Hi,

I recently create the pychemia conda forge package, now it is possible to install PyChemia via:

conda install -c conda-forge pychemia

I was wondering if one of the core developers is interested in joining me in maintaining the package.

Best,

Jan

Dear Developers,

I am trying to install pychemia by

pip3 install pychemia --user

But it fails with following errors. Any help is appreciated.

ERROR: Complete output from command python setup.py egg_info: ERROR: Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-rd5hvw21/pychemia/setup.py", line 141, in data = write_version_py() File "/tmp/pip-install-rd5hvw21/pychemia/setup.py", line 89, in write_version_py release_data, FULLVERSION, GIT_REVISION = get_version_info() File "/tmp/pip-install-rd5hvw21/pychemia/setup.py", line 47, in get_version_info rf = open('setup.json') FileNotFoundError: [Errno 2] No such file or directory: 'setup.json' Using Cython: True ---------------------------------------- ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-rd5hvw21/pychemia/

Thanks,

Best \Alex

Dear Guillermo,

Since setup.py already compiles the shared library required for lennardjones utilities for both cython and non-cython, this is unnecessary. It would be useful in the case that the shared library is not compiled and the import from the .pyx file needed to be imported directly without any compilation whatsoever.

With the current setup.py, keeping the .pyx and .c in the distribution package will make sure it will work when both cython is present and not present.

Best, Uthpala

Hello Guillermo,

I added the lines: import pyximport pyximport.install()

to init.py and lj.py in pychemia/code/lennardjones to fix an import error that occurs when installing PyChemia with pip.

Best, Uthpala

… outcar, added writing to text and returning dict to DensityOfStates object

1. Created VaspXML object as a CodeOutput object. a lot of features was added such as total,projcted and parametric density of states.
2. fixed a bug in reading outcar energies
3. added writing to text and returning dict to DensityOfStates object

This update allows the repeating order in atoms in POSCAR to be conserved.

For example:

Sr V O 1.0 3.8465199999999999 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.8465199999999999 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.8465199999999999 Sr V Sr O 1 1 1 3 Direct 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.0000000000000000 0.5000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.0000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000

Here the order Sr, V, Sr, O will be conserved when using the structure to generate POTCARs and POSCARs for kgrid, encut convergence and relaxation with PyChemia. Otherwise, it reverts to Sr, V, O ignoring the order of the repetition.

This is helpful for performing calculations for heterostructures where atoms in layers are ordered separately. The order of the POTCAR concatenation will follow this too.

-Uthpala

This update allows the repeating order in atoms in POSCAR to be conserved.

For example:

Sr V O 1.0 3.8465199999999999 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.8465199999999999 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.8465199999999999 Sr V Sr O 1 1 1 3 Direct 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.0000000000000000 0.5000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000 0.5000000000000000 0.0000000000000000 0.0000000000000000 0.5000000000000000 0.5000000000000000

Here the order Sr, V, Sr, O will be conserved when using the structure to generate POTCARs and POSCARs for kgrid, encut convergence and relaxation with PyChemia. Otherwise, it reverts to Sr, V, O ignoring the order of the repetition.

This is helpful for performing calculations for heterostructures where atoms in layers are ordered separately. The order of the POTCAR concatenation will follow this too.

-Uthpala

changed the free energy in the convergence to free energy per atom. Also fixed the bug with kpoint converges best kpoint grid. previously it was taking the last calculated kgrid as the best kgrid.

chaged La and Ac group to 'd' in pychemia/utils/periodic as they don't have f electrons. I hope I'm write

Be it composition- or structure-based, could you point to a place in the docs or provide an example that follows the general idea of:

from pychemia import Discover()
mdl = Discover()
mdl.fit(X_train)
next_experiment = mdl.suggest_next_experiment()

I'm hoping to be able to compare PyChemia with mat_discover.

Hello Guillermo,

In some of my structural relaxation I wanted to keep a lower EDIFF value so I added this in relax.py to use the EDIFF provided by the user in the INCAR. If not provided it will use the default value of EDIFF=1E-04.

I simply changed:

     # How to change EDIFF
        if vj.input_variables["EDIFF"] > -0.01 * vj.input_variables["EDIFFG"]:
            vj.input_variables["EDIFF"] = round_small(
                -0.01 * vj.input_variables["EDIFFG"]
            )
        else:
                vj.input_variables["EDIFF"] = 1e-4

to

        # How to change EDIFF
        if vj.input_variables["EDIFF"] > -0.01 * vj.input_variables["EDIFFG"]:
            vj.input_variables["EDIFF"] = round_small(
                -0.01 * vj.input_variables["EDIFFG"]
            )
        else:
            if self.extra_vars["EDIFF"]:
                vj.input_variables["EDIFF"] = self.extra_vars["EDIFF"]
            else:
                vj.input_variables["EDIFF"] = 1e-4

If you think it's something that is useful please merge it and add it to pip.

Thank you,

Best, Uthpala

Hi, I am haidi. I feel the code framework of pychemia is the best one among all CSP software i know. But more thing need to be done to make it user friendly and high effiency. I have add some code into it , would you please open a devel branch for developing ?