tomswinburne / blasa Goto Github PK

Also after the paper is accepted I would be interested to running an thermodynamic integration from the MD code to DFT or an interatomic potential - basically the work of Albert. By now we already have a class for the Hessian constructed from the dynamical matrix https://github.com/pyiron/pyiron/blob/master/pyiron/thermodynamics/hessian.py so we should be able to construct a similar class for the combination of longitudinal and transversal potential. That would allow us to integrate the method in pyiron as a quick way to calculate free energies.

I have set the output folder from a new parameter dump_folder in input.json

However, the output folder is also in Snakefile

Can we set the folder name in Snakefile from input.json?

Once the repository is publicly available we can add a link to mybinder:

This is a public jupyter notebook service which is using the conda environment to create docker containers. If we do so it is maybe reasonable to also add the output files, for the MD calculation so people can execute the notebooks directly.

To be completed after submission!

When I execute the notebooks with Snakemake, I get:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-19-8ae13d1375a5> in <module>
----> 1 r = MarginalHist[:,0]
      2 bins=r.size
      3 
      4 H=JointHist
      5 

NameError: name 'MarginalHist' is not defined
NameError: name 'MarginalHist' is not defined

Simply because the histogram files are not written. I guess we should write them by default.

Best,

Jan

I had a quick discussion with Joerg about the current status of our repository. He suggested to add documentation to the input file - basically comments of what we already have in the README and to include one set of MD results so the users can directly start with the analysis without waiting for the execution of the MD code.

I was trying to create histograms for the second notebook but I got the following error:

Successfully installed bond-lattice-0.0.1
True 2 False
True 2 False
True 2 False
True 2 False
True 2 False
True 2 False
True 2 False
True 2 False
(60777003,)
True 2 False
MORSE LATTICE SYMM:
FCC: 1
CentralForce: 0
kT/[Energy]: 0.008617
a/a0:1
CorrelationType: 2
True 2 False
Histgram Captured 1036800000/1036800000 Bond Values ; 2< b_ll <3.45348
Traceback (most recent call last):
  File "mpi_sweep.py", line 118, in <module>
    cdata = lcomm.gather(CH, root=0)
  File "mpi4py/MPI/Comm.pyx", line 1262, in mpi4py.MPI.Comm.gather
  File "mpi4py/MPI/msgpickle.pxi", line 680, in mpi4py.MPI.PyMPI_gather
  File "mpi4py/MPI/msgpickle.pxi", line 685, in mpi4py.MPI.PyMPI_gather
  File "mpi4py/MPI/msgpickle.pxi", line 148, in mpi4py.MPI.Pickle.allocv
  File "mpi4py/MPI/msgpickle.pxi", line 139, in mpi4py.MPI.Pickle.alloc
SystemError: Negative size passed to PyBytes_FromStringAndSize
mpirun: Forwarding signal 18 to job
Will exit after finishing currently running jobs.
[Fri Jun 19 23:59:01 2020]