src/gromacs/gmxlib/chargegroup.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "chargegroup.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/math/vec.h"
  44 #include "gromacs/pbcutil/pbc.h"
  45 #include "gromacs/topology/topology.h"
  46 #include "gromacs/utility/fatalerror.h"
  47 #include "gromacs/utility/smalloc.h"
  48
  49
  50 void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
  51                             real *rvdw1, real *rvdw2,
  52                             real *rcoul1, real *rcoul2)
  53 {
  54     real            r2v1, r2v2, r2c1, r2c2, r2;
  55     int             ntype, i, j, m, cg, a_mol, a0, a1, a;
  56     gmx_bool       *bLJ;
  57     rvec            cen;
  58
  59     r2v1 = 0;
  60     r2v2 = 0;
  61     r2c1 = 0;
  62     r2c2 = 0;
  63
  64     ntype = mtop->ffparams.atnr;
  65     snew(bLJ, ntype);
  66     for (i = 0; i < ntype; i++)
  67     {
  68         bLJ[i] = FALSE;
  69         for (j = 0; j < ntype; j++)
  70         {
  71             if (mtop->ffparams.iparams[i*ntype+j].lj.c6  != 0 ||
  72                 mtop->ffparams.iparams[i*ntype+j].lj.c12 != 0)
  73             {
  74                 bLJ[i] = TRUE;
  75             }
  76         }
  77     }
  78
  79     a_mol = 0;
  80     for (const gmx_molblock_t &molb : mtop->molblock)
  81     {
  82         const gmx_moltype_t *molt = &mtop->moltype[molb.type];
  83         const t_block       *cgs  = &molt->cgs;
  84         const t_atom        *atom = molt->atoms.atom;
  85         for (m = 0; m < molb.nmol; m++)
  86         {
  87             for (cg = 0; cg < cgs->nr; cg++)
  88             {
  89                 a0 = cgs->index[cg];
  90                 a1 = cgs->index[cg+1];
  91                 if (a1 - a0 > 1)
  92                 {
  93                     clear_rvec(cen);
  94                     for (a = a0; a < a1; a++)
  95                     {
  96                         rvec_inc(cen, x[a_mol+a]);
  97                     }
  98                     svmul(1.0/(a1-a0), cen, cen);
  99                     for (a = a0; a < a1; a++)
 100                     {
 101                         r2 = distance2(cen, x[a_mol+a]);
 102                         if (r2 > r2v2 && (bLJ[atom[a].type ] ||
 103                                           bLJ[atom[a].typeB]))
 104                         {
 105                             if (r2 > r2v1)
 106                             {
 107                                 r2v2 = r2v1;
 108                                 r2v1 = r2;
 109                             }
 110                             else
 111                             {
 112                                 r2v2 = r2;
 113                             }
 114                         }
 115                         if (r2 > r2c2 &&
 116                             (atom[a].q != 0 || atom[a].qB != 0))
 117                         {
 118                             if (r2 > r2c1)
 119                             {
 120                                 r2c2 = r2c1;
 121                                 r2c1 = r2;
 122                             }
 123                             else
 124                             {
 125                                 r2c2 = r2;
 126                             }
 127                         }
 128                     }
 129                 }
 130             }
 131             a_mol += molt->atoms.nr;
 132         }
 133     }
 134
 135     sfree(bLJ);
 136
 137     *rvdw1  = std::sqrt(r2v1);
 138     *rvdw2  = std::sqrt(r2v2);
 139     *rcoul1 = std::sqrt(r2c1);
 140     *rcoul2 = std::sqrt(r2c2);
 141 }
 142
 143 void calc_cgcm(FILE gmx_unused *fplog, int cg0, int cg1, const t_block *cgs,
 144                rvec pos[], rvec cg_cm[])
 145 {
 146     int      icg, k, k0, k1, d;
 147     rvec     cg;
 148     real     nrcg, inv_ncg;
 149     int     *cgindex;
 150
 151 #ifdef DEBUG
 152     fprintf(fplog, "Calculating centre of geometry for charge groups %d to %d\n",
 153             cg0, cg1);
 154 #endif
 155     cgindex = cgs->index;
 156
 157     /* Compute the center of geometry for all charge groups */
 158     for (icg = cg0; (icg < cg1); icg++)
 159     {
 160         k0      = cgindex[icg];
 161         k1      = cgindex[icg+1];
 162         nrcg    = k1-k0;
 163         if (nrcg == 1)
 164         {
 165             copy_rvec(pos[k0], cg_cm[icg]);
 166         }
 167         else
 168         {
 169             inv_ncg = 1.0/nrcg;
