potentials/albe.c

   1 /*
   2  * albe.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.h"
  21
  22 /* create mixed terms from parameters and set them */
  23 int albe_mult_set_params(t_moldyn *moldyn,int element1,int element2) {
  24
  25         t_albe_mult_params *p;
  26
  27         // set cutoff before parameters (actually only necessary for some pots)
  28         if(moldyn->cutoff==0.0) {
  29                 printf("[albe] 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] 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->d[0]=ALBE_D_SI;
  57                         p->h[0]=ALBE_H_SI;
  58                         switch(element2) {
  59                                 case C:
  60                                         /* type: carbon */
  61                                         p->S[1]=ALBE_S_C;
  62                                         p->R[1]=ALBE_R_C;
  63                                         p->A[1]=ALBE_A_C;
  64                                         p->B[1]=ALBE_B_C;
  65                                         p->r0[1]=ALBE_R0_C;
  66                                         p->lambda[1]=ALBE_LAMBDA_C;
  67                                         p->mu[1]=ALBE_MU_C;
  68                                         p->gamma[1]=ALBE_GAMMA_C;
  69                                         p->c[1]=ALBE_C_C;
  70                                         p->d[1]=ALBE_D_C;
  71                                         p->h[1]=ALBE_H_C;
  72                                         /* mixed type: silicon carbide */
  73                                         p->Smixed=ALBE_S_SIC;
  74                                         p->Rmixed=ALBE_R_SIC;
  75                                         p->Amixed=ALBE_A_SIC;
  76                                         p->Bmixed=ALBE_B_SIC;
  77                                         p->r0_mixed=ALBE_R0_SIC;
  78                                         p->lambda_m=ALBE_LAMBDA_SIC;
  79                                         p->mu_m=ALBE_MU_SIC;
  80                                         p->gamma_m=ALBE_GAMMA_SIC;
  81                                         p->c_mixed=ALBE_C_SIC;
  82                                         p->d_mixed=ALBE_D_SIC;
  83                                         p->h_mixed=ALBE_H_SIC;
  84                                         break;
  85                                 default:
  86                                         printf("[albe] WARNING: element2\n");
  87                                         return -1;
  88                         }
  89                         break;
  90                 default:
  91                         printf("[albe] WARNING: element1\n");
  92                         return -1;
  93         }
  94
  95         printf("[albe] parameter completion\n");
  96         p->S2[0]=p->S[0]*p->S[0];
  97         p->S2[1]=p->S[1]*p->S[1];
  98         p->S2mixed=p->Smixed*p->Smixed;
  99         p->c2[0]=p->c[0]*p->c[0];
 100         p->c2[1]=p->c[1]*p->c[1];
 101         p->c2_mixed=p->c_mixed*p->c_mixed;
 102         p->d2[0]=p->d[0]*p->d[0];
 103         p->d2[1]=p->d[1]*p->d[1];
 104         p->d2_mixed=p->d_mixed*p->d_mixed;
 105         p->c2d2[0]=p->c2[0]/p->d2[0];
 106         p->c2d2[1]=p->c2[1]/p->d2[1];
 107         p->c2d2_m=p->c2_mixed/p->d2_mixed;
 108
 109         printf("[albe] mult parameter info:\n");
 110         printf("  S (A)  | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
 111         printf("  R (A)  | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
 112         printf("  A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
 113         printf("  B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
 114         printf("  lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
 115                                           p->lambda_m);
 116         printf("  mu     | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
 117         printf("  gamma  | %f | %f\n",p->gamma[0],p->gamma[1]);
 118         printf("  c      | %f | %f\n",p->c[0],p->c[1]);
 119         printf("  d      | %f | %f\n",p->d[0],p->d[1]);
 120         printf("  h      | %f | %f\n",p->h[0],p->h[1]);
 121
 122         return 0;
 123 }
 124
 125 /* albe 3 body potential function (first ij loop) */
 126 int albe_mult_3bp_j1(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 127
 128         t_albe_mult_params *params;
 129         t_albe_exchange *exchange;
 130         unsigned char brand;
 131         double S2;
 132         t_3dvec dist_ij;
 133         double d_ij2,d_ij;
 134
 135         params=moldyn->pot_params;
