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 #define STAGE_FILL                              0x09
  54 #define STAGE_THERMAL_INIT                      0x10
  55 #define STAGE_DEL_ATOMS                         0x11
  56
  57 typedef struct s_mdrun {
  58         char cfile[128];                        // config file
  59
  60         char continue_file[128];                // moldyn save file to continue
  61
  62         u8 intalgo;                             // integration algorithm
  63         double timestep;                        // timestep
  64
  65         u8 potential;                           // potential
  66         double cutoff;                          // cutoff radius
  67         double nnd;                             // next neighbour distance
  68
  69         t_3dvec dim;                            // simulation volume
  70         u8 pbcx;                                // periodic boundary conditions
  71         u8 pbcy;
  72         u8 pbcz;
  73
  74         int element1;                           // element 1
  75         int element2;                           // element 2
  76
  77         double lc;                              // lattice constant
  78         u8 lattice;                             // type of lattice
  79
  80         u8 sattr;                               // system attributes
  81         double temperature;                     // temperature
  82         double pressure;                        // pressure
  83         double dp;
  84         double dt;
  85         int relax_steps;                        // amount of relaxation steps
  86
  87         int prerun;                             // amount of loops in first run
  88
  89         int elog;                               // logging
  90         int tlog;
  91         int plog;
  92         int vlog;
  93         int save;
  94         int visualize;
  95         u8 vis;
  96         int avgskip;                            // average skip
  97         char sdir[128];                         // save root
  98
  99         t_list stage;                           // stages
 100         int s_cnt;                              // stage counter
 101 } t_mdrun;
 102
 103 #define SATTR_PRELAX                            0x01
 104 #define SATTR_TRELAX                            0x02
 105 #define SATTR_AVGRST                            0x04
 106
 107 typedef struct s_displace_atom_params {
 108         int nr;
 109         double dx,dy,dz;
 110 } t_displace_atom_params;
 111
 112 typedef struct s_del_atoms_params {
 113         double r;
 114         t_3dvec o;
 115 } t_del_atoms_params;
 116
 117 typedef struct s_insert_atoms_params {
 118         u8 type;
 119         double x0,y0,z0,x1,y1,z1;
 120         double cr;
 121         int ins_steps;
 122         int cnt_steps;
 123         int ins_atoms;
 124         int element;
 125         u8 brand;
 126         u8 attr;
 127 } t_insert_atoms_params;
 128
 129 typedef struct s_insert_mixed_atoms_params {
 130         int element1;
 131         int element2;
 132         int amount1;
 133         int amount2;
 134         u8 brand1;
 135         u8 brand2;
 136         u8 attr1;
 137         u8 attr2;
 138         double crmin;
 139         double crmax;
 140 } t_insert_mixed_atoms_params;
 141
 142 #define INS_TOTAL                               0x01
 143 #define INS_RECT                                0x02
 144 #define INS_SPHERE                              0x03
 145 #define INS_POS                                 0x04
 146
 147 typedef struct s_continue_params {
 148         int runs;
 149 } t_continue_params;
 150
 151 typedef struct s_anneal_params {
 152         int runs;
 153         int count;
 154         double dt;
 155         int interval;
 156 } t_anneal_params;
 157
 158 typedef struct s_chaattr_params {
 159         u8 type;
 160         double x0,y0,z0;
 161         double x1,y1,z1;
 162         int element;
 163         u8 attr;
 164 } t_chaattr_params;
 165
 166 #define CHAATTR_TOTALV                          0x01
 167 #define CHAATTR_REGION                          0x02
 168 #define CHAATTR_ELEMENT                         0x04
 169
 170 typedef struct s_chsattr_params {
 171         u8 type;
 172         double ttau;
 173         double ptau;
 174         double dt;
 175         double dp;
 176         int rsteps;
 177         u8 avgrst;
 178 } t_chsattr_params;
 179
 180 #define CHSATTR_PCTRL                           0x01
 181 #define CHSATTR_TCTRL                           0x02
 182 #define CHSATTR_PRELAX                          0x04
 183 #define CHSATTR_TRELAX                          0x08
 184 #define CHSATTR_AVGRST                          0x10
 185 #define CHSATTR_RSTEPS                          0x20
 186
 187 typedef struct s_set_temp_params {
 188         u8 type;
 189         double val;
 190 } t_set_temp_params;
 191
 192 #define SET_TEMP_CURRENT                        0x01
 193 #define SET_TEMP_VALUE                          0x02
 194
 195 typedef struct s_set_timestep_params {
 196         double tau;
 197 } t_set_timestep_params;
 198
 199 typedef struct s_fill_params {
 200         double lc;                              // lattice constant
 201         int lx;                                 // amount of lc units
 202         int ly;
 203         int lz;
 204         u8 lattice;
 205         int fill_element;
 206         u8 fill_brand;
 207         t_part_params p_params;
 208         t_defect_params d_params;
 209 } t_fill_params;
 210
 211 /*
 212  * function prototypes
 213  */
 214
 215 #endif