src/gromacs/mdtypes/swaphistory.h

   1 /*
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  35
  36 /*
  37  * This file contains data types containing ioin/water position exchange
  38  * data to be stored in the checkpoint file.
  39  */
  40
  41 #ifndef GMX_MDLIB_SWAPHISTORY_H
  42 #define GMX_MDLIB_SWAPHISTORY_H
  43
  44 #include "gromacs/mdtypes/md_enums.h"
  45
  46 /* History of an ion type used in position swapping
  47  */
  48 typedef struct swapstateIons_t
  49 {
  50     int  nMolReq[eCompNR];      // Requested # of molecules per compartment
  51     int* nMolReq_p[eCompNR];    // Pointer to this data (for checkpoint writing)
  52     int  inflow_net[eCompNR];   // Flux determined from the # of swaps
  53     int* inflow_net_p[eCompNR]; // Pointer to this data
  54     int* nMolPast[eCompNR];     // Array with nAverage entries for history
  55     int* nMolPast_p[eCompNR];   // Pointer points to the first entry only
  56
  57     // Channel flux detection, this is counting only and has no influence on whether swaps are performed or not:                                                                 */
  58     int            fluxfromAtoB[eCompNR];   // Flux determined from the split cylinders
  59     int*           fluxfromAtoB_p[eCompNR]; // Pointer to this data
  60     int            nMol;                    // Number of molecules, size of the following arrays
  61     unsigned char* comp_from;               // Ion came from which compartment?
  62     unsigned char* channel_label;           // Through which channel did this ion pass?
  63 } swapstateIons_t;
  64
  65 /* Position swapping state
  66  *
  67  * To also make multimeric channel proteins whole, we save the last whole configuration
  68  * of the channels in the checkpoint file. If we have no checkpoint file, we assume
  69  * that the starting configuration has the correct PBC representation after making the
  70  * individual molecules whole
  71  *
  72  * \todo move out of this file to ObservablesHistory
  73  *
  74  */
  75 typedef struct swaphistory_t
  76 {
  77     int  eSwapCoords; // Swapping along x, y, or z-direction?
  78     int  nIonTypes;   // Number of ion types, this is the size of the following arrays
  79     int  nAverage; // Use average over this many swap attempt steps when determining the ion counts
  80     int  fluxleak; // Ions not going through any channel (bad!)
  81     int* fluxleak_p;               // Pointer to this data
  82     gmx_bool         bFromCpt;     // Did we start from a checkpoint file?
  83     int              nat[eChanNR]; // Size of xc_old_whole, i.e. the number of atoms in each channel
  84     rvec*            xc_old_whole[eChanNR]; // Last known whole positions of the two channels (important for multimeric ch.!)
  85     rvec**           xc_old_whole_p[eChanNR]; // Pointer to these positions
  86     swapstateIons_t* ionType;                 // History information for one ion type
  87 } swaphistory_t;
  88
  89 #endif