BUG: atomate2 failed to compute the 3rd-order elastic tensor.

[hongyi-zhao]

I try to call atomate2 via jobflow-remote to compute the 3rd-order elastic tensor with the following code:

import numpy as np
from jobflow import run_locally
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from atomate2.vasp.flows.elastic import ElasticMaker
from atomate2.vasp.powerups import (
    update_user_incar_settings,
    update_user_potcar_functional,
    update_user_kpoints_settings,
)
from pymatgen.io.vasp.inputs import Kpoints
from pymatgen.core import Structure
from mp_api.client import MPRester
from atomate2.vasp.powerups import add_metadata_to_flow
#https://github.com/materialsproject/atomate2/issues/1014#issuecomment-2454955891
from atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker, MPGGAStaticMaker

from jobflow import Flow
from jobflow_remote import submit_flow

# Based on the following checking:
#werner@x13dai-t:~/Public/hpc/vasp/pot$ ug -r 'TITEL  = PAW_PBE Pt ' -g POTCAR
#potpaw_PBE.54/Pt/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005
#potpaw_PBE.64/Pt/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005
#potpaw_PBE/Pt/POTCAR:   TITEL  = PAW_PBE Pt 05Jan2001
#potpaw_PBE/Pt_new/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005
#potpaw_PBE/Pt_ZORA/POTCAR:   TITEL  = PAW_PBE Pt 05Jan2001
#potpaw_PBE.52/Pt/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005
#potpaw_LDA_PBE_52_54_orig/potpaw_PBE.54/Pt/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005
#potpaw_LDA_PBE_52_54_orig/potpaw_PBE.52/Pt/POTCAR:   TITEL  = PAW_PBE Pt 04Feb2005

#So, all the following versions are the same one in this case:
#user_potcar_functional = "PBE_64"
#user_potcar_functional = "PBE_52"
#user_potcar_functional = "PBE_54"
#user_potcar_functional = "PBE_52_W_HASH"
#user_potcar_functional = "PBE_54_W_HASH"

#要复现MP，根据下面的检查，应该设置potcar版本与MP官方使用的一致。

#In [4]: from mp_api.client import MPRester
#   ...: 
#   ...: material_id = "mp-126"
#   ...: with MPRester() as mpr:
#   ...:     # 获取elastic数据来获取task id
#   ...:     elasticity_doc = mpr.materials.elasticity.search(material_ids=[material_id])
#   ...:     opt_id = elasticity_doc[0].fitting_data.optimization_task.string
#   ...: 
#   ...:     # 使用task id获取详细信息
#   ...:     opt_doc = mpr.materials.tasks.search([opt_id],
#   ...:         fields=["input", "calcs_reversed"])
#   ...: 
#   ...:     # 提取 potcar_spec
#   ...:     potcar_spec = opt_doc[0].calcs_reversed[0].input.potcar_spec
#   ...:     print(f"POTCAR specifications: {potcar_spec}")
#   ...: 
#Retrieving ElasticityDoc documents: 100%|█████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 7543.71it/s]
#Retrieving TaskDoc documents: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 9892.23it/s]
#POTCAR specifications: [PotcarSpec(titel='PAW_PBE Pt 05Jan2001', hash='a604ea3c6a9cc23c739b762f625cf449', summary_stats=None)]

#In [4]: opt_doc[0].calcs_reversed[0].input.potcar_spec
#Out[4]: [PotcarSpec(titel='PAW_PBE Pt 05Jan2001', hash='a604ea3c6a9cc23c739b762f625cf449', summary_stats=None)]

#https://github.com/materialsproject/api/issues/944#issuecomment-2503063154
user_potcar_functional = "PBE"

# 实际测试表明，不同的vasp版本的计算结果是一致的（差别很小，可以忽略）：
#In [5]: # MP所使用的vasp版本：
#   ...: for calc in opt_doc[0].calcs_reversed:
#   ...:     print(calc.vasp_version)
#   ...: 
#5.4.4
#5.4.4

material_id = "mp-126"
with MPRester() as mpr:
    # Obtain elastic data and the related task IDs.
    elasticity_doc = mpr.materials.elasticity.search(material_ids=[material_id])
    opt_id = elasticity_doc[0].fitting_data.optimization_task.string
    first_deform_id = str(elasticity_doc[0].fitting_data.deformation_tasks[0])
    opt_doc = mpr.materials.tasks.search([opt_id],
        fields=["input", "orig_inputs", "calcs_reversed"])

    deform_dep_doc = mpr.materials.tasks.search([first_deform_id],
        fields=["input", "orig_inputs", "calcs_reversed"])

structure = mpr.materials.get_structure_by_material_id(material_id)
#ElasticMaker的flow中有 structure_to_conventional的job，所以下面的步骤应该不是必需的：
structure = SpacegroupAnalyzer(structure).get_conventional_standard_structure()

