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 #include "visual/visual.h"
  18
  19
  20 int create_lattice(unsigned char type,int element,double mass,double lc,
  21                    int a,int b,int c,t_atom **atom) {
  22
  23         int count;
  24         int ret;
  25         t_3dvec origin;
  26
  27         count=a*b*c;
  28
  29         if(type==FCC) count*=4;
  30         if(type==DIAMOND) count*=8;
  31
  32         *atom=malloc(count*sizeof(t_atom));
  33         if(*atom==NULL) {
  34                 perror("malloc (atoms)");
  35                 return -1;
  36         }
  37
  38         v3_zero(&origin);
  39
  40         switch(type) {
  41                 case FCC:
  42                         ret=fcc_init(a,b,c,lc,*atom,&origin);
  43                         break;
  44                 case DIAMOND:
  45                         ret=diamond_init(a,b,c,lc,*atom,&origin);
  46                         break;
  47                 default:
  48                         printf("unknown lattice type (%02x)\n",type);
  49                         return -1;
  50         }
  51
  52         /* debug */
  53         if(ret!=count) {
  54                 printf("ok, there is something wrong ...\n");
  55                 printf("calculated -> %d atoms\n",count);
  56                 printf("created -> %d atoms\n",ret);
  57                 return -1;
  58         }
  59
  60         while(count) {
  61                 (*atom)[count-1].element=element;
  62                 (*atom)[count-1].mass=mass;
  63                 count-=1;
  64         }
  65
  66         return ret;
  67 }
  68
  69 int destroy_lattice(t_atom *atom) {
  70
  71         if(atom) free(atom);
  72
  73         return 0;
  74 }
  75
  76 int thermal_init(t_atom *atom,t_random *random,int count,double t) {
  77
  78         /*
  79          * - gaussian distribution of velocities
  80          * - zero total momentum
  81          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
  82          */
  83
  84         int i;
  85         double v,sigma;
  86         t_3dvec p_total,delta;
  87
  88         /* gaussian distribution of velocities */
  89         v3_zero(&p_total);
  90         for(i=0;i<count;i++) {
  91                 sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
  92                 /* x direction */
  93                 v=sigma*rand_get_gauss(random);
  94                 atom[i].v.x=v;
  95                 p_total.x+=atom[i].mass*v;
  96                 /* y direction */
  97                 v=sigma*rand_get_gauss(random);
  98                 atom[i].v.y=v;
  99                 p_total.y+=atom[i].mass*v;
 100                 /* z direction */
 101                 v=sigma*rand_get_gauss(random);
 102                 atom[i].v.z=v;
 103                 p_total.z+=atom[i].mass*v;
 104         }
 105
 106         /* zero total momentum */
 107         v3_scale(&p_total,&p_total,1.0/count);
 108         for(i=0;i<count;i++) {
 109                 v3_scale(&delta,&p_total,1.0/atom[i].mass);
 110                 v3_sub(&(atom[i].v),&(atom[i].v),&delta);
 111         }
 112
 113         /* velocity scaling */
 114         scale_velocity(atom,count,t);
 115
 116         return 0;
 117 }
 118
 119 int scale_velocity(t_atom *atom,int count,double t) {
 120
 121         int i;
 122         double e,c;
 123
 124         /*
 125          * - velocity scaling (E = 3/2 N k T), E: kinetic energy
 126          */
 127         e=0.0;
 128         for(i=0;i<count;i++)
 129                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 130         c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
 131         for(i=0;i<count;i++)
 132                 v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 133
 134         return 0;
 135 }
 136
 137 double get_e_kin(t_atom *atom,int count) {
 138
 139         int i;
 140         double e;
 141
 142         e=0.0;
 143
 144         for(i=0;i<count;i++) {
 145                 e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
 146         }
 147
 148         return e;
 149 }
 150
 151 double get_e_pot(t_moldyn *moldyn) {
 152
 153         return(moldyn->potential(moldyn));
 154 }
 155
