src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "gen_maxwell_velocities.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/math/units.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/random/tabulatednormaldistribution.h"
  47 #include "gromacs/random/threefry.h"
  48 #include "gromacs/topology/mtop_util.h"
  49 #include "gromacs/topology/topology.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 static void low_mspeed(real tempi,
  54                        gmx_mtop_t *mtop, rvec v[], gmx::ThreeFry2x64<> * rng)
  55 {
  56     int                                     i, m, nrdf;
  57     real                                    boltz, sd;
  58     real                                    ekin, temp, mass, scal;
  59     gmx_mtop_atomloop_all_t                 aloop;
  60     const t_atom                           *atom;
  61     gmx::TabulatedNormalDistribution<real>  normalDist;
  62
  63     boltz = BOLTZ*tempi;
  64     ekin  = 0.0;
  65     nrdf  = 0;
  66     aloop = gmx_mtop_atomloop_all_init(mtop);
  67     while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
  68     {
  69         mass = atom->m;
  70         if (mass > 0)
  71         {
  72             rng->restart(i, 0);
  73             sd = std::sqrt(boltz/mass);
  74             for (m = 0; (m < DIM); m++)
  75             {
  76                 v[i][m] = sd*normalDist(*rng);
  77                 ekin   += 0.5*mass*v[i][m]*v[i][m];
  78             }
  79             nrdf += DIM;
  80         }
  81     }
  82     temp = (2.0*ekin)/(nrdf*BOLTZ);
  83     if (temp > 0)
  84     {
  85         scal = std::sqrt(tempi/temp);
  86         for (i = 0; (i < mtop->natoms); i++)
  87         {
  88             for (m = 0; (m < DIM); m++)
  89             {
  90                 v[i][m] *= scal;
  91             }
  92         }
  93     }
  94     fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n",
  95             tempi);
  96     if (debug)
  97     {
  98         fprintf(debug,
  99                 "Velocities were taken from a Maxwell distribution\n"
 100                 "Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
 101                 temp, tempi);
 102     }
 103 }
 104
 105 void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t *mtop, rvec v[])
 106 {
 107
 108     if (seed == 0)
 109     {
 110         seed = static_cast<int>(gmx::makeRandomSeed());
 111         fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
 112     }
 113     gmx::ThreeFry2x64<>  rng(seed, gmx::RandomDomain::MaxwellVelocities);
 114
 115     low_mspeed(tempi, mtop, v, &rng);
 116 }
 117
 118 static real calc_cm(int natoms, real mass[], rvec x[], rvec v[],
 119                     rvec xcm, rvec vcm, rvec acm, matrix L)
 120 {
 121     rvec dx, a0;
 122     real tm, m0;
 123     int  i, m;
 124
 125     clear_rvec(xcm);
 126     clear_rvec(vcm);
 127     clear_rvec(acm);
 128     tm = 0.0;
 129     for (i = 0; (i < natoms); i++)
 130     {
 131         m0  = mass[i];
 132         tm += m0;
 133         cprod(x[i], v[i], a0);
 134         for (m = 0; (m < DIM); m++)
 135         {
 136             xcm[m] += m0*x[i][m]; /* c.o.m. position */
 137             vcm[m] += m0*v[i][m]; /* c.o.m. velocity */
 138             acm[m] += m0*a0[m];   /* rotational velocity around c.o.m. */
 139         }
 140     }
 141     cprod(xcm, vcm, a0);
 142     for (m = 0; (m < DIM); m++)
 143     {
 144         xcm[m] /= tm;
 145         vcm[m] /= tm;
 146         acm[m] -= a0[m]/tm;
 147     }
 148
 149 #define PVEC(str, v) fprintf(log, \
 150                              "%s[X]: %10.5e  %s[Y]: %10.5e  %s[Z]: %10.5e\n", \
 151                              str, v[0], str, v[1], str, v[2])
 152 #ifdef DEBUG
 153     PVEC("xcm", xcm);
 154     PVEC("acm", acm);
 155     PVEC("vcm", vcm);
 156 #endif
 157
 158     clear_mat(L);
 159     for (i = 0; (i < natoms); i++)
 160     {
 161         m0 = mass[i];
 162         for (m = 0; (m < DIM); m++)
 163         {
 164             dx[m] = x[i][m]-xcm[m];
 165         }
 166         L[XX][XX] += dx[XX]*dx[XX]*m0;
 167         L[XX][YY] += dx[XX]*dx[YY]*m0;
 168         L[XX][ZZ] += dx[XX]*dx[ZZ]*m0;
 169         L[YY][YY] += dx[YY]*dx[YY]*m0;
 170         L[YY][ZZ] += dx[YY]*dx[ZZ]*m0;
 171         L[ZZ][ZZ] += dx[ZZ]*dx[ZZ]*m0;
 172     }
 173 #ifdef DEBUG
 174     PVEC("L-x", L[XX]);
 175     PVEC("L-y", L[YY]);
 176     PVEC("L-z", L[ZZ]);
 177 #endif
 178
 179     return tm;
 180 }
 181
 182 void stop_cm(FILE gmx_unused *log, int natoms, real mass[], rvec x[], rvec v[])
 183 {
 184     rvec   xcm, vcm, acm;
 185     tensor L;
 186     int    i, m;
 187
 188 #ifdef DEBUG
 189     fprintf(log, "stopping center of mass motion...\n");
 190 #endif
 191     (void)calc_cm(natoms, mass, x, v, xcm, vcm, acm, L);
 192
 193     /* Subtract center of mass velocity */
 194     for (i = 0; (i < natoms); i++)
 195     {
 196         for (m = 0; (m < DIM); m++)
 197         {
 198             v[i][m] -= vcm[m];
 199         }
 200     }
 201
 202 #ifdef DEBUG
 203     (void)calc_cm(log, natoms, mass, x, v, xcm, vcm, acm, L);
 204 #endif
 205 }