src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwBham_GeomP1P1_c.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
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  17  * Lesser General Public License for more details.
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  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43
  44 #include "../nb_kernel.h"
  45 #include "types/simple.h"
  46 #include "vec.h"
  47 #include "nrnb.h"
  48
  49 /*
  50  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
  51  * Electrostatics interaction: GeneralizedBorn
  52  * VdW interaction:            Buckingham
  53  * Geometry:                   Particle-Particle
  54  * Calculate force/pot:        PotentialAndForce
  55  */
  56 void
  57 nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
  58                     (t_nblist                    * gmx_restrict       nlist,
  59                      rvec                        * gmx_restrict          xx,
  60                      rvec                        * gmx_restrict          ff,
  61                      t_forcerec                  * gmx_restrict          fr,
  62                      t_mdatoms                   * gmx_restrict     mdatoms,
  63                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
  64                      t_nrnb                      * gmx_restrict        nrnb)
  65 {
  66     int              i_shift_offset,i_coord_offset,j_coord_offset;
  67     int              j_index_start,j_index_end;
  68     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  69     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  70     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  71     real             *shiftvec,*fshift,*x,*f;
  72     int              vdwioffset0;
  73     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  74     int              vdwjidx0;
  75     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  76     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  77     real             velec,felec,velecsum,facel,crf,krf,krf2;
  78     real             *charge;
  79     int              gbitab;
  80     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
  81     real             *invsqrta,*dvda,*gbtab;
  82     int              nvdwtype;
  83     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  84     int              *vdwtype;
  85     real             *vdwparam;
  86     int              vfitab;
  87     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
  88     real             *vftab;
  89
  90     x                = xx[0];
  91     f                = ff[0];
  92
  93     nri              = nlist->nri;
  94     iinr             = nlist->iinr;
  95     jindex           = nlist->jindex;
  96     jjnr             = nlist->jjnr;
  97     shiftidx         = nlist->shift;
  98     gid              = nlist->gid;
  99     shiftvec         = fr->shift_vec[0];
 100     fshift           = fr->fshift[0];
 101     facel            = fr->epsfac;
 102     charge           = mdatoms->chargeA;
 103     nvdwtype         = fr->ntype;
 104     vdwparam         = fr->nbfp;
 105     vdwtype          = mdatoms->typeA;
 106
 107     invsqrta         = fr->invsqrta;
 108     dvda             = fr->dvda;
 109     gbtabscale       = fr->gbtab.scale;
 110     gbtab            = fr->gbtab.data;
 111     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
 112
 113     outeriter        = 0;
 114     inneriter        = 0;
 115
 116     /* Start outer loop over neighborlists */
 117     for(iidx=0; iidx<nri; iidx++)
 118     {
 119         /* Load shift vector for this list */
 120         i_shift_offset   = DIM*shiftidx[iidx];
 121         shX              = shiftvec[i_shift_offset+XX];
 122         shY              = shiftvec[i_shift_offset+YY];
 123         shZ              = shiftvec[i_shift_offset+ZZ];
 124
 125         /* Load limits for loop over neighbors */
 126         j_index_start    = jindex[iidx];
 127         j_index_end      = jindex[iidx+1];
 128
 129         /* Get outer coordinate index */
 130         inr              = iinr[iidx];
 131         i_coord_offset   = DIM*inr;
 132
 133         /* Load i particle coords and add shift vector */
 134         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 135         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 136         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 137
 138         fix0             = 0.0;
 139         fiy0             = 0.0;
 140         fiz0             = 0.0;
 141
 142         /* Load parameters for i particles */
 143         iq0              = facel*charge[inr+0];
 144         isai0            = invsqrta[inr+0];
 145         vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 146
 147         /* Reset potential sums */
 148         velecsum         = 0.0;
 149         vgbsum           = 0.0;
 150         vvdwsum          = 0.0;
 151         dvdasum          = 0.0;
 152
 153         /* Start inner kernel loop */
 154         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 155         {
