[QE-developers] Interfacing MBD library to QEspresso
Daniele Cesarini
d.cesarini at cineca.it
Fri Nov 20 18:22:34 CET 2020
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
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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$>
>>
>>
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