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Tracking: atomate2 PRs from Anubhav Jain's group #1591
Description
This issue tracks the atomate2 PRs from @computron's group (Hacking Materials). A workflow with several PRs gets its own issue, linked below.
Open
- Add Debye-Waller factors as an option of the phonon makers #1580 Debye-Waller factors as an option of the phonon makers (the pheasy and hiPhive flows also need Store imaginary_modes and structure in ThermalDisplacementData emmet#1536)
- Add a tutorial for the Debye-Waller workflow #1592 Debye-Waller tutorial (needs Add Debye-Waller factors as an option of the phonon makers #1580)
- Add an opt-in linear fit of the vibrational free energy for QHA volumes with imaginary modes #1632 QHA: opt-in linear fit of the vibrational free energy for the volumes with imaginary modes (plan in Plan: fix the force field QHA issues #1411 and #1412 #1611)
- [WIP] CALPHAD workflow with ATAT sqs2tdb #1574 CALPHAD phase diagrams with ATAT
- Restructure the thermal expansion tutorial with stored results and no image files #1578 Thermal expansion tutorial with stored results
- Add the jobs and schema of the finite-temperature phonon workflow #1600 Finite-temperature phonons: jobs and schema (part of Plan: split the finite-temperature phonon workflow (#1560) into PRs #1585)
- Add the force field and VASP flows of the finite-temperature phonon workflow #1601 Finite-temperature phonons: force field and VASP flows (needs Add the jobs and schema of the finite-temperature phonon workflow #1600)
- [WIP] Add the docs of the finite-temperature phonon workflow #1603 Finite-temperature phonons: docs (part of Plan: split the finite-temperature phonon workflow (#1560) into PRs #1585, needs Add the force field and VASP flows of the finite-temperature phonon workflow #1601)
- [WIP] Add the finite-temperature phonon tutorial #1604 Finite-temperature phonons: tutorial (part of Plan: split the finite-temperature phonon workflow (#1560) into PRs #1585, needs [WIP] Add the docs of the finite-temperature phonon workflow #1603)
- Raise an error for MTKNPT runs with a temperature or pressure schedule #1602 Raise an error when MTKNPT, the default NpT dynamics of
AseMDMaker, gets a temperature or pressure schedule. MTKNPT reads its targets only once at the start, so a ramp was silently ignored. - [WIP] Breaking: Read ASE MD velocities in Angstrom/fs and let MultiMDMaker chain VASP and ASE MD jobs #1606
MultiMDMakerchains ASE (force field) MD jobs, and ASE MD reads velocities in Angstrom/fs (Breaking, first part of the long MD item of Plan: split the finite-temperature phonon workflow (#1560) into PRs #1585) - [WIP] Split the MD of the finite-temperature phonon workflow into several jobs #1607 Finite-temperature phonons: split the MD into several jobs with
n_md_jobs(part of Plan: split the finite-temperature phonon workflow (#1560) into PRs #1585, needs [WIP] Add the finite-temperature phonon tutorial #1604 and [WIP] Breaking: Read ASE MD velocities in Angstrom/fs and let MultiMDMaker chain VASP and ASE MD jobs #1606) - [WIP] Fix atom positions in ASE NPT MD for non-upper-triangular cells #1608 Fix atom positions in ASE NPT MD (
nose-hoover) for cells that are not upper triangular - Use one default of 0.1 THz for tol_imaginary_modes in all phonon workflows #1633 One default of 0.1 THz for
tol_imaginary_modesin all phonon workflows (Breaking, closes Different default tolerances for imaginary modes in the phonon workflows #1630) - Use VASP_NCL_CMD when the INCAR sets LSORBIT or LNONCOLLINEAR #1637 Use
VASP_NCL_CMDwhen the INCAR setsLSORBITorLNONCOLLINEAR(closes VASP_NCL_CMD is not used anywhere? #1636)
Planned
- Lattice thermal conductivity with phono3py, ShengBTE, FourPhonon and kALDo.. from @leslie-zheng , @ZKC19940412 and me
- Melting point workflow by @amelia-codes
- CALPHAD workflow with VASP (after [WIP] CALPHAD workflow with ATAT sqs2tdb #1574) .. from @ZKC19940412 and me
- CALPHAD workflow with calphy, free energies from thermodynamic integration (after [WIP] CALPHAD workflow with ATAT sqs2tdb #1574) .. from me
- Volume resolved at 0K and finite temp for CTE @ZKC19940412
- Extend the finite temperature phonon to include 3rd IFCs .. from @ZKC19940412
- Born and Huang elastic tensor to obtain elastic constants at high temperature .. from @ZKC19940412
- error metrics for phase diagram (calphad) workflow. from @ZKC19940412
- Can we also add energy above hull workflow, which is required by @amelia-codes
- Phonon renormalization methods that do not need MD, such as SCPH and SSCHA (open question in Phonon renormalization methods that do not need MD #1634) .. from me
Merged
#1631, #1629, #1628, #1620, #1610, #1609, #1590, #1589, #1587, #1586, #1584, #1576, #1575, #1573, #1568, #1559, #1558
Reacted by zkunchen and Aaron Kaplan
Activity
ZKC19940412 commentedon Oct 12, 2026
Two more needed features within the upcoming PR:1). Extend the finite temperature phonon to include 3rd IFCs and 2). Born and Huang elastic tensor to obtain elastic constants at high temperature
hrushikesh-s commentedon Oct 12, 2026
@JaGeo, should we add #1411 and #1412 to this plan as well? Both are open since March and come from the force field QHA workflow, which builds on the phonon workflow. I can try to fix these two open issues in case there's no one is working on them right now.
JaGeo commentedon Oct 13, 2026
@hrushikesh-s Sure.
From my side, no one is working on it.
computron commentedon Oct 14, 2026
@JaGeo @esoteric-ephemera @utf
Could you let me know which of these PRs you would be able to review (e.g., within the next week or two), and which ones you would want to punt to our group for review? If you'd like, we can stick to review and iteration on our side rather than merge, but at least the secondary pre-review could help resolve any immediate issues.
JaGeo commentedon Oct 15, 2026
i am suggesting a pre-review for all of them from your group but I am happy to to take a look at the ones that are ticked. Nevetheless I would like to ask to be considerate with the timelines given the number of PRs in this short time frame.
esoteric-ephemera commentedon Oct 15, 2026
Some of these are still WIP - how would you rank these in priority @computron?
computron commentedon Oct 15, 2026
@hrushikesh-s can probably prioritize, but the WIP can of course wait ...
hrushikesh-s commentedon Oct 15, 2026
@esoteric-ephemera @computron @JaGeo, thanks!
My priority order is #1589 --> #1590 --> #1578 --> #1580 --> #1592
There are more planned PRs (including the WIP #1574), which I will soon start, and @ZKC19940412 will pre-review each PR before we ask you.
JaGeo commentedon Oct 16, 2026
Just to state this here: i have an important deadline on the 31st of October myself and I will prioritize this deadline. Thus, if anyone is faster than me, please feel free to volunteer.
For some of the PRs, we now wait for a pymatgen release. They are nearly ready otherwise.
ZKC19940412 commentedon Oct 23, 2026
It will be useful and also add on error metrics on calphad modeled phase diagrams with known ground truth, with classification based metrics for example.
ZKC19940412 commentedon Oct 23, 2026
Also energy above Hull as atomate2 workflow, versus say single point energy/forces and then post-adhoc constructions.