src/gromacs/mdlib/ewald.c

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  37 #include "config.h"
  38
  39 #include <math.h>
  40 #include <stdio.h>
  41 #include <stdlib.h>
  42
  43 #include "typedefs.h"
  44 #include "types/commrec.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/utility/smalloc.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/math/units.h"
  49 #include "coulomb.h"
  50 #include "macros.h"
  51
  52 #include "gromacs/utility/futil.h"
  53 #include "gromacs/math/gmxcomplex.h"
  54
  55 #define TOL 2e-5
  56
  57 struct ewald_tab
  58 {
  59     int        nx, ny, nz, kmax;
  60     cvec     **eir;
  61     t_complex *tab_xy, *tab_qxyz;
  62 };
  63
  64
  65
  66 /* TODO: fix thread-safety */
  67
  68 /* the other routines are in complex.h */
  69 static t_complex conjmul(t_complex a, t_complex b)
  70 {
  71     t_complex c;
  72
  73     c.re = a.re*b.re + a.im*b.im;
  74     c.im = a.im*b.re - a.re*b.im;
  75
  76     return c;
  77 }
  78
  79
  80
  81
  82 static void tabulate_eir(int natom, rvec x[], int kmax, cvec **eir, rvec lll)
  83 {
  84     int  i, j, m;
  85
  86     if (kmax < 1)
  87     {
  88         printf("Go away! kmax = %d\n", kmax);
  89         exit(1);
  90     }
  91
  92     for (i = 0; (i < natom); i++)
  93     {
  94         for (m = 0; (m < 3); m++)
  95         {
  96             eir[0][i][m].re = 1;
  97             eir[0][i][m].im = 0;
  98         }
  99
 100         for (m = 0; (m < 3); m++)
 101         {
 102             eir[1][i][m].re = cos(x[i][m]*lll[m]);
 103             eir[1][i][m].im = sin(x[i][m]*lll[m]);
 104         }
 105         for (j = 2; (j < kmax); j++)
 106         {
 107             for (m = 0; (m < 3); m++)
 108             {
 109                 eir[j][i][m] = cmul(eir[j-1][i][m], eir[1][i][m]);
 110             }
 111         }
 112     }
 113 }
 114
 115 void init_ewald_tab(ewald_tab_t *et, const t_inputrec *ir, FILE *fp)
 116 {
 117     int n;
 118
 119     snew(*et, 1);
 120     if (fp)
 121     {
 122         fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
 123     }
 124
 125     (*et)->nx       = ir->nkx+1;
 126     (*et)->ny       = ir->nky+1;
 127     (*et)->nz       = ir->nkz+1;
 128     (*et)->kmax     = max((*et)->nx, max((*et)->ny, (*et)->nz));
 129     (*et)->eir      = NULL;
 130     (*et)->tab_xy   = NULL;
 131     (*et)->tab_qxyz = NULL;
 132 }
 133
 134
 135
 136 real do_ewald(t_inputrec *ir,
 137               rvec x[],        rvec f[],
 138               real chargeA[],  real chargeB[],
 139               rvec box,
 140               t_commrec *cr,   int natoms,
 141               matrix lrvir,    real ewaldcoeff,
 142               real lambda,     real *dvdlambda,
 143               ewald_tab_t et)
 144 {
 145     real     factor     = -1.0/(4*ewaldcoeff*ewaldcoeff);
 146     real     scaleRecip = 4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r; /* 1/(Vol*e0) */
 147     real    *charge, energy_AB[2], energy;
 148     rvec     lll;
 149     int      lowiy, lowiz, ix, iy, iz, n, q;
 150     real     tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
 151     gmx_bool bFreeEnergy;
 152
 153     if (cr != NULL)
 154     {
 155         if (PAR(cr))
 156         {
 157             gmx_fatal(FARGS, "No parallel Ewald. Use PME instead.\n");
 158         }
 159     }
 160
 161
 162     if (!et->eir) /* allocate if we need to */
 163     {
 164         snew(et->eir, et->kmax);
 165         for (n = 0; n < et->kmax; n++)
 166         {
 167             snew(et->eir[n], natoms);
 168         }
 169         snew(et->tab_xy, natoms);
 170         snew(et->tab_qxyz, natoms);
 171     }
 172
 173     bFreeEnergy = (ir->efep != efepNO);
 174
 175     clear_mat(lrvir);
 176
 177     calc_lll(box, lll);
 178     /* make tables for the structure factor parts */
 179     tabulate_eir(natoms, x, et->kmax, et->eir, lll);
 180
 181     for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
 182     {
 183         if (!bFreeEnergy)
 184         {
 185             charge = chargeA;
 186             scale  = 1.0;
 187         }
 188         else if (q == 0)
 189         {
 190             charge = chargeA;
 191             scale  = 1.0 - lambda;
 192         }
 193         else
 194         {
 195             charge = chargeB;
