elcorto / pwtools Goto Github PK

Hey,

since I could not find any other contact I'll try like this:

I've been using your pwtools a lot for reading the dcd files produced by CP2K. Since it seems you're one of the few to have knowledge about the exact file format used by CP2K I am asking you:

Would you allow me to use your file format information from pwtools/dcd.py to implement a direct reader in ASE and PLAMS?

Your tool has been working fine for me now for a long time, but always skipping between modules creates some problems over time (not taking into account the inefficiency every time I read a dcd file). Since ASE is now a pretty well developed piece that a lot of people use, I would like it to be able to read CP2Ks dcd files natively there. If you're not happy with the licencing of PLAMS I can stick with ASE, that would already be a big help.

Thanks for considering!
Cheers,
Patrick

It seems that pip install -e used to build extensions, as discussed in #2. While investigating #4 we find that this is (no longer) the case. Only pip install calls python setup.py build_py which triggers make.

The line

crys.rpdf(coords, rmax=5.0, cell=cell, ...)

uses and older API that is no longer supported. It needs to be converted to using a Structure as input, where we build the latter using coords, cell and symbols.

This is not critical since the generated data is part of the repo in test/files/rpdf/, just has to be fixed if new data is to be generated.

Dear developers,
thanks for the very interesting code. I have some questions:
As far as I understood,pwtools yields the normalized power densities, while sometimes we would need unnormalized one. would you provide some details how the code can be modified to yield such unnormalized power density?

As the second request, I am wondering, are there some strightforward way/examples for pwtools users who are not experts in python (like myself) to get spectral power density (unnormalized) from CP2K generated velocity xyz file which has a structure like the one bellow? (first column is the atomic labels and the next columns are xyz components of velocities).
Thanks in advance and best regards,
Amin
####################
the sample CP2K velocity output
192
i = 0, time = 0.000, E = -368.9974887553
O 0.0000886641 -0.0000911669 -0.0001021906
H -0.0002956863 -0.0004934272 -0.0007190413
H 0.0014825795 -0.0010745990 0.0005481207
O 0.0003332422 -0.0001536368 0.0000391431
H 0.0004673263 -0.0005194924 0.0010338811
H 0.0000057824 -0.0005089213 0.0006525857
O -0.0002933685 -0.0002304744 -0.0001533996
H -0.0008513052 0.0007130663 -0.0006748945

hi

i tried installing the one go installation, but it did not make the fortran extension automatically.

after reading through the rest of the installation page i was able to make the extensions and load the package

i wonder if this is a bug in the installation script worth reporting

details below:

i installed via git clone and pip install .

then i was getting the error

from pwtools import pydos                                                                                                                                       
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-79e08d090104> in <module>
----> 1 from pwtools import pydos

~/pwtools/pwtools/pydos.py in <module>
     17 from scipy.fftpack import fft
     18 from scipy.signal import convolve, gaussian
---> 19 from pwtools import constants, _flib, num
     20 from pwtools.verbose import verbose
     21 from pwtools.signal import pad_zeros, welch, mirror

~/pwtools/pwtools/num.py in <module>
      8     bisplev, splev, splrep
      9 from scipy.integrate import simps, trapz
---> 10 from pwtools import _flib
     11 import warnings
     12 ##warnings.simplefilter('always')

ImportError: cannot import name '_flib'

the dependency test seemed fine

$ python pwtools/test/check_dependencies.py 
required packages:
    numpy ... ok
    scipy ... ok
    ase ... ok
    pyspglib ... ok
    CifFile ... ok
    h5py ... ok
    nose ... ok
    matplotlib ... ok
    sphinx ... ok
    numpydoc ... ok
optional executables:
    eos.x ... NOT FOUND

then i went into src and ran make following hints from
( http://elcorto.github.io/pwtools/written/install.html )

now it seems to work :)

I'm trying to install Pwtools on Windows and I'm having a hard time

I've installed Pwtool using

git clone https://github.com/elcorto/pwtools.git
pip install -e pwtools

Everything went well, at least no errors. But when I try to run

from pwtools import io
from ase.visualize import view

traj = io.read_cp2k_md('zeo_opti.log')
view(traj)`

I get the following error

cannot import name '_flib' from 'pwtools' (c:\users\cb\pwtools\pwtools\__init__.py)

Is there a way to troubleshoot this?