potentials/albe_orig.c

   1 /*
   2  * albe_orig.c - albe potential
   3  *
   4  * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 #include <stdlib.h>
  11 #include <string.h>
  12 #include <sys/types.h>
  13 #include <sys/stat.h>
  14 #include <fcntl.h>
  15 #include <unistd.h>
  16 #include <math.h>
  17
  18 #include "../moldyn.h"
  19 #include "../math/math.h"
  20 #include "albe_orig.h"
  21
  22 /* create mixed terms from parameters and set them */
  23 int albe_orig_mult_set_params(t_moldyn *moldyn,int element1,int element2) {
  24
  25         t_albe_orig_mult_params *p;
  26
  27         // set cutoff before parameters (actually only necessary for some pots)
  28         if(moldyn->cutoff==0.0) {
  29                 printf("[albe orig] WARNING: no cutoff!\n");
  30                 return -1;
  31         }
  32
  33         /* alloc mem for potential parameters */
  34         moldyn->pot_params=malloc(sizeof(t_albe_mult_params));
  35         if(moldyn->pot_params==NULL) {
  36                 perror("[albe orig] pot params alloc");
  37                 return -1;
  38         }
  39
  40         /* these are now albe parameters */
  41         p=moldyn->pot_params;
  42
  43         // only 1 combination by now :p
  44         switch(element1) {
  45                 case SI:
  46                         /* type: silicon */
  47                         p->S[0]=ALBE_S_SI;
  48                         p->R[0]=ALBE_R_SI;
  49                         p->A[0]=ALBE_A_SI;
  50                         p->B[0]=ALBE_B_SI;
  51                         p->r0[0]=ALBE_R0_SI;
  52                         p->lambda[0]=ALBE_LAMBDA_SI;
  53                         p->mu[0]=ALBE_MU_SI;
  54                         p->gamma[0]=ALBE_GAMMA_SI;
  55                         p->c[0]=ALBE_C_SI;
  56                         p->c2[0]=p->c[0]*p->c[0];
  57                         p->d[0]=ALBE_D_SI;
  58                         p->d2[0]=p->d[0]*p->d[0];
  59                         p->c2d2[0]=p->c2[0]/p->d2[0];
  60                         p->h[0]=ALBE_H_SI;
  61                         switch(element2) {
  62                                 case C:
  63                                         /* type: carbon */
  64                                         p->S[1]=ALBE_S_C;
  65                                         p->R[1]=ALBE_R_C;
  66                                         p->A[1]=ALBE_A_C;
  67                                         p->B[1]=ALBE_B_C;
  68                                         p->r0[1]=ALBE_R0_C;
  69                                         p->lambda[1]=ALBE_LAMBDA_C;
  70                                         p->mu[1]=ALBE_MU_C;
  71                                         p->gamma[1]=ALBE_GAMMA_C;
  72                                         p->c[1]=ALBE_C_C;
  73                                         p->c2[1]=p->c[1]*p->c[1];
  74                                         p->d[1]=ALBE_D_C;
  75                                         p->d2[1]=p->d[1]*p->d[1];
  76                                         p->c2d2[1]=p->c2[1]/p->d2[1];
  77                                         p->h[1]=ALBE_H_C;
  78                                         /* mixed type: silicon carbide */
  79                                         p->Smixed=ALBE_S_SIC;
  80                                         p->Rmixed=ALBE_R_SIC;
  81                                         p->Amixed=ALBE_A_SIC;
  82                                         p->Bmixed=ALBE_B_SIC;
  83                                         p->r0_mixed=ALBE_R0_SIC;
  84                                         p->lambda_m=ALBE_LAMBDA_SIC;
  85                                         p->mu_m=ALBE_MU_SIC;
  86                                         p->gamma_m=ALBE_GAMMA_SIC;
  87                                         p->c_mixed=ALBE_C_SIC;
  88                                         p->c2_m=p->c_mixed*p->c_mixed;
  89                                         p->d_mixed=ALBE_D_SIC;
  90                                         p->d2_m=p->d_mixed*p->d_mixed;
  91                                         p->c2d2_m=p->c2_m/p->d2_m;
  92                                         p->h_mixed=ALBE_H_SIC;
  93                                         break;
