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39 #include "gen_maxwell_velocities.h"
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"
53 static void low_mspeed(real tempi
,
54 gmx_mtop_t
*mtop
, rvec v
[], gmx::ThreeFry2x64
<> * rng
)
59 gmx::TabulatedNormalDistribution
<real
> normalDist
;
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",
98 "Velocities were taken from a Maxwell distribution\n"
99 "Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
104 void maxwell_speed(real tempi
, unsigned int seed
, gmx_mtop_t
*mtop
, rvec v
[])
109 seed
= static_cast<int>(gmx::makeRandomSeed());
110 fprintf(stderr
, "Using random seed %u for generating velocities\n", seed
);
112 gmx::ThreeFry2x64
<> rng(seed
, gmx::RandomDomain::MaxwellVelocities
);
114 low_mspeed(tempi
, mtop
, v
, &rng
);
117 static real
calc_cm(int natoms
, const 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
);