 156             /* Get j neighbor index, and coordinate index */
 157             jnr              = jjnr[jidx];
 158             j_coord_offset   = DIM*jnr;
 159
 160             /* load j atom coordinates */
 161             jx0              = x[j_coord_offset+DIM*0+XX];
 162             jy0              = x[j_coord_offset+DIM*0+YY];
 163             jz0              = x[j_coord_offset+DIM*0+ZZ];
 164
 165             /* Calculate displacement vector */
 166             dx00             = ix0 - jx0;
 167             dy00             = iy0 - jy0;
 168             dz00             = iz0 - jz0;
 169
 170             /* Calculate squared distance and things based on it */
 171             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 172
 173             rinv00           = gmx_invsqrt(rsq00);
 174
 175             rinvsq00         = rinv00*rinv00;
 176
 177             /* Load parameters for j particles */
 178             jq0              = charge[jnr+0];
 179             isaj0           = invsqrta[jnr+0];
 180             vdwjidx0         = 3*vdwtype[jnr+0];
 181
 182             /**************************
 183              * CALCULATE INTERACTIONS *
 184              **************************/
 185
 186             r00              = rsq00*rinv00;
 187
 188             qq00             = iq0*jq0;
 189             c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 190             cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 191             cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 192
 193             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 194             isaprod          = isai0*isaj0;
 195             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 196             gbscale          = isaprod*gbtabscale;
 197             dvdaj            = dvda[jnr+0];
 198
 199             /* Calculate generalized born table index - this is a separate table from the normal one,
 200              * but we use the same procedure by multiplying r with scale and truncating to integer.
 201              */
 202             rt               = r00*gbscale;
 203             gbitab           = rt;
 204             gbeps            = rt-gbitab;
 205             gbitab           = 4*gbitab;
 206
 207             Y                = gbtab[gbitab];
 208             F                = gbtab[gbitab+1];
 209             Geps             = gbeps*gbtab[gbitab+2];
 210             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 211             Fp               = F+Geps+Heps2;
 212             VV               = Y+gbeps*Fp;
 213             vgb              = gbqqfactor*VV;
 214
 215             FF               = Fp+Geps+2.0*Heps2;
 216             fgb              = gbqqfactor*FF*gbscale;
 217             dvdatmp          = -0.5*(vgb+fgb*r00);
 218             dvdasum          = dvdasum + dvdatmp;
 219             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 220             velec            = qq00*rinv00;
 221             felec            = (velec*rinv00-fgb)*rinv00;
 222
 223             /* BUCKINGHAM DISPERSION/REPULSION */
 224             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 225             vvdw6            = c6_00*rinvsix;
 226             br               = cexp2_00*r00;
 227             vvdwexp          = cexp1_00*exp(-br);
 228             vvdw             = vvdwexp - vvdw6*(1.0/6.0);
 229             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 230
 231             /* Update potential sums from outer loop */
 232             velecsum        += velec;
 233             vgbsum          += vgb;
 234             vvdwsum         += vvdw;
 235
 236             fscal            = felec+fvdw;
 237
 238             /* Calculate temporary vectorial force */
 239             tx               = fscal*dx00;
 240             ty               = fscal*dy00;
 241             tz               = fscal*dz00;
 242
 243             /* Update vectorial force */
 244             fix0            += tx;
 245             fiy0            += ty;
 246             fiz0            += tz;
 247             f[j_coord_offset+DIM*0+XX] -= tx;
 248             f[j_coord_offset+DIM*0+YY] -= ty;
 249             f[j_coord_offset+DIM*0+ZZ] -= tz;
 250
 251             /* Inner loop uses 97 flops */
 252         }
 253         /* End of innermost loop */
 254
 255         tx = ty = tz = 0;
 256         f[i_coord_offset+DIM*0+XX] += fix0;
 257         f[i_coord_offset+DIM*0+YY] += fiy0;
 258         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 259         tx                         += fix0;
 260         ty                         += fiy0;
 261         tz                         += fiz0;
 262         fshift[i_shift_offset+XX]  += tx;
 263         fshift[i_shift_offset+YY]  += ty;
 264         fshift[i_shift_offset+ZZ]  += tz;
 265
 266         ggid                        = gid[iidx];
 267         /* Update potential energies */
 268         kernel_data->energygrp_elec[ggid] += velecsum;
