mogroupumd / aimd Goto Github PK

@alberthxf
Xingfeng,
Let's do the following to make sure people use our code cite our papers. I think the key papers are:
Your NPJ CM, Your NC, and don't forget pymatgen (we still use a lot of their code).

Let's make this very explicit in the documentation, and tutorial. Let's also print a message for citatoin, every time the output is generated.

Hello,
I have installed the AIMD package in a virtual environment according to the instructions, but running either of the tests fails with the error:

Traceback (most recent call last):
File "/work/04391/tg836903/stampede2/atomate/atomate_env/bin/analyze_aimd", line 11, in
load_entry_point('aimd==0.1', 'console_scripts', 'analyze_aimd')()
File "/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/aimd-0.1-py3.6.egg/aimd/script/analyze_aimd.py", line 321, in main
File "/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/aimd-0.1-py3.6.egg/aimd/script/analyze_aimd.py", line 156, in Analyze_arrhenius
File "/work/04391/tg836903/stampede2/atomate/atomate_env/lib/python3.6/site-packages/aimd-0.1-py3.6.egg/aimd/diffusion.py", line 570, in get_conversion_factor
TypeError: 'ItemsView' object does not support indexing

Here are some comments: May overlap with Qiang's comments.

We need to Provide sample of submit.SLURM script, especially those with how to put thing in RUN folders. Seems this has confused some people (e.g. @shaolin055 ). Maybe we can also provide a sample submit folder with submit.slurm, INCAR, POSCAR, KPOINT (but we need to leave POTCAR blank).

We shall also provide a sample data so people can run it directly. Esp. with RUN_ folders. We may reuse the one for Toyota but make sure the other log generated by the Toyota code is removed.

Xingfeng,
We discussed a long time ago about the release of easy-install package to help resolving the dependence issue.
Let's also implement that.

I suggest we also output sigma*T with its error bound, as D and sigma.

For Arrhenius plot, let's also give an option of plotting sigma*T with proper error bounds (this can even be the default).

The drift correction in DiffusivityAnalyzer is automatically applied when calculating ionic diffusivity.
(1) Is it always required to include the drift correction for a trajectory?
(2) It makes sense to include it if all the ions moving in the same direction, but what if the ions are randomly moving around?
(3) If I want to calculate the diffusivities of different species in a same trajectory, should I use a same framework? For example, I have an AIMD calculated trajectory for LiAlO2. When using DiffusivityAnalyzer to calculate Li diffusivity, Al+O will be the framework and the drift correction will be calculated based on Al+O displacements. Now, I also want to calculate the O diffusivity. Should I use the same framework (Al+O), or use Li+Al as the framework ions and recalculate the drift correction? Using the same framework makes more sense to me as the calculated Li and O diffusivities are based on the same framework.

Hello, I run the test lapt with the command: analyze_aimd diffusivity Li+ RUN_ 10 13 3.2
The following error appears. Can anyone please help?

/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/inputs.py:1737: UserWarning: Ignoring unknown variable type SHA256
  warnings.warn(f"Ignoring unknown variable type {key}")
/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/inputs.py:1737: UserWarning: Ignoring unknown variable type COPYR
  warnings.warn(f"Ignoring unknown variable type {key}")
/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:1098: UserWarning: No POTCAR file with matching TITEL fields was found in /Users/thienbinh/Downloads/aimd-master/aimd/tests/test_files/latp_md/RUN_10
  warnings.warn(f"No POTCAR file with matching TITEL fields was found in {os.path.abspath(p)}")
/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:1098: UserWarning: No POTCAR file with matching TITEL fields was found in /Users/thienbinh/Downloads/aimd-master/aimd/tests/test_files/latp_md/RUN_11
  warnings.warn(f"No POTCAR file with matching TITEL fields was found in {os.path.abspath(p)}")
/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:1098: UserWarning: No POTCAR file with matching TITEL fields was found in /Users/thienbinh/Downloads/aimd-master/aimd/tests/test_files/latp_md/RUN_12
  warnings.warn(f"No POTCAR file with matching TITEL fields was found in {os.path.abspath(p)}")
/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:1098: UserWarning: No POTCAR file with matching TITEL fields was found in /Users/thienbinh/Downloads/aimd-master/aimd/tests/test_files/latp_md/RUN_13
  warnings.warn(f"No POTCAR file with matching TITEL fields was found in {os.path.abspath(p)}")
Traceback (most recent call last):
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/diffusion.py", line 566, in get_conversion_factor
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/pymatgen/core/periodic_table.py", line 1173, in from_string
    m = re.search(r"([A-Z][a-z]*)([0-9.]*)([+\-]*)(.*)", species_string)
  File "/Users/thienbinh/miniconda3/lib/python3.8/re.py", line 201, in search
    return _compile(pattern, flags).search(string)
TypeError: expected string or bytes-like object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/thienbinh/miniconda3/bin/analyze_aimd", line 33, in <module>
    sys.exit(load_entry_point('aimd==0.1', 'console_scripts', 'analyze_aimd')())
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/script/analyze_aimd.py", line 321, in main
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/script/analyze_aimd.py", line 72, in Analyze_VASP_MD
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/diffusion.py", line 430, in get_summary_dict
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/diffusion.py", line 228, in get_summary_dict
  File "/Users/thienbinh/miniconda3/lib/python3.8/site-packages/aimd-0.1-py3.8.egg/aimd/diffusion.py", line 568, in get_conversion_factor
Exception: Please provide oxidation decorated specie, like Li+, O2-

Another issue is that Github is not accessible in China. Though some knowledgable ones know how to get across the wall, we shall still do our best to make our code accessible to those researchers.
This may also affect our required dependence such as pymatgen.

Any idea?

The code now is really good. It is better for the respectful author to provide (output) the parameters (slope, intercept) of the fitted Arrhenius� relationship. Then users can depict the relationship elsewhere.