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         char continue_file[128];                // moldyn save file to continue
  55
  56         u8 intalgo;                             // integration algorithm
  57         double timestep;                        // timestep
  58
  59         u8 potential;                           // potential
  60         double cutoff;                          // cutoff radius
  61         double nnd;                             // next neighbour distance
  62
  63         t_3dvec dim;                            // simulation volume
  64         u8 pbcx;                                // periodic boundary conditions
  65         u8 pbcy;
  66         u8 pbcz;
  67
  68         int element1;                           // element 1
  69         double m1;
  70         int element2;                           // element 2
  71         double m2;
  72         double lc;                              // lattice constant
  73         int lx;                                 // amount of lc units
  74         int ly;
  75         int lz;
  76         u8 lattice;                             // type of lattice
  77
  78         u8 sattr;                               // system attributes
  79         double temperature;                     // temperature
  80         double pressure;                        // pressure
  81         double dp;
  82         double dt;
  83         int relax_steps;                        // amount of relaxation steps
  84
  85         int prerun;                             // amount of loops in first run
  86
  87         int elog;                               // logging
  88         int tlog;
  89         int plog;
  90         int vlog;
  91         int save;
  92         int visualize;
  93         u8 vis;
  94         int avgskip;                            // average skip
  95         char sdir[128];                         // save root
  96
  97         t_list stage;                           // stages
  98         int s_cnt;                              // stage counter
  99 } t_mdrun;
 100
 101 #define SATTR_PRELAX                            0x01
 102 #define SATTR_TRELAX                            0x02
 103 #define SATTR_AVGRST                            0x04
 104
 105 typedef struct s_displace_atom_params {
 106         int nr;
 107         double dx,dy,dz;
 108 } t_displace_atom_params;
 109
 110 typedef struct s_insert_atoms_params {
 111         u8 type;
 112         double x0,y0,z0,x1,y1,z1;
 113         double cr;
 114         int ins_steps;
 115         int cnt_steps;
 116         int ins_atoms;
 117         int element;
 118         u8 brand;
 119         u8 attr;
 120 } t_insert_atoms_params;
 121
 122 #define INS_TOTAL                               0x01
 123 #define INS_REGION                              0x02
 124 #define INS_POS                                 0x03
 125
 126 typedef struct s_continue_params {
 127         int runs;
 128 } t_continue_params;
 129
 130 typedef struct s_anneal_params {
 131         int runs;
 132         int count;
 133         double dt;
 134 } t_anneal_params;
 135
 136 typedef struct s_chaattr_params {
 137         u8 type;
 138         double x0,y0,z0;
 139         double x1,y1,z1;
 140         int element;
 141         u8 attr;
 142 } t_chaattr_params;
 143
 144 #define CHAATTR_TOTALV                          0x01
 145 #define CHAATTR_REGION                          0x02
 146 #define CHAATTR_ELEMENT                         0x04
 147
 148 typedef struct s_chsattr_params {
 149         u8 type;
 150         double ttau;
 151         double ptau;
 152         double dt;
 153         double dp;
 154         int rsteps;
 155         u8 avgrst;
 156 } t_chsattr_params;
 157
 158 #define CHSATTR_PCTRL                           0x01
 159 #define CHSATTR_TCTRL                           0x02
 160 #define CHSATTR_PRELAX                          0x04
 161 #define CHSATTR_TRELAX                          0x08
 162 #define CHSATTR_AVGRST                          0x10
 163 #define CHSATTR_RSTEPS                          0x20
 164
 165 /*
 166  * function prototypes
 167  */
 168
 169
 170 #endif