pychemia.code.octopus package¶

Set of classes and functions to manipulate

OCTOPUS ‘inp’ input files

pychemia.code.octopus.coordinates(dirname)[source]¶

Reads the ‘coordinates’ file and extracts its data as the numpy arrays ‘positions’,’velocities’ and ‘forces’.

Each of those arrays has the following structure:

Args:

dirname:: The path were the octopus data is produced

Returns:

natom:: Number of atoms
iterations:: Array with iterations
times:: Array with times
positions:: positions[0:MaxIteration,0:natom,0:3]
velocities:: velocities[0:MaxIteration,0:natom,0:3]
forces:: forces[0:MaxIteration,0:natom,0:3]

pychemia.code.octopus.energy(dirname)[source]¶

Reads the ‘energy’ file and extracts its data as the numpy arrays ‘Total’,’Kinetic’, etc.

Args:

dirname:: The directory where the octopus data was produced

Returns:

iterations:: numpy array of iterations recorded
times:: numpy array with time for each iteration
energy_dict:: dictionary of numpy arrays with values of Total, Kinetic (ions), Ion-Ion, Electronic, Eigenvalues, Hartree, Int[n v_xc], Exchange and Correlation

Submodules¶

pychemia.code.octopus.analysis module¶

Useful routines to get physical data from octopus TD runs

pychemia.code.octopus.analysis.change_kinetic_energy(dirname, iteration=None)[source]¶

Change of Kinetic energy respect to initial value

Parameters:	dirname – (str) Directory to read iteration – (int) Iteration number to read
Returns:

pychemia.code.octopus.analysis.charge_in_sphere(dirname, iteration=None, radius=4.5, spin=None)[source]¶

Get the value at a given index of the data stored in the NetCDF file

Parameters:	dirname – (str) Directory to read iteration – (int) Number of iteration to read radius – (float) Radius of the sphere to integrate spin – (int) Spin contribution to read
Returns:

pychemia.code.octopus.analysis.deflection(dirname, iteration=None)[source]¶

Get the deflection angle respect to the initial velocity for all the atoms and for a given iteration and spin.

Args:

dirname:: The directory where the octopus data was produced
iteration:: Iteration to make the difference, if absent the last iteration will be taken

Returns:

A numpy array for the number of atoms with the Hirsfeld charges

pychemia.code.octopus.analysis.dipolx_in_sphere(dirname, iteration=None, radius=4.5, spin=None)[source]¶

Get the value at a given index of the data stored in the NetCDF file

Parameters:	dirname – (str) Directory to read iteration – (int) Number of iteration to read radius – (float) Radius of the sphere to integrate spin – (int) Spin contribution to read
Returns:

pychemia.code.octopus.analysis.get_last_iteration(dirname)[source]¶

Get the last “td.xxxxxxx” found in dirname

Parameters:	dirname – (str) Directory to take last information
Returns:

pychemia.code.octopus.analysis.hirshfeld(dirname, iteration=None, spin=None)[source]¶

Get the Hirshfeld charge analysis for all the atoms comparing for a given iteration and spin.

Args:

dirname:: The directory where the octopus data was produced
iteration:: Iteration to make the difference, if absent the last iteration will be taken
spin:: Integer with the spin for which the data will be taken, if absent the addition of both spins will be returned

Returns:

A numpy array for the number of atoms with the Hirsfeld charges

pychemia.code.octopus.analysis.magnitude_velocity(dirname, iteration=None)[source]¶

Magnitude of velocity for each atom

Parameters:	dirname – (str) Directory to analyse velocities iteration – (int) Number of iteration to use
Returns:

pychemia.code.octopus.analysis.value_in_sphere(dirname, keys, iteration=None, radius=4.5, spin=None)[source]¶

Compute the value of a certain scalar quantity inside a sphere of a given radius

Parameters:	dirname – (str) Directory to read keys – (list) Variables to read the scalar quantity iteration – (int) Number of iteration to read radius – (float) Radius of the sphere to integrate spin – (int) Spin contribution to read
Returns:

pychemia.code.octopus.input module¶

Routines anc Classes to manipulate Octopus Inputs

class pychemia.code.octopus.input.InputVariables(filename=None)[source]¶

Bases: object

Manipulate an octopus input file

write(filename)[source]¶

Write an input dictionary into a file the variables are sort by kind and written in their respective place

Parameters:	filename – (str) Filename for the octopus input that will be created

class pychemia.code.octopus.input.OpenDX(filename)[source]¶

Bases: object

Manipulate the OpenDX file generated by octopus

integrate_x()[source]¶: Compute the Integral in the X direction

pychemia.code.octopus.input.execute(basedir, num_threads=1, num_procs=2)[source]¶

Call octopus in parallel with a given number of threads and MPI process

Parameters:	basedir – (str) Working directory for execution num_threads – (int) Number of OpenMP Threads to use num_procs – (int) Number of MPI processes to create

pychemia.code.octopus.input.get_vars()[source]¶: Get a list of all the variables in octopus

pychemia.code.octopus.merge module¶

class pychemia.code.octopus.merge.OctopusOccupancies(basedir)[source]¶

Bases: object

write(filename)[source]¶

class pychemia.code.octopus.merge.OctopusRestart(basedir)[source]¶: Bases: object

class pychemia.code.octopus.merge.OctopusStates(basedir)[source]¶

Bases: object

write(filename)[source]¶

class pychemia.code.octopus.merge.OctopusStatesFile(basedir)[source]¶: Bases: object

class pychemia.code.octopus.merge.OctopusWavefunctions(basedir)[source]¶

Bases: object

write(filename)[source]¶

pychemia.code.octopus.merge.merge_restart(dir1, dir2, dest, mksym1=True, mksym2=False)[source]¶: Merge the restart directories (dir1 and dir2) into the destination (dest)

pychemia.code.octopus.merge.oct_merge(res1, res2, basedir, mksym1, mksym2)[source]¶