src/gromacs/mdlib/vcm.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "vcm.h"
  41
  42 #include "gromacs/gmxlib/network.h"
  43 #include "gromacs/math/vec.h"
  44 #include "gromacs/math/vecdump.h"
  45 #include "gromacs/mdtypes/md_enums.h"
  46 #include "gromacs/pbcutil/pbc.h"
  47 #include "gromacs/topology/topology.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir)
  52 {
  53     t_vcm *vcm;
  54     int    g;
  55
  56     snew(vcm, 1);
  57
  58     vcm->mode = (ir->nstcomm > 0) ? ir->comm_mode : ecmNO;
  59     vcm->ndim = ndof_com(ir);
  60
  61     if (vcm->mode == ecmANGULAR && vcm->ndim < 3)
  62     {
  63         gmx_fatal(FARGS, "Can not have angular comm removal with pbc=%s",
  64                   epbc_names[ir->ePBC]);
  65     }
  66
  67     if (vcm->mode != ecmNO)
  68     {
  69         vcm->nr = groups->grps[egcVCM].nr;
  70         /* Allocate one extra for a possible rest group */
  71         if (vcm->mode == ecmANGULAR)
  72         {
  73             snew(vcm->group_j, vcm->nr+1);
  74             snew(vcm->group_x, vcm->nr+1);
  75             snew(vcm->group_i, vcm->nr+1);
  76             snew(vcm->group_w, vcm->nr+1);
  77         }
  78         snew(vcm->group_p, vcm->nr+1);
  79         snew(vcm->group_v, vcm->nr+1);
  80         snew(vcm->group_mass, vcm->nr+1);
  81         snew(vcm->group_name, vcm->nr);
  82         snew(vcm->group_ndf, vcm->nr);
  83         for (g = 0; (g < vcm->nr); g++)
  84         {
  85             vcm->group_ndf[g] = ir->opts.nrdf[g];
  86         }
  87
  88         /* Copy pointer to group names and print it. */
  89         if (fp)
  90         {
  91             fprintf(fp, "Center of mass motion removal mode is %s\n",
  92                     ECOM(vcm->mode));
  93             fprintf(fp, "We have the following groups for center of"
  94                     " mass motion removal:\n");
  95         }
  96         for (g = 0; (g < vcm->nr); g++)
  97         {
  98             vcm->group_name[g] = *groups->grpname[groups->grps[egcVCM].nm_ind[g]];
  99             if (fp)
 100             {
 101                 fprintf(fp, "%3d:  %s\n", g, vcm->group_name[g]);
 102             }
 103         }
 104     }
 105
 106     return vcm;
 107 }
 108
 109 static void update_tensor(rvec x, real m0, tensor I)
 110 {
 111     real xy, xz, yz;
 112
 113     /* Compute inertia tensor contribution due to this atom */
 114     xy         = x[XX]*x[YY]*m0;
 115     xz         = x[XX]*x[ZZ]*m0;
 116     yz         = x[YY]*x[ZZ]*m0;
 117     I[XX][XX] += x[XX]*x[XX]*m0;
 118     I[YY][YY] += x[YY]*x[YY]*m0;
 119     I[ZZ][ZZ] += x[ZZ]*x[ZZ]*m0;
 120     I[XX][YY] += xy;
 121     I[YY][XX] += xy;
 122     I[XX][ZZ] += xz;
 123     I[ZZ][XX] += xz;
 124     I[YY][ZZ] += yz;
 125     I[ZZ][YY] += yz;
 126 }
 127
 128 /* Center of mass code for groups */
 129 void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
 130                   rvec x[], rvec v[], t_vcm *vcm)
 131 {
 132     int    i, g, m;
 133     real   m0;
 134     rvec   j0;
 135
 136     if (vcm->mode != ecmNO)
 137     {
 138         /* Also clear a possible rest group */
 139         for (g = 0; (g < vcm->nr+1); g++)
 140         {
 141             /* Reset linear momentum */
 142             vcm->group_mass[g] = 0;
 143             clear_rvec(vcm->group_p[g]);
 144
 145             if (vcm->mode == ecmANGULAR)
 146             {
 147                 /* Reset anular momentum */
 148                 clear_rvec(vcm->group_j[g]);
 149                 clear_rvec(vcm->group_x[g]);
 150                 clear_rvec(vcm->group_w[g]);
 151                 clear_mat(vcm->group_i[g]);
 152             }
 153         }
 154
 155         g = 0;
 156         for (i = start; (i < start+homenr); i++)
 157         {
 158             m0 = md->massT[i];
 159             if (md->cVCM)
 160             {
 161                 g = md->cVCM[i];
 162             }
 163
 164             /* Calculate linear momentum */
 165             vcm->group_mass[g]  += m0;
 166             for (m = 0; (m < DIM); m++)
 167             {
 168                 vcm->group_p[g][m] += m0*v[i][m];
 169             }
 170
 171             if (vcm->mode == ecmANGULAR)
 172             {
 173                 /* Calculate angular momentum */
 174                 cprod(x[i], v[i], j0);
 175
 176                 for (m = 0; (m < DIM); m++)
 177                 {
 178                     vcm->group_j[g][m] += m0*j0[m];
 179                     vcm->group_x[g][m] += m0*x[i][m];
 180                 }
 181                 /* Update inertia tensor */
 182                 update_tensor(x[i], m0, vcm->group_i[g]);
 183             }
 184         }
 185     }
 186 }
 187
 188 void do_stopcm_grp(int start, int homenr, unsigned short *group_id,
 189                    rvec x[], rvec v[], t_vcm *vcm)
 190 {
