[QE-developers] Interfacing MBD library to QEspresso

Fri Nov 20 19:45:55 CET 2020

Hi Daniele,

Thank you so much for your help. We really appreciate it!

Best,
Hsin-Yu

On Fri, Nov 20, 2020 at 12:22 PM Daniele Cesarini <d.cesarini at cineca.it>
wrote:

> Dear Hsin-Yu and Szabi,
>
> I will take a look in the week end, I will report you back.
>
> Best,
> Daniele
> On 20/11/20 18:00, Hsin-Yu Ko wrote:
>
> Dear Daniele,
>
> Szabi and I have been working on patching `libmbd` for a non-cmake version
> to be compliant with the current build system in QE; we just got a
> tentative public version (with documentation and a test-suite case `pw_vdw/
> vdw-mbd.in
> <https://urldefense.com/v3/__http://vdw-mbd.in__;!!P1tgJ-3e!Q88m3i-9H7v5sXetSNpUQcH6PcwtZg1FSvNLqNzOtSYxgnk0Y8sW7gTdLh-IJzXb3w$>`
> prepared). The repo (https://gitlab.com/szabi_public/q-e
> <https://urldefense.com/v3/__https://gitlab.com/szabi_public/q-e__;!!P1tgJ-3e!Q88m3i-9H7v5sXetSNpUQcH6PcwtZg1FSvNLqNzOtSYxgnk0Y8sW7gTdLh_xiK0xtg$>)
> passes the Gitlab pipelines (build:cp, build:pw, build:ph, and build:pgi)
> except for build:cmake-gnu. We wonder if we could use your kind help to
> enable this remaining CMake build feature. Could you please let us know?
> Thank you so much!
>
> Best,
> Hsin-Yu and Szabi
>
>
> On Tue, Nov 17, 2020 at 9:22 AM Hsin-Yu Ko <hk945 at cornell.edu> wrote:
>
>> Sorry, typing it too fast. I meant: "... We will give it a try and let
>> you know if **we** should encounter any issues."
>>
>> On Tue, Nov 17, 2020 at 9:19 AM Hsin-Yu Ko <hk945 at cornell.edu> wrote:
>>
>>> Dear Paolo and Daniele,
>>>
>>> Thank you so much for your prompt response! Regarding Paolo's question,
>>> libmbd is currently built using CMake; however, Szabolcs and I should
>>> be able to write an alternative makefile without too much issue (which
>>> seems to be the right way to proceed at least for now).
>>>
>>> Daniele, thank you for kindly offering help. We really appreciate it! We
>>> will give it a try and let you know if you should encounter any issues.
>>>
>>> Best Regards,
>>> Hsin-Yu
>>>
>>>
>>> On Tue, Nov 17, 2020 at 8:59 AM Daniele Cesarini <d.cesarini at cineca.it>
>>> wrote:
>>>
>>>> Dear Hsin-Yu,
>>>>
>>>> yes, we are working to move on CMake build system, this is a
>>>> work-in-progress activity but we are in a good shape.
>>>>
>>>> To add an external library to QE using CMake is quite straightforward
>>>> (I am sorry, it currently lacks of documentation), just follow the example
>>>> of FoX library. You can add a git submodule to the project and call it from
>>>> the CMakeLists.txt located in the "external" directory of the project. You
>>>> can copy the CMake code of 'external/CMakeLists.txt' between line 4 and 27
>>>> and adapt it to MBD library. You just need to define the appropriate CMake
>>>> targets and create a new CMake target library, which you can link to QE
>>>> libraries/executables as well as other targets.
>>>>
>>>> Let me know you if you have questions/problems, I would happy to help
>>>> you!
>>>>
>>>> BTW, if you need help just point me to your QE fork, I can help/assist
>>>> you.
>>>>
>>>> Best,
>>>> Daniele
>>>> On 17/11/20 14:10, Hsin-Yu Ko wrote:
>>>>
>>>> Dear All,
>>>>
>>>> I just wanted to add to this thread some more details: We forked the
>>>> official QEF/q-e repo and followed closely the currently implemented
>>>> `ts_vdw` (Tkatchenko-Scheffler van der Waals) procedure.
>>>>
>>>> The issue that we could really use your help is in the `configure` and
>>>> the new `cmake` building mechanism. What we currently have is the below (following
>>>> FoX library mechanism):
>>>> 1. We (manually) download the most recent release of the `libmbd` to
