src/tools/nsc.h

   1 /*
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   9  *                        VERSION 3.2.0
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  35 #include "typedefs.h"
  36
  37 #define FLAG_DOTS       01
  38 #define FLAG_VOLUME     02
  39 #define FLAG_ATOM_AREA  04
  40
  41
  42
  43 extern int nsc_dclm_pbc(rvec *coords, real *radius, int nat,
  44                         int  densit, int mode,
  45                         real *value_of_area, real **at_area,
  46                         real *value_of_vol,
  47                         real **lidots, int *nu_dots,
  48                         atom_id index[],int ePBC,matrix box);
  49
  50 /*
  51     User notes :
  52 The input requirements :
  53   The arrays with atom coordinates and radii are thought to start
  54   with index 0, i.e., places 0, 1, and 2 are the x-, y-, and z-
  55   coordinates of the zero-th atom and place 0 in the other array
  56   is its radius.
  57
  58   PLEASE TAKE INTO ACCOUNT THAT THE RADII GIVEN HERE ARE DIRECTLY
  59   USED FOR SURFACE CALCULATION. NSC does not increment with a probe
  60   radius.
  61
  62   The user can define any number of dots. The program selects a
  63   dot density that is the lowest possible with at least the required
  64   number of dots. The points are distributed in accordance with the
  65   icosahedron-based or the dodecahedron-based method as described in
  66   ref. 1.
  67
  68 The output requirements are :
  69   1 and 3 :  pointer to an existing real
  70   2 and 4 :  pointer to an existing pointer to real
  71              NSC allocates memory for an array
  72   5       :  pointer to an existing integer
  73
  74 The subroutine NSC makes use of variant 2 described in reference 1.
  75 By selecting the necessary output via flags, the requirements for
  76 cpu-time and computer memory can be adapted to the actual needs.
  77
  78 Example : flag = FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS
  79           The routine calculates the area, volume and the dot surface. The
  80           program allocates arrays for the atomwise areas and for the surface
  81           dots. The addresses are returned in the pointers to pointers to
  82           real.
  83           This variant is not recommended because normally the dot surface
  84           is needed for low point density (e.g.42) at which area and volume
  85           are inaccurate. The sign "|" is used as binary AND !
  86
  87           flag = FLAG_VOLUME | FLAG_ATOM_AREA
  88           In this case the large arrays for storing the surface dots
  89           are not allocated. A large point number of the fully accessible
  90           sphere can be selected. Good accuracy is already achieved with
  91           600-700 points per sphere (accuracy of about 1.5 square Angstrem
  92           per atomic sphere).
  93           Output pointers 4 and 5 may be NULL.
  94
  95           flag = FLAG_DOTS
  96           Only the dot surface is produced.
  97           Output pointers 2 and 3 may be NULL.
  98
  99 The output pointer 1 cannot be set to NULL in any circumstances. The
 100 overall area value is returned in every mode.
 101
 102 All files calling NSC should include nsc.h !!
 103
 104
 105 Example for calling NSC (contents of user file):
 106
 107   ...
 108 #include "nsc.h"
 109
 110 int routine_calling_NSC(int n_atom, real *coordinates, real *radii) {
 111   real area, volume, *atomwise_area, *surface_dots;
 112   int    i, density = 300, n_dots;
 113
 114   ...
 115
 116   for (i=0; i<n_atom; i++) {
 117    radii[i]  += 1.4      /# add the probe radius if necessary #/
 118
 119   if (NSC(coordinates, radii, n_atom, density,
 120           FLAG_AREA | FLAG_VOLUME | FLAG_DOTS,
 121           &area, &atomwise_area, &volume, &surface_dots, &n_dots))
 122     printf("error occured\n");
 123     return 1;
 124     }
 125
 126   ...
 127
 128 /# do something with areas, volume and surface dots #/
 129
 130   ...
 131
 132   return 0;
 133   }
 134
 135 */