 191     int  i, g;
 192     rvec dv, dx;
 193
 194     if (vcm->mode != ecmNO)
 195     {
 196         /* Subtract linear momentum */
 197         g = 0;
 198         switch (vcm->ndim)
 199         {
 200             case 1:
 201                 for (i = start; (i < start+homenr); i++)
 202                 {
 203                     if (group_id)
 204                     {
 205                         g = group_id[i];
 206                     }
 207                     v[i][XX] -= vcm->group_v[g][XX];
 208                 }
 209                 break;
 210             case 2:
 211                 for (i = start; (i < start+homenr); i++)
 212                 {
 213                     if (group_id)
 214                     {
 215                         g = group_id[i];
 216                     }
 217                     v[i][XX] -= vcm->group_v[g][XX];
 218                     v[i][YY] -= vcm->group_v[g][YY];
 219                 }
 220                 break;
 221             case 3:
 222                 for (i = start; (i < start+homenr); i++)
 223                 {
 224                     if (group_id)
 225                     {
 226                         g = group_id[i];
 227                     }
 228                     rvec_dec(v[i], vcm->group_v[g]);
 229                 }
 230                 break;
 231         }
 232         if (vcm->mode == ecmANGULAR)
 233         {
 234             /* Subtract angular momentum */
 235             for (i = start; (i < start+homenr); i++)
 236             {
 237                 if (group_id)
 238                 {
 239                     g = group_id[i];
 240                 }
 241                 /* Compute the correction to the velocity for each atom */
 242                 rvec_sub(x[i], vcm->group_x[g], dx);
 243                 cprod(vcm->group_w[g], dx, dv);
 244                 rvec_dec(v[i], dv);
 245             }
 246         }
 247     }
 248 }
 249
 250 static void get_minv(tensor A, tensor B)
 251 {
 252     int    m, n;
 253     double fac, rfac;
 254     tensor tmp;
 255
 256     tmp[XX][XX] =  A[YY][YY] + A[ZZ][ZZ];
 257     tmp[YY][XX] = -A[XX][YY];
 258     tmp[ZZ][XX] = -A[XX][ZZ];
 259     tmp[XX][YY] = -A[XX][YY];
 260     tmp[YY][YY] =  A[XX][XX] + A[ZZ][ZZ];
 261     tmp[ZZ][YY] = -A[YY][ZZ];
 262     tmp[XX][ZZ] = -A[XX][ZZ];
 263     tmp[YY][ZZ] = -A[YY][ZZ];
 264     tmp[ZZ][ZZ] =  A[XX][XX] + A[YY][YY];
 265
 266     /* This is a hack to prevent very large determinants */
 267     rfac  = (tmp[XX][XX]+tmp[YY][YY]+tmp[ZZ][ZZ])/3;
 268     if (rfac == 0.0)
 269     {
 270         gmx_fatal(FARGS, "Can not stop center of mass: maybe 2dimensional system");
 271     }
 272     fac = 1.0/rfac;
 273     for (m = 0; (m < DIM); m++)
 274     {
 275         for (n = 0; (n < DIM); n++)
 276         {
 277             tmp[m][n] *= fac;
 278         }
 279     }
 280     m_inv(tmp, B);
 281     for (m = 0; (m < DIM); m++)
 282     {
 283         for (n = 0; (n < DIM); n++)
 284         {
 285             B[m][n] *= fac;
 286         }
 287     }
 288 }
 289
 290 void check_cm_grp(FILE *fp, t_vcm *vcm, t_inputrec *ir, real Temp_Max)
 291 {
 292     int    m, g;
 293     real   ekcm, ekrot, tm, tm_1, Temp_cm;
 294     rvec   jcm;
 295     tensor Icm;
 296
 297     /* First analyse the total results */
 298     if (vcm->mode != ecmNO)
 299     {
 300         for (g = 0; (g < vcm->nr); g++)
 301         {
 302             tm = vcm->group_mass[g];
 303             if (tm != 0)
 304             {
 305                 tm_1 = 1.0/tm;
 306                 svmul(tm_1, vcm->group_p[g], vcm->group_v[g]);
 307             }
 308             /* Else it's zero anyway! */
 309         }
 310         if (vcm->mode == ecmANGULAR)
 311         {
 312             for (g = 0; (g < vcm->nr); g++)
 313             {
 314                 tm = vcm->group_mass[g];
 315                 if (tm != 0)
 316                 {
 317                     tm_1 = 1.0/tm;
 318
 319                     /* Compute center of mass for this group */
 320                     for (m = 0; (m < DIM); m++)
 321                     {
 322                         vcm->group_x[g][m] *= tm_1;
 323                     }
 324
 325                     /* Subtract the center of mass contribution to the
 326                      * angular momentum
 327                      */
 328                     cprod(vcm->group_x[g], vcm->group_v[g], jcm);
 329                     for (m = 0; (m < DIM); m++)
 330                     {
 331                         vcm->group_j[g][m] -= tm*jcm[m];
 332                     }
 333
 334                     /* Subtract the center of mass contribution from the inertia
 335                      * tensor (this is not as trivial as it seems, but due to
 336                      * some cancellation we can still do it, even in parallel).
