Properties

• Output <number>

  At output level $>=$ 5, type line(s) with some data (time step, energies, etc) each <number> of steps

  Default: 1

• Serie_average <number>

  Compute and remember intermediate averages over series of <number> steps

  Default: 10000

• Average_from <number>

  Begin final averaging over series (see Serie_average keyword) from series with the given <number>

• Average_internal yes/no

  Whether to compute average values of all bond lengths, angles and their energies

  Default: no

• Dump_XMOL yes/no

  Dump the final configuration in ``XMOL'' format

  Default: no

• Trajectory <format> <step> <num_conf> <list>

  Dump trajectory.

  <format> may be one of:

  bincrd - binary with coordinates only

  binvel - binary with coordinates and velocities

  asccrd - ACSII (XMOL-format) with coordinates only

  ascvel - ACSII (XMOL-format) with coordinates and velocities

  <step> is time interval (in femtoseconds) between the configurations saved in the trajectory file

  <num_conf> - number of configurations in each trajectory file. After filling <num_conf> configuration in a trajectory file, the program begins to write configurations in the next file. Trajectory files acquire extensions .001, .002, .003, etc

  <list> - list (in the form of numbers 0 or 1 for each molecule type) which signals whether to include molecules of this type into trajectory. <list> may be set also to ``all'' (all molecules)

  Units for velocities in the trajectory file are Å/fs.

• Bond_list yes/no

  Generate list of all bonds and put it in file bond.list

  Default:no

• RDF_calc <restart_option> <RDFcutoff> <nbins>

  Calculate RDFs.

  <restart_option> may be one of the following

  RW - read restart rdf file and dump updated rdf-restart file

  RO - only read restart RDF file but do not dump updated rdf file

  (these two options have an effect only if simulation is continued from restart)

  WO - start a new collection of RDFs (that is, ignore restart file even if it is present) and dump a new RDF-restart file.

  NOR - do not read and do not write restart-RDF file

  <RDFcutoff> - Cutoff for RDF

  <nbins> - number of bins to compute RDFs

  This keyword must be followed by a description which RDFs need to be calculated. This part consists of the following lines (commentary symbols are allowed):

  <n> - number of RDFs

  followed by a list of atom pairs (site numbers) for RDFs. Symbol &n can be used for averaging of RDFs from several atom pairs. Such a group is counted as a single RDF.

  Note On-the-fly computation of RDF is obsolete and will be removed in future releases. Use rdf utility from the tranal suite.

• TCF_calc <restart_option> <N-steps> <jump>

  Calculate TCFs.

  <restart_option> may be one of the following

  RW - read restart TCF file and dump updated tcf-restart file

  RO - only read restart TCF file but do not dump updated tcf file

  (these two options have an effect only if simulation is continued from restart)

  WO - start new collection of TCFs (that is, ignore restart file even if it is present) and dump new restart TCF file

  NOR - do not read and do not write restart TCF file

  <N-steps> - number of steps to compute TCFs

  <jump> - number of (long) MD time steps for one step of TCF

  This means that TCF will be calculated with step ``dt*jump'' during ``dt*jump*<N-steps>'' time

  This keyword must be followed by a description which TCFs need to be calculated. This part consists of the following lines (commentary symbols are allowed):

  A line of 12 symbols ``0'', ``1'' or ``2'' which specify which of 12 types of TCFs are to compute:

    1 - velocity autocorellations
    2 - angular velocity autocorellations
    3 - 1 order Legendre polynom for dipole moment
    4 - 2 order Legendre polynom for dipole moment
    5 - 1 order Legendre polynom for reorintational tcf for a 
          specific vector
    6 - 2 order Legendre polynom for reorintational tcf for a 
          specific vector
    7 - X projection of velocity TCF
    8 - Y projection of velocity TCF
    9 - Z projection of velocity TCF
    10 - X projection of angular velocity TCF
    11 - Y projection of angular velocity TCF
    12 - Z projection of angular velocity TCF
  

  ``0'' means do not compute, ``1'' or ``2'' signals that this type of TCF must be computed. "2" can be specified for tcf 7-9 or 10-12, then tcf projections are calculated in the molecular principal coordinate system; otherwise (1) they are calculated in the laboratory's coordinate system

  If TCF of type 5 or 6 are given for computation, then two additional lines should be given which specify two atom number on each molecular type which define the unit vectors for reorientational TCF.

  Note. On-the-fly computation of TCF is obsolete and will be removed in future releases. TCF calculations are not parallelized and therefore not recommended for parallel computations. Use the trajectory analysis instead.

• End

  end of the input file. This line is compulsory