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 #define STAGE_CRT                               0x13
  58
  59 typedef struct s_mdrun {
  60         char cfile[128];                        // config file
  61
  62         char continue_file[128];                // moldyn save file to continue
  63
  64         u8 intalgo;                             // integration algorithm
  65         double timestep;                        // timestep
  66
  67         u8 potential;                           // potential
  68         double cutoff;                          // cutoff radius
  69         double nnd;                             // next neighbour distance
  70
  71         t_3dvec dim;                            // simulation volume
  72         u8 pbcx;                                // periodic boundary conditions
  73         u8 pbcy;
  74         u8 pbcz;
  75
  76         int element1;                           // element 1
  77         int element2;                           // element 2
  78
  79         double lc;                              // lattice constant
  80         u8 lattice;                             // type of lattice
  81
  82         u8 sattr;                               // system attributes
  83         double temperature;                     // temperature
  84         double pressure;                        // pressure
  85         double dp;
  86         double dt;
  87         int relax_steps;                        // amount of relaxation steps
  88
  89         int prerun;                             // amount of loops in first run
  90
  91         int elog;                               // logging
  92         int tlog;
  93         int plog;
  94         int vlog;
  95         int save;
  96         int visualize;
  97         u8 vis;
  98         int avgskip;                            // average skip
  99         char sdir[128];                         // save root
 100
 101         t_list stage;                           // stages
 102         int s_cnt;                              // stage counter
 103 } t_mdrun;
 104
 105 #define SATTR_PRELAX                            0x01
 106 #define SATTR_TRELAX                            0x02
 107 #define SATTR_AVGRST                            0x04
 108
 109 typedef struct s_displace_atom_params {
 110         int nr;
 111         double dx,dy,dz;
 112 } t_displace_atom_params;
 113
 114 typedef struct s_del_atoms_params {
 115         double r;
 116         t_3dvec o;
 117 } t_del_atoms_params;
 118
 119 typedef struct s_modify_aoms_params {
 120         u8 type;
 121         int tag;
 122         t_3dvec ekin;
 123 } t_modify_atoms_params;
 124
 125 typedef struct s_insert_atoms_params {
 126         u8 type;
 127         double x0,y0,z0,x1,y1,z1;
 128         double cr;
 129         int ins_steps;
 130         int cnt_steps;
 131         int ins_atoms;
 132         int element;
 133         u8 brand;
 134         u8 attr;
 135 } t_insert_atoms_params;
 136
 137 typedef struct s_insert_mixed_atoms_params {
 138         int element1;
 139         int element2;
 140         int amount1;
 141         int amount2;
 142         u8 brand1;
 143         u8 brand2;
 144         u8 attr1;
 145         u8 attr2;
 146         double crmin;
 147         double crmax;
 148 } t_insert_mixed_atoms_params;
 149
 150 #define INS_TOTAL                               0x01
 151 #define INS_RECT                                0x02
 152 #define INS_SPHERE                              0x03
 153 #define INS_POS                                 0x04
 154 #define INS_RELPOS                              0x05
 155
 156 typedef struct s_continue_params {
 157         int runs;
 158 } t_continue_params;
 159
 160 typedef struct s_anneal_params {
 161         int runs;
 162         int count;
 163         double dt;
 164         int interval;
 165 } t_anneal_params;
 166
 167 typedef struct s_chaattr_params {
 168         u8 type;
 169         double x0,y0,z0;
 170         double x1,y1,z1;
 171         int element;
 172         u8 attr;
 173 } t_chaattr_params;
 174
 175 #define CHAATTR_TOTALV                          0x01
 176 #define CHAATTR_REGION                          0x02
 177 #define CHAATTR_ELEMENT                         0x04
 178 #define CHAATTR_NUMBER                          0x08
 179
 180 typedef struct s_chsattr_params {
 181         u8 type;
 182         double ttau;
 183         double ptau;
 184         double dt;
 185         double dp;
 186         int rsteps;
 187         u8 avgrst;
 188 } t_chsattr_params;
 189
 190 #define CHSATTR_PCTRL                           0x01
 191 #define CHSATTR_TCTRL                           0x02
 192 #define CHSATTR_PRELAX                          0x04
 193 #define CHSATTR_TRELAX                          0x08
 194 #define CHSATTR_AVGRST                          0x10
 195 #define CHSATTR_RSTEPS                          0x20
 196
 197 typedef struct s_set_temp_params {
 198         u8 type;
 199         double val;
 200 } t_set_temp_params;
 201
 202 #define SET_TEMP_CURRENT                        0x01
 203 #define SET_TEMP_VALUE                          0x02
 204
 205 typedef struct s_set_timestep_params {
 206         double tau;
 207 } t_set_timestep_params;
 208
 209 typedef struct s_fill_params {
 210         double lc;                              // lattice constant
 211         int lx;                                 // amount of lc units
 212         int ly;
 213         int lz;
 214         u8 lattice;
 215         int fill_element;
 216         u8 fill_brand;
 217         t_part_params p_params;
 218         t_defect_params d_params;
 219         t_offset_params o_params;
 220 } t_fill_params;
 221
 222 typedef struct s_crt_params {
 223         u8 type;
 224         char file[128];
 225         t_3dvec *r_fin;
 226         u8 *constraints;
 227         int steps;
 228         int count;
 229 } t_crt_params;
 230
 231 /*
 232  * extern variables
 233  */
 234
 235 // constraint relaxation technique
 236 extern u8 crtt;
 237 extern u8 *constraints;
 238 extern double *trafo_angle;
 239
 240 /*
 241  * function prototypes
 242  */
 243
 244 #endif