Introduction

from py2sambvca import p2s

import numpy as np

Potential setup for the program. At this point no graphical interface is implemented.

For remove_H, orient_z and write_surf_files only the values 0 and 1 are possible

nhc_p2s = p2s(
    xyz_filepath="../test/data/nhc.xyz",
    sphere_center_atom_ids=[22],
    z_ax_atom_ids=[5],
    xz_plane_atoms_ids=[1],
    atoms_to_delete_ids=None,
    sphere_radius=3.5,
    displacement=0.0,
    mesh_size=0.10,
    remove_H=True,
    orient_z=True,
    write_surf_files=True,
)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Input In [2], in <cell line: 1>()
----> 1 nhc_p2s = p2s(
      2     xyz_filepath="../test/data/nhc.xyz",
      3     sphere_center_atom_ids=[22],
      4     z_ax_atom_ids=[5],
      5     xz_plane_atoms_ids=[1],
      6     atoms_to_delete_ids=None,
      7     sphere_radius=3.5,
      8     displacement=0.0,
      9     mesh_size=0.10,
     10     remove_H=True,
     11     orient_z=True,
     12     write_surf_files=True,
     13 )

File ~/checkouts/readthedocs.org/user_builds/py2sambvca/conda/latest/lib/python3.9/site-packages/py2sambvca/py2sambvca.py:94, in py2sambvca.__init__(self, xyz_filepath, sphere_center_atom_ids, z_ax_atom_ids, xz_plane_atoms_ids, atoms_to_delete_ids, sphere_radius, displacement, mesh_size, remove_H, orient_z, write_surf_files, path_to_sambvcax, verbose)
     92 self.write_surf_files = int(write_surf_files)
     93 # open the xyz file, read the data
---> 94 with open(xyz_filepath, "r") as file:
     95     self.xyz_data = file.readlines()
     97 # assign the path to the calculator

FileNotFoundError: [Errno 2] No such file or directory: '../test/data/nhc.xyz'

The run_range function is designed to quickly scan a range of radii values.

df_test = nhc_p2s.run_range(2, 4)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [3], in <cell line: 1>()
----> 1 df_test = nhc_p2s.run_range(2, 4)

NameError: name 'nhc_p2s' is not defined

df_test.plot("r", "buried_volume")

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [4], in <cell line: 1>()
----> 1 df_test.plot("r", "buried_volume")

NameError: name 'df_test' is not defined