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, mb, m, cg, a_mol, a0, a1, a;
  56     gmx_bool       *bLJ;
  57     gmx_molblock_t *molb;
  58     gmx_moltype_t  *molt;
  59     t_block        *cgs;
  60     t_atom         *atom;
  61     rvec            cen;
  62
  63     r2v1 = 0;
  64     r2v2 = 0;
  65     r2c1 = 0;
  66     r2c2 = 0;
  67
  68     ntype = mtop->ffparams.atnr;
  69     snew(bLJ, ntype);
  70     for (i = 0; i < ntype; i++)
  71     {
  72         bLJ[i] = FALSE;
  73         for (j = 0; j < ntype; j++)
  74         {
  75             if (mtop->ffparams.iparams[i*ntype+j].lj.c6  != 0 ||
  76                 mtop->ffparams.iparams[i*ntype+j].lj.c12 != 0)
  77             {
  78                 bLJ[i] = TRUE;
  79             }
  80         }
  81     }
  82
  83     a_mol = 0;
  84     for (mb = 0; mb < mtop->nmolblock; mb++)
  85     {
  86         molb = &mtop->molblock[mb];
  87         molt = &mtop->moltype[molb->type];
  88         cgs  = &molt->cgs;
  89         atom = molt->atoms.atom;
  90         for (m = 0; m < molb->nmol; m++)
  91         {
  92             for (cg = 0; cg < cgs->nr; cg++)
  93             {
  94                 a0 = cgs->index[cg];
  95                 a1 = cgs->index[cg+1];
  96                 if (a1 - a0 > 1)
  97                 {
  98                     clear_rvec(cen);
  99                     for (a = a0; a < a1; a++)
 100                     {
 101                         rvec_inc(cen, x[a_mol+a]);
 102                     }
 103                     svmul(1.0/(a1-a0), cen, cen);
 104                     for (a = a0; a < a1; a++)
 105                     {
 106                         r2 = distance2(cen, x[a_mol+a]);
 107                         if (r2 > r2v2 && (bLJ[atom[a].type ] ||
 108                                           bLJ[atom[a].typeB]))
 109                         {
 110                             if (r2 > r2v1)
 111                             {
 112                                 r2v2 = r2v1;
 113                                 r2v1 = r2;
 114                             }
 115                             else
 116                             {
 117                                 r2v2 = r2;
 118                             }
 119                         }
 120                         if (r2 > r2c2 &&
 121                             (atom[a].q != 0 || atom[a].qB != 0))
 122                         {
 123                             if (r2 > r2c1)
 124                             {
 125                                 r2c2 = r2c1;
 126                                 r2c1 = r2;
 127                             }
 128                             else
 129                             {
 130                                 r2c2 = r2;
 131                             }
 132                         }
 133                     }
 134                 }
 135             }
 136             a_mol += molb->natoms_mol;
 137         }
 138     }
 139
 140     sfree(bLJ);
 141
 142     *rvdw1  = std::sqrt(r2v1);
 143     *rvdw2  = std::sqrt(r2v2);
 144     *rcoul1 = std::sqrt(r2c1);
 145     *rcoul2 = std::sqrt(r2c2);
 146 }
 147
 148 void calc_cgcm(FILE gmx_unused *fplog, int cg0, int cg1, const t_block *cgs,
 149                rvec pos[], rvec cg_cm[])
 150 {
 151     int      icg, k, k0, k1, d;
 152     rvec     cg;
 153     real     nrcg, inv_ncg;
 154     int     *cgindex;
 155
 156 #ifdef DEBUG
 157     fprintf(fplog, "Calculating centre of geometry for charge groups %d to %d\n",
 158             cg0, cg1);
 159 #endif
 160     cgindex = cgs->index;
 161
 162     /* Compute the center of geometry for all charge groups */
 163     for (icg = cg0; (icg < cg1); icg++)
 164     {
 165         k0      = cgindex[icg];
 166         k1      = cgindex[icg+1];
 167         nrcg    = k1-k0;
 168         if (nrcg == 1)
 169         {
 170             copy_rvec(pos[k0], cg_cm[icg]);
 171         }
 172         else
 173         {
 174             inv_ncg = 1.0/nrcg;
 175
 176             clear_rvec(cg);
 177             for (k = k0; (k < k1); k++)
 178             {
 179                 for (d = 0; (d < DIM); d++)
 180                 {
 181                     cg[d] += pos[k][d];