 156 double get_total_energy(t_moldyn *moldyn) {
 157
 158         double e;
 159
 160         e=get_e_kin(moldyn->atom,moldyn->count);
 161         e+=get_e_pot(moldyn);
 162
 163         return e;
 164 }
 165
 166 t_3dvec get_total_p(t_atom *atom, int count) {
 167
 168         t_3dvec p,p_total;
 169         int i;
 170
 171         v3_zero(&p_total);
 172         for(i=0;i<count;i++) {
 173                 v3_scale(&p,&(atom[i].v),atom[i].mass);
 174                 v3_add(&p_total,&p_total,&p);
 175         }
 176
 177         return p_total;
 178 }
 179
 180 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 181
 182         double tau;
 183
 184         tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
 185         tau*=1.0E-9;
 186         if(tau<moldyn->tau)
 187                 printf("[moldyn] warning: time step  (%f > %.15f)\n",
 188                        moldyn->tau,tau);
 189
 190         return tau;
 191 }
 192
 193
 194 /*
 195  *
 196  * 'integration of newtons equation' - algorithms
 197  *
 198  */
 199
 200 /* start the integration */
 201
 202 int moldyn_integrate(t_moldyn *moldyn) {
 203
 204         int i;
 205         int write;
 206
 207         write=moldyn->write;
 208
 209         /* calculate initial forces */
 210         moldyn->force(moldyn);
 211
 212         for(i=0;i<moldyn->time_steps;i++) {
 213                 /* integration step */
 214                 moldyn->integrate(moldyn);
 215
 216                 /* check for visualiziation */
 217                 if(!(i%write)) {
 218                         visual_atoms(moldyn->visual,i*moldyn->tau,
 219                                      moldyn->atom,moldyn->count);
 220                 }
 221         }
 222
 223         return 0;
 224 }
 225
 226 /* velocity verlet */
 227
 228 int velocity_verlet(t_moldyn *moldyn) {
 229
 230         int i,count;
 231         double tau,tau_square;
 232         t_3dvec delta;
 233         t_atom *atom;
 234
 235         atom=moldyn->atom;
 236         count=moldyn->count;
 237         tau=moldyn->tau;
 238
 239         tau_square=tau*tau;
 240
 241         for(i=0;i<count;i++) {
 242                 /* new positions */
 243                 v3_scale(&delta,&(atom[i].v),tau);
 244                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 245                 v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 246                 v3_add(&(atom[i].r),&(atom[i].r),&delta);
 247                 v3_per_bound(&(atom[i].r),&(moldyn->dim));
 248
 249                 /* velocities */
 250                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 251                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 252         }
 253
 254         /* forces depending on chosen potential */
 255         moldyn->force(moldyn);
 256
 257         for(i=0;i<count;i++) {
 258                 /* again velocities */
 259                 v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 260                 v3_add(&(atom[i].v),&(atom[i].v),&delta);
 261         }
 262
 263         return 0;
 264 }
 265
 266
 267 /*
 268  *
 269  * potentials & corresponding forces
 270  *
 271  */
 272
 273 /* harmonic oscillator potential and force */
 274
 275 double potential_harmonic_oscillator(t_moldyn *moldyn) {
 276
 277         t_ho_params *params;
 278         t_atom *atom;
 279         int i,j;
 280         int count;
 281         t_3dvec distance;
 282         double d,u;
 283         double sc,equi_dist;
 284
 285         params=moldyn->pot_params;
 286         atom=moldyn->atom;
 287         sc=params->spring_constant;
 288         equi_dist=params->equilibrium_distance;
 289         count=moldyn->count;
 290
 291         u=0.0;
 292         for(i=0;i<count;i++) {
 293                 for(j=0;j<i;j++) {
 294                         v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 295                         d=v3_norm(&distance);
 296                         u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
 297                 }
 298         }
 299
 300         return u;
 301 }
 302
 303 int force_harmonic_oscillator(t_moldyn *moldyn) {
 304
 305         t_ho_params *params;
 306         int i,j,count;
