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 /* elements */
  22 #include "pse.h"
  23
  24 /* list api */
  25 #include "list/list.h"
  26
  27 /* potentials */
  28 #include "potentials/harmonic_oscillator.h"
  29 #include "potentials/lennard_jones.h"
  30 #include "potentials/albe.h"
  31 #ifdef TERSOFF_ORIG
  32 #include "potentials/tersoff_orig.h"
  33 #else
  34 #include "potentials/tersoff.h"
  35 #endif
  36
  37 /*
  38  * datatypes & definitions
  39  */
  40
  41 typedef struct s_stage {
  42         u8 type;
  43         void *params;
  44         u8 executed;
  45 } t_stage;
  46
  47 #define STAGE_INSERT_ATOMS                      0x01
  48 #define STAGE_CONTINUE                          0x02
  49 #define STAGE_ANNEAL                            0x03
  50 #define STAGE_CHAATTR                           0x04
  51 #define STAGE_CHSATTR                           0x05
  52
  53 typedef struct s_mdrun {
  54         char cfile[128];                        // config file
  55
  56         u8 intalgo;                             // integration algorithm
  57         double timestep;                        // timestep
  58
  59         u8 potential;                           // potential
  60
  61         double cutoff;                          // cutoff radius
  62         t_3dvec dim;                            // simulation volume
  63         u8 pbcx;                                // periodic boundary conditions
  64         u8 pbcy;
  65         u8 pbcz;
  66
  67         int element1;                           // element 1
  68         double m1;
  69         int element2;                           // element 2
  70         double m2;
  71         double lc;                              // lattice constant
  72         int lx;                                 // amount of lc units
  73         int ly;
  74         int lz;
  75         u8 lattice;                             // type of lattice
  76
  77         u8 sattr;                               // system attributes
  78         double temperature;                     // temperature
  79         double pressure;                        // pressure
  80         double dp;
  81         double dt;
  82         int relax_steps;                        // amount of relaxation steps
  83
  84         int prerun;                             // amount of loops in first run
  85
  86         int elog;                               // logging
  87         int tlog;
  88         int plog;
  89         int vlog;
  90         int save;
  91         int visualize;
  92         u8 vis;
  93         int avgskip;                            // average skip
  94         char sdir[128];                         // save root
  95
  96         t_list stage;                           // stages
  97         int s_cnt;                              // stage counter
  98 } t_mdrun;
  99
 100 #define SATTR_PRELAX                            0x01
 101 #define SATTR_TRELAX                            0x02
 102 #define SATTR_AVGRST                            0x04
 103
 104 typedef struct s_insert_atoms_params {
 105         u8 type;
 106         double x0,y0,z0,x1,y1,z1;
 107         double cr;
 108         int ins_steps;
 109         int cnt_steps;
 110         int ins_atoms;
 111         int element;
 112         u8 brand;
 113         u8 attr;
 114 } t_insert_atoms_params;
 115
 116 #define INS_TOTAL                               0x01
 117 #define INS_REGION                              0x02
 118
 119 typedef struct s_continue_params {
 120         int runs;
 121 } t_continue_params;
 122
 123 typedef struct s_anneal_params {
 124         int runs;
 125         int count;
 126         double dt;
 127 } t_anneal_params;
 128
 129 typedef struct s_chaattr_params {
 130         u8 type;
 131         double x0,y0,z0;
 132         double x1,y1,z1;
 133         int element;
 134         u8 attr;
 135 } t_chaattr_params;
 136
 137 #define CHAATTR_TOTALV                          0x01
 138 #define CHAATTR_REGION                          0x02
 139 #define CHAATTR_ELEMENT                         0x04
 140
 141 typedef struct s_chsattr_params {
 142         u8 type;
 143         double ttau;
 144         double ptau;
 145         double dt;
 146         double dp;
 147         int rsteps;
 148         u8 avgrst;
 149 } t_chsattr_params;
 150
 151 #define CHSATTR_PCTRL                           0x01
 152 #define CHSATTR_TCTRL                           0x02
 153 #define CHSATTR_PRELAX                          0x04
 154 #define CHSATTR_TRELAX                          0x08
 155 #define CHSATTR_AVGRST                          0x10
 156 #define CHSATTR_RSTEPS                          0x20
 157
 158 /*
 159  * function prototypes
 160  */
 161
 162
 163 #endif