 337                      */
 338                     clear_mat(Icm);
 339                     update_tensor(vcm->group_x[g], tm, Icm);
 340                     m_sub(vcm->group_i[g], Icm, vcm->group_i[g]);
 341
 342                     /* Compute angular velocity, using matrix operation
 343                      * Since J = I w
 344                      * we have
 345                      * w = I^-1 J
 346                      */
 347                     get_minv(vcm->group_i[g], Icm);
 348                     mvmul(Icm, vcm->group_j[g], vcm->group_w[g]);
 349                 }
 350                 /* Else it's zero anyway! */
 351             }
 352         }
 353     }
 354     for (g = 0; (g < vcm->nr); g++)
 355     {
 356         ekcm    = 0;
 357         if (vcm->group_mass[g] != 0 && vcm->group_ndf[g] > 0)
 358         {
 359             for (m = 0; m < vcm->ndim; m++)
 360             {
 361                 ekcm += sqr(vcm->group_v[g][m]);
 362             }
 363             ekcm   *= 0.5*vcm->group_mass[g];
 364             Temp_cm = 2*ekcm/vcm->group_ndf[g];
 365
 366             if ((Temp_cm > Temp_Max) && fp)
 367             {
 368                 fprintf(fp, "Large VCM(group %s): %12.5f, %12.5f, %12.5f, Temp-cm: %12.5e\n",
 369                         vcm->group_name[g], vcm->group_v[g][XX],
 370                         vcm->group_v[g][YY], vcm->group_v[g][ZZ], Temp_cm);
 371             }
 372
 373             if (vcm->mode == ecmANGULAR)
 374             {
 375                 ekrot = 0.5*iprod(vcm->group_j[g], vcm->group_w[g]);
 376                 if ((ekrot > 1) && fp && !EI_RANDOM(ir->eI))
 377                 {
 378                     /* if we have an integrator that may not conserve momenta, skip */
 379                     tm    = vcm->group_mass[g];
 380                     fprintf(fp, "Group %s with mass %12.5e, Ekrot %12.5e Det(I) = %12.5e\n",
 381                             vcm->group_name[g], tm, ekrot, det(vcm->group_i[g]));
 382                     fprintf(fp, "  COM: %12.5f  %12.5f  %12.5f\n",
 383                             vcm->group_x[g][XX], vcm->group_x[g][YY], vcm->group_x[g][ZZ]);
 384                     fprintf(fp, "  P:   %12.5f  %12.5f  %12.5f\n",
 385                             vcm->group_p[g][XX], vcm->group_p[g][YY], vcm->group_p[g][ZZ]);
 386                     fprintf(fp, "  V:   %12.5f  %12.5f  %12.5f\n",
 387                             vcm->group_v[g][XX], vcm->group_v[g][YY], vcm->group_v[g][ZZ]);
 388                     fprintf(fp, "  J:   %12.5f  %12.5f  %12.5f\n",
 389                             vcm->group_j[g][XX], vcm->group_j[g][YY], vcm->group_j[g][ZZ]);
 390                     fprintf(fp, "  w:   %12.5f  %12.5f  %12.5f\n",
 391                             vcm->group_w[g][XX], vcm->group_w[g][YY], vcm->group_w[g][ZZ]);
 392                     pr_rvecs(fp, 0, "Inertia tensor", vcm->group_i[g], DIM);
 393                 }
 394             }
 395         }
 396     }
 397 }