geom

geom calculates specific geometric parameters (i.e. bond distances, bond angles, and torsion angles) for a given species, reporting the average, minimum, and maximum values it finds, along with the standard deviation. It can be useful when a quick check on the 'rigidity' of the intramolecular structure is required. Either specific bonds, angles, and torsions may be specified on the command line, or a file containing the required data can be provided.

Related programs:

  • To calculate a single torsion angle histogram, see intratorsion.
  • To calculate a torsion angle formed between two species, see intertorsion.
  • To calculate a torsion angle map between two torsions, see intratorsion2.
  • To calculate average geometry parameters (not histograms), see geom.

Basic Usage

geom <HISTORYfile|CONFIGfile> <OUTPUTfile> <sp> <nframes>

Where:

  • <HISTORYfile|CONFIGfile> is the name of the DL_POLY HISTORY file or, alternatively, a DL_POLY CONFIG file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <sp> is the integer index of the target species
  • <nframes> specifies the number of frames to use in the calculation

Switches

-angle i j k

Adds calculation of the geometry of the angle i-j-k.

-bond i j

Adds calculation of the geometry of the bond i-j.

-data file

Specifies a file from which bond, angle, and torsion definitions should be read (in addition to any specified on the command line). The format of the file is to contain, one per line, "bond i j", "angle i j k", or "torsion i j k l" where i, j, k, l are atom indices.

-discard n

Discard n frames at the start of the trajectory.

-torsion i j k l

Adds calculation of the geometry of the torsion i-j-k-l.

-warnangle maxangle

Print a warning if any of the target bond angles exceed the supplied maxangle.

-warndist maxdist

Print a warning if any of the target bond distances exceed the supplied maxdist.

Output Files

No output files are produced. Minimum, maximum, average, and standard deviation values are printed to the screen.