 196             scale  = lambda;
 197         }
 198         lowiy        = 0;
 199         lowiz        = 1;
 200         energy_AB[q] = 0;
 201         for (ix = 0; ix < et->nx; ix++)
 202         {
 203             mx = ix*lll[XX];
 204             for (iy = lowiy; iy < et->ny; iy++)
 205             {
 206                 my = iy*lll[YY];
 207                 if (iy >= 0)
 208                 {
 209                     for (n = 0; n < natoms; n++)
 210                     {
 211                         et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
 212                     }
 213                 }
 214                 else
 215                 {
 216                     for (n = 0; n < natoms; n++)
 217                     {
 218                         et->tab_xy[n] = conjmul(et->eir[ix][n][XX], et->eir[-iy][n][YY]);
 219                     }
 220                 }
 221                 for (iz = lowiz; iz < et->nz; iz++)
 222                 {
 223                     mz  = iz*lll[ZZ];
 224                     m2  = mx*mx+my*my+mz*mz;
 225                     ak  = exp(m2*factor)/m2;
 226                     akv = 2.0*ak*(1.0/m2-factor);
 227                     if (iz >= 0)
 228                     {
 229                         for (n = 0; n < natoms; n++)
 230                         {
 231                             et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n],
 232                                                                     et->eir[iz][n][ZZ]));
 233                         }
 234                     }
 235                     else
 236                     {
 237                         for (n = 0; n < natoms; n++)
 238                         {
 239                             et->tab_qxyz[n] = rcmul(charge[n], conjmul(et->tab_xy[n],
 240                                                                        et->eir[-iz][n][ZZ]));
 241                         }
 242                     }
 243
 244                     cs = ss = 0;
 245                     for (n = 0; n < natoms; n++)
 246                     {
 247                         cs += et->tab_qxyz[n].re;
 248                         ss += et->tab_qxyz[n].im;
 249                     }
 250                     energy_AB[q]  += ak*(cs*cs+ss*ss);
 251                     tmp            = scale*akv*(cs*cs+ss*ss);
 252                     lrvir[XX][XX] -= tmp*mx*mx;
 253                     lrvir[XX][YY] -= tmp*mx*my;
 254                     lrvir[XX][ZZ] -= tmp*mx*mz;
 255                     lrvir[YY][YY] -= tmp*my*my;
 256                     lrvir[YY][ZZ] -= tmp*my*mz;
 257                     lrvir[ZZ][ZZ] -= tmp*mz*mz;
 258                     for (n = 0; n < natoms; n++)
 259                     {
 260                         /*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
 261                         tmp       = scale*ak*(cs*et->tab_qxyz[n].im-ss*et->tab_qxyz[n].re);
 262                         f[n][XX] += tmp*mx*2*scaleRecip;
 263                         f[n][YY] += tmp*my*2*scaleRecip;
 264                         f[n][ZZ] += tmp*mz*2*scaleRecip;
 265 #if 0
 266                         f[n][XX] += tmp*mx;
 267                         f[n][YY] += tmp*my;
 268                         f[n][ZZ] += tmp*mz;
 269 #endif
 270                     }
 271                     lowiz = 1-et->nz;
 272                 }
 273                 lowiy = 1-et->ny;
 274             }
 275         }
 276     }
 277
 278     if (!bFreeEnergy)
 279     {
 280         energy = energy_AB[0];
 281     }
 282     else
 283     {
 284         energy      = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
 285         *dvdlambda += scaleRecip*(energy_AB[1] - energy_AB[0]);
 286     }
 287
 288     lrvir[XX][XX] = -0.5*scaleRecip*(lrvir[XX][XX]+energy);
 289     lrvir[XX][YY] = -0.5*scaleRecip*(lrvir[XX][YY]);
 290     lrvir[XX][ZZ] = -0.5*scaleRecip*(lrvir[XX][ZZ]);
 291     lrvir[YY][YY] = -0.5*scaleRecip*(lrvir[YY][YY]+energy);
 292     lrvir[YY][ZZ] = -0.5*scaleRecip*(lrvir[YY][ZZ]);
 293     lrvir[ZZ][ZZ] = -0.5*scaleRecip*(lrvir[ZZ][ZZ]+energy);
 294
 295     lrvir[YY][XX] = lrvir[XX][YY];
 296     lrvir[ZZ][XX] = lrvir[XX][ZZ];
 297     lrvir[ZZ][YY] = lrvir[YY][ZZ];
 298
 299     energy *= scaleRecip;
 300
 301     return energy;
 302 }