Give us some tutorials for calculation of 2D material and polar material

[Guodonglin-cqust]

Dear jenny
For electrical transport, could you give us some tutorials for calculation of 2D material and polar material?
Best regards
Guo

[jcoulter12]

Hi Guo,

Actually, the reason we don't have specific tutorials for this is because the main electron transport tutorial should be the same for 2D materials.

The only difference is, you can speed up the calculation and change the output units to those for 2D materials by adding:
dimensionality = 2 in your Phoebe input file (the one used in step 8). I can definitely add a note about this to the tutorial to make it clearer.
Otherwise, as you might expect, you would converge your transport calculation using only in-plane sampling, such as kMesh = [25,25,1].

For polar materials, the polar electron-phonon coupling contribution is added automatically so long as the relevant information is in your QE calculation. By this, I simply mean you shouldn't use smearing for insulators (as is standard practice) so that dielectric information is determined during the ph.x calculation.

The only other note I can think to make is that for a long time there was a bug in QE related to using Coloumb truncation during el-ph calculations, which caused the code to mysteriously crash. As far as I know it's still there and you just need to use vacuum in your calculation.

If you think there's other features needed for 2D materials, or this doesn't answer your question in some way, feel free to ask further questions and I can help you set up the calculation.

Best,
Jenny

[Guodonglin-cqust]

Dear jenny

For polar materials, the epsil=.true. and nk1, nk2, nk3 should be added into file of ph.in.
For 2D materials, the assume_isolated =2D and enough vacuum thickness along the Z axis should be added into file of scf.in and nscf.in.
Am I right to understand your suggestion?

For el-ph scarttering, i hope to output the el-ph intra valley scattering rate and el-ph inter valley scattering rate. Meanwhile, these scattering rate, including total scattering rate , intra scattering rate and inter scattering rate, could be decomposed into different phonon modes, such as, ZA, TA, LA, ZO, TO, LO.

For ph-el scattering, i want to output the similar file, eg,

Phonon-Electron Scattering Rate (THz)
Q-point Mode Phonon freq (THz) Phonon linewidth(THz)
1 1 -0.76597277E-06 0.0000000000E+00
1 2 -0.38541311E-06 0.0000000000E+00
1 3 0.27423343E-06 0.0000000000E+00
1 4 0.26901937E+02 0.0000000000E+00
1 5 0.47264404E+02 0.0000000000E+00
1 6 0.47264404E+02 0.0000000000E+00
2 1 0.14638393E+00 0.2761765016E-05
2 2 0.13033857E+01 0.1437154065E-05
2 3 0.20516776E+01 0.9122152384E-05
2 4 0.26892357E+02 0.8136636253E-05

I want to study the effect of ph-el scattering on the thermal conductivity by considring the 4ph scattering with te ShengBTE code.

For 2D materials, Whether phoebe code has a default thickness in electrical transport calculation. For perturbo, there is a default thickness, namely, 6Å. See the website https://perturbo-code.github.io/mydoc_param_qe2pert.html#thickness_2d

thickness_2d

Variable type: real
Default value: 6.0
Units: Å

Thickness of the 2d system, used in the 2D polar e-ph correction. Only needed when system_2d=.true.

Could you help me, thank you very much.

Best regards
Guo

[jcoulter12]

Hi Guo,

I'm going to answer all of the questions I can off the top of my head now, then think about the last thing from the Perturbo code -- I'm not familiar with the need to set this, it is likely related to a specific method for 2d polar scattering corrections. This will take a little more thought, so I'll reply on this later.

For polar materials, the epsil=.true. and nk1, nk2, nk3 should be added into file of ph.in.

The epsil information is calculated automatically in QE during the phonon calculation if smearing is not used and ldisp = true. As you can see from the QE docs on epsil, it will automatically be set to true if you have an insulator and ldisp = true (which it is for Phoebe phonon calculations, if you see the ph.in example files).
You shouldn't set nk1, nk2, nk3, this is for a different kind of electron phonon calculation.
If you follow the ph.in of the Phoebe tutorials, you don't have to use either of these.

For 2D materials, the assume_isolated =2D and enough vacuum thickness along the Z axis should be added into file of scf.in and nscf.in.

I think I mentioned this in the last message -- I'm pretty sure the part of QE that does electron-phonon calculations will seg fault if Coulomb truncation is used in the scf calculation (this is what assume_isolated=2D does). This is not something the Phoebe team has control over, unless it's been fixed in a more recent version of QE, in which case let me know.
Instead, you should use a unit cell with a larger amount of vacuum along the z direction to try to avoid periodic interactions. I think given this bug in QE, this is the best that can be done.

For ph-el scattering, i want to output the similar file

The phonon-electron scattering rates will be output to a file called rta_phel_relaxation_times.json. It can be read in with python and contains, for each q point and mode pair, the phonon energies and relaxation times (inverse of linewidths).
We also have a plot script to help plot the lifetimes vs energies, which I can demonstrate for you if you want.

I want to study the effect of ph-el scattering on the thermal conductivity by considering the 4ph scattering with the ShengBTE code.

Just to be super clear, we don't currently offer 4-ph scattering -- I think you're saying you'll use ShengBTE for this, which is perfectly fine. I'd love to have it, and I hope we will at some point.

I'll also answer shortly about the 2D polar correction, thanks for the questions and for your patience!
Jenny

[Guodonglin-cqust]

Dear jenny

    Can your team develop the conda version of  phoebe software, we can more easily install and use.

Best regards

Guo

[jcoulter12]

Hi Guo,

I can look into doing this, I haven't done it before so it's hard to guess how long it will take.
I'll let you know soon.

Best,
Jenny

[jcoulter12]

Hi Guo,

I gave this a try, and it seems close to working, however, the cluster I'm currently using, SLURM requires a copy of openmpi built with pmix support, and it seems I cannot get that in a conda env.

In general, and if you're running on a cluster especially, it's better to use the native system copies of things like c++ compilers and mpi implementations, as these are tailored to the compute environment of the cluster by administrators. Even if this works, the code performance may still be compromised.

If you would like help building Phoebe in the normal way on a cluster, let me know and we can walk through any errors. I have built Phoebe on a number of systems now without much trouble.