  94                                 default:
  95                                         printf("[albe orig] WARNING: element2");
  96                                         printf("\n");
  97                                         return -1;
  98                         }
  99                         break;
 100                 default:
 101                         printf("[albe orig] WARNING: element1\n");
 102                         return -1;
 103         }
 104
 105         printf("[albe orig] parameter completion\n");
 106         p->S2[0]=p->S[0]*p->S[0];
 107         p->S2[1]=p->S[1]*p->S[1];
 108         p->S2mixed=p->Smixed*p->Smixed;
 109
 110         printf("[albe orig] mult parameter info:\n");
 111         printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
 112         printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
 113         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
 114         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
 115         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
 116                                           p->lambda_m);
 117         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
 118         printf("  gamma  | %f | %f | %f\n",p->gamma[0],p->gamma[1],p->gamma_m);
 119         printf("  c      | %f | %f | %f\n",p->c[0],p->c[1],p->c_mixed);
 120         printf("  d      | %f | %f | %f\n",p->d[0],p->d[1],p->d_mixed);
 121         printf("  h      | %f | %f | %f\n",p->h[0],p->h[1],p->h_mixed);
 122
 123         return 0;
 124 }
 125
 126 /* albe 3 body potential function (first ij loop) */
 127 int albe_orig_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 128
 129         t_albe_orig_mult_params *params;
 130         t_albe_orig_exchange *exchange;
 131         unsigned char brand;
 132         double S2;
 133         t_3dvec dist_ij;
 134         double d_ij2,d_ij;
 135
 136         params=moldyn->pot_params;
 137         exchange=&(params->exchange);
 138
 139         /* reset zeta sum */
 140         exchange->zeta_ij=0.0;
 141
 142         /*
 143          * set ij depending values
 144          */
 145
 146         brand=ai->brand;
 147         if(brand==aj->brand) {
 148                 S2=params->S2[brand];
 149         }
 150         else {
 151                 S2=params->S2mixed;
 152         }
 153
 154         /* dist_ij, d_ij2 */
 155         v3_sub(&dist_ij,&(aj->r),&(ai->r));
 156         if(bc) check_per_bound(moldyn,&dist_ij);
 157         d_ij2=v3_absolute_square(&dist_ij);
 158
 159         /* if d_ij2 > S2 => no force & potential energy contribution */
 160         if(d_ij2>S2) {
 161                 moldyn->run3bp=0;
 162                 return 0;
 163         }
 164
 165         /* d_ij */
 166         d_ij=sqrt(d_ij2);
 167
 168         /* store values */
 169         exchange->dist_ij=dist_ij;
 170         exchange->d_ij2=d_ij2;
 171         exchange->d_ij=d_ij;
 172
 173         /* reset k counter for first k loop */
 174         exchange->kcount=0;
 175
 176         return 0;
 177 }
 178
 179 /* albe 3 body potential function (first k loop) */
 180 int albe_orig_mult_3bp_k1(t_moldyn *moldyn,
 181                           t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 182
 183         t_albe_orig_mult_params *params;
 184         t_albe_orig_exchange *exchange;
 185         unsigned char brand;
 186         double R,S,S2;
 187         t_3dvec dist_ij,dist_ik;
 188         double d_ik2,d_ik,d_ij;
 189         double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
 190         double f_c_ik,df_c_ik;
 191         int kcount;
 192
 193         /* continue if aj equals ak */
 194         if(aj==ak)
 195                 return 0;
 196
 197         params=moldyn->pot_params;
 198         exchange=&(params->exchange);
 199         kcount=exchange->kcount;
 200
 201         if(kcount>ALBE_ORIG_MAXN) {
 202                 printf("FATAL: neighbours = %d\n",kcount);
 203                 printf("  -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
 204         }
 205
 206         /* ik constants */
 207         brand=ai->brand;
 208         if(brand==ak->brand) {
 209                 R=params->R[brand];
 210                 S=params->S[brand];