 269         kernel_data->energygrp_polarization[ggid] += vgbsum;
 270         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 271         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 272
 273         /* Increment number of inner iterations */
 274         inneriter                  += j_index_end - j_index_start;
 275
 276         /* Outer loop uses 16 flops */
 277     }
 278
 279     /* Increment number of outer iterations */
 280     outeriter        += nri;
 281
 282     /* Update outer/inner flops */
 283
 284     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*97);
 285 }
 286 /*
 287  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
 288  * Electrostatics interaction: GeneralizedBorn
 289  * VdW interaction:            Buckingham
 290  * Geometry:                   Particle-Particle
 291  * Calculate force/pot:        Force
 292  */
 293 void
 294 nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
 295                     (t_nblist                    * gmx_restrict       nlist,
 296                      rvec                        * gmx_restrict          xx,
 297                      rvec                        * gmx_restrict          ff,
 298                      t_forcerec                  * gmx_restrict          fr,
 299                      t_mdatoms                   * gmx_restrict     mdatoms,
 300                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 301                      t_nrnb                      * gmx_restrict        nrnb)
 302 {
 303     int              i_shift_offset,i_coord_offset,j_coord_offset;
 304     int              j_index_start,j_index_end;
 305     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 306     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 307     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 308     real             *shiftvec,*fshift,*x,*f;
 309     int              vdwioffset0;
 310     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 311     int              vdwjidx0;
 312     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 313     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 314     real             velec,felec,velecsum,facel,crf,krf,krf2;
 315     real             *charge;
 316     int              gbitab;
 317     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
 318     real             *invsqrta,*dvda,*gbtab;
 319     int              nvdwtype;
 320     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 321     int              *vdwtype;
 322     real             *vdwparam;
 323     int              vfitab;
 324     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
 325     real             *vftab;
 326
 327     x                = xx[0];
 328     f                = ff[0];
 329
 330     nri              = nlist->nri;
 331     iinr             = nlist->iinr;
 332     jindex           = nlist->jindex;
 333     jjnr             = nlist->jjnr;
 334     shiftidx         = nlist->shift;
 335     gid              = nlist->gid;
 336     shiftvec         = fr->shift_vec[0];
 337     fshift           = fr->fshift[0];
 338     facel            = fr->epsfac;
 339     charge           = mdatoms->chargeA;
 340     nvdwtype         = fr->ntype;
 341     vdwparam         = fr->nbfp;
 342     vdwtype          = mdatoms->typeA;
 343
 344     invsqrta         = fr->invsqrta;
 345     dvda             = fr->dvda;
 346     gbtabscale       = fr->gbtab.scale;
 347     gbtab            = fr->gbtab.data;
 348     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
 349
 350     outeriter        = 0;
 351     inneriter        = 0;
 352
 353     /* Start outer loop over neighborlists */
 354     for(iidx=0; iidx<nri; iidx++)
 355     {
 356         /* Load shift vector for this list */
 357         i_shift_offset   = DIM*shiftidx[iidx];
 358         shX              = shiftvec[i_shift_offset+XX];
 359         shY              = shiftvec[i_shift_offset+YY];
 360         shZ              = shiftvec[i_shift_offset+ZZ];
 361
 362         /* Load limits for loop over neighbors */
 363         j_index_start    = jindex[iidx];
 364         j_index_end      = jindex[iidx+1];
 365
 366         /* Get outer coordinate index */
 367         inr              = iinr[iidx];
 368         i_coord_offset   = DIM*inr;
 369
 370         /* Load i particle coords and add shift vector */
 371         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 372         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 373         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 374
 375         fix0             = 0.0;
 376         fiy0             = 0.0;
 377         fiz0             = 0.0;
 378
 379         /* Load parameters for i particles */
 380         iq0              = facel*charge[inr+0];
 381         isai0            = invsqrta[inr+0];
 382         vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 383
 384         dvdasum          = 0.0;
 385
 386         /* Start inner kernel loop */
 387         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 388         {
