nappy -- NAP PYthon utilities¶

nappy is a set of python utilities. It is contained in nap/nappy/ directory, but currenly it is not exactly a python module. Users may have to use those utilities by calling them directly from the shell.

Setup¶

See Install.

Quick start¶

`napsys.py` command (older than rev220118 or v0.10.12)¶

Once nappy is installed correctly, you can use napsys.py as an utility command.

It is recommended to make symlink of /path/to/nap/nappy/napsys.py in some directory lised in your PATH environment, so that it is found by just typing napsys.py.

The following commend will give you some information about the system described in pmdini.

$ napsys.py analyze /path/to/nap/example/test_W/pmdini

If you want to convert the file between some formats available in nappy, the following command convert infile to the format guessed from the filename outfile, such as POSCAR, dump_0, or pmd_0.

$ napsys.py convert infile outfile

To show the help message,

$ napsys.py -h

Since rev220118 or v0.10.12¶

Once nappy is installed using pip as described in the Install section, napsys is placed in the command search scope and you will be able to use napsys without making symlink to napsys.py. Thus, it is recommended.

nappy on jupyter or ipython¶

Some modules nappy can be called within jupyter notebook or ipython, for example,

import nappy
from nappy.napsys import analyze
nsys = nappy.io.read('/path/to/nap/examples/pmd_W/pmdini')
print(nsys)

Above code will show the following result.

 a1 vector = [    10.254,      0.000,      0.000]
 a2 vector = [     0.000,      9.613,      0.000]
 a3 vector = [     0.000,      0.000,      9.613]
 a =     10.254 A
 b =      9.613 A
 c =      9.613 A
 alpha =   90.00 deg.
 beta  =   90.00 deg.
 gamma =   90.00 deg.
 volume=    947.617 A^3
 number of atoms   =  54

Read and write files¶

To read atomic structures from files of several formats,

import nappy
nsys = nappy.io.read('POSCAR')
nsys = nappy.io.read(fname='structure.dat', format='xsf')

Current available formats are:

pmd: file format specific for pmd program
POSCAR: VASP POSCAR file
dump: LAMMPS dump file
xsf
akr: file format for Akira viewer

And to write the structure to a file,

import nappy
nappy.io.write(nsys,'POSCAR')
nappy.io.write(nsys,'pmdini')
nappy.io.write(nsys,'dump')

The write function will parse file name and choose appropriate file format from the name.

Convert to/from ASE atoms¶

Conversion between nappy.napsys.NAPSystem object and ASE atoms object can be done with the following code,

import nappy
nsys = nappy.io.from_ase(atoms)
atoms = nsys.to_ase_atoms()

Call pmd from python¶

If pmd_wrapper was compiled using f2py, pmd can be called from python as following.

import nappy
nsys = nappy.io.from_ase(atoms)
pmd = nappy.pmd.PMD(nsys)  # <== Set napsys as an atomic system used in pmd
pmd.load_inpmd()           # <== assuming there is in.pmd file in the working directory
pmd.run()                  # <== Run MD
nsys = pmd.get_system()    # <== Get the new system that contains MD results
nsys.get_potential_energy()
  -11389.735335774534

nappy.pmd.PMD() class provides some functions for performing pmd using napsys object. PMD assumes that there are some input files, e.g. in.params.XXX used to perform pmd, in the working directory.

Viewing the system on jupyter notebook¶

The nappy can visualize the system easily on jupyter notebooks. By default, the nappy uses the Py3Dmol as a backend and it should be installed.

nsys.view()

It is not recommended to visualize the system with a huge number of atoms. Use other visalization apps instead.