 136         exchange=&(params->exchange);
 137
 138         /* reset zeta sum */
 139         exchange->zeta_ij=0.0;
 140
 141         /*
 142          * set ij depending values
 143          */
 144
 145         brand=ai->brand;
 146         if(brand==aj->brand) {
 147                 S2=params->S2[brand];
 148         }
 149         else {
 150                 S2=params->S2mixed;
 151         }
 152
 153         /* dist_ij, d_ij2 */
 154         v3_sub(&dist_ij,&(aj->r),&(ai->r));
 155         if(bc) check_per_bound(moldyn,&dist_ij);
 156         d_ij2=v3_absolute_square(&dist_ij);
 157
 158         /* if d_ij2 > S2 => no force & potential energy contribution */
 159         if(d_ij2>S2) {
 160                 moldyn->run3bp=0;
 161                 return 0;
 162         }
 163
 164         /* d_ij */
 165         d_ij=sqrt(d_ij2);
 166
 167         /* store values */
 168         exchange->dist_ij=dist_ij;
 169         exchange->d_ij2=d_ij2;
 170         exchange->d_ij=d_ij;
 171
 172         /* reset k counter for first k loop */
 173         exchange->kcount=0;
 174
 175         return 0;
 176 }
 177
 178 /* albe 3 body potential function (first k loop) */
 179 #ifdef PTHREADS
 180 void *albe_mult_3bp_k1(void *ptr) {
 181 #else
 182 int albe_mult_3bp_k1(t_moldyn *moldyn,
 183                      t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 184 #endif
 185
 186         t_albe_mult_params *params;
 187         t_albe_exchange *exchange;
 188         unsigned char brand;
 189         double R,S,S2;
 190         t_3dvec dist_ij,dist_ik;
 191         double d_ik2,d_ik,d_ij;
 192         double cos_theta,h_cos,d2_h_cos2,frac,g,dg,s_r,arg;
 193         double f_c_ik,df_c_ik;
 194         int kcount;
 195 #ifdef PTHREADS
 196         t_kdata *kdata;
 197         t_moldyn *moldyn;
 198         t_atom *ai,*aj,*ak;
 199         u8 bc;
 200
 201         kdata=ptr;
 202         moldyn=kdata->moldyn;
 203         ai=kdata->ai;
 204         aj=kdata->aj;
 205         ak=kdata->ak;
 206         bc=kdata->bc;
 207 #endif
 208
 209         params=moldyn->pot_params;
 210         exchange=&(params->exchange);
 211         kcount=exchange->kcount;
 212
 213         if(kcount>ALBE_MAXN) {
 214                 printf("FATAL: neighbours = %d\n",kcount);
 215                 printf("  -> %d %d %d\n",ai->tag,aj->tag,ak->tag);
 216         }
 217
 218         /* ik constants */
 219         brand=ai->brand;
 220         if(brand==ak->brand) {
 221                 R=params->R[brand];
 222                 S=params->S[brand];
 223                 S2=params->S2[brand];
 224                 /* albe needs i,k depending c,d,h and gamma values */
 225                 exchange->gamma_i=&(params->gamma[brand]);
 226                 exchange->c_i=&(params->c[brand]);
 227                 exchange->d_i=&(params->d[brand]);
 228                 exchange->h_i=&(params->h[brand]);
 229         }
 230         else {
 231                 R=params->Rmixed;
 232                 S=params->Smixed;
 233                 S2=params->S2mixed;
 234                 /* albe needs i,k depending c,d,h and gamma values */
 235                 exchange->gamma_i=&(params->gamma_m);
 236                 exchange->c_i=&(params->c_mixed);
 237                 exchange->d_i=&(params->d_mixed);
 238                 exchange->h_i=&(params->h_mixed);
 239         }
 240         exchange->ci2=*(exchange->c_i)**(exchange->c_i);
 241         exchange->di2=*(exchange->d_i)**(exchange->d_i);
 242         exchange->ci2di2=exchange->ci2/exchange->di2;
 243
 244         /* dist_ik, d_ik2 */
 245         v3_sub(&dist_ik,&(ak->r),&(ai->r));
 246         if(bc) check_per_bound(moldyn,&dist_ik);
 247         d_ik2=v3_absolute_square(&dist_ik);
 248
 249         /* store data for second k loop */
 250         exchange->dist_ik[kcount]=dist_ik;
 251         exchange->d_ik2[kcount]=d_ik2;
 252
 253         /* return if not within cutoff */
 254         if(d_ik2>S2) {
 255                 exchange->kcount++;
 256                 return 0;
 257         }
 258
 259         /* d_ik */
 260         d_ik=sqrt(d_ik2);
 261
 262         /* dist_ij, d_ij */
 263         dist_ij=exchange->dist_ij;
 264         d_ij=exchange->d_ij;
 265
 266         /* cos theta */
 267         cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
 268
 269         /* g_ijk */
 270         h_cos=*(exchange->h_i)+cos_theta; // + in albe formalism
 271         d2_h_cos2=exchange->di2+(h_cos*h_cos);
 272         frac=exchange->ci2/d2_h_cos2;
 273         g=*(exchange->gamma_i)*(1.0+exchange->ci2di2-frac);
 274         dg=2.0*frac**(exchange->gamma_i)*h_cos/d2_h_cos2; // + in albe f..