 211                 S2=params->S2[brand];
 212                 /* albe needs i,k depending c,d,h and gamma values */
 213                 exchange->gamma_i=&(params->gamma[brand]);
 214                 exchange->c_i=&(params->c[brand]);
 215                 exchange->d_i=&(params->d[brand]);
 216                 exchange->h_i=&(params->h[brand]);
 217                 exchange->ci2=&(params->c2[brand]);
 218                 exchange->di2=&(params->d2[brand]);
 219                 exchange->ci2di2=&(params->c2d2[brand]);
 220         }
 221         else {
 222                 R=params->Rmixed;
 223                 S=params->Smixed;
 224                 S2=params->S2mixed;
 225                 /* albe needs i,k depending c,d,h and gamma values */
 226                 exchange->gamma_i=&(params->gamma_m);
 227                 exchange->c_i=&(params->c_mixed);
 228                 exchange->d_i=&(params->d_mixed);
 229                 exchange->h_i=&(params->h_mixed);
 230                 exchange->ci2=&(params->c2_m);
 231                 exchange->di2=&(params->d2_m);
 232                 exchange->ci2di2=&(params->c2d2_m);
 233         }
 234
 235         /* dist_ik, d_ik2 */
 236         v3_sub(&dist_ik,&(ak->r),&(ai->r));
 237         if(bc) check_per_bound(moldyn,&dist_ik);
 238         d_ik2=v3_absolute_square(&dist_ik);
 239
 240         /* store data for second k loop */
 241         exchange->dist_ik[kcount]=dist_ik;
 242         exchange->d_ik2[kcount]=d_ik2;
 243
 244         /* return if not within cutoff */
 245         if(d_ik2>S2) {
 246                 exchange->kcount++;
 247                 return 0;
 248         }
 249
 250         /* d_ik */
 251         d_ik=sqrt(d_ik2);
 252
 253         /* dist_ij, d_ij */
 254         dist_ij=exchange->dist_ij;
 255         d_ij=exchange->d_ij;
 256
 257         /* cos theta */
 258         cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
 259
 260         /* g_ijk */
 261         h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
 262         d2_h_cos2=*(exchange->di2)+(h_cos*h_cos);
 263         frac=*(exchange->ci2)/d2_h_cos2;
 264         g=*(exchange->gamma_i)*(1.0+*(exchange->ci2di2)-frac);
 265         dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
 266
 267         /* zeta sum += f_c_ik * g_ijk */
 268         if(d_ik<=R) {
 269                 exchange->zeta_ij+=g;
 270                 f_c_ik=1.0;
 271                 df_c_ik=0.0;
 272         }
 273         else {
 274                 s_r=S-R;
 275                 arg=M_PI*(d_ik-R)/s_r;
 276                 f_c_ik=0.5+0.5*cos(arg);
 277                 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 278                 exchange->zeta_ij+=f_c_ik*g;
 279         }
 280
 281         /* store even more data for second k loop */
 282         exchange->g[kcount]=g;
 283         exchange->dg[kcount]=dg;
 284         exchange->d_ik[kcount]=d_ik;
 285         exchange->cos_theta[kcount]=cos_theta;
 286         exchange->f_c_ik[kcount]=f_c_ik;
 287         exchange->df_c_ik[kcount]=df_c_ik;
 288
 289         /* increase k counter */
 290         exchange->kcount++;
 291
 292         return 0;
 293 }
 294
 295 int albe_orig_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 296
 297         t_albe_orig_mult_params *params;
 298         t_albe_orig_exchange *exchange;
 299         t_3dvec force;
 300         double f_a,df_a,b,db,f_c,df_c;
 301         double f_r,df_r;
 302         double scale;
 303         double mu,B;
 304         double lambda,A;
 305         double d_ij,r0;
 306         unsigned char brand;
 307         double S,R,s_r,arg;
 308         double energy;
 309
 310         params=moldyn->pot_params;
 311         exchange=&(params->exchange);
 312
 313         brand=aj->brand;
 314         if(brand==ai->brand) {
 315                 S=params->S[brand];
 316                 R=params->R[brand];
 317                 B=params->B[brand];
 318                 A=params->A[brand];
 319                 r0=params->r0[brand];
 320                 mu=params->mu[brand];
 321                 lambda=params->lambda[brand];
 322         }
 323         else {
 324                 S=params->Smixed;
 325                 R=params->Rmixed;
