# HYDRONIUM_SHELL

Section to define the formation of a hydronium as a collective variable. Number of oxygens in the 1st shell of the hydronium. Adapted from Equation (3) in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318, i.e. omitting the cutoff function and summing only over the oxygens of water. [Edit on GitHub]

## Keywords

- HYDROGENS

- LAMBDA

- NH

- OXYGENS

- PM

- POH

- POO

- QM

- QOH

- QOO

- ROH

- ROO

## Keyword descriptions

HYDROGENS: integer[ ]

  Keyword can be repeated.

  Usage: HYDROGENS {integer} {integer} ..

  Specifies indexes of atoms building the coordination variable. Hydrogens of the water molecules. [Edit on GitHub]

LAMBDA: real = 1.00000000E+001

  Usage: LAMBDA {real}

  Specify the LAMBDA parameter in the hydronium function. [Edit on GitHub]

NH: real = 3.00000000E+000

  Usage: NH {real}

  Specifies the NH parameter in the M function. [Edit on GitHub]

OXYGENS: integer[ ]

  Keyword can be repeated.

  Usage: OXYGENS {integer} {integer} ..

  Specifies indexes of atoms building the coordination variable. Oxygens of the water molecules. [Edit on GitHub]

PM: integer = 8

  Aliases: EXPON_NUMERATOR

  Usage: pM {integer}

  Sets the value of the numerator of the exponential factor in the M function. [Edit on GitHub]

POH: integer = 6

  Aliases: EXPON_NUMERATORB

  Usage: pOH {integer}

  Sets the value of the numerator of the exponential factor in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]

POO: integer = 6

  Aliases: EXPON_NUMERATORA

  Usage: pOO {integer}

  Sets the value of the numerator of the exponential factor in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]

QM: integer = 16

  Aliases: EXPON_DENOMINATOR

  Usage: qM {integer}

  Sets the value of the denominator of the exponential factor in the M function. [Edit on GitHub]

QOH: integer = 12

  Aliases: EXPON_DENOMINATORB

  Usage: qOH {integer}

  Sets the value of the denominator of the exponential factor in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]

QOO: integer = 12

  Aliases: EXPON_DENOMINATORA

  Usage: qOO {integer}

  Sets the value of the denominator of the exponential factor in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]

ROH: real = 3.00000000E+000 [bohr]

  Usage: ROH {real}

  Specifies the rc parameter in the coordination function: number of hydrogens per water molecule. [Edit on GitHub]

ROO: real = 3.00000000E+000 [bohr]

  Usage: ROO {real}

  Specifies the rc parameter in the coordination function: number of oxygens per water oxygen. [Edit on GitHub]