If you would like to attempt the conda env build, and perhaps you have a system that behaves differently than my local cluster, this might work:

conda create --name phoebe
conda activate phoebe
conda install -c conda-forge cxx-compiler c-compiler libgfortran5
conda install -c conda-forge cmake openmpi scalapack
conda install -c conda-forge hdf5=*=mpi* 

and then as usual, you can attempt to build the code by running:

git clone --recurse-submodules https://github.com/mir-group/phoebe.git
cd phoebe
mkdir build
cd build
cmake ..
# use more than one processor below if you have them
make -j 1 phoebe
make -j 1 runTests

and then, if this is successful, you should run the test suite to confirm it works by typing:
mpirun -np 1 ./runTests
(where again 1 can be replaced by the number of cores you have available).

It's possible that HDF5 won't be properly found at the stage "cmake ..". Let me know if this happens or you encounter other issues.

Jenny

[jcoulter12]

Additionally, to run the electronic transport tutorial, you will need to build the patched copy of Quantum Espresso. Quantum Espresso requires the same things as Phoebe, so ideally this env setup will work for that as well.

To note, the benefit of the patched version of Quantum Espresso is that we can use many kinds of pseudopotentials that other codes cannot, potentially do DFT+U calculations, things like this, but in return, there's this extra step of building a special copy of QE.

Thanks, and again feel free to ask questions,
Jenny

[Guodonglin-cqust]

Hi jenny
Using the conda, i install the phoebe code, but i can not find the commond "phoebe" in the folder of build.

The installation process is as follows

(phoebe) cqwl111@cqwl111:~/Videos/phoebe/build$ cmake ..
-- The C compiler identification is GNU 12.3.0
-- The CXX compiler identification is GNU 12.3.0
-- The Fortran compiler identification is GNU 9.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
/home/cqwl111/Videos/phoebe
/home/cqwl111/Videos/phoebe/src/algebra/Matrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/PMatrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/SMatrix.cpp/home/cqwl111/Videos/phoebe/src/apps/app.cpp/home/cqwl111/Videos/phoebe/src/apps/bands_app.cpp/home/cqwl111/Videos/phoebe/src/apps/dos_app.cpp/home/cqwl111/Videos/phoebe/src/apps/electron_wannier_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_plot_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_qe_to_phoebe_app.cpp/home/cqwl111/Videos/phoebe/src/apps/lifetimes_app.cpp/home/cqwl111/Videos/phoebe/src/apps/ph_el_lifetimes.cpp/home/cqwl111/Videos/phoebe/src/apps/phonon_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_epa.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_utils.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_wannier.cpp/home/cqwl111/Videos/phoebe/src/apps/transport_epa_app.cpp/home/cqwl111/Videos/phoebe/src/bands/active_bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/window.cpp/home/cqwl111/Videos/phoebe/src/bte/drift.cpp/home/cqwl111/Videos/phoebe/src/bte/el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_3rd_state.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/ph_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/phel_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_bte.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_epa.cpp/home/cqwl111/Videos/phoebe/src/common_kokkos.cpp/home/cqwl111/Videos/phoebe/src/constants/periodic_table.cpp/home/cqwl111/Videos/phoebe/src/context.cpp/home/cqwl111/Videos/phoebe/src/crystal.cpp/home/cqwl111/Videos/phoebe/src/delta_function.cpp/home/cqwl111/Videos/phoebe/src/exceptions.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_fourier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_wannier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/harmonic.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_kokkos.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_sum_rule.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_3ph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph_parsing.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_epa.cpp/home/cqwl111/Videos/phoebe/src/io.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiController.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiHelper.cpp/home/cqwl111/Videos/phoebe/src/observable/electron_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/observable.cpp/home/cqwl111/Videos/phoebe/src/observable/onsager.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/specific_heat.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_electron.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/parser/ifc3_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/parser.cpp/home/cqwl111/Videos/phoebe/src/parser/phonopy_input_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/qe_input_parser.cpp/home/cqwl111/Videos/phoebe/src/particle.cpp/home/cqwl111/Videos/phoebe/src/points.cpp/home/cqwl111/Videos/phoebe/src/statistics_sweep.cpp/home/cqwl111/Videos/phoebe/src/utilities.cpp
-- Setting default Kokkos CXX standard to 14
-- Setting policy CMP0074 to use _ROOT variables
-- The project name is: Kokkos
-- Using -std=c++14 for C++14 standard as feature
-- Built-in Execution Spaces:
-- Device Parallel: NoTypeDefined
-- Host Parallel: Kokkos::OpenMP
-- Host Serial: NONE

-- Architectures:
-- Found TPLLIBDL: /home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so
-- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP
CMake Deprecation Warning at build/googletest/CMakeLists.txt:4 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest/googlemock/CMakeLists.txt:45 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

CMake Deprecation Warning at build/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Found Python: /home/cqwl111/anaconda3/bin/python3.9 (found version "3.9.12") found components: Interpreter
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
CMake Deprecation Warning at build/json_src/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Using the multi-header code from /home/cqwl111/Videos/phoebe/build/json_src/include/
-- Found MPI_C: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1")
-- Found MPI_Fortran: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found SCALAPACK: /home/cqwl111/anaconda3/envs/phoebe/lib/libscalapack.so
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - not found
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Found BLAS: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Found LAPACK: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP_Fortran: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found HDF5: /home/cqwl111/anaconda3/envs/phoebe/lib/libhdf5.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcrypto.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcurl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libsz.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libz.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libm.so (found version "1.14.2")
-- Found Doxygen: /home/cqwl111/anaconda3/envs/phoebe/bin/doxygen (found version "1.9.8") found components: doxygen missing components: dot
-- Found Sphinx: /home/cqwl111/anaconda3/bin/sphinx-build
Doxygen configured
-- Configuring done (42.8s)
-- Generating done (0.1s)
-- Build files have been written to: /home/cqwl111/Videos/phoebe/build
(phoebe) cqwl111@cqwl111:~/Videos/phoebe/build$

Guo

[jcoulter12]

Hi Guo, You ran the line “cmake ..” which creates a makefile for the code, but didn’t run the other lines I mentioned you need to run following that. Can you revisit the previous message and run all the lines necessary to run the code (the next one is make -j 1 phoebe, but there are others following that one too). Jenny

