src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwNone_GeomP1P1_c.c

   1 /*
   2  * Note: this file was generated by the Gromacs c kernel generator.
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  * Copyright (c) 2001-2012, The GROMACS Development Team
   9  *
  10  * Gromacs is a library for molecular simulation and trajectory analysis,
  11  * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
  12  * a full list of developers and information, check out http://www.gromacs.org
  13  *
  14  * This program is free software; you can redistribute it and/or modify it under
  15  * the terms of the GNU Lesser General Public License as published by the Free
  16  * Software Foundation; either version 2 of the License, or (at your option) any
  17  * later version.
  18  *
  19  * To help fund GROMACS development, we humbly ask that you cite
  20  * the papers people have written on it - you can find them on the website.
  21  */
  22 #ifdef HAVE_CONFIG_H
  23 #include <config.h>
  24 #endif
  25
  26 #include <math.h>
  27
  28 #include "../nb_kernel.h"
  29 #include "types/simple.h"
  30 #include "vec.h"
  31 #include "nrnb.h"
  32
  33 /*
  34  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
  35  * Electrostatics interaction: GeneralizedBorn
  36  * VdW interaction:            None
  37  * Geometry:                   Particle-Particle
  38  * Calculate force/pot:        PotentialAndForce
  39  */
  40 void
  41 nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
  42                     (t_nblist * gmx_restrict                nlist,
  43                      rvec * gmx_restrict                    xx,
  44                      rvec * gmx_restrict                    ff,
  45                      t_forcerec * gmx_restrict              fr,
  46                      t_mdatoms * gmx_restrict               mdatoms,
  47                      nb_kernel_data_t * gmx_restrict        kernel_data,
  48                      t_nrnb * gmx_restrict                  nrnb)
  49 {
  50     int              i_shift_offset,i_coord_offset,j_coord_offset;
  51     int              j_index_start,j_index_end;
  52     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  53     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  54     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  55     real             *shiftvec,*fshift,*x,*f;
  56     int              vdwioffset0;
  57     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  58     int              vdwjidx0;
  59     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  60     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  61     real             velec,felec,velecsum,facel,crf,krf,krf2;
  62     real             *charge;
  63     int              gbitab;
  64     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
  65     real             *invsqrta,*dvda,*gbtab;
  66     int              vfitab;
  67     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
  68     real             *vftab;
  69
  70     x                = xx[0];
  71     f                = ff[0];
  72
  73     nri              = nlist->nri;
  74     iinr             = nlist->iinr;
  75     jindex           = nlist->jindex;
  76     jjnr             = nlist->jjnr;
  77     shiftidx         = nlist->shift;
  78     gid              = nlist->gid;
  79     shiftvec         = fr->shift_vec[0];
  80     fshift           = fr->fshift[0];
  81     facel            = fr->epsfac;
  82     charge           = mdatoms->chargeA;
  83
  84     invsqrta         = fr->invsqrta;
  85     dvda             = fr->dvda;
  86     gbtabscale       = fr->gbtab.scale;
  87     gbtab            = fr->gbtab.data;
  88     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
  89
  90     outeriter        = 0;
  91     inneriter        = 0;
  92
  93     /* Start outer loop over neighborlists */
  94     for(iidx=0; iidx<nri; iidx++)
  95     {
  96         /* Load shift vector for this list */
  97         i_shift_offset   = DIM*shiftidx[iidx];
  98         shX              = shiftvec[i_shift_offset+XX];
  99         shY              = shiftvec[i_shift_offset+YY];
 100         shZ              = shiftvec[i_shift_offset+ZZ];
 101
 102         /* Load limits for loop over neighbors */
 103         j_index_start    = jindex[iidx];
 104         j_index_end      = jindex[iidx+1];
 105
 106         /* Get outer coordinate index */
 107         inr              = iinr[iidx];
 108         i_coord_offset   = DIM*inr;
 109
 110         /* Load i particle coords and add shift vector */