 170
 171             clear_rvec(cg);
 172             for (k = k0; (k < k1); k++)
 173             {
 174                 for (d = 0; (d < DIM); d++)
 175                 {
 176                     cg[d] += pos[k][d];
 177                 }
 178             }
 179             for (d = 0; (d < DIM); d++)
 180             {
 181                 cg_cm[icg][d] = inv_ncg*cg[d];
 182             }
 183         }
 184     }
 185 }
 186
 187 void put_charge_groups_in_box(FILE gmx_unused *fplog, int cg0, int cg1,
 188                               int ePBC, matrix box, const t_block *cgs,
 189                               rvec pos[], rvec cg_cm[])
 190
 191 {
 192     int      npbcdim, icg, k, k0, k1, d, e;
 193     rvec     cg;
 194     real     nrcg, inv_ncg;
 195     int     *cgindex;
 196     gmx_bool bTric;
 197
 198     if (ePBC == epbcNONE)
 199     {
 200         gmx_incons("Calling put_charge_groups_in_box for a system without PBC");
 201     }
 202
 203 #ifdef DEBUG
 204     fprintf(fplog, "Putting cgs %d to %d in box\n", cg0, cg1);
 205 #endif
 206     cgindex = cgs->index;
 207
 208     if (ePBC == epbcXY)
 209     {
 210         npbcdim = 2;
 211     }
 212     else
 213     {
 214         npbcdim = 3;
 215     }
 216
 217     bTric = TRICLINIC(box);
 218
 219     for (icg = cg0; (icg < cg1); icg++)
 220     {
 221         /* First compute the center of geometry for this charge group */
 222         k0      = cgindex[icg];
 223         k1      = cgindex[icg+1];
 224         nrcg    = k1-k0;
 225
 226         if (nrcg == 1)
 227         {
 228             copy_rvec(pos[k0], cg_cm[icg]);
 229         }
 230         else
 231         {
 232             inv_ncg = 1.0/nrcg;
 233
 234             clear_rvec(cg);
 235             for (k = k0; (k < k1); k++)
 236             {
 237                 for (d = 0; d < DIM; d++)
 238                 {
 239                     cg[d] += pos[k][d];
 240                 }
 241             }
 242             for (d = 0; d < DIM; d++)
 243             {
 244                 cg_cm[icg][d] = inv_ncg*cg[d];
 245             }
 246         }
 247         /* Now check pbc for this cg */
 248         if (bTric)
 249         {
 250             for (d = npbcdim-1; d >= 0; d--)
 251             {
 252                 while (cg_cm[icg][d] < 0)
 253                 {
 254                     for (e = d; e >= 0; e--)
 255                     {
 256                         cg_cm[icg][e] += box[d][e];
 257                         for (k = k0; (k < k1); k++)
 258                         {
 259                             pos[k][e] += box[d][e];
 260                         }
 261                     }
 262                 }
 263                 while (cg_cm[icg][d] >= box[d][d])
 264                 {
 265                     for (e = d; e >= 0; e--)
 266                     {
 267                         cg_cm[icg][e] -= box[d][e];
 268                         for (k = k0; (k < k1); k++)
 269                         {
 270                             pos[k][e] -= box[d][e];
 271                         }
 272                     }
 273                 }
 274             }
 275         }
 276         else
 277         {
 278             for (d = 0; d < npbcdim; d++)
 279             {
 280                 while (cg_cm[icg][d] < 0)
 281                 {
 282                     cg_cm[icg][d] += box[d][d];
 283                     for (k = k0; (k < k1); k++)
 284                     {
 285                         pos[k][d] += box[d][d];
 286                     }
 287                 }
 288                 while (cg_cm[icg][d] >= box[d][d])
 289                 {
 290                     cg_cm[icg][d] -= box[d][d];
 291                     for (k = k0; (k < k1); k++)
 292                     {
 293                         pos[k][d] -= box[d][d];
 294                     }
 295                 }
 296             }
 297         }
 298 #ifdef DEBUG_PBC
 299         for (d = 0; (d < npbcdim); d++)
 300         {
 301             if ((cg_cm[icg][d] < 0) || (cg_cm[icg][d] >= box[d][d]))
 302             {
 303                 gmx_fatal(FARGS, "cg_cm[%d] = %15f  %15f  %15f\n"
 304                           "box = %15f  %15f  %15f\n",
 305                           icg, cg_cm[icg][XX], cg_cm[icg][YY], cg_cm[icg][ZZ],
 306                           box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
 307             }
 308         }
 309 #endif
 310     }
 311 }