…

On Mon, Sep 18, 2023 at 6:02 AM Guodonglin-cqust ***@***.***> wrote: Hi jenny Using the conda, i install the phoebe code, but i can not find the commond "phoebe" in the folder of build. The installation process is as follows (phoebe) ***@***.***:~/Videos/phoebe/build$ cmake .. -- The C compiler identification is GNU 12.3.0 -- The CXX compiler identification is GNU 12.3.0 -- The Fortran compiler identification is GNU 9.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped /home/cqwl111/Videos/phoebe /home/cqwl111/Videos/phoebe/src/algebra/Matrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/PMatrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/SMatrix.cpp/home/cqwl111/Videos/phoebe/src/apps/app.cpp/home/cqwl111/Videos/phoebe/src/apps/bands_app.cpp/home/cqwl111/Videos/phoebe/src/apps/dos_app.cpp/home/cqwl111/Videos/phoebe/src/apps/electron_wannier_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_plot_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_qe_to_phoebe_app.cpp/home/cqwl111/Videos/phoebe/src/apps/lifetimes_app.cpp/home/cqwl111/Videos/phoebe/src/apps/ph_el_lifetimes.cpp/home/cqwl111/Videos/phoebe/src/apps/phonon_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_epa.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_utils.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_wannier.cpp/home/cqwl111/Videos/phoebe/src/apps/transport_epa_app.cpp/home/cqwl111/Videos/phoebe/src/bands/active_bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/window.cpp/home/cqwl111/Videos/phoebe/src/bte/drift.cpp/home/cqwl111/Videos/phoebe/src/bte/el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_3rd_state.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/ph_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/phel_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_bte.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_epa.cpp/home/cqwl111/Videos/phoebe/src/common_kokkos.cpp/home/cqwl111/Videos/phoebe/src/constants/periodic_table.cpp/home/cqwl111/Videos/phoebe/src/context.cpp/home/cqwl111/Videos/phoebe/src/crystal.cpp/home/cqwl111/Videos/phoebe/src/delta_function.cpp/home/cqwl111/Videos/phoebe/src/exceptions.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_fourier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_wannier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/harmonic.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_kokkos.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_sum_rule.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_3ph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph_parsing.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_epa.cpp/home/cqwl111/Videos/phoebe/src/io.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiController.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiHelper.cpp/home/cqwl111/Videos/phoebe/src/observable/electron_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/observable.cpp/home/cqwl111/Videos/phoebe/src/observable/onsager.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/specific_heat.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_electron.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/parser/ifc3_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/parser.cpp/home/cqwl111/Videos/phoebe/src/parser/phonopy_input_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/qe_input_parser.cpp/home/cqwl111/Videos/phoebe/src/particle.cpp/home/cqwl111/Videos/phoebe/src/points.cpp/home/cqwl111/Videos/phoebe/src/statistics_sweep.cpp/home/cqwl111/Videos/phoebe/src/utilities.cpp -- Setting default Kokkos CXX standard to 14 -- Setting policy CMP0074 to use _ROOT variables -- The project name is: Kokkos -- Using -std=c++14 for C++14 standard as feature -- Built-in Execution Spaces: -- Device Parallel: NoTypeDefined -- Host Parallel: Kokkos::OpenMP -- Host Serial: NONE -- Architectures: -- Found TPLLIBDL: /home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so -- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP CMake Deprecation Warning at build/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at build/googletest/googlemock/CMakeLists.txt:45 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at build/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found Python: /home/cqwl111/anaconda3/bin/python3.9 (found version "3.9.12") found components: Interpreter -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE CMake Deprecation Warning at build/json_src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Using the multi-header code from /home/cqwl111/Videos/phoebe/build/json_src/include/ -- Found MPI_C: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1") -- Found MPI_Fortran: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found SCALAPACK: /home/cqwl111/anaconda3/envs/phoebe/lib/libscalapack.so -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found HDF5: /home/cqwl111/anaconda3/envs/phoebe/lib/libhdf5.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcrypto.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcurl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libsz.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libz.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libm.so (found version "1.14.2") -- Found Doxygen: /home/cqwl111/anaconda3/envs/phoebe/bin/doxygen (found version "1.9.8") found components: doxygen missing components: dot -- Found Sphinx: /home/cqwl111/anaconda3/bin/sphinx-build Doxygen configured -- Configuring done (42.8s) -- Generating done (0.1s) -- Build files have been written to: /home/cqwl111/Videos/phoebe/build (phoebe) ***@***.***:~/Videos/phoebe/build$ [image: 1695031315547] <https://user-images.githubusercontent.com/111854127/268612693-e0eed504-9c1b-4043-adca-47e3a01670a1.png> Guo — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADLC27ACJDTWCR6JUWQKSU3X3AL4LANCNFSM6AAAAAA4RPW3SU> . You are receiving this because you commented.Message ID: ***@***.***>

[jcoulter12]