>>>> `archive/` as a tarball
>>>> 2. We add `libmbd` build procedures (added as a dependency of `mods`)
>>>> as `libfox` in `Makefile` and `install/extlibs_makefile`
>>>> 3. We append the include/library paths to `IFLAGS`/`LD_LIBS` in
>>>> `install/make.inc.in
>>>> <https://urldefense.com/v3/__http://make.inc.in__;!!P1tgJ-3e!Wb0faV2y6SftYRg3KV3mgtAdi-0a_69XJor6LylnF5qXkcaf3rYa-jaYudERPn6btA$>
>>>> `.
>>>>
>>>> By doing so, it seems to build no problem from our local machines.
>>>> However, there is an issue when we use it in the GitLab pipeline. The issue
>>>> is that `libmbd` depends on `cmake` which is not present in the docker
>>>> image. As such, we had to include the cmake installation in the
>>>> `.gitlab-cl.yml` file. We also noticed that there is a new
>>>> `build:cmake-gnu` pipeline. Since there seems to be some tendency of moving
>>>> to `cmake`, we were wondering if we could ask for some advice on the how to
>>>> proceed. Thank you!
>>>>
>>>> Best Regards,
>>>> Hsin-Yu
>>>>
>>>> --
>>>> Hsin-Yu Ko
>>>> Postdoctoral Research Fellow
>>>> Department of Chemistry and Chemical Biology
>>>> Cornell University
>>>>
>>>> On Tue, Nov 17, 2020 at 7:31 AM Szabolcs GOGER <szabolcs.goger at uni.lu>
>>>> wrote:
>>>>
>>>>> Dear Developers,
>>>>>
>>>>>
>>>>> We are currently working on writing a module for Many-Body Dispersion
>>>>> correction (MBD) for Quantum Espresso here in Luxembourg in Alexandre
>>>>> Tkatchenko's group. We are doing this in collaboration with Cornell
>>>>> University, in particular, Hsin-Yu Ko from the group of Robert DiStasio is
>>>>> closely invested in the project. With his technical assistance we are
>>>>> getting to a state when our personal implementation might be ready for
>>>>> becoming public.
>>>>>
>>>>>
>>>>> The main idea behind the implementation is to use a portable library
>>>>> (called libMBD) which can be readily called from a Fortran code. The
>>>>> library has already been linked to other DFT codes so using it ensures
>>>>> reproducibility and transferability. Currently our code can be used in the
>>>>> SCF energy calculations, while using the MBD forces for structure
>>>>> optimization is still an ongoing project. Since most of the development is
>>>>> done in the portable library itself, this new feature would only need a
>>>>> minimal amount of modification in the main code. We are also working on
>>>>> preparing a well-rounded test suite.
>>>>>
>>>>>
>>>>> We would be grateful if someone, who has experience in building
>>>>> projects using an external library, could assist us in finding an efficient
>>>>> way of preparing our code to be compatible with the main release.
>>>>>
>>>>>
>>>>> Kind Regards,
>>>>> Szabolcs Goger
>>>>> Szabolcs Goger
>>>>> Ph.D. student
>>>>> Department of Physics and Materials Science
>>>>>
>>>>> UNIVERSITÉ DU LUXEMBOURG
>>>>>
>>>>> CAMPUS LIMPERTSBERG
>>>>> 162a, avenue de la Faïencerie
>>>>> L-1511 Luxembourg
>>>>> T +352 46 66 44 6694
>>>>> szabolcs.goger at uni.lu /www.uni.lu
>>>>> <https://urldefense.com/v3/__http://www.uni.lu/__;!!P1tgJ-3e!Wb0faV2y6SftYRg3KV3mgtAdi-0a_69XJor6LylnF5qXkcaf3rYa-jaYudHuJ6vdLg$>
>>>>> / www.tcpunilu.com
>>>>> <https://urldefense.com/v3/__http://www.tcpunilu.com/__;!!P1tgJ-3e!Wb0faV2y6SftYRg3KV3mgtAdi-0a_69XJor6LylnF5qXkcaf3rYa-jaYudG0jk8qWA$>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> developers mailing listdevelopers at lists.quantum-espresso.orghttps://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/developers__;!!P1tgJ-3e!Wb0faV2y6SftYRg3KV3mgtAdi-0a_69XJor6LylnF5qXkcaf3rYa-jaYudHo49vfeA$
>>>>
>>>>
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