 326                 B=params->Bmixed;
 327                 A=params->Amixed;
 328                 r0=params->r0_mixed;
 329                 mu=params->mu_m;
 330                 lambda=params->lambda_m;
 331         }
 332
 333         d_ij=exchange->d_ij;
 334
 335         /* f_c, df_c */
 336         if(d_ij<R) {
 337                 f_c=1.0;
 338                 df_c=0.0;
 339         }
 340         else {
 341                 s_r=S-R;
 342                 arg=M_PI*(d_ij-R)/s_r;
 343                 f_c=0.5+0.5*cos(arg);
 344                 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 345         }
 346
 347         /* f_a, df_a */
 348         f_a=-B*exp(-mu*(d_ij-r0));
 349         df_a=mu*f_a/d_ij;
 350
 351         /* f_r, df_r */
 352         f_r=A*exp(-lambda*(d_ij-r0));
 353         df_r=lambda*f_r/d_ij;
 354
 355         /* b, db */
 356         if(exchange->zeta_ij==0.0) {
 357                 b=1.0;
 358                 db=0.0;
 359         }
 360         else {
 361                 b=1.0/sqrt(1.0+exchange->zeta_ij);
 362                 db=-0.5*b/(1.0+exchange->zeta_ij);
 363         }
 364
 365         /* force contribution for atom i */
 366         scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism
 367         v3_scale(&force,&(exchange->dist_ij),scale);
 368         v3_add(&(ai->f),&(ai->f),&force);
 369
 370         /* force contribution for atom j */
 371         v3_scale(&force,&force,-1.0); // dri rij = - drj rij
 372         v3_add(&(aj->f),&(aj->f),&force);
 373
 374         /* virial */
 375         virial_calc(ai,&force,&(exchange->dist_ij));
 376
 377 #ifdef DEBUG
 378 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 379         if((ai==&(moldyn->atom[DATOM]))|(aj==&(moldyn->atom[DATOM]))) {
 380                 printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag);
 381                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 382                 if(ai==&(moldyn->atom[0]))
 383                         printf("  total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
 384                 if(aj==&(moldyn->atom[0]))
 385                         printf("  total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
 386                 printf("  energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r),
 387                                                     f_c,b,f_a,f_r);
 388                 printf("          %f %f %f\n",exchange->zeta_ij,.0,.0);
 389         }
 390 }
 391 #endif
 392
 393         /* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */
 394         exchange->pre_dzeta=0.5*f_a*f_c*db;
 395
 396         /* energy contribution */
 397         energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
 398         moldyn->energy+=energy;
 399         ai->e+=energy;
 400
 401         /* reset k counter for second k loop */
 402         exchange->kcount=0;
 403
 404         return 0;
 405 }
 406
 407 /* albe 3 body potential function (second k loop) */
 408 int albe_orig_mult_3bp_k2(t_moldyn *moldyn,
 409                           t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 410
 411         t_albe_orig_mult_params *params;
 412         t_albe_orig_exchange *exchange;
 413         int kcount;
 414         t_3dvec dist_ik,dist_ij;
 415         double d_ik2,d_ik,d_ij2,d_ij;
 416         unsigned char brand;
 417         double S2;
 418         double g,dg,cos_theta;
 419         double pre_dzeta;
 420         double f_c_ik,df_c_ik;
 421         double dijdik_inv,fcdg,dfcg;
 422         t_3dvec dcosdrj,dcosdrk;
 423         t_3dvec force,tmp;
 424
 425         /* continue if aj equals ak */
 426         if(aj==ak)
 427                 return 0;
 428
 429         params=moldyn->pot_params;
 430         exchange=&(params->exchange);
 431         kcount=exchange->kcount;
 432
 433         if(kcount>ALBE_ORIG_MAXN)
 434                 printf("FATAL: neighbours!\n");
 435
 436         /* d_ik2 */
 437         d_ik2=exchange->d_ik2[kcount];
 438
 439         brand=ak->brand;
 440         if(brand==ai->brand)
 441                 S2=params->S2[brand];
 442         else
 443                 S2=params->S2mixed;
 444
 445         /* return if d_ik > S */
 446         if(d_ik2>S2) {
 447                 exchange->kcount++;