Also, are you attempting to install Phoebe on a windows-based laptop? That may not work well, as Windows is generally not recommended for scientific computing. If you have access to a cluster or linux-based computer this process will be much better.JennyOn Sep 18, 2023, at 6:02 AM, Guodonglin-cqust ***@***.***> wrote: Hi jenny Using the conda, i install the phoebe code, but i can not find the commond "phoebe" in the folder of build. The installation process is as follows (phoebe) ***@***.***:~/Videos/phoebe/build$ cmake .. -- The C compiler identification is GNU 12.3.0 -- The CXX compiler identification is GNU 12.3.0 -- The Fortran compiler identification is GNU 9.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/cqwl111/anaconda3/envs/phoebe/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped /home/cqwl111/Videos/phoebe /home/cqwl111/Videos/phoebe/src/algebra/Matrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/PMatrix.cpp/home/cqwl111/Videos/phoebe/src/algebra/SMatrix.cpp/home/cqwl111/Videos/phoebe/src/apps/app.cpp/home/cqwl111/Videos/phoebe/src/apps/bands_app.cpp/home/cqwl111/Videos/phoebe/src/apps/dos_app.cpp/home/cqwl111/Videos/phoebe/src/apps/electron_wannier_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_plot_app.cpp/home/cqwl111/Videos/phoebe/src/apps/elph_qe_to_phoebe_app.cpp/home/cqwl111/Videos/phoebe/src/apps/lifetimes_app.cpp/home/cqwl111/Videos/phoebe/src/apps/ph_el_lifetimes.cpp/home/cqwl111/Videos/phoebe/src/apps/phonon_transport_app.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_epa.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_utils.cpp/home/cqwl111/Videos/phoebe/src/apps/qe_to_phoebe_wannier.cpp/home/cqwl111/Videos/phoebe/src/apps/transport_epa_app.cpp/home/cqwl111/Videos/phoebe/src/bands/active_bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/bandstructure.cpp/home/cqwl111/Videos/phoebe/src/bands/window.cpp/home/cqwl111/Videos/phoebe/src/bte/drift.cpp/home/cqwl111/Videos/phoebe/src/bte/el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_3rd_state.cpp/home/cqwl111/Videos/phoebe/src/bte/helper_el_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/ph_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/phel_scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/scattering.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_bte.cpp/home/cqwl111/Videos/phoebe/src/bte/vector_epa.cpp/home/cqwl111/Videos/phoebe/src/common_kokkos.cpp/home/cqwl111/Videos/phoebe/src/constants/periodic_table.cpp/home/cqwl111/Videos/phoebe/src/context.cpp/home/cqwl111/Videos/phoebe/src/crystal.cpp/home/cqwl111/Videos/phoebe/src/delta_function.cpp/home/cqwl111/Videos/phoebe/src/exceptions.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_fourier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/electron_h0_wannier.cpp/home/cqwl111/Videos/phoebe/src/harmonic/harmonic.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_kokkos.cpp/home/cqwl111/Videos/phoebe/src/harmonic/phonon_h0_sum_rule.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_3ph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_elph_parsing.cpp/home/cqwl111/Videos/phoebe/src/interaction/interaction_epa.cpp/home/cqwl111/Videos/phoebe/src/io.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiController.cpp/home/cqwl111/Videos/phoebe/src/mpi/mpiHelper.cpp/home/cqwl111/Videos/phoebe/src/observable/electron_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/observable.cpp/home/cqwl111/Videos/phoebe/src/observable/onsager.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/observable/phonon_viscosity.cpp/home/cqwl111/Videos/phoebe/src/observable/specific_heat.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_electron.cpp/home/cqwl111/Videos/phoebe/src/observable/wigner_phonon_thermal_cond.cpp/home/cqwl111/Videos/phoebe/src/parser/ifc3_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/parser.cpp/home/cqwl111/Videos/phoebe/src/parser/phonopy_input_parser.cpp/home/cqwl111/Videos/phoebe/src/parser/qe_input_parser.cpp/home/cqwl111/Videos/phoebe/src/particle.cpp/home/cqwl111/Videos/phoebe/src/points.cpp/home/cqwl111/Videos/phoebe/src/statistics_sweep.cpp/home/cqwl111/Videos/phoebe/src/utilities.cpp -- Setting default Kokkos CXX standard to 14 -- Setting policy CMP0074 to use _ROOT variables -- The project name is: Kokkos -- Using -std=c++14 for C++14 standard as feature -- Built-in Execution Spaces: -- Device Parallel: NoTypeDefined -- Host Parallel: Kokkos::OpenMP -- Host Serial: NONE -- Architectures: -- Found TPLLIBDL: /home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so -- Kokkos Devices: OPENMP, Kokkos Backends: OPENMP CMake Deprecation Warning at build/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at build/googletest/googlemock/CMakeLists.txt:45 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at build/googletest/googletest/CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Found Python: /home/cqwl111/anaconda3/bin/python3.9 (found version "3.9.12") found components: Interpreter -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE CMake Deprecation Warning at build/json_src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Using the multi-header code from /home/cqwl111/Videos/phoebe/build/json_src/include/ -- Found MPI_C: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi.so (found version "3.1") -- Found MPI_Fortran: /home/cqwl111/anaconda3/envs/phoebe/lib/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found SCALAPACK: /home/cqwl111/anaconda3/envs/phoebe/lib/libscalapack.so -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/2020u1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64_lin/libmkl_core.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found HDF5: /home/cqwl111/anaconda3/envs/phoebe/lib/libhdf5.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcrypto.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libcurl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libsz.so;/home/cqwl111/anaconda3/envs/phoebe/lib/libz.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so;/home/cqwl111/anaconda3/envs/phoebe/x86_64-conda-linux-gnu/sysroot/usr/lib/libm.so (found version "1.14.2") -- Found Doxygen: /home/cqwl111/anaconda3/envs/phoebe/bin/doxygen (found version "1.9.8") found components: doxygen missing components: dot -- Found Sphinx: /home/cqwl111/anaconda3/bin/sphinx-build Doxygen configured -- Configuring done (42.8s) -- Generating done (0.1s) -- Build files have been written to: /home/cqwl111/Videos/phoebe/build (phoebe) ***@***.***:~/Videos/phoebe/build$ Guo —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>

[Guodonglin-cqust]

Hi jenny

 I install the code on ubantu system. 

 I forget the commond line "make -j 1 phoebe   make -j 1 runTests", and i have  successfully compiled the code. When i run the 

"runTests", i encounter some problems about HDF5, and the process of runTests is like this:

(phoebe) cqwl111@cqwl111:~/Videos/phoebe/build$ mpirun -np 1 ./runTests
Started on Mon Sep 18 18:56:34 2023
Kokkos::OpenMP::initialize WARNING: OMP_PROC_BIND environment variable not set
In general, for best performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads
For best performance with OpenMP 3.1 set OMP_PROC_BIND=true
For unit testing set OMP_PROC_BIND=false
[==========] Running 26 tests from 16 test suites.
[----------] Global test environment set-up.
[----------] 1 test from PMatrixTest
[ RUN ] PMatrixTest.diagonalize
Starting matrix diagonalization.
Time for rank 0 : 0.020179
Matrix diagonalization completed.
Time for rank 0 : 0.084618

WARNING: Relaxons diagonalization found negative eigenvalues.
This can happen when there's a bit of numerical noise on the scattering matrix,
and finding them may indicate the calculation is unconverged.
While we simply do not include these when computing transport,
and likely if they are small the calculation will be unaffected,
you may want to consider using with more wavevectors or an improved DFT calculation.
Additionally, setting symmetrizeMatrix = true in your input file will help.

These eigenvalues are (in atomic units):
0 -1

[ OK ] PMatrixTest.diagonalize (64 ms)
[----------] 1 test from PMatrixTest (64 ms total)

[----------] 2 tests from ActiveBandStructureTest
[ RUN ] ActiveBandStructureTest.BandStructureStorage
Reading in ../test/data/444_silicon.fc.
Found 48 symmetries

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 300.000000 (K)

Applying an energy window discarding states outside of [0.000000, 0.054423] eV range.
Applying an energy window discarding states outside of [0.000000, 0.054423] eV range.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 300.000000 (K)

Reading in ../test/data/444_silicon.fc.
Found 48 symmetries

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 300.000000 (K)

Applying a population window discarding states with dn/dT < 5.000000e-09.
Applying a population window discarding states with dn/dT < 5.000000e-09.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 300.000000 (K)

[ OK ] ActiveBandStructureTest.BandStructureStorage (2915 ms)
[ RUN ] ActiveBandStructureTest.WindowFilter
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 50.000000 (K)

Applying a population window discarding states with dn/dT < 1.000000e-02.
Applying a population window discarding states with dn/dT < 1.000000e-02.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 50.000000 (K)

[ OK ] ActiveBandStructureTest.WindowFilter (1248 ms)
[----------] 2 tests from ActiveBandStructureTest (4163 ms total)

[----------] 1 test from ABS
[ RUN ] ABS.Symmetries
Reading in ../test/data/444_silicon.fc.
Found 48 symmetries

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Applying an energy window discarding states outside of [0.00000000, 0.05714391] eV range.

