moldyn.c

   1 /*
   2  * moldyn.c - molecular dynamics library main file
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #include "moldyn.h"
   9
  10 #include <stdio.h>
  11 #include <stdlib.h>
  12 #include <math.h>
  13
  14 #include "math/math.h"
  15 #include "init/init.h"
  16 #include "random/random.h"
  17
  18
  19 int create_lattice(unsigned char type,int element,double mass,double lc,
  20                    int a,int b,int c,t_atom **atom) {
  21
  22         int count;
  23         int ret;
  24         t_3dvec origin;
  25
  26         count=a*b*c;
  27
  28         if(type==FCC) count*=4;
  29         if(type==DIAMOND) count*=8;
  30
  31         *atom=malloc(count*sizeof(t_atom));
  32         if(*atom==NULL) {
  33                 perror("malloc (atoms)");
  34                 return -1;
  35         }
  36
  37         v3_zero(&origin);
  38
  39         switch(type) {
  40                 case FCC:
  41                         ret=fcc_init(a,b,c,lc,*atom,&origin);
  42                         break;
  43                 case DIAMOND:
  44                         ret=diamond_init(a,b,c,lc,*atom,&origin);
  45                         break;
  46                 default:
  47                         printf("unknown lattice type (%02x)\n",type);
  48                         return -1;
  49         }
  50
  51         /* debug */
  52         if(ret!=count) {
  53                 printf("ok, there is something wrong ...\n");
  54                 printf("calculated -> %d atoms\n",count);
  55                 printf("created -> %d atoms\n",ret);
  56                 return -1;
  57         }
  58
  59         while(count) {
  60                 (*atom)[count-1].element=element;
  61                 (*atom)[count-1].mass=mass;
  62                 count-=1;
  63         }
  64
  65         return ret;
  66 }
  67
  68 int destroy_lattice(t_atom *atom) {
  69
  70         if(atom) free(atom);
  71
  72         return 0;
  73 }
  74
  75 int thermal_init(t_atom *atom,t_random *random,int count,double t) {
  76
  77         /*
  78          * - gaussian distribution of velocities
  79          * - zero total momentum
  80          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
  81          */
  82
  83         int i;
  84         double v,sigma;
  85         t_3dvec p_total,delta;
  86
  87         /* gaussian distribution of velocities */
  88         v3_zero(&p_total);
  89         for(i=0;i<count;i++) {
  90                 sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
  91                 /* x direction */
  92                 v=sigma*rand_get_gauss(random);
  93                 atom[i].v.x=v;
  94                 p_total.x+=atom[i].mass*v;
  95                 /* y direction */
  96                 v=sigma*rand_get_gauss(random);
  97                 atom[i].v.y=v;
  98                 p_total.y+=atom[i].mass*v;
  99                 /* z direction */
 100                 v=sigma*rand_get_gauss(random);
 101                 atom[i].v.z=v;
 102                 p_total.z+=atom[i].mass*v;
 103         }
 104
 105         /* zero total momentum */
 106         v3_scale(&p_total,&p_total,1.0/count);
 107         for(i=0;i<count;i++) {
 108                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 109                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 110         }
 111
 112         /* velocity scaling */
 113         scale_velocity(atom,count,t);
 114
 115         return 0;
 116 }
 117
 118 int scale_velocity(t_atom *atom,int count,double t) {
 119
 120         int i;
 121         double e,c;
 122
 123         /*
 124          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 125          */
 126         e=0.0;
 127         for(i=0;i<count;i++)
 128                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 129         c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
 130         for(i=0;i<count;i++)
 131                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 132
 133         return 0;
 134 }
 135
 136 double get_e_kin(t_atom *atom,int count) {
 137
 138         int i;
 139         double e;
 140
 141         e=0.0;
 142
 143         for(i=0;i<count;i++) {
 144                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 145         }
 146
 147         return e;
 148 }
 149
 150 t_3dvec get_total_p(t_atom *atom, int count) {
 151
 152         t_3dvec p,p_total;
 153         int i;
 154
 155         v3_zero(&p_total);
 156         for(i=0;i<count;i++) {
 157                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 158                 v3_add(&p_total,&p_total,&p);
 159         }
 160
 161         return p_total;
 162 }
 163
 164 double potential_lennard_jones_2(t_moldyn *moldyn,void *ptr) {
 165
 166         t_lj_params *params;
 167         t_atom *atom;
 168         int i,j;
 169         int count;
 170         t_3dvec distance;
 171         double d,help;
 172         double u;
 173         double eps,sig6,sig12;
 174
 175         params=ptr;
 176         atom=moldyn->atom;
 177         count=moldyn->count;
 178         eps=params->epsilon;
 179         sig6=params->sigma6;
 180         sig12=params->sigma12;
 181
 182         u=0.0;
 183         for(i=0;i<count;i++) {
 184                 for(j=0;j<i;j++) {
 185                         v3_sub(&distance,&(atom[j].r),&(atom[i].r));
 186                         d=v3_absolute_square(&distance);        /* 1/r^2 */
 187                         help=d*d;                               /* 1/r^4 */
 188                         help*=d;                                /* 1/r^6 */
 189                         d=help*help;                            /* 1/r^12 */
 190                         u+=eps*(sig12*d-sig6*help);
 191                 }
 192         }
 193
 194         return u;
 195 }
 196
 197