# Process kpoints settings
#opt_kpoints_settings = opt_doc[0].orig_inputs.kpoints
#deform_kpoints_settings = deform_dep_doc[0].orig_inputs.kpoints

# Use calcs-reversed to do the trick:
#https://materialsproject.github.io/atomate2/user/docs_schemas_emmet.html#calcs-reversed
opt_kpoints_settings = opt_doc[0].calcs_reversed[0].input.kpoints
deform_kpoints_settings = deform_dep_doc[0].calcs_reversed[0].input.kpoints

# Process INCAR settings
# Adopt the following strategy: based on the keys in `orig_inputs.incar`, use the corresponding values from `input.parameters`.
# This can be simplified into a one-liner dictionary comprehension:

#opt_incar_settings = {key: opt_doc[0].input.parameters[key] for key in opt_doc[0].orig_inputs.incar.keys() if key in opt_doc[0].input.parameters}
#deform_incar_settings = {key: deform_dep_doc[0].input.parameters[key] for key in deform_dep_doc[0].orig_inputs.incar.keys() if key in deform_dep_doc[0].input.parameters}

# Or, for better readability, you can first define variables and then achieve it as following:
#orig_incar = opt_doc[0].orig_inputs.incar
#input_params = opt_doc[0].input.parameters
#opt_incar_settings = {key: input_params[key] for key in orig_incar.keys() if key in input_params}

#orig_incar = deform_dep_doc[0].orig_inputs.incar
#input_params = deform_dep_doc[0].input.parameters
#deform_incar_settings = {key: input_params[key] for key in orig_incar.keys() if key in input_params}

# Use calcs-reversed to do the trick:
#https://materialsproject.github.io/atomate2/user/docs_schemas_emmet.html#calcs-reversed
opt_incar_settings = opt_doc[0].calcs_reversed[0].input.incar
deform_incar_settings = deform_dep_doc[0].calcs_reversed[0].input.incar

# Handle MAGMOM settings correctly.
if isinstance(opt_incar_settings.get("MAGMOM", []), list):
    magmoms = {}
    for idx, site in enumerate(structure):
        if idx < len(opt_incar_settings.get("MAGMOM", [])):
            magmoms[site.species_string] = opt_incar_settings["MAGMOM"][idx]
    opt_incar_settings["MAGMOM"] = magmoms


if isinstance(deform_incar_settings.get("MAGMOM", []), list):
    magmoms = {}
    for idx, site in enumerate(structure):
        if idx < len(deform_incar_settings.get("MAGMOM", [])):
            magmoms[site.species_string] = deform_incar_settings["MAGMOM"][idx]
    deform_incar_settings["MAGMOM"] = magmoms


#Re: The meaning of "GGA = --".
#https://www.vasp.at/forum/viewtopic.php?p=29678#p29678
#If the GGA tag is not explicitly specified in INCAR, then the functional from the POTCAR (usually PBE) is used. With older VASP versions, this was indicated with "GGA = --" in OUTCAR. Since VASP.6.4.3 this is properly indicated with "GGA = PE".

#In [3]: opt_doc[0].input.parameters['GGA']
#Out[3]: '--'

#In [34]: opt_doc[0].calcs_reversed[0].input.potcar
#Out[34]: ['Pt']

#In [35]: opt_doc[0].calcs_reversed[0].input.potcar_spec
#Out[35]: [PotcarSpec(titel='PAW_PBE Pt 05Jan2001', hash='a604ea3c6a9cc23c739b762f625cf449', summary_stats=None)]

#In [36]: opt_doc[0].calcs_reversed[0].input.potcar_type
#Out[36]: ['PAW_PBE']

flow = ElasticMaker(
    # 展示3阶弹性张量的计算：
    order=3, # Order of the tensor expansion to be determined. Can be either 2 or 3. default value is 2
    bulk_relax_maker=MPGGADoubleRelaxMaker(),  # 使用MP的双重优化设置
    elastic_relax_maker=MPGGAStaticMaker(),    # 使用MP的静态计算设置
    ).make(structure, conventional=True)
flow = update_user_potcar_functional(flow, user_potcar_functional)

flow = update_user_kpoints_settings(flow, opt_kpoints_settings, name_filter="MP GGA relax")
flow = update_user_kpoints_settings(flow, deform_kpoints_settings, name_filter="MP GGA static")

flow = update_user_incar_settings(flow, opt_incar_settings, name_filter="MP GGA relax" )
flow = update_user_incar_settings(flow, deform_incar_settings, name_filter="MP GGA static")

