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40 #include "gromacs/random/random.h"
41 #include "gromacs/utility/smalloc.h"
42 #include "gromacs/math/units.h"
43 #include "gromacs/legacyheaders/typedefs.h"
44 #include "gromacs/math/vec.h"
45 #include "gen_maxwell_velocities.h"
46 #include "gromacs/topology/mtop_util.h"
48 static void low_mspeed(real tempi,
49 gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)
53 real ekin, temp, mass, scal;
54 gmx_mtop_atomloop_all_t aloop;
60 aloop = gmx_mtop_atomloop_all_init(mtop);
61 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
66 sd = sqrt(boltz/mass);
67 for (m = 0; (m < DIM); m++)
69 v[i][m] = sd*gmx_rng_gaussian_real(rng);
70 ekin += 0.5*mass*v[i][m]*v[i][m];
75 temp = (2.0*ekin)/(nrdf*BOLTZ);
78 scal = sqrt(tempi/temp);
79 for (i = 0; (i < mtop->natoms); i++)
81 for (m = 0; (m < DIM); m++)
87 fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n",
92 "Velocities were taken from a Maxwell distribution\n"
93 "Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
98 void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t *mtop, rvec v[])
106 seed = gmx_rng_make_seed();
107 fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
110 rng = gmx_rng_init(seed);
112 low_mspeed(tempi, mtop, v, rng);
114 gmx_rng_destroy(rng);
117 static real calc_cm(int natoms, real mass[], rvec x[], rvec v[],
118 rvec xcm, rvec vcm, rvec acm, matrix L)
128 for (i = 0; (i < natoms); i++)
132 cprod(x[i], v[i], a0);
133 for (m = 0; (m < DIM); m++)
135 xcm[m] += m0*x[i][m]; /* c.o.m. position */
136 vcm[m] += m0*v[i][m]; /* c.o.m. velocity */
137 acm[m] += m0*a0[m]; /* rotational velocity around c.o.m. */
141 for (m = 0; (m < DIM); m++)
148 #define PVEC(str, v) fprintf(log, \
149 "%s[X]: %10.5e %s[Y]: %10.5e %s[Z]: %10.5e\n", \
150 str, v[0], str, v[1], str, v[2])
158 for (i = 0; (i < natoms); i++)
161 for (m = 0; (m < DIM); m++)
163 dx[m] = x[i][m]-xcm[m];
165 L[XX][XX] += dx[XX]*dx[XX]*m0;
166 L[XX][YY] += dx[XX]*dx[YY]*m0;
167 L[XX][ZZ] += dx[XX]*dx[ZZ]*m0;
168 L[YY][YY] += dx[YY]*dx[YY]*m0;
169 L[YY][ZZ] += dx[YY]*dx[ZZ]*m0;
170 L[ZZ][ZZ] += dx[ZZ]*dx[ZZ]*m0;
181 void stop_cm(FILE gmx_unused *log, int natoms, real mass[], rvec x[], rvec v[])
188 fprintf(log, "stopping center of mass motion...\n");
190 (void)calc_cm(natoms, mass, x, v, xcm, vcm, acm, L);
192 /* Subtract center of mass velocity */
193 for (i = 0; (i < natoms); i++)
195 for (m = 0; (m < DIM); m++)
202 (void)calc_cm(log, natoms, mass, x, v, xcm, vcm, acm, L);