votca-csg-scripts 1.2.4-1 / usr / share / votca / xml / cginteraction.xml

<tags>
  <item>
    <name>name</name>
    <desc>
      Name of the interaction. The name can be arbitrary but should be unique. For bonded interactions, this
      should match the name specified in the mapping file.
    </desc>
  </item>
  
  <item>
   <name>type1</name>
    <desc>
      Only for non-bonded. **Bead** type 1 of non-bonded interaction.
    </desc>
  </item>
  <item>
   <name>type2</name>
    <desc>
      Only for non-bonded. **Bead** type 2 of non-bonded interaction.
    </desc>
  </item>
  <item>
   <name>bondtype</name>
    <desc>
      Internal alias for non-bonded and bonded, set automatically
    </desc>
  </item>
  <item>
    <name>min</name>
    <desc>
      lower bound of interval for potential table in which calculations are performed.
      Should be set based on reference distributions.
    </desc>
  </item>
  <item>
    <name>max</name>
    <desc>
      upper bound of interval for potential table in which calculations are performed.
      Should be set based on reference distributions.
    </desc>
  </item>
  <item>
    <name>step</name>
    <desc>
      step size of interval for potential table in which calculations are performed.
      If step site is too small, lots of statistics is needed ( long runs ). If it's too big,
      features in the distribtuion/potentials might get lost.
    </desc>
  </item>
  <!-- inverse options -->
  <item><name>inverse</name><desc>Contains all information relevant to iterative process</desc></item>
  <item>
   <name>inverse.target</name>
   <desc>
     target distribution (e.g. rdf) which is tried to match during iterations to match
   </desc>
  </item>
  <item>
    <name>inverse.do_potential</name>
    <default>1</default>
    <desc>
      Update cycle for the potential update. 1 means update, 0 don't update. 1 1 0 means
      update 2 iterations, then don't update, then repeat.
    </desc>
  </item>
  <item>
    <name>inverse.post_update</name>
    <desc>
      Additional post-processing of dU before added to potential. This is a list of
      scripts separated by spaces which are called. See section on iterative framework for details.
    </desc>
  </item>
  <item>
    <name>inverse.post_add</name>
    <desc>
      Additional post processing of U after dU added to potential. This is a list of
      scripts separated by spaces which are called. See section on iterative framework for details.
    </desc>
  </item>
  <item><name>inverse.post_add_options</name><desc>Contains all options of post add scripts</desc></item>
  <item><name>inverse.post_add_options.overwrite</name><desc>Contains all options of the overwrite postadd scripts</desc></item>
  <item>
    <name>inverse.post_add_options.overwrite.do</name>
    <desc>
      pattern for overwrite postadd script (1 do, 0 do not).
    </desc>
  </item>
  <item>
    <name>inverse.p_target</name>
    <desc>
      partial pressure of this species
    </desc>
  </item>

  <item>
    <name>inverse.particle_dens</name>
    <desc>
      particle density of this species (for wjk pressure correction)
    </desc>
  </item>
  <item><name>inverse.post_update_options</name><desc>Contains all options of post update scripts</desc></item>
  <item><name>inverse.post_update_options.pressure</name><desc>Contains all options of the pressure correction scripts</desc></item>
  <item>
    <name>inverse.post_update_options.pressure.do</name>
    <desc>
      pattern for pressure correction (1 do, 0 do not). To do pressure correction every third
      step specify "0 0 1", similar to inverse.do_update
    </desc>
  </item>
  <item>
    <name>inverse.post_update_options.pressure.type</name>
    <desc>
      Pressure correction algoritm, can be simple or wjk
    </desc>
  </item>
  <item><name>inverse.post_update_options.pressure.simple</name><desc>Contains all options of the simple pressure correction script</desc></item>
  <item>
    <name>inverse.post_update_options.pressure.simple.scale</name>
    <desc>
      slope of the simple pressure correction
    </desc>
  </item>
  <item><name>inverse.post_update_options.pressure.wjk</name><desc>Contains all options of the wjk pressure correction script</desc></item>
  <item>
    <name>inverse.post_update_options.pressure.wjk.scale</name>
    <desc>
      extra scaling factor of pressure correction
    </desc>
  </item>
  <item><name>inverse.post_update_options.smooth</name><desc>Contains all options of the smooth script</desc></item>
  <item>
    <name>inverse.post_update_options.smooth.iterations</name>
    <desc>
      number of iterations for triangular smooth
    </desc>
  </item>
  <item><name>inverse.post_update_options.splinesmooth</name><desc>Contains all options of the spline smooth script</desc></item>
  <item>
    <name>inverse.post_update_options.splinesmooth.step</name>
    <desc>
      grid spacing for spline fit when doing spline smoothing
    </desc>
  </item>
  <item>
    <name>inverse.post_update_options.scale</name>
    <desc>scale factor for the update</desc>
  </item>

