/***************************************************************************
                          rundoc.h  -  description
                             -------------------
    begin                : Tue Nov 18 01:45:35 2003
    copyright            : (C) 1999-2006 by Cavalli Andrea
    author               : : cavalli $
    date                 : : 2003/12/09 11:10:33 $
    id                   : : coor.h,v 1.1.2.2 2003/12/09 11:10:33 cavalli Exp $
    email                : cavalli@bioc.unizh.ch amc82@cam.ac.uk
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU General Public License as published by  *
 *   the Free Software Foundation; either version 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/
#ifndef __RUNDOC__
#define __RUNDOC__

#include <almost.h>

namespace Almost {
  namespace RunDoc {

    static const string algorithm = 
      "";

    //Geometry
    static const string geometry = 
      "Acceptable Values: PLAIN or CUBIC. Geometric boundary conditions.\n";

    static const string Lx = 
      "Acceptable Values: positive real number. X size of the simulation box.\n"
      "Used only if geometry is CUBIC.\n"
      ;

    static const string Ly = 
      "Acceptable Values: positive real number. Y size of the simulation box.\n"
      "Used only if geometry is CUBIC.\n"
      ;

    static const string Lz = 
      "Acceptable Values: positive real number. Z size of the simulation box.\n"
      "Used only if geometry is CUBIC.\n"
      ;

    static const string granularity = 
      "Acceptable Values: positive integer. Granularity of the the grid\n"
      "used for non-bonded list update. Used only if geometry is  CUBIC.\n"
      ;


    static const string trj = 
      "Acceptable Values: string. Name of the file on which the coordinates\n"
      "of the dynamics run are to be saved.\n"
      ;

    static const string vtrj = 
      "Acceptable Values: string. Name of the file on which the velocities\n"
      "of the dynamics run are to be saved.\n"
      ;


    static const string rst = 
      "Acceptable Values: string. Name of the file on which the dynamics\n"
      "restart file for the present run is to be written.\n"
      ;


    static const string log = 
      "Acceptable Values: string. If different from \"none\", name of the\n"
      "file on which the energies of the dynamics run are to be written.\n"
      ;

    static const string dat = 
      "Acceptable Values: string. If different from \"none\", name of the\n"
      "file on which the energies of the dynamics run are to be written.\n"
      "Differs from log file in the format.\n"
      ;

    static const string steps = 
      "Acceptable Values: positive integer. The number of steps to be taken.\n"
      "This is the number of dynamics steps which is also equal to the\n"
      "number of energy evaluations.\n"
      ;

    static const string nprint = 
      "Acceptable Values: positive integer. The step frequency for printing\n"
      "or saving energy data\n"
      ;

    static const string nsave = 
      "Acceptable Values: positive integer. The step frequency for writing\n"
      "coordinates (and velocities) in the trajectories and restart files.\n"
      ;

    static const string nupdate = 
      "Acceptable Values: positive integer. The frequency of regenerating\n"
      "the non-bonded list."
      ;

    static const string nrottrans = 
      "Acceptable Values: positive integer. The frequency for stopping the\n"
      "rotation and translation of the molecule during dynamics.\n"
      "Only used with the Berendsen thermostat.\n"
      ;


    static const string nsurf = 
      "Acceptable Values: positive integer.Not used.";
    static const string shake_mode = 
      "Acceptable Values: BONDH, BONDALL or NONE. Fix selected bonds with the\n"
      "SHAKE algorithm.\n"
      ;

    static const string shake_tol = 
      "Acceptable Values: positive real number. The shake tolerance (if SHAKE is in use).\n"
      ;

    static const string temp = 
      "Acceptable Values: positive real number. Temperature in degrees Kelvin\n"
      "of the dynamics simulation.\n"
      ;

    static const string time_step = 
      "Acceptable Values: positive real number. Time step for dynamics in picoseconds.\n"
      ;

    static const string tau = 
      "Acceptable Values: positive real number. The coupling decay time in picoseconds for the temperature.\n"
      "Only used with the Berendsen thermostat.\n"
      ;
    static const string gamma_water =       
      "Acceptable Values: positive real number. \"Solvent\" friction\n"
      "coefficient to be used in Langevin molecular dynamics simulation\n."
      ;

    static const string vect = 
      "Acceptable Values: bool. Not used.\n"
      ;

    static const string seed = 
      "Acceptable Values: positive integer. The seed for the random number\n"
      "generator used for assigning velocities."
      ;

    static const string save_fitted = 
      "Acceptable Values: bool. Not used.";

    static const string selection = 
      "Acceptable Values: string. Not used.";

    static const string nreplica = 
      "Acceptable Values: positive integer. Number of replicas to be used\n"
      "in dynamics run.\n"
      ;
  }
}

#endif
// Local Variables:
// mode:C++
// End: