src/gromacs/mdtypes/pull_params.h

   1 /*
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  35
  36 /*! \libinternal \file
  37  *
  38  *
  39  * \brief
  40  * This file contains datatypes for the mdp options used by the pull code.
  41  *
  42  * \author Berk Hess
  43  *
  44  * \inlibraryapi
  45  * \ingroup module_mdtypes
  46  */
  47
  48 #ifndef GMX_MDTYPES_PULL_PARAMS_H
  49 #define GMX_MDTYPES_PULL_PARAMS_H
  50
  51 #include <array>
  52 #include <string>
  53 #include <vector>
  54
  55 #include "gromacs/math/vectypes.h"
  56 #include "gromacs/mdtypes/md_enums.h"
  57 #include "gromacs/utility/basedefinitions.h"
  58 #include "gromacs/utility/real.h"
  59
  60 /*! \cond INTERNAL */
  61
  62 /*! \brief Struct that defines a pull group */
  63 struct t_pull_group
  64 {
  65     std::vector<int>  ind;     /**< The global atoms numbers */
  66     std::vector<real> weight;  /**< Weights (use all 1 when weight==NULL) */
  67     int               pbcatom; /**< The reference atom for pbc (global number) */
  68     int               pbcatom_input; /**< The reference atom for pbc (global number) as specified in the input parameters */
  69 };
  70
  71 /*! Maximum number of pull groups that can be used in a pull coordinate */
  72 static const int c_pullCoordNgroupMax = 6;
  73
  74 /*! \brief Struct that defines a pull coordinate */
  75 struct t_pull_coord
  76 {
  77     //! The pull type: umbrella, constraint, ...
  78     int eType = 0;
  79     //! Name of the module providing   the external potential, only used with eType==epullEXTERNAL
  80     std::string externalPotentialProvider;
  81     //! The pull geometry
  82     int eGeom = 0;
  83     //! The number of groups, depends on eGeom
  84     int ngroup = 0;
  85     /*! \brief The pull groups:
  86      *
  87      *  indices into the group arrays in pull_t and pull_params_t,
  88      *   ngroup indices are used
  89      */
  90     std::array<int, c_pullCoordNgroupMax> group;
  91     //! Used to select components for constraint
  92     gmx::IVec dim = { 0, 0, 0 };
  93     //! The origin for the absolute reference
  94     gmx::RVec origin = { 0, 0, 0 };
  95     //! The pull vector, direction or position
  96     gmx::RVec vec = { 0, 0, 0 };
  97     //! Set init based on the initial structure
  98     bool bStart = false;
  99     //! Initial reference displacement (nm) or (deg)
 100     real init = 0.0;
 101     //! Rate of motion (nm/ps) or (deg/ps)
 102     real rate = 0.0;
 103     /*! \brief Force constant
 104      *
 105      * For umbrella pull type this is (kJ/(mol nm^2) or kJ/(mol rad^2).
 106      * For constant force pull type it is kJ/(mol nm) or kJ/(mol rad).
 107      */
 108     real k = 0.0;
 109     //! Force constant for state B
 110     real kB = 0.0;
 111 };
 112
 113 /*! \brief Struct containing all pull parameters */
 114 struct pull_params_t
 115 {
 116     //! Number of pull groups
 117     int ngroup = 0;
 118     //! Number of pull coordinates
 119     int ncoord = 0;
 120     //! Radius of cylinder for dynamic COM (nm)
 121     real cylinder_r = 0.0;
 122     //! Absolute tolerance for constraints in (nm)
 123     real constr_tol = 0.0;
 124     //! Print coordinates of COM for each coord
 125     bool bPrintCOM = false;
 126     //! Print the reference value for each coord
 127     bool bPrintRefValue = false;
 128     //! Print cartesian components for each coord with geometry=distance
 129     bool bPrintComp = false;
 130     //! Use the COM of each group from the previous step as reference
 131     bool bSetPbcRefToPrevStepCOM = false;
 132     //! Output interval for pull x
 133     int nstxout = 0;
 134     //! Output interval for pull f
 135     int nstfout = 0;
 136     //! Write the average coordinate during the output interval
 137     bool bXOutAverage = false;
 138     //! Write the average force during the output interval
 139     bool bFOutAverage = false;
 140     //! groups to pull/restrain/etc/
 141     std::vector<t_pull_group> group;
 142     //! the pull coordinates
 143     std::vector<t_pull_coord> coord;
 144 };
 145
 146 /*! \endcond */
 147
 148 #endif /* GMX_MDTYPES_PULL_PARAMS_H */