  <item>
    <name>inverse.post_add_options</name>
    <desc>
      This section contains all options for post add scripts.
    </desc>
  </item>
  <item>
    <name>inverse.post_add_options.copyback.filelist</name>
    <desc>list of files to copy to the main dir</desc>
  </item>
  <item>
    <name>inverse.post_add_options.convergence.weight</name>
    <desc>weight factors for the convergence of the interaction, should be a list of same length as inverse.post_add_options.convergence.what (default 1)</desc>
  </item>
  <item>
    <name>inverse.post_add_options.convergence.what</name>
    <desc>list for what to calc the convergence: dist pot, .. (default dist)</desc>
  </item>
  <item>
    <name>inverse.post_add_options.plot.gnuplot_bin</name>
    <desc>gnuplot binary to use (default gnuplot)</desc>
  </item>
  <item>
    <name>inverse.post_add_options.plot.gnuplot_opts</name>
    <desc>extra options to give to gnuplot_bin (e.g. -persist, if one uses kill)</desc>
  </item>
  <item>
    <name>inverse.post_add_options.plot.fd</name>
    <desc>file descriptor to use (default 8), make it unique if you want to plot multiple things</desc>
  </item>
  <item>
    <name>inverse.post_add_options.plot.script</name>
    <desc>plot script to give to gnuplot</desc>
  </item>
  <item>
    <name>inverse.post_add_options.plot.kill</name>
    <desc>kill all processes with that name before ploting (e.g. gnuplot_x11), this is more reliable than using multiplot</desc>

  </item>
  
<!-- imc specific stuff -->

  <item>
    <name>inverse.imc</name>
    <desc>Section containing inverse monte carlo specific options.</desc>
  </item>
  <item>
    <name>inverse.imc.group</name>
    <desc>
      Group of interaction. Cross-correlations of all members of a group are taken into account for calculating the update.
        If no cross correlations should be calculated, interactions have to be put into different groups.
    </desc>
  </item>
  <item>
    <name>inverse.gromacs</name>
    <desc>
        This section contains gromacs specific options in case gromacs is used as simulation program.
    </desc>
  </item>
  
  <item>
    <name>inverse.gromacs.table</name>
    <desc>
      Name of file for tabulated potential of this interaction. This fill will be created from the internal tabulated potential format for every run.
    </desc>
  </item>

  <item>
    <name>inverse.gromacs.grp1</name>
    <desc>
      Name of energy group of bead type1 using in the g_rdf index file.
    </desc>
  </item>

  <item>
    <name>inverse.gromacs.grp2</name>
    <desc>
      Name of energy group of bead type2 using in the g_rdf index file.
    </desc>
  </item>

  <item>
    <name>inverse.espresso</name>
    <desc>
        This section contains espresso specific options in case espresso is used as simulation program.
    </desc>
  </item>

  <item>
    <name>inverse.espresso.table</name>
    <desc>
      Name of file for tabulated potential of this interaction. This file will
be created from the internal tabulated potential format for every run. Note,
though, that the original espresso blockfile needs to contain the name of that
table as the tabulated interaction (see tutorial methanol ibi_espresso for details).
    </desc>
  </item>

  <item>
    <name>inverse.espresso.index1</name>
    <desc>
      Index list of type1 -- Name of the Tcl variable containing all index1
particles that is contained in the espresso blockfile.
    </desc>
  </item>

  <item>
    <name>inverse.espresso.index2</name>
    <desc>
      Index list of type2 -- Name of the Tcl variable containing all index2
particles that is contained in the espresso blockfile.
    </desc>
  </item>

  <item>
    <name>fmatch</name>
    <desc>
      Force matching options
    </desc>
  </item>

  <item>
    <name>fmatch.min</name>
    <desc>
      Minimum value of interval for distribution sampled in atomistic MD simulation. One can get this
      number by looking at the distribution function for this interaction. For non-bonded interactions
      it's the distance to the rdf start. For CG bonds and angles the variable has the similar meaning
      ( note, that for angles it is specified in radians ).
    </desc>
  </item>
  
  <item>
    <name>fmatch.max</name>
    <desc>
      Maximum value of interval for distribution sampled in atomistic MD simulation. One can get this
      number by looking at the distribution function for this interaction. For non-bonded interactions
      it's the cut-off of the interaction.
    </desc>
  </item>

  <item>
    <name>fmatch.step</name>
    <desc>
      grid spacing for the spline, which represents the interaction. This parameter should not be too big,
      otherwise you might lose some features of the interaction potential, and not too small either, otherwise you
      will have unsampled bins which result in an ill-defined equation system and NaNs in the output.
    </desc>
  </item>

  <item>
    <name>fmatch.out_step</name>
    <desc>
      Grid spacing for the output grid. Normally, one wants to have this parameter smaller than fmatch.step, 
      to have a smooth curve, without additional spline interpolation. As a rule of thumb we normally use
      fmatch.out_step which is approximately 5 times smaller than fmatch.step.
    </desc>
  </item>
  <item><name>tf</name><desc>Contains all information relevant to thermoforce iteration</desc></item>
  <item><name>tf.spline_start</name><desc>Start of the spline used to smooth the density</desc></item>
  <item><name>tf.spline_end</name><desc>End of the spline used to smooth the density</desc></item>
  <item><name>tf.spline_step</name><desc>Grid of the spline used to smooth the density</desc></item>
  <item><name>tf.molname</name><desc>Molecule name of this gropu used in gromacs topology</desc></item>
  <item><name>tf.prefactor</name><desc>Prefactor for the thermoforce (f=-prefactor * grad density)</desc></item>
  <item><name>tf.cg_prefactor</name><desc>Second Prefactor for the thermoforce will be linear interpolated with tf.prefactor</desc></item>

</tags>