ectoolkits.analysis.atom_density module#

class ectoolkits.analysis.atom_density.AtomDensity(inp)[source]#

Bases: object

get_all_z() → array[source]#

get the z coordinates of atoms along trajectory

_extended_summary_

Returns:

the z coordinates of atoms

Return type:

np.array

get_atom_density(param, idx_list)[source]#
get_ave_density(width_list)[source]#
get_idx_list(param)[source]#
get_idx_list_all(param)[source]#
get_idx_list_manual(param)[source]#
get_surf1_z_list() → array[source]#

calculate the surface 1 average position

_extended_summary_

Returns:

axis 0: traj

Return type:

np.array

get_surf2_z_list() → array[source]#

calculate the surface 2 average position

_extended_summary_

Returns:

axis 0: traj

Return type:

np.array

get_unit_conversion(param, dz)[source]#
get_water_cent_list() → array[source]#
plot_density(sym=False)[source]#
run()[source]#
water_O_idx()[source]#
class ectoolkits.analysis.atom_density.Density(atomgroup, **kwargs)[source]#

Bases: AnalysisBase

Calculate the density profile of a group of atoms along the z-axis for interface systems

get_unit_conversion()[source]#
ectoolkits.analysis.atom_density.analysis_run(args)[source]#