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