 448                 return 0;
 449         }
 450
 451         /* prefactor dzeta */
 452         pre_dzeta=exchange->pre_dzeta;
 453
 454         /* dist_ik, d_ik */
 455         dist_ik=exchange->dist_ik[kcount];
 456         d_ik=exchange->d_ik[kcount];
 457
 458         /* f_c_ik, df_c_ik */
 459         f_c_ik=exchange->f_c_ik[kcount];
 460         df_c_ik=exchange->df_c_ik[kcount];
 461
 462         /* dist_ij, d_ij2, d_ij */
 463         dist_ij=exchange->dist_ij;
 464         d_ij2=exchange->d_ij2;
 465         d_ij=exchange->d_ij;
 466
 467         /* g, dg, cos_theta */
 468         g=exchange->g[kcount];
 469         dg=exchange->dg[kcount];
 470         cos_theta=exchange->cos_theta[kcount];
 471
 472         /* cos_theta derivatives wrt j,k */
 473         dijdik_inv=1.0/(d_ij*d_ik);
 474         v3_scale(&dcosdrj,&dist_ik,dijdik_inv);         // j
 475         v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
 476         v3_add(&dcosdrj,&dcosdrj,&tmp);
 477         v3_scale(&dcosdrk,&dist_ij,dijdik_inv);         // k
 478         v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
 479         v3_add(&dcosdrk,&dcosdrk,&tmp);
 480
 481         /* f_c_ik * dg, df_c_ik * g */
 482         fcdg=f_c_ik*dg;
 483         dfcg=df_c_ik*g;
 484
 485         /* derivative wrt j */
 486         v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
 487
 488         /* force contribution */
 489         v3_add(&(aj->f),&(aj->f),&force);
 490
 491 #ifdef DEBUG
 492 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 493         if(aj==&(moldyn->atom[DATOM])) {
 494                 printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
 495                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 496                 printf("  total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
 497                 printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
 498                 printf("    d ij ik = %f %f\n",d_ij,d_ik);
 499         }
 500 }
 501 #endif
 502
 503         /* virial */
 504         virial_calc(ai,&force,&dist_ij);
 505
 506         /* force contribution to atom i */
 507         v3_scale(&force,&force,-1.0);
 508         v3_add(&(ai->f),&(ai->f),&force);
 509
 510         /* derivative wrt k */
 511         v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
 512         v3_scale(&tmp,&dcosdrk,fcdg);
 513         v3_add(&force,&force,&tmp);
 514         v3_scale(&force,&force,pre_dzeta);
 515
 516         /* force contribution */
 517         v3_add(&(ak->f),&(ak->f),&force);
 518
 519 #ifdef DEBUG
 520 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 521         if(ak==&(moldyn->atom[DATOM])) {
 522                 printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
 523                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 524                 printf("  total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
 525                 printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
 526                 printf("    d ij ik = %f %f\n",d_ij,d_ik);
 527         }
 528 }
 529 #endif
 530
 531         /* virial */
 532         virial_calc(ai,&force,&dist_ik);
 533
 534         /* force contribution to atom i */
 535         v3_scale(&force,&force,-1.0);
 536         v3_add(&(ai->f),&(ai->f),&force);
 537
 538         /* increase k counter */
 539         exchange->kcount++;
 540
 541         return 0;
 542
 543 }
 544
 545 int albe_orig_mult_check_2b_bond(t_moldyn *moldyn,
 546                                  t_atom *itom,t_atom *jtom,u8 bc) {
 547
 548         t_albe_orig_mult_params *params;
 549         t_3dvec dist;
 550         double d;
 551         u8 brand;
 552
 553         v3_sub(&dist,&(jtom->r),&(itom->r));
 554         if(bc) check_per_bound(moldyn,&dist);
 555         d=v3_absolute_square(&dist);
 556
 557         params=moldyn->pot_params;
 558         brand=itom->brand;
 559
 560         if(brand==jtom->brand) {
 561                 if(d<=params->S2[brand])
 562                         return TRUE;
 563         }
 564         else {
 565                 if(d<=params->S2mixed)
 566                         return TRUE;
 567         }
 568
 569         return FALSE;
 570 }