# Add metadata.
#flow = add_metadata_to_flow(
#    flow=flow,
#    additional_fields={
#        "mp_id": "mp-126", 
#        "submission_label": "mp-126_elastic_tensor-GGA-PE"
#    },
#)

# Run the flow
#responses = run_locally(flow, create_folders=True, ensure_success=True)
#elastic_output = responses[flow.jobs[-1].uuid][1].output
#matrix = np.array(elastic_output.elastic_tensor.ieee_format)
#np.set_printoptions(precision=4, suppress=True)
#print(matrix)

# 基于jobflow-remote:
jf_flow = Flow(flow, name='reproduce-mp-elastic')

# 提交计算
#https://github.com/Matgenix/jobflow-remote/issues/277#issuecomment-2759941413
#$ cd "/home/werner/Public/repo/github.com/Matgenix/qtoolkit.git" && ug -i 'SBATCH --mem'
#src/qtoolkit/io/slurm.py
#   157: #SBATCH --mem=$${mem}
#   158: #SBATCH --mem-per-cpu=$${mem_per_cpu}
resources = {
    "nodes": 1,
    "ntasks": 16,
    "mem": "80G",
    "partition": "batch",
    "time": "2400:00:00"
}

#https://github.com/Matgenix/jobflow-remote/issues/277#issuecomment-2759918475
print(submit_flow(jf_flow, project='std', worker="vasp_slurm", resources=resources, exec_config="vasp_slurm"))

But the job fit_elastic_tensor in the flow failed as shown below:

In [11]: ! jf -p std job info 211f2834-2c16-4ed4-be09-6c59085abdfd
The selected project is std from config file /home/werner/.jfremote/std.yaml
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│      db_id = '390'                                                                                                                                           │
│       uuid = '211f2834-2c16-4ed4-be09-6c59085abdfd'                                                                                                          │
│      index = 1                                                                                                                                               │
│       name = 'fit_elastic_tensor'                                                                                                                            │
│      state = 'FAILED'                                                                                                                                        │
│      error = Traceback (most recent call last):                                                                                                              │
│                File "/home/werner/Public/repo/github.com/Matgenix/jobflow-remote.git/src/jobflow_remote/jobs/run.py", line 69, in run_remote_job             │
│                  response = job.run(store=store)                                                                                                             │
│                             ^^^^^^^^^^^^^^^^^^^^                                                                                                             │
│                File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/jobflow/core/job.py", line 604, in run                    │
│                  response = function(*self.function_args, **self.function_kwargs)                                                                            │
│                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                            │
│                File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/common/jobs/elastic.py", line 245, in fit_elastic_tensor │
│                  return ElasticDocument.from_stresses(                                                                                                       │
│                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                       │
│                File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/common/schemas/elastic.py", line 267, in from_stresses   │
│                  raw=result.voigt.tolist(), ieee_format=ieee.voigt.tolist()                                                                                  │
│                      ^^^^^^^^^^^^^^^^^^^                                                                                                                     │
│              AttributeError: 'list' object has no attribute 'tolist'                                                                                         │
│     remote = {'step_attempts': 0, 'process_id': '998', 'prerun_cleanup': False}                                                                              │
│ created_on = '2025-06-06 13:21'                                                                                                                              │
│ updated_on = '2025-06-06 14:08'                                                                                                                              │
│ start_time = '2025-06-06 14:08'                                                                                                                              │
│   end_time = '2025-06-06 14:08'                                                                                                                              │
│   metadata = {}                                                                                                                                              │
│    run_dir = '/home/werner/Desktop/std_vasp_slurm/21/1f/28/211f2834-2c16-4ed4-be09-6c59085abdfd_1'                                                           │
│    parents = ['485e627d-8e43-412a-994d-3fe6572b8d8d', '2615a673-a0c5-4805-9cc9-3acb49570594', '804865f9-d32e-4268-a623-e12d34425c59']                        │
│   priority = 0                                                                                                                                               │
│     worker = 'vasp_slurm'                                                                                                                                    │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

See below for the related discussions:

https://www.vasp.at/forum/viewtopic.php?p=31597#p31597
Neraaz/HTESP#1 (comment)