Statistical parameters for the calculation
Index, temperature
iCalc = 0, T = 300.000000 (K)

[ OK ] ABS.Symmetries (29 ms)
[----------] 1 test from ABS (29 ms total)

[----------] 1 test from FullBandStructureTest
[ RUN ] FullBandStructureTest.BandStructureStorage
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

[ OK ] FullBandStructureTest.BandStructureStorage (593 ms)
[----------] 1 test from FullBandStructureTest (593 ms total)

[----------] 1 test from Crystal
[ RUN ] Crystal.Test1
Found 48 symmetries
[ OK ] Crystal.Test1 (11 ms)
[----------] 1 test from Crystal (11 ms total)

[----------] 1 test from TetrahedronTest
[ RUN ] TetrahedronTest.Normalization
Reading in ../test/data/444_silicon.fc.
Found 48 symmetries

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
[ OK ] TetrahedronTest.Normalization (4533 ms)
[----------] 1 test from TetrahedronTest (4533 ms total)

[----------] 2 tests from SquareRootTest
[ RUN ] SquareRootTest.PositiveNos
[ OK ] SquareRootTest.PositiveNos (0 ms)
[ RUN ] SquareRootTest.ZeroAndNegativeNos
[ OK ] SquareRootTest.ZeroAndNegativeNos (0 ms)
[----------] 2 tests from SquareRootTest (0 ms total)

[----------] 3 tests from Interaction3Ph
[ RUN ] Interaction3Ph.Coupling3Ph000
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
Using anharmonic force constants from ShengBTE.
Reading in ../test/data/FORCE_CONSTANTS_3RD.
Allocating 0.00008489 (GB) (per MPI process) for the 3-ph coupling matrix.

Successfully parsed anharmonic ShengBTE files.

[ OK ] Interaction3Ph.Coupling3Ph000 (28 ms)
[ RUN ] Interaction3Ph.Coupling3Ph210
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
Reading in ../test/data/FORCE_CONSTANTS_3RD.
Allocating 0.00008489 (GB) (per MPI process) for the 3-ph coupling matrix.

Successfully parsed anharmonic ShengBTE files.

**[ OK ] Interaction3Ph.Coupling3Ph210 (4749 ms)
[ RUN ] Interaction3Ph.Coupling3Ph000_p3py
Using harmonic force constants from phonopy.
Reading in ../test/data/phono3py/phono3py_disp.yaml.
Reading in ../test/data/phono3py/fc2.hdf5.
HDF5-DIAG: Error detected in HDF5 (1.14.2) MPI-process 0:
#000: H5D.c line 403 in H5Dopen2(): unable to synchronously open dataset
major: Dataset
minor: Can't open object
#1: H5D.c line 364 in H5D__open_api_common(): unable to open dataset
major: Dataset
minor: Can't open object
#2: H5VLcallback.c line 1980 in H5VL_dataset_open(): dataset open failed
major: Virtual Object Layer
minor: Can't open object
#3: H5VLcallback.c line 1947 in H5VL__dataset_open(): dataset open failed
major: Virtual Object Layer
minor: Can't open object
#4: H5VLnative_dataset.c line 321 in H5VL__native_dataset_open(): unable to open dataset
major: Dataset
minor: Can't open object
#5: H5Dint.c line 1418 in H5D__open_name(): not found
major: Dataset
minor: Object not found
#6: H5Gloc.c line 421 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#7: H5Gtraverse.c line 816 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#8: H5Gtraverse.c line 596 in H5G__traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#9: H5Gloc.c line 381 in H5G__loc_find_cb(): object 'physical_unit' doesn't exist
major: Symbol table
minor: Object not found

Phonopy fc file did not include units.
This is likely ok, defaulting to eV/angstrom^2.
However, you should check to be sure the magnitude of your phonon frequencies is sensible.**

Successfully parsed harmonic phonopy files.

Direct lattice vectors (ang)
a1 | a2 | a3
0.00000000 2.73313145 2.73313145
2.73313145 0.00000000 2.73313145
2.73313145 2.73313145 0.00000000
Atomic Positions (Cartesian, ang)
Si 4.09969717 4.09969717 4.09969717
Si 2.73313145 2.73313145 2.73313145

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
Using anharmonic force constants from phono3py.
Reading in ../test/data/phono3py/phono3py_disp.yaml.
Reading in ../test/data/phono3py/fc3.hdf5.
Allocating 0.00082397 (GB) (per MPI process) for the 3-ph coupling matrix.
Successfully parsed anharmonic phono3py files.

[ OK ] Interaction3Ph.Coupling3Ph000_p3py (19 ms)
[----------] 3 tests from Interaction3Ph (4797 ms total)

[----------] 1 test from InteractionElPh
[ RUN ] InteractionElPh.Test1
Reading in ../test/data/silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Starting Wannier post-processing

Started Wannier transform of coupling with 3 irreducible q-points.
2023-09-18, 18:56:48 | 33% | 1 / 3
2023-09-18, 18:56:48 | 66% | 2 / 3
2023-09-18, 18:56:48 | 100% | 3 / 3
Elapsed time: 0.132 s.
Done Wannier-transform of g

Start writing el-ph coupling to file.

WARNING: HDF5 with <4 MPI process may crash (due to a library's bug),
use more MPI processes if that happens

Done writing el-ph coupling to file.

Start reading el-ph coupling from file.
The app will now allocate 0.000366 (GB) of memory per MPI process.
Done reading el-ph coupling from file.

