Atomic systems

fix_no_of_elements (integer)

The number of elements in the input list. This list should be exhaustive and should contains all the elements of the database. This number should be equal to the numbers of chemical symbols (and correspondings weigths in chemical_elements and weigth_per_element or weigth_per_element_3ch)

Default no_of_elements=1

chemical_elements (character(len=80))

The chemical symbols of the elements contained in the database. The elements should be among the 109 elements of the periodic table. E.g. for there elements should be like that: chemical_elements= ” Fe W Re ”. The custom weigths associated with those elements are defined in weigth_per_element.

Default chemical_elements= ” ”

weighted (logical)

Take into accout the chemical type of atoms. It can be weighted=.true. or weighted=.false.. If .true. the descriptors are built using the regular geometric channel and a supplementary channel for descriptors both with exactelly the same dimension. The chemical weights for atoms are controlled with the option weight_per_element or weighted_auto.

Default weighted= .false.

weighted_3ch (logical)

Take into accout the chemical type of atoms: the 3rd channel. It can be weighted_3ch=.true. or weighted_3ch=.false.. If .true. the descriptors are built using the regular geometric channel, the second channel and a supplementary third channel. The chemical weights for atoms are controlled with the option weight_per_element_3ch or weighted_auto.

Default weighted_3ch = .false.

weighted_auto (logical)

If this option is valid .true. the chemical weights are chosen automatically by MILADY for weight_per_element and weight_per_element_3ch, if necessary. If this option is .true. the current value of weight_per_element and weight_per_element_3ch are redefined with the default values.

For the second channel the weighted_auto=.true gives for the weigth for the species \(w_I\) as:

\[w_I^{\textrm{2nd ch}} = \frac{ \sqrt{m_I} \sqrt{N_{\textrm{all species} } } }{ \sqrt{ \sum_{J \in \textrm{all species}} m_J } }\]

For the third channel the weighted_auto=.true assign the weigth for the species \(w_I\) as:

\[w_I^{\textrm{3rd ch}} = \frac {Z_I N_{\textrm{all species} } } {\sum_{J \in \textrm{all species}} Z_J}\]

Default weighted_auto = .true.

chemical_elements_invisible (character(len=80))

The chemical symbols of the elements that will be invisible by the other atoms i.e. any information of then will not be included in the computation of descriptors.

Default chemical_elements_invisible= ” ”

weight_per_element (character(len=80))

The weigths associated with the chemical elements defined in the list chemical_elements.

This list should be formatted as: weight_per_element= ” 1.0 2.0 3.0 ” i.e. for the example given in the examle given above chemical_elements= ” Fe W Re ” the weigths are 1.0, 2.0 and 3.0, respectivelly.

For the particular case when the weight_per_element= ” ” is empty list the weight of the atoms of \(i^{th}\) type are automatically put proportional to square root of the mass of that type \(\sqrt(m_i)\) (see weighted_auto keyword section for the exact formulae).

Default weight_per_element= " "

weight_per_element_3ch (character(len=80))

The weigths associated with the chemical elements defined in the list chemical_elements. These weights define the accuracy of the 3rd channel.

This list should be formatted anf follows exactelly the same rules as weight_per_element.

For the particular case when the weight_per_element_3ch= ” ” is empty list the weight of the atoms of \(i^{th}\) type are automatically proportional to the atomic number \(Z_i\) (see weighted_auto keyword section for the exact formulae)

Default weight_per_element_3ch= " "