 389             /* Get j neighbor index, and coordinate index */
 390             jnr              = jjnr[jidx];
 391             j_coord_offset   = DIM*jnr;
 392
 393             /* load j atom coordinates */
 394             jx0              = x[j_coord_offset+DIM*0+XX];
 395             jy0              = x[j_coord_offset+DIM*0+YY];
 396             jz0              = x[j_coord_offset+DIM*0+ZZ];
 397
 398             /* Calculate displacement vector */
 399             dx00             = ix0 - jx0;
 400             dy00             = iy0 - jy0;
 401             dz00             = iz0 - jz0;
 402
 403             /* Calculate squared distance and things based on it */
 404             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 405
 406             rinv00           = gmx_invsqrt(rsq00);
 407
 408             rinvsq00         = rinv00*rinv00;
 409
 410             /* Load parameters for j particles */
 411             jq0              = charge[jnr+0];
 412             isaj0           = invsqrta[jnr+0];
 413             vdwjidx0         = 3*vdwtype[jnr+0];
 414
 415             /**************************
 416              * CALCULATE INTERACTIONS *
 417              **************************/
 418
 419             r00              = rsq00*rinv00;
 420
 421             qq00             = iq0*jq0;
 422             c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 423             cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 424             cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 425
 426             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 427             isaprod          = isai0*isaj0;
 428             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 429             gbscale          = isaprod*gbtabscale;
 430             dvdaj            = dvda[jnr+0];
 431
 432             /* Calculate generalized born table index - this is a separate table from the normal one,
 433              * but we use the same procedure by multiplying r with scale and truncating to integer.
 434              */
 435             rt               = r00*gbscale;
 436             gbitab           = rt;
 437             gbeps            = rt-gbitab;
 438             gbitab           = 4*gbitab;
 439
 440             Y                = gbtab[gbitab];
 441             F                = gbtab[gbitab+1];
 442             Geps             = gbeps*gbtab[gbitab+2];
 443             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 444             Fp               = F+Geps+Heps2;
 445             VV               = Y+gbeps*Fp;
 446             vgb              = gbqqfactor*VV;
 447
 448             FF               = Fp+Geps+2.0*Heps2;
 449             fgb              = gbqqfactor*FF*gbscale;
 450             dvdatmp          = -0.5*(vgb+fgb*r00);
 451             dvdasum          = dvdasum + dvdatmp;
 452             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 453             velec            = qq00*rinv00;
 454             felec            = (velec*rinv00-fgb)*rinv00;
 455
 456             /* BUCKINGHAM DISPERSION/REPULSION */
 457             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 458             vvdw6            = c6_00*rinvsix;
 459             br               = cexp2_00*r00;
 460             vvdwexp          = cexp1_00*exp(-br);
 461             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 462
 463             fscal            = felec+fvdw;
 464
 465             /* Calculate temporary vectorial force */
 466             tx               = fscal*dx00;
 467             ty               = fscal*dy00;
 468             tz               = fscal*dz00;
 469
 470             /* Update vectorial force */
 471             fix0            += tx;
 472             fiy0            += ty;
 473             fiz0            += tz;
 474             f[j_coord_offset+DIM*0+XX] -= tx;
 475             f[j_coord_offset+DIM*0+YY] -= ty;
 476             f[j_coord_offset+DIM*0+ZZ] -= tz;
 477
 478             /* Inner loop uses 92 flops */
 479         }
 480         /* End of innermost loop */
 481
 482         tx = ty = tz = 0;
 483         f[i_coord_offset+DIM*0+XX] += fix0;
 484         f[i_coord_offset+DIM*0+YY] += fiy0;
 485         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 486         tx                         += fix0;
 487         ty                         += fiy0;
 488         tz                         += fiz0;
 489         fshift[i_shift_offset+XX]  += tx;
 490         fshift[i_shift_offset+YY]  += ty;
 491         fshift[i_shift_offset+ZZ]  += tz;
 492
 493         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 494
 495         /* Increment number of inner iterations */
 496         inneriter                  += j_index_end - j_index_start;
 497
 498         /* Outer loop uses 13 flops */
 499     }
 500
 501     /* Increment number of outer iterations */
 502     outeriter        += nri;
 503
 504     /* Update outer/inner flops */
 505
 506     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*92);
 507 }