 275
 276         /* zeta sum += f_c_ik * g_ijk */
 277         if(d_ik<=R) {
 278                 exchange->zeta_ij+=g;
 279                 f_c_ik=1.0;
 280                 df_c_ik=0.0;
 281         }
 282         else {
 283                 s_r=S-R;
 284                 arg=M_PI*(d_ik-R)/s_r;
 285                 f_c_ik=0.5+0.5*cos(arg);
 286                 df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 287                 exchange->zeta_ij+=f_c_ik*g;
 288         }
 289
 290         /* store even more data for second k loop */
 291         exchange->g[kcount]=g;
 292         exchange->dg[kcount]=dg;
 293         exchange->d_ik[kcount]=d_ik;
 294         exchange->cos_theta[kcount]=cos_theta;
 295         exchange->f_c_ik[kcount]=f_c_ik;
 296         exchange->df_c_ik[kcount]=df_c_ik;
 297
 298         /* increase k counter */
 299         exchange->kcount++;
 300
 301 #ifdef PTHREADS
 302 }
 303 #else
 304         return 0;
 305 }
 306 #endif
 307
 308 int albe_mult_3bp_j2(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 309
 310         t_albe_mult_params *params;
 311         t_albe_exchange *exchange;
 312         t_3dvec force;
 313         double f_a,df_a,b,db,f_c,df_c;
 314         double f_r,df_r;
 315         double scale;
 316         double mu,B;
 317         double lambda,A;
 318         double d_ij,r0;
 319         unsigned char brand;
 320         double S,R,s_r,arg;
 321         double energy;
 322
 323         params=moldyn->pot_params;
 324         exchange=&(params->exchange);
 325
 326         brand=aj->brand;
 327         if(brand==ai->brand) {
 328                 S=params->S[brand];
 329                 R=params->R[brand];
 330                 B=params->B[brand];
 331                 A=params->A[brand];
 332                 r0=params->r0[brand];
 333                 mu=params->mu[brand];
 334                 lambda=params->lambda[brand];
 335         }
 336         else {
 337                 S=params->Smixed;
 338                 R=params->Rmixed;
 339                 B=params->Bmixed;
 340                 A=params->Amixed;
 341                 r0=params->r0_mixed;
 342                 mu=params->mu_m;
 343                 lambda=params->lambda_m;
 344         }
 345
 346         d_ij=exchange->d_ij;
 347
 348         /* f_c, df_c */
 349         if(d_ij<R) {
 350                 f_c=1.0;
 351                 df_c=0.0;
 352         }
 353         else {
 354                 s_r=S-R;
 355                 arg=M_PI*(d_ij-R)/s_r;
 356                 f_c=0.5+0.5*cos(arg);
 357                 df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
 358         }
 359
 360         /* f_a, df_a */
 361         f_a=-B*exp(-mu*(d_ij-r0));
 362         df_a=mu*f_a/d_ij;
 363
 364         /* f_r, df_r */
 365         f_r=A*exp(-lambda*(d_ij-r0));
 366         df_r=lambda*f_r/d_ij;
 367
 368         /* b, db */
 369         if(exchange->zeta_ij==0.0) {
 370                 b=1.0;
 371                 db=0.0;
 372         }
 373         else {
 374                 b=1.0/sqrt(1.0+exchange->zeta_ij);
 375                 db=-0.5*b/(1.0+exchange->zeta_ij);
 376         }
 377
 378         /* force contribution for atom i */
 379         scale=-0.5*(f_c*(df_r-b*df_a)+df_c*(f_r-b*f_a)); // - in albe formalism
 380         v3_scale(&force,&(exchange->dist_ij),scale);
 381         v3_add(&(ai->f),&(ai->f),&force);
 382
 383         /* force contribution for atom j */
