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.

• 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. 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