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 #define STAGE_MODIFY_ATOMS                      0x12
  57
  58 typedef struct s_mdrun {
  59         char cfile[128];                        // config file
  60
  61         char continue_file[128];                // moldyn save file to continue
  62
  63         u8 intalgo;                             // integration algorithm
  64         double timestep;                        // timestep
  65
  66         u8 potential;                           // potential
  67         double cutoff;                          // cutoff radius
  68         double nnd;                             // next neighbour distance
  69
  70         t_3dvec dim;                            // simulation volume
  71         u8 pbcx;                                // periodic boundary conditions
  72         u8 pbcy;
  73         u8 pbcz;
  74
  75         int element1;                           // element 1
  76         int element2;                           // element 2
  77
  78         double lc;                              // lattice constant
  79         u8 lattice;                             // type of lattice
  80
  81         u8 sattr;                               // system attributes
  82         double temperature;                     // temperature
  83         double pressure;                        // pressure
  84         double dp;
  85         double dt;
  86         int relax_steps;                        // amount of relaxation steps
  87
  88         int prerun;                             // amount of loops in first run
  89
  90         int elog;                               // logging
  91         int tlog;
  92         int plog;
  93         int vlog;
  94         int save;
  95         int visualize;
  96         u8 vis;
  97         int avgskip;                            // average skip
  98         char sdir[128];                         // save root
  99
 100         t_list stage;                           // stages
 101         int s_cnt;                              // stage counter
 102 } t_mdrun;
 103
 104 #define SATTR_PRELAX                            0x01
 105 #define SATTR_TRELAX                            0x02
 106 #define SATTR_AVGRST                            0x04
 107
 108 typedef struct s_displace_atom_params {
 109         int nr;
 110         double dx,dy,dz;
 111 } t_displace_atom_params;
 112
 113 typedef struct s_del_atoms_params {
 114         double r;
 115         t_3dvec o;
 116 } t_del_atoms_params;
 117
 118 typedef struct s_modify_aoms_params {
 119         u8 type;
 120         int tag;
 121         t_3dvec ekin;
 122 } t_modify_atoms_params;
 123
 124 typedef struct s_insert_atoms_params {
 125         u8 type;
 126         double x0,y0,z0,x1,y1,z1;
 127         double cr;
 128         int ins_steps;
 129         int cnt_steps;
 130         int ins_atoms;
 131         int element;
 132         u8 brand;
 133         u8 attr;
 134 } t_insert_atoms_params;
 135
 136 typedef struct s_insert_mixed_atoms_params {
 137         int element1;
 138         int element2;
 139         int amount1;
 140         int amount2;
 141         u8 brand1;
 142         u8 brand2;
 143         u8 attr1;
 144         u8 attr2;
 145         double crmin;
 146         double crmax;
 147 } t_insert_mixed_atoms_params;
 148
 149 #define INS_TOTAL                               0x01
 150 #define INS_RECT                                0x02
 151 #define INS_SPHERE                              0x03
 152 #define INS_POS                                 0x04
 153 #define INS_RELPOS                              0x05
 154
 155 typedef struct s_continue_params {
 156         int runs;
 157 } t_continue_params;
 158
 159 typedef struct s_anneal_params {
 160         int runs;
 161         int count;
 162         double dt;
 163         int interval;
 164 } t_anneal_params;
 165
 166 typedef struct s_chaattr_params {
 167         u8 type;
 168         double x0,y0,z0;
 169         double x1,y1,z1;
 170         int element;
 171         u8 attr;
 172 } t_chaattr_params;
 173
 174 #define CHAATTR_TOTALV                          0x01
 175 #define CHAATTR_REGION                          0x02
 176 #define CHAATTR_ELEMENT                         0x04
 177 #define CHAATTR_NUMBER                          0x08
 178
 179 typedef struct s_chsattr_params {
 180         u8 type;
 181         double ttau;
 182         double ptau;
 183         double dt;
 184         double dp;
 185         int rsteps;
 186         u8 avgrst;
 187 } t_chsattr_params;
 188
 189 #define CHSATTR_PCTRL                           0x01
 190 #define CHSATTR_TCTRL                           0x02
 191 #define CHSATTR_PRELAX                          0x04
 192 #define CHSATTR_TRELAX                          0x08
 193 #define CHSATTR_AVGRST                          0x10
 194 #define CHSATTR_RSTEPS                          0x20
 195
 196 typedef struct s_set_temp_params {
 197         u8 type;
 198         double val;
 199 } t_set_temp_params;
 200
 201 #define SET_TEMP_CURRENT                        0x01
 202 #define SET_TEMP_VALUE                          0x02
 203
 204 typedef struct s_set_timestep_params {
 205         double tau;
 206 } t_set_timestep_params;
 207
 208 typedef struct s_fill_params {
 209         double lc;                              // lattice constant
 210         int lx;                                 // amount of lc units
 211         int ly;
 212         int lz;
 213         u8 lattice;
 214         int fill_element;
 215         u8 fill_brand;
 216         t_part_params p_params;
 217         t_defect_params d_params;
 218         t_offset_params o_params;
 219 } t_fill_params;
 220
 221 /*
 222  * function prototypes
 223  */
 224
 225 #endif