 384         v3_scale(&force,&force,-1.0); // dri rij = - drj rij
 385         v3_add(&(aj->f),&(aj->f),&force);
 386
 387         /* virial */
 388         virial_calc(ai,&force,&(exchange->dist_ij));
 389
 390 #ifdef DEBUG
 391 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 392         if((ai==&(moldyn->atom[DATOM]))|(aj==&(moldyn->atom[DATOM]))) {
 393                 printf("force 3bp (j2): [%d %d sum]\n",ai->tag,aj->tag);
 394                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 395                 if(ai==&(moldyn->atom[0]))
 396                         printf("  total i: %f %f %f\n",ai->f.x,ai->f.y,ai->f.z);
 397                 if(aj==&(moldyn->atom[0]))
 398                         printf("  total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
 399                 printf("  energy: %f = %f %f %f %f\n",0.5*f_c*(b*f_a+f_r),
 400                                                     f_c,b,f_a,f_r);
 401                 printf("          %f %f %f\n",exchange->zeta_ij,.0,.0);
 402         }
 403 }
 404 #endif
 405
 406         /* dzeta prefactor = - f_c f_a db, (* -0.5 due to force calc) */
 407         exchange->pre_dzeta=0.5*f_a*f_c*db;
 408
 409         /* energy contribution */
 410         energy=0.5*f_c*(f_r-b*f_a); // - in albe formalism
 411         moldyn->energy+=energy;
 412         ai->e+=energy;
 413
 414         /* reset k counter for second k loop */
 415         exchange->kcount=0;
 416
 417         return 0;
 418 }
 419
 420 /* albe 3 body potential function (second k loop) */
 421 int albe_mult_3bp_k2(t_moldyn *moldyn,
 422                      t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
 423
 424         t_albe_mult_params *params;
 425         t_albe_exchange *exchange;
 426         int kcount;
 427         t_3dvec dist_ik,dist_ij;
 428         double d_ik2,d_ik,d_ij2,d_ij;
 429         unsigned char brand;
 430         double S2;
 431         double g,dg,cos_theta;
 432         double pre_dzeta;
 433         double f_c_ik,df_c_ik;
 434         double dijdik_inv,fcdg,dfcg;
 435         t_3dvec dcosdrj,dcosdrk;
 436         t_3dvec force,tmp;
 437
 438         params=moldyn->pot_params;
 439         exchange=&(params->exchange);
 440         kcount=exchange->kcount;
 441
 442         if(kcount>ALBE_MAXN)
 443                 printf("FATAL: neighbours!\n");
 444
 445         /* d_ik2 */
 446         d_ik2=exchange->d_ik2[kcount];
 447
 448         brand=ak->brand;
 449         if(brand==ai->brand)
 450                 S2=params->S2[brand];
 451         else
 452                 S2=params->S2mixed;
 453
 454         /* return if d_ik > S */
 455         if(d_ik2>S2) {
 456                 exchange->kcount++;
 457                 return 0;
 458         }
 459
 460         /* prefactor dzeta */
 461         pre_dzeta=exchange->pre_dzeta;
 462
 463         /* dist_ik, d_ik */
 464         dist_ik=exchange->dist_ik[kcount];
 465         d_ik=exchange->d_ik[kcount];
 466
 467         /* f_c_ik, df_c_ik */
 468         f_c_ik=exchange->f_c_ik[kcount];
 469         df_c_ik=exchange->df_c_ik[kcount];
 470
 471         /* dist_ij, d_ij2, d_ij */
 472         dist_ij=exchange->dist_ij;
 473         d_ij2=exchange->d_ij2;
 474         d_ij=exchange->d_ij;
 475
 476         /* g, dg, cos_theta */
 477         g=exchange->g[kcount];
 478         dg=exchange->dg[kcount];
 479         cos_theta=exchange->cos_theta[kcount];
 480