Started parsing of el-ph interaction.
Allocating 0.00207 (GB) (per MPI process) for the el-ph coupling matrix.
Finished parsing of el-ph interaction.
[ OK ] InteractionElPh.Test1 (288 ms)
[----------] 1 test from InteractionElPh (288 ms total)

[----------] 1 test from InteractionIsotope
[ RUN ] InteractionIsotope.Wphisoiq4
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
[ OK ] InteractionIsotope.Wphisoiq4 (64 ms)
[----------] 1 test from InteractionIsotope (64 ms total)

[----------] 2 tests from IrrPointsTest
[ RUN ] IrrPointsTest.Symmetries
Found 48 symmetries
[ OK ] IrrPointsTest.Symmetries (11 ms)
[ RUN ] IrrPointsTest.SymmetriesGaN
Found 12 symmetries
[ OK ] IrrPointsTest.SymmetriesGaN (0 ms)
[----------] 2 tests from IrrPointsTest (12 ms total)

[----------] 5 tests from Kokkos
[ RUN ] Kokkos.KokkosDeviceManager
[ OK ] Kokkos.KokkosDeviceManager (0 ms)
[ RUN ] Kokkos.Wannier1

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880376 0.00000000 -2.69880376
0.00000000 2.69880376 2.69880376
2.69880376 2.69880376 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 0.71407173 0.71407173 0.71407173

[ OK ] Kokkos.Wannier1 (60 ms)
[ RUN ] Kokkos.Wannier2

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880376 0.00000000 -2.69880376
0.00000000 2.69880376 2.69880376
2.69880376 2.69880376 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 0.71407173 0.71407173 0.71407173

[ OK ] Kokkos.Wannier2 (61 ms)
[ RUN ] Kokkos.Wannier3

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880376 0.00000000 -2.69880376
0.00000000 2.69880376 2.69880376
2.69880376 2.69880376 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 0.71407173 0.71407173 0.71407173

[ OK ] Kokkos.Wannier3 (61 ms)
[ RUN ] Kokkos.PhononH0
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
[ OK ] Kokkos.PhononH0 (10 ms)
[----------] 5 tests from Kokkos (195 ms total)

[----------] 1 test from MPITest
[ RUN ] MPITest.AllReduceSum
[ OK ] MPITest.AllReduceSum (0 ms)
[----------] 1 test from MPITest (0 ms total)

[----------] 1 test from PointsTest
[ RUN ] PointsTest.PointsHandling
[ OK ] PointsTest.PointsHandling (0 ms)
[----------] 1 test from PointsTest (0 ms total)

[----------] 1 test from PhononH0
[ RUN ] PhononH0.Velocity
Reading in ../test/data/444_silicon.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880377 0.00000000 -2.69880377
0.00000000 2.69880377 2.69880377
2.69880377 2.69880377 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 1.34940189 1.34940189 1.34940189

Successfully parsed harmonic QE files.

Start imposing simple acoustic sum rule.
Finished imposing simple acoustic sum rule.
[ OK ] PhononH0.Velocity (10 ms)
[----------] 1 test from PhononH0 (10 ms total)

[----------] 2 tests from WannierH0
[ RUN ] WannierH0.Velocity

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880376 0.00000000 -2.69880376
0.00000000 2.69880376 2.69880376
2.69880376 2.69880376 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 0.71407173 0.71407173 0.71407173

[ OK ] WannierH0.Velocity (60 ms)
[ RUN ] WannierH0.Velocity2

Direct lattice vectors (ang)
a1 | a2 | a3
-2.69880376 0.00000000 -2.69880376
0.00000000 2.69880376 2.69880376
2.69880376 2.69880376 0.00000000
Atomic Positions (Cartesian, ang)
Si 0.00000000 0.00000000 0.00000000
Si 0.71407173 0.71407173 0.71407173

[ OK ] WannierH0.Velocity2 (61 ms)
[----------] 2 tests from WannierH0 (122 ms total)

[----------] Global test environment tear-down
[==========] 26 tests from 16 test suites ran. (14886 ms total)
[ PASSED ] 26 tests.
Finished on Mon Sep 18 18:56:49 2023
Run time: 14.906100 s
(phoebe) cqwl111@cqwl111:~/Videos/phoebe/build$

[jcoulter12]

Hi Guo, All the tests passed, so it’s working. Great news! If you encounter any issues later, it is really easy to build Phoebe and we have some specific instructions on our installation page about how to do it. However, this seems to work. Best, Jenny