 111         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 112         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 113         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 114
 115         fix0             = 0.0;
 116         fiy0             = 0.0;
 117         fiz0             = 0.0;
 118
 119         /* Load parameters for i particles */
 120         iq0              = facel*charge[inr+0];
 121         isai0            = invsqrta[inr+0];
 122
 123         /* Reset potential sums */
 124         velecsum         = 0.0;
 125         vgbsum           = 0.0;
 126         dvdasum          = 0.0;
 127
 128         /* Start inner kernel loop */
 129         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 130         {
 131             /* Get j neighbor index, and coordinate index */
 132             jnr              = jjnr[jidx];
 133             j_coord_offset   = DIM*jnr;
 134
 135             /* load j atom coordinates */
 136             jx0              = x[j_coord_offset+DIM*0+XX];
 137             jy0              = x[j_coord_offset+DIM*0+YY];
 138             jz0              = x[j_coord_offset+DIM*0+ZZ];
 139
 140             /* Calculate displacement vector */
 141             dx00             = ix0 - jx0;
 142             dy00             = iy0 - jy0;
 143             dz00             = iz0 - jz0;
 144
 145             /* Calculate squared distance and things based on it */
 146             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 147
 148             rinv00           = gmx_invsqrt(rsq00);
 149
 150             /* Load parameters for j particles */
 151             jq0              = charge[jnr+0];
 152             isaj0           = invsqrta[jnr+0];
 153
 154             /**************************
 155              * CALCULATE INTERACTIONS *
 156              **************************/
 157
 158             r00              = rsq00*rinv00;
 159
 160             qq00             = iq0*jq0;
 161
 162             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 163             isaprod          = isai0*isaj0;
 164             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 165             gbscale          = isaprod*gbtabscale;
 166             dvdaj            = dvda[jnr+0];
 167
 168             /* Calculate generalized born table index - this is a separate table from the normal one,
 169              * but we use the same procedure by multiplying r with scale and truncating to integer.
 170              */
 171             rt               = r00*gbscale;
 172             gbitab           = rt;
 173             gbeps            = rt-gbitab;
 174             gbitab           = 4*gbitab;
 175
 176             Y                = gbtab[gbitab];
 177             F                = gbtab[gbitab+1];
 178             Geps             = gbeps*gbtab[gbitab+2];
 179             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 180             Fp               = F+Geps+Heps2;
 181             VV               = Y+gbeps*Fp;
 182             vgb              = gbqqfactor*VV;
 183
 184             FF               = Fp+Geps+2.0*Heps2;
 185             fgb              = gbqqfactor*FF*gbscale;
 186             dvdatmp          = -0.5*(vgb+fgb*r00);
 187             dvdasum          = dvdasum + dvdatmp;
 188             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 189             velec            = qq00*rinv00;
 190             felec            = (velec*rinv00-fgb)*rinv00;
 191
 192             /* Update potential sums from outer loop */
 193             velecsum        += velec;
 194             vgbsum          += vgb;
 195
 196             fscal            = felec;
 197
 198             /* Calculate temporary vectorial force */
 199             tx               = fscal*dx00;
 200             ty               = fscal*dy00;
 201             tz               = fscal*dz00;
 202
 203             /* Update vectorial force */
 204             fix0            += tx;
 205             fiy0            += ty;
 206             fiz0            += tz;
 207             f[j_coord_offset+DIM*0+XX] -= tx;
 208             f[j_coord_offset+DIM*0+YY] -= ty;
 209             f[j_coord_offset+DIM*0+ZZ] -= tz;
 210
 211             /* Inner loop uses 58 flops */
 212         }
 213         /* End of innermost loop */
 214
 215         tx = ty = tz = 0;
 216         f[i_coord_offset+DIM*0+XX] += fix0;
 217         f[i_coord_offset+DIM*0+YY] += fiy0;
 218         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 219         tx                         += fix0;
 220         ty                         += fiy0;
 221         tz                         += fiz0;