 481         /* cos_theta derivatives wrt j,k */
 482         dijdik_inv=1.0/(d_ij*d_ik);
 483         v3_scale(&dcosdrj,&dist_ik,dijdik_inv);         // j
 484         v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
 485         v3_add(&dcosdrj,&dcosdrj,&tmp);
 486         v3_scale(&dcosdrk,&dist_ij,dijdik_inv);         // k
 487         v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
 488         v3_add(&dcosdrk,&dcosdrk,&tmp);
 489
 490         /* f_c_ik * dg, df_c_ik * g */
 491         fcdg=f_c_ik*dg;
 492         dfcg=df_c_ik*g;
 493
 494         /* derivative wrt j */
 495         v3_scale(&force,&dcosdrj,fcdg*pre_dzeta);
 496
 497         /* force contribution */
 498         v3_add(&(aj->f),&(aj->f),&force);
 499
 500 #ifdef DEBUG
 501 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 502         if(aj==&(moldyn->atom[DATOM])) {
 503                 printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
 504                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 505                 printf("  total j: %f %f %f\n",aj->f.x,aj->f.y,aj->f.z);
 506                 printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
 507                 printf("    d ij ik = %f %f\n",d_ij,d_ik);
 508         }
 509 }
 510 #endif
 511
 512         /* virial */
 513         virial_calc(ai,&force,&dist_ij);
 514
 515         /* force contribution to atom i */
 516         v3_scale(&force,&force,-1.0);
 517         v3_add(&(ai->f),&(ai->f),&force);
 518
 519         /* derivative wrt k */
 520         v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
 521         v3_scale(&tmp,&dcosdrk,fcdg);
 522         v3_add(&force,&force,&tmp);
 523         v3_scale(&force,&force,pre_dzeta);
 524
 525         /* force contribution */
 526         v3_add(&(ak->f),&(ak->f),&force);
 527
 528 #ifdef DEBUG
 529 if(moldyn->time>DSTART&&moldyn->time<DEND) {
 530         if(ak==&(moldyn->atom[DATOM])) {
 531                 printf("force 3bp (k2): [%d %d %d]\n",ai->tag,aj->tag,ak->tag);
 532                 printf("  adding %f %f %f\n",force.x,force.y,force.z);
 533                 printf("  total k: %f %f %f\n",ak->f.x,ak->f.y,ak->f.z);
 534                 printf("  angle: %f\n",acos(cos_theta)*360.0/(2*M_PI));
 535                 printf("    d ij ik = %f %f\n",d_ij,d_ik);
 536         }
 537 }
 538 #endif
 539
 540         /* virial */
 541         virial_calc(ai,&force,&dist_ik);
 542
 543         /* force contribution to atom i */
 544         v3_scale(&force,&force,-1.0);
 545         v3_add(&(ai->f),&(ai->f),&force);
 546
 547         /* increase k counter */
 548         exchange->kcount++;
 549
 550         return 0;
 551
 552 }
 553
 554 int albe_mult_check_2b_bond(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,u8 bc) {
 555
 556         t_albe_mult_params *params;
 557         t_3dvec dist;
 558         double d;
 559         u8 brand;
 560
 561         v3_sub(&dist,&(jtom->r),&(itom->r));
 562         if(bc) check_per_bound(moldyn,&dist);
 563         d=v3_absolute_square(&dist);
 564
 565         params=moldyn->pot_params;
 566         brand=itom->brand;
 567
 568         if(brand==jtom->brand) {
 569                 if(d<=params->S2[brand])
 570                         return TRUE;
 571         }
 572         else {
 573                 if(d<=params->S2mixed)
 574                         return TRUE;
 575         }
 576
 577         return FALSE;
 578 }