mdrun.h

   1 /*
   2  * mdrun.h - mdrun header file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #ifndef MDRUN_H
   9 #define MDRUN_H
  10
  11 #include <sys/types.h>
  12 #include <sys/stat.h>
  13 #include <fcntl.h>
  14 #include <unistd.h>
  15
  16 #include <math.h>
  17
  18 /* main molecular dynamics api */
  19 #include "moldyn.h"
  20
  21 /* list api */
  22 #include "list/list.h"
  23
  24 /* potentials */
  25 #include "potentials/harmonic_oscillator.h"
  26 #include "potentials/lennard_jones.h"
  27 #include "potentials/albe.h"
  28 #ifdef TERSOFF_ORIG
  29 #include "potentials/tersoff_orig.h"
  30 #else
  31 #include "potentials/tersoff.h"
  32 #endif
  33
  34 /*
  35  * datatypes & definitions
  36  */
  37
  38 typedef struct s_stage {
  39         u8 type;
  40         void *params;
  41         u8 executed;
  42 } t_stage;
  43
  44 #define STAGE_DISPLACE_ATOM                     0x00
  45 #define STAGE_INSERT_ATOMS                      0x01
  46 #define STAGE_CONTINUE                          0x02
  47 #define STAGE_ANNEAL                            0x03
  48 #define STAGE_CHAATTR                           0x04
  49 #define STAGE_CHSATTR                           0x05
  50
  51 typedef struct s_mdrun {
  52         char cfile[128];                        // config file
  53
  54         u8 intalgo;                             // integration algorithm
  55         double timestep;                        // timestep
  56
  57         u8 potential;                           // potential
  58         double cutoff;                          // cutoff radius
  59         double nnd;                             // next neighbour distance
  60
  61         t_3dvec dim;                            // simulation volume
  62         u8 pbcx;                                // periodic boundary conditions
  63         u8 pbcy;
  64         u8 pbcz;
  65
  66         int element1;                           // element 1
  67         double m1;
  68         int element2;                           // element 2
  69         double m2;
  70         double lc;                              // lattice constant
  71         int lx;                                 // amount of lc units
  72         int ly;
  73         int lz;
  74         u8 lattice;                             // type of lattice
  75
  76         u8 sattr;                               // system attributes
  77         double temperature;                     // temperature
  78         double pressure;                        // pressure
  79         double dp;
  80         double dt;
  81         int relax_steps;                        // amount of relaxation steps
  82
  83         int prerun;                             // amount of loops in first run
  84
  85         int elog;                               // logging
  86         int tlog;
  87         int plog;
  88         int vlog;
  89         int save;
  90         int visualize;
  91         u8 vis;
  92         int avgskip;                            // average skip
  93         char sdir[128];                         // save root
  94
  95         t_list stage;                           // stages
  96         int s_cnt;                              // stage counter
  97 } t_mdrun;
  98
  99 #define SATTR_PRELAX                            0x01
 100 #define SATTR_TRELAX                            0x02
 101 #define SATTR_AVGRST                            0x04
 102
 103 typedef struct s_displace_atom_params {
 104         int nr;
 105         double dx,dy,dz;
 106 } t_displace_atom_params;
 107
 108 typedef struct s_insert_atoms_params {
 109         u8 type;
 110         double x0,y0,z0,x1,y1,z1;
 111         double cr;
 112         int ins_steps;
 113         int cnt_steps;
 114         int ins_atoms;
 115         int element;
 116         u8 brand;
 117         u8 attr;
 118 } t_insert_atoms_params;
 119
 120 #define INS_TOTAL                               0x01
 121 #define INS_REGION                              0x02
 122 #define INS_POS                                 0x03
 123
 124 typedef struct s_continue_params {
 125         int runs;
 126 } t_continue_params;
 127
 128 typedef struct s_anneal_params {
 129         int runs;
 130         int count;
 131         double dt;
 132 } t_anneal_params;
 133
 134 typedef struct s_chaattr_params {
 135         u8 type;
 136         double x0,y0,z0;
 137         double x1,y1,z1;
 138         int element;
 139         u8 attr;
 140 } t_chaattr_params;
 141
 142 #define CHAATTR_TOTALV                          0x01
 143 #define CHAATTR_REGION                          0x02
 144 #define CHAATTR_ELEMENT                         0x04
 145
 146 typedef struct s_chsattr_params {
 147         u8 type;
 148         double ttau;
 149         double ptau;
 150         double dt;
 151         double dp;
 152         int rsteps;
 153         u8 avgrst;
 154 } t_chsattr_params;
 155
 156 #define CHSATTR_PCTRL                           0x01
 157 #define CHSATTR_TCTRL                           0x02
 158 #define CHSATTR_PRELAX                          0x04
 159 #define CHSATTR_TRELAX                          0x08
 160 #define CHSATTR_AVGRST                          0x10
 161 #define CHSATTR_RSTEPS                          0x20
 162
 163 /*
 164  * function prototypes
 165  */
 166
 167
 168 #endif