 222         fshift[i_shift_offset+XX]  += tx;
 223         fshift[i_shift_offset+YY]  += ty;
 224         fshift[i_shift_offset+ZZ]  += tz;
 225
 226         ggid                        = gid[iidx];
 227         /* Update potential energies */
 228         kernel_data->energygrp_elec[ggid] += velecsum;
 229         kernel_data->energygrp_polarization[ggid] += vgbsum;
 230         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 231
 232         /* Increment number of inner iterations */
 233         inneriter                  += j_index_end - j_index_start;
 234
 235         /* Outer loop uses 15 flops */
 236     }
 237
 238     /* Increment number of outer iterations */
 239     outeriter        += nri;
 240
 241     /* Update outer/inner flops */
 242
 243     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58);
 244 }
 245 /*
 246  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
 247  * Electrostatics interaction: GeneralizedBorn
 248  * VdW interaction:            None
 249  * Geometry:                   Particle-Particle
 250  * Calculate force/pot:        Force
 251  */
 252 void
 253 nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
 254                     (t_nblist * gmx_restrict                nlist,
 255                      rvec * gmx_restrict                    xx,
 256                      rvec * gmx_restrict                    ff,
 257                      t_forcerec * gmx_restrict              fr,
 258                      t_mdatoms * gmx_restrict               mdatoms,
 259                      nb_kernel_data_t * gmx_restrict        kernel_data,
 260                      t_nrnb * gmx_restrict                  nrnb)
 261 {
 262     int              i_shift_offset,i_coord_offset,j_coord_offset;
 263     int              j_index_start,j_index_end;
 264     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 265     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 266     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 267     real             *shiftvec,*fshift,*x,*f;
 268     int              vdwioffset0;
 269     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 270     int              vdwjidx0;
 271     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 272     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 273     real             velec,felec,velecsum,facel,crf,krf,krf2;
 274     real             *charge;
 275     int              gbitab;
 276     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
 277     real             *invsqrta,*dvda,*gbtab;
 278     int              vfitab;
 279     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
 280     real             *vftab;
 281
 282     x                = xx[0];
 283     f                = ff[0];
 284
 285     nri              = nlist->nri;
 286     iinr             = nlist->iinr;
 287     jindex           = nlist->jindex;
 288     jjnr             = nlist->jjnr;
 289     shiftidx         = nlist->shift;
 290     gid              = nlist->gid;
 291     shiftvec         = fr->shift_vec[0];
 292     fshift           = fr->fshift[0];
 293     facel            = fr->epsfac;
 294     charge           = mdatoms->chargeA;
 295
 296     invsqrta         = fr->invsqrta;
 297     dvda             = fr->dvda;
 298     gbtabscale       = fr->gbtab.scale;
 299     gbtab            = fr->gbtab.data;
 300     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
 301
 302     outeriter        = 0;
 303     inneriter        = 0;
 304
 305     /* Start outer loop over neighborlists */
 306     for(iidx=0; iidx<nri; iidx++)
 307     {
 308         /* Load shift vector for this list */
 309         i_shift_offset   = DIM*shiftidx[iidx];
 310         shX              = shiftvec[i_shift_offset+XX];
 311         shY              = shiftvec[i_shift_offset+YY];
 312         shZ              = shiftvec[i_shift_offset+ZZ];
 313
 314         /* Load limits for loop over neighbors */
 315         j_index_start    = jindex[iidx];
 316         j_index_end      = jindex[iidx+1];
 317
 318         /* Get outer coordinate index */
 319         inr              = iinr[iidx];
 320         i_coord_offset   = DIM*inr;
 321
 322         /* Load i particle coords and add shift vector */
 323         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 324         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 325         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 326
 327         fix0             = 0.0;
 328         fiy0             = 0.0;
 329         fiz0             = 0.0;
 330
 331         /* Load parameters for i particles */
 332         iq0              = facel*charge[inr+0];