Regards,
Zhao

[hongyi-zhao]

Below is a minimal working example for this issue:

from pymatgen.core.structure import Structure
from atomate2.vasp.flows.elastic import ElasticMaker

structure = Structure(
    lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
    species=["Mg", "O"],
    coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)

phonon_flow = ElasticMaker(order=3).make(
    structure=structure, conventional=True
)

from jobflow_remote import submit_flow

ncores = 16
resources = {"nodes": 1, "partition": "batch", "mem":"80g", "time": "2400:00:00", "ntasks": ncores}


submit_flow(
#    bandstructure_flow, worker="my_worker", resources=resources, project="my_project"
    phonon_flow, worker="vasp_slurm", resources=resources, project="std", exec_config="vasp_slurm"
)

# run the flow
#$ jf -p std runner start
# watch the flow's status of execution:
#$ watch -n 1 "jf -p std job list"

Show the bug:

werner@x13dai-t:~/Public/repo/github.com/materialsproject/atomate2.git$ git log -1
commit e22dccf367785db7be54f128ae6b43afcbd631cf (HEAD -> main, origin/main, origin/HEAD)
Author: Aaron Kaplan <33381112+esoteric-ephemera@users.noreply.github.com>
Date:   Fri Jun 13 15:50:48 2025 -0700

    ML forcefields bug fixes (#1220)
    
    * ff bug fixes
    
    * make filter_kwargs an optional kwarg for AseRelaxer
    
    * temporarily disable ASE energy checks - runs are inconsistent even with same initial input
    
    * skip optimizer instantiation when steps <= 1 in ase/mlff flows
    
    * ensure lj test runs one step
    
    * bump ase bc of inconsistent behavior between 3.24 and 3.25
    
    * bump emmet-core

$ jf -p std job info 6620f48c-fc76-46c5-974a-74b67ee0f60b
The selected project is std from config file /home/werner/.jfremote/std.yaml
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│      db_id = '691'                                                                                                                                           │
│       uuid = '6620f48c-fc76-46c5-974a-74b67ee0f60b'                                                                                                          │
│      index = 1                                                                                                                                               │
│       name = 'fit_elastic_tensor'                                                                                                                            │
│      state = 'FAILED'                                                                                                                                        │
│      error = Traceback (most recent call last):                                                                                                              │
│                File "/home/werner/Public/repo/github.com/Matgenix/jobflow-remote.git/src/jobflow_remote/jobs/run.py", line 69, in run_remote_job             │
│                  response = job.run(store=store)                                                                                                             │
│                             ^^^^^^^^^^^^^^^^^^^^                                                                                                             │
│                File "/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/jobflow/core/job.py", line 604, in run                    │
│                  response = function(*self.function_args, **self.function_kwargs)                                                                            │
│                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                            │
│                File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/common/jobs/elastic.py", line 245, in fit_elastic_tensor │
│                  return ElasticDocument.from_stresses(                                                                                                       │
│                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                       │
│                File "/home/werner/Public/repo/github.com/materialsproject/atomate2.git/src/atomate2/common/schemas/elastic.py", line 267, in from_stresses   │
│                  raw=result.voigt.tolist(), ieee_format=ieee.voigt.tolist()                                                                                  │
│                      ^^^^^^^^^^^^^^^^^^^                                                                                                                     │
│              AttributeError: 'list' object has no attribute 'tolist'                                                                                         │
│     remote = {'step_attempts': 0, 'process_id': '1301', 'prerun_cleanup': False}                                                                             │
│ created_on = '2025-06-14 15:43'                                                                                                                              │
│ updated_on = '2025-06-14 15:51'                                                                                                                              │
│ start_time = '2025-06-14 15:51'                                                                                                                              │
│   end_time = '2025-06-14 15:51'                                                                                                                              │
│   metadata = {}                                                                                                                                              │
│    run_dir = '/home/werner/Desktop/std_vasp_slurm/66/20/f4/6620f48c-fc76-46c5-974a-74b67ee0f60b_1'                                                           │
│    parents = ['b3922361-a2ad-462d-b071-80c75202af84', '155e45a9-84c6-4989-8d70-ba156bd8caaf', 'b4d6ff01-a28d-4e31-8737-40dd0e44eb6a']                        │
│   priority = 0                                                                                                                                               │
│     worker = 'vasp_slurm'                                                                                                                                    │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

[hongyi-zhao]

See https://matsci.org/t/bug-atomate2-failed-to-compute-the-3rd-order-elastic-tensor/64029 for the related discussion.