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40 #include "gen_maxwell_velocities.h"
44 #include "gromacs/math/units.h"
45 #include "gromacs/math/vec.h"
46 #include "gromacs/math/vectypes.h"
47 #include "gromacs/random/tabulatednormaldistribution.h"
48 #include "gromacs/random/threefry.h"
49 #include "gromacs/topology/mtop_util.h"
50 #include "gromacs/topology/topology.h"
51 #include "gromacs/utility/fatalerror.h"
52 #include "gromacs/utility/smalloc.h"
54 static void low_mspeed(real tempi, gmx_mtop_t* mtop, rvec v[], gmx::ThreeFry2x64<>* rng)
59 gmx::TabulatedNormalDistribution<real> normalDist;
61 boltz = BOLTZ * tempi;
64 for (const AtomProxy atomP : AtomRange(*mtop))
66 const t_atom& local = atomP.atom();
67 int i = atomP.globalAtomNumber();
72 real sd = std::sqrt(boltz / mass);
73 for (int m = 0; (m < DIM); m++)
75 v[i][m] = sd * normalDist(*rng);
76 ekin += 0.5 * mass * v[i][m] * v[i][m];
81 temp = (2.0 * ekin) / (nrdf * BOLTZ);
84 real scal = std::sqrt(tempi / temp);
85 for (int i = 0; (i < mtop->natoms); i++)
87 for (int m = 0; (m < DIM); m++)
93 fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n", tempi);
97 "Velocities were taken from a Maxwell distribution\n"
98 "Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
103 void maxwell_speed(real tempi, unsigned int seed, gmx_mtop_t* mtop, rvec v[])
108 seed = static_cast<int>(gmx::makeRandomSeed());
109 fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
111 gmx::ThreeFry2x64<> rng(seed, gmx::RandomDomain::MaxwellVelocities);
113 low_mspeed(tempi, mtop, v, &rng);
116 static real calc_cm(int natoms, const real mass[], rvec x[], rvec v[], rvec xcm, rvec vcm, rvec acm, matrix L)
126 for (i = 0; (i < natoms); i++)
130 cprod(x[i], v[i], a0);
131 for (m = 0; (m < DIM); m++)
133 xcm[m] += m0 * x[i][m]; /* c.o.m. position */
134 vcm[m] += m0 * v[i][m]; /* c.o.m. velocity */
135 acm[m] += m0 * a0[m]; /* rotational velocity around c.o.m. */
139 for (m = 0; (m < DIM); m++)
143 acm[m] -= a0[m] / tm;
146 #define PVEC(str, v) \
147 fprintf(log, "%s[X]: %10.5e %s[Y]: %10.5e %s[Z]: %10.5e\n", str, (v)[0], str, (v)[1], str, (v)[2])
155 for (i = 0; (i < natoms); i++)
158 for (m = 0; (m < DIM); m++)
160 dx[m] = x[i][m] - xcm[m];
162 L[XX][XX] += dx[XX] * dx[XX] * m0;
163 L[XX][YY] += dx[XX] * dx[YY] * m0;
164 L[XX][ZZ] += dx[XX] * dx[ZZ] * m0;
165 L[YY][YY] += dx[YY] * dx[YY] * m0;
166 L[YY][ZZ] += dx[YY] * dx[ZZ] * m0;
167 L[ZZ][ZZ] += dx[ZZ] * dx[ZZ] * m0;
178 void stop_cm(FILE gmx_unused* log, int natoms, real mass[], rvec x[], rvec v[])
185 fprintf(log, "stopping center of mass motion...\n");
187 (void)calc_cm(natoms, mass, x, v, xcm, vcm, acm, L);
189 /* Subtract center of mass velocity */
190 for (i = 0; (i < natoms); i++)
192 for (m = 0; (m < DIM); m++)
199 (void)calc_cm(log, natoms, mass, x, v, xcm, vcm, acm, L);