 333         isai0            = invsqrta[inr+0];
 334
 335         dvdasum          = 0.0;
 336
 337         /* Start inner kernel loop */
 338         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 339         {
 340             /* Get j neighbor index, and coordinate index */
 341             jnr              = jjnr[jidx];
 342             j_coord_offset   = DIM*jnr;
 343
 344             /* load j atom coordinates */
 345             jx0              = x[j_coord_offset+DIM*0+XX];
 346             jy0              = x[j_coord_offset+DIM*0+YY];
 347             jz0              = x[j_coord_offset+DIM*0+ZZ];
 348
 349             /* Calculate displacement vector */
 350             dx00             = ix0 - jx0;
 351             dy00             = iy0 - jy0;
 352             dz00             = iz0 - jz0;
 353
 354             /* Calculate squared distance and things based on it */
 355             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 356
 357             rinv00           = gmx_invsqrt(rsq00);
 358
 359             /* Load parameters for j particles */
 360             jq0              = charge[jnr+0];
 361             isaj0           = invsqrta[jnr+0];
 362
 363             /**************************
 364              * CALCULATE INTERACTIONS *
 365              **************************/
 366
 367             r00              = rsq00*rinv00;
 368
 369             qq00             = iq0*jq0;
 370
 371             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 372             isaprod          = isai0*isaj0;
 373             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 374             gbscale          = isaprod*gbtabscale;
 375             dvdaj            = dvda[jnr+0];
 376
 377             /* Calculate generalized born table index - this is a separate table from the normal one,
 378              * but we use the same procedure by multiplying r with scale and truncating to integer.
 379              */
 380             rt               = r00*gbscale;
 381             gbitab           = rt;
 382             gbeps            = rt-gbitab;
 383             gbitab           = 4*gbitab;
 384
 385             Y                = gbtab[gbitab];
 386             F                = gbtab[gbitab+1];
 387             Geps             = gbeps*gbtab[gbitab+2];
 388             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 389             Fp               = F+Geps+Heps2;
 390             VV               = Y+gbeps*Fp;
 391             vgb              = gbqqfactor*VV;
 392
 393             FF               = Fp+Geps+2.0*Heps2;
 394             fgb              = gbqqfactor*FF*gbscale;
 395             dvdatmp          = -0.5*(vgb+fgb*r00);
 396             dvdasum          = dvdasum + dvdatmp;
 397             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 398             velec            = qq00*rinv00;
 399             felec            = (velec*rinv00-fgb)*rinv00;
 400
 401             fscal            = felec;
 402
 403             /* Calculate temporary vectorial force */
 404             tx               = fscal*dx00;
 405             ty               = fscal*dy00;
 406             tz               = fscal*dz00;
 407
 408             /* Update vectorial force */
 409             fix0            += tx;
 410             fiy0            += ty;
 411             fiz0            += tz;
 412             f[j_coord_offset+DIM*0+XX] -= tx;
 413             f[j_coord_offset+DIM*0+YY] -= ty;
 414             f[j_coord_offset+DIM*0+ZZ] -= tz;
 415
 416             /* Inner loop uses 56 flops */
 417         }
 418         /* End of innermost loop */
 419
 420         tx = ty = tz = 0;
 421         f[i_coord_offset+DIM*0+XX] += fix0;
 422         f[i_coord_offset+DIM*0+YY] += fiy0;
 423         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 424         tx                         += fix0;
 425         ty                         += fiy0;
 426         tz                         += fiz0;
 427         fshift[i_shift_offset+XX]  += tx;
 428         fshift[i_shift_offset+YY]  += ty;
 429         fshift[i_shift_offset+ZZ]  += tz;
 430
 431         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 432
 433         /* Increment number of inner iterations */
 434         inneriter                  += j_index_end - j_index_start;
 435
 436         /* Outer loop uses 13 flops */
 437     }
 438
 439     /* Increment number of outer iterations */
 440     outeriter        += nri;
 441
 442     /* Update outer/inner flops */
 443
 444     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56);
 445 }