 182                 }
 183             }
 184             for (d = 0; (d < DIM); d++)
 185             {
 186                 cg_cm[icg][d] = inv_ncg*cg[d];
 187             }
 188         }
 189     }
 190 }
 191
 192 void put_charge_groups_in_box(FILE gmx_unused *fplog, int cg0, int cg1,
 193                               int ePBC, matrix box, t_block *cgs,
 194                               rvec pos[], rvec cg_cm[])
 195
 196 {
 197     int      npbcdim, icg, k, k0, k1, d, e;
 198     rvec     cg;
 199     real     nrcg, inv_ncg;
 200     int     *cgindex;
 201     gmx_bool bTric;
 202
 203     if (ePBC == epbcNONE)
 204     {
 205         gmx_incons("Calling put_charge_groups_in_box for a system without PBC");
 206     }
 207
 208 #ifdef DEBUG
 209     fprintf(fplog, "Putting cgs %d to %d in box\n", cg0, cg1);
 210 #endif
 211     cgindex = cgs->index;
 212
 213     if (ePBC == epbcXY)
 214     {
 215         npbcdim = 2;
 216     }
 217     else
 218     {
 219         npbcdim = 3;
 220     }
 221
 222     bTric = TRICLINIC(box);
 223
 224     for (icg = cg0; (icg < cg1); icg++)
 225     {
 226         /* First compute the center of geometry for this charge group */
 227         k0      = cgindex[icg];
 228         k1      = cgindex[icg+1];
 229         nrcg    = k1-k0;
 230
 231         if (nrcg == 1)
 232         {
 233             copy_rvec(pos[k0], cg_cm[icg]);
 234         }
 235         else
 236         {
 237             inv_ncg = 1.0/nrcg;
 238
 239             clear_rvec(cg);
 240             for (k = k0; (k < k1); k++)
 241             {
 242                 for (d = 0; d < DIM; d++)
 243                 {
 244                     cg[d] += pos[k][d];
 245                 }
 246             }
 247             for (d = 0; d < DIM; d++)
 248             {
 249                 cg_cm[icg][d] = inv_ncg*cg[d];
 250             }
 251         }
 252         /* Now check pbc for this cg */
 253         if (bTric)
 254         {
 255             for (d = npbcdim-1; d >= 0; d--)
 256             {
 257                 while (cg_cm[icg][d] < 0)
 258                 {
 259                     for (e = d; e >= 0; e--)
 260                     {
 261                         cg_cm[icg][e] += box[d][e];
 262                         for (k = k0; (k < k1); k++)
 263                         {
 264                             pos[k][e] += box[d][e];
 265                         }
 266                     }
 267                 }
 268                 while (cg_cm[icg][d] >= box[d][d])
 269                 {
 270                     for (e = d; e >= 0; e--)
 271                     {
 272                         cg_cm[icg][e] -= box[d][e];
 273                         for (k = k0; (k < k1); k++)
 274                         {
 275                             pos[k][e] -= box[d][e];
 276                         }
 277                     }
 278                 }
 279             }
 280         }
 281         else
 282         {
 283             for (d = 0; d < npbcdim; d++)
 284             {
 285                 while (cg_cm[icg][d] < 0)
 286                 {
 287                     cg_cm[icg][d] += box[d][d];
 288                     for (k = k0; (k < k1); k++)
 289                     {
 290                         pos[k][d] += box[d][d];
 291                     }
 292                 }
 293                 while (cg_cm[icg][d] >= box[d][d])
 294                 {
 295                     cg_cm[icg][d] -= box[d][d];
 296                     for (k = k0; (k < k1); k++)
 297                     {
 298                         pos[k][d] -= box[d][d];
 299                     }
 300                 }
 301             }
 302         }
 303 #ifdef DEBUG_PBC
 304         for (d = 0; (d < npbcdim); d++)
 305         {
 306             if ((cg_cm[icg][d] < 0) || (cg_cm[icg][d] >= box[d][d]))
 307             {
 308                 gmx_fatal(FARGS, "cg_cm[%d] = %15f  %15f  %15f\n"
 309                           "box = %15f  %15f  %15f\n",
 310                           icg, cg_cm[icg][XX], cg_cm[icg][YY], cg_cm[icg][ZZ],
 311                           box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
 312             }
 313         }
 314 #endif
 315     }
 316 }