Update outputs of EPA app #212

jcoulter12 · 2024-04-26T13:08:49Z

This is a small PR updating various outputs and print statements.

Summary of changes:

tau.py plot script is updated to match some relatively recent change by matplotlib which was causing it to crash.
1 and 2D unit conversions for Wigner transport output were previously flipped
Chemical potential determination could previously crash if far too many MPI procs were used
EPA app now properly prints progress during Fourier bands calculation
EPA app now outputs DoS to json
General increase in verbosity in print statements of EPA app
Added "thickness" input variable for use with 2D systems
Variational solver now runs for at least several iterations by default to avoid spurious convergence claims
Added a function to print the dynmat to HDF5 if needed

… points in the bands app

…therwise

…cation of cell thickness

…ies are negative Co-authored-by: Changpeng Lin <[email protected]>

…termination segfaulted when more processes than kpoints were used

…mments in the code

…and add a few extra variables to the tutorial files

…s of the code

…t dos to json during the run

… works, remove useless copy/assignment constructors from fourier bands class

…ages

…but an alternative memory tracking scheme is needed

…ew requirement that solver run at least 3 iterations

jcoulter12 and others added 30 commits January 3, 2024 16:41

Update the features in the read README.md file

13eac1e

Update features on the introduction page of the website

9c87378

add thickness parameter to user documentation

56d2e02

add thickness variable and input sanity check function

5eb3edd

update units and ensure only the dimensions set in input are looped over

9dac301

further updates to check that only selected dims are looped over

5163337

a few comments about other places this might be needed

25da46a

Merge remote-tracking branch 'origin/develop' into minorFixes

60ee015

Merge branch 'minorFixes' of github.com:mir-group/phoebe into minorFixes

1d645bc

Further dimensionality unit improvements to Wigner thermal transport.

9d4a492

fix a typo in phonon bte docs

d4822d1

warn a user if they select an even relaxons mesh

c88126d

fix the warning for even relaxons meshes

961a4a6

account for possible floating point errors when finding the high symm…

a183f25

… points in the bands app

unblock tetrahedron method for phonons

3d30427

add a minimum number of iters for variational transport calculations

5f9ad12

add many print fixes for 2d case to the viscosity output functions

6222795

initialize specific heat to zero, as this sometimes resulted in nan o…

86becf2

…therwise

previously thermal conductivity had dims 3 and 1 flipped in the appli…

2f5bb58

…cation of cell thickness

wigner transport had dims flipped for thermal cond units

a7a74a0

update error message for tetrahedron scattering

a7b4f14

update two error messages to be more informative when phonon frequenc…

0db1b7d

…ies are negative Co-authored-by: Changpeng Lin <[email protected]>

demo call to print dyn to hdf5 in phonon bands app

8a0c416

add functions to convert coordinates to the crystal object

7f241c0

add function to write to hdf5

5c4ea98

phonon dynamical matrix to file mistake fixed

99162d8

minor bugfix in chemical potential determination -- max/min energy de…

943fd61

…termination segfaulted when more processes than kpoints were used

Create epa_tau.py, to plot epa_relaxation_times.json [ci skip]

d8deffa

Update elEpaTransport.rst to reflect the name of the proper plot script

9f50c84

Update postProcessing.rst to have a note about epa_tau.py

49694a5

jcoulter12 added 11 commits March 26, 2024 11:10

improvement of a few error messages, print statements, and spacing/co…

3e0c4a4

…mments in the code

minor updates to the epa transport app tutorial docs, update outputs …

893df42

…and add a few extra variables to the tutorial files

make function to write a dos to json publicly available to other part…

745f459

…s of the code

update print functions to be more descriptive in epa app and to outpu…

e70140b

…t dos to json during the run

update loop print on fourier bandstructure calculation so that it now…

e3a3dd9

… works, remove useless copy/assignment constructors from fourier bands class

Merge branch 'minorFixes' of github.com:mir-group/phoebe into minorFixes

8f16a5b

update the plot tau script to work with newer versions of python pack…

301cc00

…ages

merge from develop

bf58fc7

add a script to read the output of elph_plot_app [ci skip]

aeb243d

remove test statement in bands app which was printing the dynmat to hdf5

28b28ee

replace copy and assignment constructors -- these should be removed, …

5331522

…but an alternative memory tracking scheme is needed

jcoulter12 added documentation Improvements or additions to documentation enhancement New feature or request labels Apr 26, 2024

jcoulter12 self-assigned this Apr 26, 2024

jcoulter12 added 3 commits April 26, 2024 09:35

add epa_dos to reference files

d76e45b

update the variational onsager coefficients reference file to match n…

b4d1291

…ew requirement that solver run at least 3 iterations

update the variational onsager coefficients reference file to match n…

433d544

…ew requirement that solver run at least 3 iterations

jcoulter12 merged commit f69a90b into develop Apr 26, 2024
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Update outputs of EPA app #212

Update outputs of EPA app #212

jcoulter12 commented Apr 26, 2024

Update outputs of EPA app #212

Update outputs of EPA app #212

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jcoulter12 commented Apr 26, 2024