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_INSERT_MIXED_ATOMS                0x02
  47 #define STAGE_CONTINUE                          0x03
  48 #define STAGE_ANNEAL                            0x04
  49 #define STAGE_CHAATTR                           0x05
  50 #define STAGE_CHSATTR                           0x06
  51 #define STAGE_SET_TEMP                          0x07
  52 #define STAGE_SET_TIMESTEP                      0x08
  53
  54 typedef struct s_mdrun {
  55         char cfile[128];                        // config file
  56
  57         char continue_file[128];                // moldyn save file to continue
  58
  59         u8 intalgo;                             // integration algorithm
  60         double timestep;                        // timestep
  61
  62         u8 potential;                           // potential
  63         double cutoff;                          // cutoff radius
  64         double nnd;                             // next neighbour distance
  65
  66         t_3dvec dim;                            // simulation volume
  67         u8 pbcx;                                // periodic boundary conditions
  68         u8 pbcy;
  69         u8 pbcz;
  70
  71         int element1;                           // element 1
  72         double m1;
  73         int element2;                           // element 2
  74         double m2;
  75         double lc;                              // lattice constant
  76         int lx;                                 // amount of lc units
  77         int ly;
  78         int lz;
  79         u8 lattice;                             // type of lattice
  80
  81         int fill_element;
  82         u8 fill_brand;
  83
  84         u8 sattr;                               // system attributes
  85         double temperature;                     // temperature
  86         double pressure;                        // pressure
  87         double dp;
  88         double dt;
  89         int relax_steps;                        // amount of relaxation steps
  90
  91         int prerun;                             // amount of loops in first run
  92
  93         int elog;                               // logging
  94         int tlog;
  95         int plog;
  96         int vlog;
  97         int save;
  98         int visualize;
  99         u8 vis;
 100         int avgskip;                            // average skip
 101         char sdir[128];                         // save root
 102
 103         t_list stage;                           // stages
 104         int s_cnt;                              // stage counter
 105 } t_mdrun;
 106
 107 #define SATTR_PRELAX                            0x01
 108 #define SATTR_TRELAX                            0x02
 109 #define SATTR_AVGRST                            0x04
 110
 111 typedef struct s_displace_atom_params {
 112         int nr;
 113         double dx,dy,dz;
 114 } t_displace_atom_params;
 115
 116 typedef struct s_insert_atoms_params {
 117         u8 type;
 118         double x0,y0,z0,x1,y1,z1;
 119         double cr;
 120         int ins_steps;
 121         int cnt_steps;
 122         int ins_atoms;
 123         int element;
 124         u8 brand;
 125         u8 attr;
 126 } t_insert_atoms_params;
 127
 128 typedef struct s_insert_mixed_atoms_params {
 129         int element1;
 130         int element2;
 131         int amount1;
 132         int amount2;
 133         u8 brand1;
 134         u8 brand2;
 135         u8 attr1;
 136         u8 attr2;
 137         double crmin;
 138         double crmax;
 139 } t_insert_mixed_atoms_params;
 140
 141 #define INS_TOTAL                               0x01
 142 #define INS_REGION                              0x02
 143 #define INS_POS                                 0x03
 144
 145 typedef struct s_continue_params {
 146         int runs;
 147 } t_continue_params;
 148
 149 typedef struct s_anneal_params {
 150         int runs;
 151         int count;
 152         double dt;
 153         int interval;
 154 } t_anneal_params;
 155
 156 typedef struct s_chaattr_params {
 157         u8 type;
 158         double x0,y0,z0;
 159         double x1,y1,z1;
 160         int element;
 161         u8 attr;
 162 } t_chaattr_params;
 163
 164 #define CHAATTR_TOTALV                          0x01
 165 #define CHAATTR_REGION                          0x02
 166 #define CHAATTR_ELEMENT                         0x04
 167
 168 typedef struct s_chsattr_params {
 169         u8 type;
 170         double ttau;
 171         double ptau;
 172         double dt;
 173         double dp;
 174         int rsteps;
 175         u8 avgrst;
 176 } t_chsattr_params;
 177
 178 #define CHSATTR_PCTRL                           0x01
 179 #define CHSATTR_TCTRL                           0x02
 180 #define CHSATTR_PRELAX                          0x04
 181 #define CHSATTR_TRELAX                          0x08
 182 #define CHSATTR_AVGRST                          0x10
 183 #define CHSATTR_RSTEPS                          0x20
 184
 185 typedef struct s_set_temp_params {
 186         u8 type;
 187         double val;
 188 } t_set_temp_params;
 189
 190 #define SET_TEMP_CURRENT                        0x01
 191 #define SET_TEMP_VALUE                          0x02
 192
 193 typedef struct s_set_timestep_params {
 194         double tau;
 195 } t_set_timestep_params;
 196
 197 /*
 198  * function prototypes
 199  */
 200
 201
 202 #endif