2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
7 * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
9 * and including many others, as listed in the AUTHORS file in the
10 * top-level source directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
38 /* This file is completely threadsafe - keep it that way! */
43 #include "gromacs/math/vec.h"
44 #include "gromacs/mdlib/coupling.h"
45 #include "gromacs/mdtypes/group.h"
46 #include "gromacs/mdtypes/inputrec.h"
49 real sum_ekin(const t_grpopts* opts, gmx_ekindata_t* ekind, real* dekindlambda, gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
62 clear_mat(ekind->ekin);
64 for (i = 0; (i < ngtc); i++)
68 tcstat = &ekind->tcstat[i];
69 /* Sometimes a group does not have degrees of freedom, e.g.
70 * when it consists of shells and virtual sites, then we just
71 * set the temperatue to 0 and also neglect the kinetic
72 * energy, which should be zero anyway.
81 /* in this case, kinetic energy is from the current velocities already */
82 msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
87 /* Calculate the full step Ekin as the average of the half steps */
88 for (j = 0; (j < DIM); j++)
90 for (m = 0; (m < DIM); m++)
92 tcstat->ekinf[j][m] = 0.5
93 * (tcstat->ekinh[j][m] * tcstat->ekinscaleh_nhc
94 + tcstat->ekinh_old[j][m]);
98 m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
100 tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
101 tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
103 /* after the scaling factors have been multiplied in, we can remove them */
106 tcstat->ekinscalef_nhc = 1.0;
110 tcstat->ekinscaleh_nhc = 1.0;
129 *dekindlambda = ekind->dekindl;
133 *dekindlambda = 0.5 * (ekind->dekindl + ekind->dekindl_old);