…

On Mon, Sep 18, 2023 at 7:10 AM Guodonglin-cqust ***@***.***> wrote: Hi jenny I install the code on ubantu system. I forget the commond line "make -j 1 phoebe make -j 1 runTests", and i have successfully compiled the code. When i run the "runTests", i encounter some problems about HDF5, and the process of runTests is like this: (phoebe) ***@***.***:~/Videos/phoebe/build$ mpirun -np 1 ./runTests Started on Mon Sep 18 18:56:34 2023 Kokkos::OpenMP::initialize WARNING: OMP_PROC_BIND environment variable not set In general, for best performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads For best performance with OpenMP 3.1 set OMP_PROC_BIND=true For unit testing set OMP_PROC_BIND=false [==========] Running 26 tests from 16 test suites. [----------] Global test environment set-up. [----------] 1 test from PMatrixTest [ RUN ] PMatrixTest.diagonalize Starting matrix diagonalization. Time for rank 0 : 0.020179 Matrix diagonalization completed. Time for rank 0 : 0.084618 WARNING: Relaxons diagonalization found negative eigenvalues. This can happen when there's a bit of numerical noise on the scattering matrix, and finding them may indicate the calculation is unconverged. While we simply do not include these when computing transport, and likely if they are small the calculation will be unaffected, you may want to consider using with more wavevectors or an improved DFT calculation. Additionally, setting symmetrizeMatrix = true in your input file will help. These eigenvalues are (in atomic units): 0 -1 [ OK ] PMatrixTest.diagonalize (64 ms) [----------] 1 test from PMatrixTest (64 ms total) [----------] 2 tests from ActiveBandStructureTest [ RUN ] ActiveBandStructureTest.BandStructureStorage Reading in ../test/data/444_silicon.fc. Found 48 symmetries Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 300.000000 (K) Applying an energy window discarding states outside of [0.000000, 0.054423] eV range. Applying an energy window discarding states outside of [0.000000, 0.054423] eV range. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 300.000000 (K) Reading in ../test/data/444_silicon.fc. Found 48 symmetries Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 300.000000 (K) Applying a population window discarding states with dn/dT < 5.000000e-09. Applying a population window discarding states with dn/dT < 5.000000e-09. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 300.000000 (K) [ OK ] ActiveBandStructureTest.BandStructureStorage (2915 ms) [ RUN ] ActiveBandStructureTest.WindowFilter Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 50.000000 (K) Applying a population window discarding states with dn/dT < 1.000000e-02. Applying a population window discarding states with dn/dT < 1.000000e-02. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 50.000000 (K) [ OK ] ActiveBandStructureTest.WindowFilter (1248 ms) [----------] 2 tests from ActiveBandStructureTest (4163 ms total) [----------] 1 test from ABS [ RUN ] ABS.Symmetries Reading in ../test/data/444_silicon.fc. Found 48 symmetries Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Applying an energy window discarding states outside of [0.00000000, 0.05714391] eV range. Statistical parameters for the calculation Index, temperature iCalc = 0, T = 300.000000 (K) [ OK ] ABS.Symmetries (29 ms) [----------] 1 test from ABS (29 ms total) [----------] 1 test from FullBandStructureTest [ RUN ] FullBandStructureTest.BandStructureStorage Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. [ OK ] FullBandStructureTest.BandStructureStorage (593 ms) [----------] 1 test from FullBandStructureTest (593 ms total) [----------] 1 test from Crystal [ RUN ] Crystal.Test1 Found 48 symmetries [ OK ] Crystal.Test1 (11 ms) [----------] 1 test from Crystal (11 ms total) [----------] 1 test from TetrahedronTest [ RUN ] TetrahedronTest.Normalization Reading in ../test/data/444_silicon.fc. Found 48 symmetries Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. [ OK ] TetrahedronTest.Normalization (4533 ms) [----------] 1 test from TetrahedronTest (4533 ms total) [----------] 2 tests from SquareRootTest [ RUN ] SquareRootTest.PositiveNos [ OK ] SquareRootTest.PositiveNos (0 ms) [ RUN ] SquareRootTest.ZeroAndNegativeNos [ OK ] SquareRootTest.ZeroAndNegativeNos (0 ms) [----------] 2 tests from SquareRootTest (0 ms total) [----------] 3 tests from Interaction3Ph [ RUN ] Interaction3Ph.Coupling3Ph000 Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. Using anharmonic force constants from ShengBTE. Reading in ../test/data/FORCE_CONSTANTS_3RD. Allocating 0.00008489 (GB) (per MPI process) for the 3-ph coupling matrix. Successfully parsed anharmonic ShengBTE files. [ OK ] Interaction3Ph.Coupling3Ph000 (28 ms) [ RUN ] Interaction3Ph.Coupling3Ph210 Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. Reading in ../test/data/FORCE_CONSTANTS_3RD. Allocating 0.00008489 (GB) (per MPI process) for the 3-ph coupling matrix. Successfully parsed anharmonic ShengBTE files. **[ OK ] Interaction3Ph.Coupling3Ph210 (4749 ms) [ RUN ] Interaction3Ph.Coupling3Ph000_p3py Using harmonic force constants from phonopy. Reading in ../test/data/phono3py/phono3py_disp.yaml. Reading in ../test/data/phono3py/fc2.hdf5. HDF5-DIAG: Error detected in HDF5 (1.14.2) MPI-process 0: #000: H5D.c line 403 in H5Dopen2(): unable to synchronously open dataset major: Dataset minor: Can't open object #1 <#1>: H5D.c line 364 in H5D__open_api_common(): unable to open dataset major: Dataset minor: Can't open object #2 <#2>: H5VLcallback.c line 1980 in H5VL_dataset_open(): dataset open failed major: Virtual Object Layer minor: Can't open object #3 <#3>: H5VLcallback.c line 1947 in H5VL__dataset_open(): dataset open failed major: Virtual Object Layer minor: Can't open object #4 <#4>: H5VLnative_dataset.c line 321 in H5VL__native_dataset_open(): unable to open dataset major: Dataset minor: Can't open object #5 <#5>: H5Dint.c line 1418 in H5D__open_name(): not found major: Dataset minor: Object not found #6 <#6>: H5Gloc.c line 421 in H5G_loc_find(): can't find object major: Symbol table minor: Object not found #7 <#7>: H5Gtraverse.c line 816 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #8 <#8>: H5Gtraverse.c line 596 in H5G__traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #9 <#9>: H5Gloc.c line 381 in H5G__loc_find_cb(): object 'physical_unit' doesn't exist major: Symbol table minor: Object not found Phonopy fc file did not include units. This is likely ok, defaulting to eV/angstrom^2. However, you should check to be sure the magnitude of your phonon frequencies is sensible.** Successfully parsed harmonic phonopy files. Direct lattice vectors (ang) a1 | a2 | a3 0.00000000 2.73313145 2.73313145 2.73313145 0.00000000 2.73313145 2.73313145 2.73313145 0.00000000 Atomic Positions (Cartesian, ang) Si 4.09969717 4.09969717 4.09969717 Si 2.73313145 2.73313145 2.73313145 Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. Using anharmonic force constants from phono3py. Reading in ../test/data/phono3py/phono3py_disp.yaml. Reading in ../test/data/phono3py/fc3.hdf5. Allocating 0.00082397 (GB) (per MPI process) for the 3-ph coupling matrix. Successfully parsed anharmonic phono3py files. [ OK ] Interaction3Ph.Coupling3Ph000_p3py (19 ms) [----------] 3 tests from Interaction3Ph (4797 ms total) [----------] 1 test from InteractionElPh [ RUN ] InteractionElPh.Test1 Reading in ../test/data/silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Starting Wannier post-processing Started Wannier transform of coupling with 3 irreducible q-points. 2023-09-18, 18:56:48 | 33% | 1 / 3 2023-09-18, 18:56:48 | 66% | 2 / 3 2023-09-18, 18:56:48 | 100% | 3 / 3 Elapsed time: 0.132 s. Done Wannier-transform of g Start writing el-ph coupling to file. WARNING: HDF5 with <4 MPI process may crash (due to a library's bug), use more MPI processes if that happens Done writing el-ph coupling to file. Start reading el-ph coupling from file. The app will now allocate 0.000366 (GB) of memory per MPI process. Done reading el-ph coupling from file. Started parsing of el-ph interaction. Allocating 0.00207 (GB) (per MPI process) for the el-ph coupling matrix. Finished parsing of el-ph interaction. [ OK ] InteractionElPh.Test1 (288 ms) [----------] 1 test from InteractionElPh (288 ms total) [----------] 1 test from InteractionIsotope [ RUN ] InteractionIsotope.Wphisoiq4 Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. [ OK ] InteractionIsotope.Wphisoiq4 (64 ms) [----------] 1 test from InteractionIsotope (64 ms total) [----------] 2 tests from IrrPointsTest [ RUN ] IrrPointsTest.Symmetries Found 48 symmetries [ OK ] IrrPointsTest.Symmetries (11 ms) [ RUN ] IrrPointsTest.SymmetriesGaN Found 12 symmetries [ OK ] IrrPointsTest.SymmetriesGaN (0 ms) [----------] 2 tests from IrrPointsTest (12 ms total) [----------] 5 tests from Kokkos [ RUN ] Kokkos.KokkosDeviceManager [ OK ] Kokkos.KokkosDeviceManager (0 ms) [ RUN ] Kokkos.Wannier1 Direct lattice vectors (ang) a1 | a2 | a3 -2.69880376 0.00000000 -2.69880376 0.00000000 2.69880376 2.69880376 2.69880376 2.69880376 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 0.71407173 0.71407173 0.71407173 [ OK ] Kokkos.Wannier1 (60 ms) [ RUN ] Kokkos.Wannier2 Direct lattice vectors (ang) a1 | a2 | a3 -2.69880376 0.00000000 -2.69880376 0.00000000 2.69880376 2.69880376 2.69880376 2.69880376 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 0.71407173 0.71407173 0.71407173 [ OK ] Kokkos.Wannier2 (61 ms) [ RUN ] Kokkos.Wannier3 Direct lattice vectors (ang) a1 | a2 | a3 -2.69880376 0.00000000 -2.69880376 0.00000000 2.69880376 2.69880376 2.69880376 2.69880376 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 0.71407173 0.71407173 0.71407173 [ OK ] Kokkos.Wannier3 (61 ms) [ RUN ] Kokkos.PhononH0 Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. [ OK ] Kokkos.PhononH0 (10 ms) [----------] 5 tests from Kokkos (195 ms total) [----------] 1 test from MPITest [ RUN ] MPITest.AllReduceSum [ OK ] MPITest.AllReduceSum (0 ms) [----------] 1 test from MPITest (0 ms total) [----------] 1 test from PointsTest [ RUN ] PointsTest.PointsHandling [ OK ] PointsTest.PointsHandling (0 ms) [----------] 1 test from PointsTest (0 ms total) [----------] 1 test from PhononH0 [ RUN ] PhononH0.Velocity Reading in ../test/data/444_silicon.fc. Direct lattice vectors (ang) a1 | a2 | a3 -2.69880377 0.00000000 -2.69880377 0.00000000 2.69880377 2.69880377 2.69880377 2.69880377 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 1.34940189 1.34940189 1.34940189 Successfully parsed harmonic QE files. Start imposing simple acoustic sum rule. Finished imposing simple acoustic sum rule. [ OK ] PhononH0.Velocity (10 ms) [----------] 1 test from PhononH0 (10 ms total) [----------] 2 tests from WannierH0 [ RUN ] WannierH0.Velocity Direct lattice vectors (ang) a1 | a2 | a3 -2.69880376 0.00000000 -2.69880376 0.00000000 2.69880376 2.69880376 2.69880376 2.69880376 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 0.71407173 0.71407173 0.71407173 [ OK ] WannierH0.Velocity (60 ms) [ RUN ] WannierH0.Velocity2 Direct lattice vectors (ang) a1 | a2 | a3 -2.69880376 0.00000000 -2.69880376 0.00000000 2.69880376 2.69880376 2.69880376 2.69880376 0.00000000 Atomic Positions (Cartesian, ang) Si 0.00000000 0.00000000 0.00000000 Si 0.71407173 0.71407173 0.71407173 [ OK ] WannierH0.Velocity2 (61 ms) [----------] 2 tests from WannierH0 (122 ms total) [----------] Global test environment tear-down [==========] 26 tests from 16 test suites ran. (14886 ms total) [ PASSED ] 26 tests. Finished on Mon Sep 18 18:56:49 2023 Run time: 14.906100 s (phoebe) ***@***.***:~/Videos/phoebe/build$ — Reply to this email directly, view it on GitHub <#195 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADLC27AGPLUHCFYWNZUUSHTX3AT2LANCNFSM6AAAAAA4RPW3SU> . You are receiving this because you commented.Message ID: ***@***.***>