 307         t_atom *atom;
 308         t_3dvec distance;
 309         t_3dvec force;
 310         double d;
 311         double sc,equi_dist;
 312
 313         atom=moldyn->atom;
 314         count=moldyn->count;
 315         params=moldyn->pot_params;
 316         sc=params->spring_constant;
 317         equi_dist=params->equilibrium_distance;
 318
 319         for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 320
 321         for(i=0;i<count;i++) {
 322                 for(j=0;j<i;j++) {
 323                         v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 324                         v3_per_bound(&distance,&(moldyn->dim));
 325                         d=v3_norm(&distance);
 326                         if(d<=moldyn->cutoff) {
 327                                 v3_scale(&force,&distance,
 328                                          (-sc*(1.0-(equi_dist/d))));
 329                                 v3_add(&(atom[i].f),&(atom[i].f),&force);
 330                                 v3_sub(&(atom[j].f),&(atom[j].f),&force);
 331                         }
 332                 }
 333         }
 334
 335         return 0;
 336 }
 337
 338
 339 /* lennard jones potential & force for one sort of atoms */
 340
 341 double potential_lennard_jones(t_moldyn *moldyn) {
 342
 343         t_lj_params *params;
 344         t_atom *atom;
 345         int i,j;
 346         int count;
 347         t_3dvec distance;
 348         double d,help;
 349         double u;
 350         double eps,sig6,sig12;
 351
 352         params=moldyn->pot_params;
 353         atom=moldyn->atom;
 354         count=moldyn->count;
 355         eps=params->epsilon;
 356         sig6=params->sigma6;
 357         sig12=params->sigma12;
 358
 359         u=0.0;
 360         for(i=0;i<count;i++) {
 361                 for(j=0;j<i;j++) {
 362                         v3_sub(&distance,&(atom[j].r),&(atom[i].r));
 363                         d=1.0/v3_absolute_square(&distance);    /* 1/r^2 */
 364                         help=d*d;                               /* 1/r^4 */
 365                         help*=d;                                /* 1/r^6 */
 366                         d=help*help;                            /* 1/r^12 */
 367                         u+=eps*(sig12*d-sig6*help);
 368                 }
 369         }
 370
 371         return u;
 372 }
 373
 374 int force_lennard_jones(t_moldyn *moldyn) {
 375
 376         t_lj_params *params;
 377         int i,j,count;
 378         t_atom *atom;
 379         t_3dvec distance;
 380         t_3dvec force;
 381         double d,h1,h2;
 382         double eps,sig6,sig12;
 383
 384         atom=moldyn->atom;
 385         count=moldyn->count;
 386         params=moldyn->pot_params;
 387         eps=params->epsilon;
 388         sig6=params->sigma6;
 389         sig12=params->sigma12;
 390
 391         for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 392
 393         for(i=0;i<count;i++) {
 394                 for(j=0;j<i;j++) {
 395                         v3_sub(&distance,&(atom[j].r),&(atom[i].r));
 396                         v3_per_bound(&distance,&(moldyn->dim));
 397                         d=v3_absolute_square(&distance);
 398                         if(d<=moldyn->cutoff_square) {
 399                                 h1=1.0/d;                       /* 1/r^2 */
 400                                 d=h1*h1;                        /* 1/r^4 */
 401                                 h2=d*d;                         /* 1/r^8 */
 402                                 h1*=d;                          /* 1/r^6 */
 403                                 h1*=h2;                         /* 1/r^14 */
 404                                 h1*=sig12;
 405                                 h2*=sig6;
 406                                 d=12.0*h1-6.0*h2;
 407                                 d*=eps;
 408                                 v3_scale(&force,&distance,d);
 409                                 v3_add(&(atom[j].f),&(atom[j].f),&force);
 410                                 v3_sub(&(atom[i].f),&(atom[i].f),&force);
 411                         }
 412                 }
 413         }
 414
 415         return 0;
 416 }
 417