Dissociation degree analysis

Dissociation degree affects the interfacial dipoles, hence, the band alignments of semiconductor-electrolyte interfaces. To calculate the dissociation degree for a given trajectory, we implemented the classes CNState and DisDeg, which are briefly introduced below.

The CNState Class

Analysis

The necessity of dissociation degree is the coordination number of atoms. For example, the dissociation degree of interfacial water molecules is the ratio of the number of adsorbed water molecules to the dissociated water molecules(usually the adsorbed OH groups). Therefore, one needs to count the coordination number of the adsorbed oxygen atoms for identifying the OH groups, then calculates the dissociation degrees. To this end, the CNState class calculates the coordination number of a list of atoms for a given trajectory.

# First, read a trajectory using Universe. Do not forget add dimensions.
>>> from MDAnalysis import Universe
>>> xyzfile = "./tio2-water.xyz"
>>> cellpar = np.array([12.4, 11.238, 38.42, 90, 90, 90])
>>> u = Universe(xyzfile)
>>> u.dimensions = cellpar
# Second, use CNState class to analyze the trajectory
>>> from ectoolkits.analysis.disdeg import CNState
# O_idx_dw is the indexes of adsorbed oxygen atoms. You may obtained by yourself.
>>> O_idx_dw = [264, 267, 270, 273, 276, 279, 282, 285]
>>> cnstate = CNState(atomgroup=u.atoms,
>>>          center_atom_idx=np.array(O_idx_dw),
>>>          coordinated_elements=['H'],
>>>          max_cutoff=1.2)
>>> cnstate.run()
>>> cnstate._cnstate
array([[2, 2, 2, 2, 2, 2, 1, 2],
[2, 2, 2, 2, 2, 2, 1, 2],
[2, 2, 2, 2, 2, 2, 1, 2],
[2, 2, 2, 2, 2, 2, 1, 2],
[2, 2, 2, 2, 2, 2, 1, 2]])

The result is an array with shape of (num_frames, num_center_atom_idx). Each row of the array is the coordination numbers of center_atoms with respect to Hydrogen atoms. If one would like to calculate coordination numbers with respect to other elements, such as, “C”, “N”, one can set coordinated_elements as ["C", "N"] etc.

Plot CNStates

After finishing the analysis, the method cnstate.plot(cn_list=[0, 1, 2, 3]) could quickly plot the percentages of all coordination number states.

Save CNStates

The results are saved to npy files using the method cnstate.save_cnstate(filename='cn.npy')

Restore the Analysis

CNState Class could also be restored from the cn.npy file using the method CNState.read_cnstate_from(npyfile='cn.npy')

The DisDeg Class

The DisDeg class adds extra features to calculate dissociation degree, such as, get_disdeg,save_disdeg, and plot_disdeg. The DisDeg is inherited from the CNState class, which means that the initialization is the same as CNState.

Analysis

# First, read a trajectory using Universe. Do not forget add dimensions.
>>> from MDAnalysis import Universe
>>> xyzfile = "./tio2-water.xyz"
>>> cellpar = np.array([12.4, 11.238, 38.42, 90, 90, 90])
>>> u = Universe(xyzfile)
>>> u.dimensions = cellpar
# Second, use CNState class to analyze the trajectory
>>> from ectoolkits.analysis.disdeg import DisDeg
# O_idx_dw is the indexes of adsorbed oxygen atoms. You may obtained by yourself.
>>> O_idx_dw = [264, 267, 270, 273, 276, 279, 282, 285]
>>> disdeg = DisDeg(atomgroup=u.atoms,
>>>          center_atom_idx=np.array(O_idx_dw),
>>>          coordinated_elements=['H'],
>>>          max_cutoff=1.2)
>>> disdeg.run()
# Third, obtain the dissociation degree
# Assign the coordination numbers of 2 and 3 to the intact water molecules and the coordination numbers of 0 and 1 to the dissociated water molecules.
# one can customize the cn_list_no_dis and cn_list_dis
cn_list_no_dis= [2, 3]
cn_list_dis= [0, 1]
>>> disdeg.get_disdeg(cn_list_no_dis=cn_list_no_dis, cn_list_dis=cn_list_dis)

Plot DisDeg

After finishing the analysis, the method disdeg.plot_disdeg() could quickly plot the percentages of non-dissociated and dissociated degree.

Save DisDeg

The results are saved to npy files using the method disdeg.save_disdeg(filename='disdeg.npy')