[Guodonglin-cqust]

Hi jenny

 During the "runTests" process, whether this problem "HDF5-DIAG: Error detected in HDF5 (1.14.2) MPI-process 0:" is serious, and 

whether it is necessary to solve.

 Could you give us some informations,  how to deal with the two-dimensional Fröhlich interaction in phoebe code？

is it the same with the following paper?

Thank you very much.
Guo

[jcoulter12]

Hi Guo,

Nope, this is just a warning related to the phonon transport test, it's actually expected -- it happens because sometimes phono3py writes a unit conversion to file, and sometimes it doesn't, which is out of our control. We therefore try to read it in, and if it fails, we know this means the units are in SI, the default from phono3py. This is normal, and also not related to your desired calculation -- you should be good to run tutorials.

On this 2D front, I may need to do a small amount of implementation to offer this feature. It's on our todo list for this week, so I'll keep you closely updated about how to use it. It's a feature we wanted to offer anyway, but now that you've asked, we've moved it to a higher priority.

Thanks for understanding, and happy to answer any more questions,
Jenny

[Guodonglin-cqust]

Hi jenny
i run the sample cu with phoebe-quantum-espresso, including scf, ph,in, q2r.in, wannier. but i run the "phoebe -in qeToPhoebeWannier.in -out qeToPhoebeWannier.out", the error is shown, like this

Launching App "elPhQeToPhoebe".

Reading in cu.fc.

Direct lattice vectors (ang)
a1 | a2 | a3
0.00000000 1.76692271 1.76692271
1.76692271 0.00000000 1.76692271
1.76692271 1.76692271 0.00000000
Atomic Positions (Cartesian, ang)
Cu 0.00000000 0.00000000 0.00000000

Successfully parsed harmonic QE files.

Error!
cu.phoebe.0000.dat file not found.

Finished on Wed Sep 20 21:29:04 2023

i do not know which step could the file of cu.phoebe.0000.dat.

Guo

[jcoulter12]

Hi Guo,

Did you run step 1, and build the patched copy of quantum espresso?
https://phoebe.readthedocs.io/en/develop/tutorials/elWanTransport.html#step-1-patch-quantum-espresso

If not, those files will not be generated.
Otherwise, if you did build the patched QE and are using it, those files will be generated during step 3, in which the phonon calculation is run.
https://phoebe.readthedocs.io/en/develop/tutorials/elWanTransport.html#step-3-phonons-and-electron-phonon-coupling

Thanks,
Jenny