrex platform developer,

I'm quite newbie on Amrex, and using Fortran-interface to undertake my calculation.
My question could be seperated into two steps.
For the first one, I've almost gone through all of the case files for Fortran interface, but I have not found there is a checkpoint file writer interface for Fortran. May I check if writing the Fortran interface for checkpoint write is the only way for me to continue my calculation from previous data?

For the second one, I am facing a problem that asked me to "patch" part of the data from previously calculated results instead of the whole fields, and that data patching process needed me to place that data patch on other positons instead of its original place.

A good example to explain my question is the shockwave. After a period of time of calculation, the shockwave traveled from the initial side to the end side. After that, I need to take a patch of data that covers the shockwave's leeward and upwind side. And place it at the beginning side to continue the calculation.

Is there any advice on my question?

Looking forward to hearing from you.

Many thanks.

[WeiqunZhang]

Different applications need different data for their checkpoints. So you need to write your functions. Nevertheless, you can use amrex_multifab_write and amrex_multifab_read to write and read binary MultiFab data. For many applications, the other data in checkpoint files are just some clear text files that are written out by the I/O process.

Re: "patch", is that just periodic boundary?

[paradoxknight1]

Dear Weiqun,
thanks for your timely reply.

For the "patch" process, it is more likely a trick to limit the calculation domain. For my problem, the shock wave needs to go through a nozzle first. And then, impainge a droplet. if the whole process is being calculated all at once, the RAM and time consumption will be extremely high. Therefore, the usual way to handle this issue is to calculate the shockwave interaction with nozzle first, and then patch the result to the droplet.

Therefore, a regular periodic boundary is not working for my cases, since I only need part of the data to "patch" it to the initial side, and at the same time, to initial a droplet at the "patched" shockwave front.

And the whole process is more likely to use a amrex_multifab_read, to continue the calculation but needs to modify it first.

Since the dataptr() is only works with the mfi(mpi process), and it only works within each mpi_rank. I have no idea on how to move all the data(the box array, refinement information, mesh data, etc.) from one side to the other. As shown in the attached figure, the black box's data wants to be moved to the red box position. and fill the black box with initial field information.

Looking forwards to hearing from you.

Many thanks.

[nataraj2]

@paradoxknight1
Here is a possible way for the issue. @WeiqunZhang will let you know if there is anything better or if there are any issues with this.

1. Here is an example of the fortran advection routine with restart . Go through the README section in the page for details.

2. For copying the data as you described you can do the following.

This routine gives a way of reading in the data in a plotfile and writing out another plotfile with the modified data. Hence, you can use this routine to do the data manipulation you need. Incorporate the Restart routine with this routine so that a checkpoint file can be written as in here
. Once a checkpoint file is written, you can restart the simulation with the modified data.

For the data manipulation, you can do as follows.

1. Run the code and get the plotfiles.
2. Read in the plotfile you want using the routine above.
3. Create a multifab with only 1 level. The idea is that the level 0 data in the plotfile will be copied on to this new multifab. So, this step is only doing things with level 0. Use the i indices to do the data manipulation as follows

• Find the i indices to copy from - say i_copyfrom_1 to i_copyfrom_2.
• Find the i indices to copy to - say i_copyto_1 to i_copyto_2.
• Loop over the level0 multifab data in the plotfile 2 times.
• In the first for loop pass, store the data that you need to copy from (using the i indices) in an intermediate data object -- vector or array (or anything of your choice)
• In the second for loop pass, copy that data from the intermediate object to the indices that you want to copy it to in the new multifab that was created.

4. Write the plotfile with the modified data (to verify things are correct) and also the checkpoint file of the modified data.
5. Now you can restart the simulation with the checkpoint file. While restarting, you can specify the amr.max_level variable in the inputs to what you want. The code will automatically fill the finer levels.

[WeiqunZhang]

For copying data from one MultiFab to another with index shifting, there is a ParallelCopy function for it. For example,

        MultiBlockIndexMapping dtos{};                                                                                                                                       
        dtos.offset = IntVect(-100,0,0); // Copy data from (i,j,k) in srcmf to (i-100,j,k) in destmf
        ParallelCopy(destmf, geom.Domain(), srcmf, 0, 0, ncomp, IntVect(0), dtos);