Section MSD

• Loads an external trajectory file and performs analysis on the loaded snapshots.

• Section path: CP2K_INPUT / MOTION / MD / REFTRAJ / MSD

• This section cannot be repeated and can be optional.

• Subsections

  • DEFINE_REGION

• Keywords

  • SECTION_PARAMETERS
  • DISPLACED_ATOM
  • DISPLACEMENT_TOL
  • MSD_PER_KIND
  • MSD_PER_MOLKIND
  • MSD_PER_REGION
  • REF0_FILENAME

• Keyword descriptions

  SECTION_PARAMETERS
  	&MSD T
  	controls the activation of core-level spectroscopy simulations
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  DISPLACED_ATOM
  	DISPLACED_ATOM <LOGICAL>
  	Identify the atoms that moved from their initialposition of a distance larger than a given tolerance (see msd%displacement_tol).
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  DISPLACEMENT_TOL
  	DISPLACEMENT_TOL REAL
  	Lower limit to define displaced atoms
  	This optional keyword cannot be repeated and it expects precisely one real.
  	Default value: 0.00000000E+00
  	Default unit: [bohr]

  MSD_PER_KIND
  	MSD_PER_KIND <LOGICAL>
  	Set up the calculation of the MSD for each atomic kind
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  MSD_PER_MOLKIND
  	MSD_PER_MOLKIND <LOGICAL>
  	Set up the calculation of the MSD for each molecule kind.The position of the center of mass of the molecule is considered.
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  MSD_PER_REGION
  	MSD_PER_REGION <LOGICAL>
  	Set up the calculation of the MSD for each defined region.
  	This optional keyword cannot be repeated and it expects precisely one logical.
  	The lone keyword behaves as a switch to .TRUE.
  	Default value: .FALSE.

  REF0_FILENAME
  	REF0_FILENAME <CHARACTER>
  	Specify the filename where the initial reference configuration is stored.
  	This optional keyword cannot be repeated and it expects precisely one string.