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42 #include "gromacs/random/random.h"
43 #include "gromacs/utility/smalloc.h"
44 #include "gromacs/math/units.h"
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/math/vec.h"
47 #include "gen_maxwell_velocities.h"
48 #include "gromacs/topology/mtop_util.h"
50 static void low_mspeed(real tempi,
51 gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)
55 real ekin, temp, mass, scal;
56 gmx_mtop_atomloop_all_t aloop;
62 aloop = gmx_mtop_atomloop_all_init(mtop);
63 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
68 sd = sqrt(boltz/mass);
69 for (m = 0; (m < DIM); m++)
71 v[i][m] = sd*gmx_rng_gaussian_real(rng);
72 ekin += 0.5*mass*v[i][m]*v[i][m];
77 temp = (2.0*ekin)/(nrdf*BOLTZ);
80 scal = sqrt(tempi/temp);
81 for (i = 0; (i < mtop->natoms); i++)
83 for (m = 0; (m < DIM); m++)
89 fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n",
94 "Velocities were taken from a Maxwell distribution\n"
95 "Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
100 void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t *mtop, rvec v[])
108 seed = gmx_rng_make_seed();
109 fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
112 rng = gmx_rng_init(seed);
114 low_mspeed(tempi, mtop, v, rng);
116 gmx_rng_destroy(rng);
119 static real calc_cm(int natoms, real mass[], rvec x[], rvec v[],
120 rvec xcm, rvec vcm, rvec acm, matrix L)
130 for (i = 0; (i < natoms); i++)
134 cprod(x[i], v[i], a0);
135 for (m = 0; (m < DIM); m++)
137 xcm[m] += m0*x[i][m]; /* c.o.m. position */
138 vcm[m] += m0*v[i][m]; /* c.o.m. velocity */
139 acm[m] += m0*a0[m]; /* rotational velocity around c.o.m. */
143 for (m = 0; (m < DIM); m++)
150 #define PVEC(str, v) fprintf(log, \
151 "%s[X]: %10.5e %s[Y]: %10.5e %s[Z]: %10.5e\n", \
152 str, v[0], str, v[1], str, v[2])
160 for (i = 0; (i < natoms); i++)
163 for (m = 0; (m < DIM); m++)
165 dx[m] = x[i][m]-xcm[m];
167 L[XX][XX] += dx[XX]*dx[XX]*m0;
168 L[XX][YY] += dx[XX]*dx[YY]*m0;
169 L[XX][ZZ] += dx[XX]*dx[ZZ]*m0;
170 L[YY][YY] += dx[YY]*dx[YY]*m0;
171 L[YY][ZZ] += dx[YY]*dx[ZZ]*m0;
172 L[ZZ][ZZ] += dx[ZZ]*dx[ZZ]*m0;
183 void stop_cm(FILE gmx_unused *log, int natoms, real mass[], rvec x[], rvec v[])
190 fprintf(log, "stopping center of mass motion...\n");
192 (void)calc_cm(natoms, mass, x, v, xcm, vcm, acm, L);
194 /* Subtract center of mass velocity */
195 for (i = 0; (i < natoms); i++)
197 for (m = 0; (m < DIM); m++)
204 (void)calc_cm(log, natoms, mass, x, v, xcm, vcm, acm, L);