src/gromacs/mdtypes/pull-params.h

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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 "gromacs/math/vectypes.h"
  52 #include "gromacs/mdtypes/md_enums.h"
  53 #include "gromacs/utility/basedefinitions.h"
  54 #include "gromacs/utility/real.h"
  55
  56 /*! \cond INTERNAL */
  57
  58 /*! \brief Struct that defines a pull group */
  59 typedef struct {
  60     int      nat;                    /**< Number of atoms in the pull group */
  61     int     *ind;                    /**< The global atoms numbers */
  62     int      nweight;                /**< The number of weights (0 or nat) */
  63     real    *weight;                 /**< Weights (use all 1 when weight==NULL) */
  64     int      pbcatom;                /**< The reference atom for pbc (global number) */
  65     int      pbcatom_input;          /**< The reference atom for pbc (global number) as specified in the input parameters */
  66 } t_pull_group;
  67
  68 /*! Maximum number of pull groups that can be used in a pull coordinate */
  69 static const int c_pullCoordNgroupMax = 6;
  70
  71 /*! \brief Struct that defines a pull coordinate */
  72 typedef struct {
  73     int      eType;                        /**< The pull type: umbrella, constraint, ... */
  74     char    *externalPotentialProvider;    /**< Name of the module providing the external potential, only used with eType==epullEXTERNAL */
  75     int      eGeom;                        /**< The pull geometry */
  76     int      ngroup;                       /**< The number of groups, depends on eGeom */
  77     int      group[c_pullCoordNgroupMax];  /**< The pull groups: indices into the group arrays in pull_t and pull_params_t, ngroup indices are used */
  78     ivec     dim;                          /**< Used to select components for constraint */
  79     rvec     origin;                       /**< The origin for the absolute reference */
  80     rvec     vec;                          /**< The pull vector, direction or position */
  81     gmx_bool bStart;                       /**< Set init based on the initial structure */
  82     real     init;                         /**< Initial reference displacement (nm) or (deg) */
  83     real     rate;                         /**< Rate of motion (nm/ps) or (deg/ps) */
  84     real     k;                            /**< Force constant (kJ/(mol nm^2) or kJ/(mol rad^2) for umbrella pull type, or kJ/(mol nm) or kJ/(mol rad) for constant force pull type */
  85     real     kB;                           /**< Force constant for state B */
  86 } t_pull_coord;
  87
  88 /*! \brief Struct containing all pull parameters */
  89 typedef struct pull_params_t {
  90     int            ngroup;                  /**< Number of pull groups */
  91     int            ncoord;                  /**< Number of pull coordinates */
  92     real           cylinder_r;              /**< Radius of cylinder for dynamic COM (nm) */
  93     real           constr_tol;              /**< Absolute tolerance for constraints in (nm) */
  94     gmx_bool       bPrintCOM;               /**< Print coordinates of COM for each coord */
  95     gmx_bool       bPrintRefValue;          /**< Print the reference value for each coord */
  96     gmx_bool       bPrintComp;              /**< Print cartesian components for each coord with geometry=distance */
  97     gmx_bool       bSetPbcRefToPrevStepCOM; /**< Use the COM of each group from the previous step as reference */
  98     int            nstxout;                 /**< Output interval for pull x */
  99     int            nstfout;                 /**< Output interval for pull f */
 100     bool           bXOutAverage;            /**< Write the average coordinate during the output interval */
 101     bool           bFOutAverage;            /**< Write the average force during the output interval */
 102
 103     t_pull_group  *group;                   /**< groups to pull/restrain/etc/ */
 104     t_pull_coord  *coord;                   /**< the pull coordinates */
 105 } pull_params_t;
 106
 107 /*! \endcond */
 108
 109 #endif /* GMX_MDTYPES_PULL_PARAMS_H */