-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * For more info, check our website at http://www.gromacs.org
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
- * And Hey:
- * GROwing Monsters And Cloning Shrimps
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
int flags,
float *cycles_pme)
{
- int i, j, status;
+ int i, j;
int donb_flags;
gmx_bool bDoEpot, bSepDVDL, bSB;
int pme_flags;
matrix boxs;
rvec box_size;
- real Vsr, Vlr, Vcorr = 0;
t_pbc pbc;
- real dvdgb;
char buf[22];
double clam_i, vlam_i;
- real dvdl_dum[efptNR], dvdl, dvdl_nb[efptNR], lam_i[efptNR];
- real dvdlsum;
+ real dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
if (ir->nwall)
{
/* foreign lambda component for walls */
- dvdl = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
- enerd->grpp.ener[egLJSR], nrnb);
- PRINT_SEPDVDL("Walls", 0.0, dvdl);
- enerd->dvdl_lin[efptVDW] += dvdl;
+ real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
+ enerd->grpp.ener[egLJSR], nrnb);
+ PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
+ enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
/* If doing GB, reset dvda and calculate the Born radii */
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
- Vsr = 0;
if (bSepDVDL)
{
+ real V_short_range = 0;
+ real dvdl_short_range;
+
for (i = 0; i < enerd->grpp.nener; i++)
{
- Vsr +=
+ V_short_range +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
- dvdlsum = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
- PRINT_SEPDVDL("VdW and Coulomb SR particle-p.", Vsr, dvdlsum);
+ dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
+ PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
+ V_short_range,
+ dvdl_short_range);
}
debug_gmx();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype))
{
+ real Vlr = 0, Vcorr = 0;
+ real dvdl_long_range = 0;
+ int status = 0;
+
bSB = (ir->nwall == 2);
if (bSB)
{
if (fr->bEwald)
{
- Vcorr = 0;
- dvdl = 0;
+ real dvdl_long_range_correction = 0;
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
fnv = fr->f_novirsum;
vir = &fr->vir_el_recip;
Vcorrt = &Vcorr;
- dvdlt = &dvdl;
+ dvdlt = &dvdl_long_range_correction;
}
else
{
{
reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
fr->vir_el_recip,
- &Vcorr, efptCOUL, &dvdl,
+ &Vcorr, efptCOUL, &dvdl_long_range_correction,
nthreads, fr->f_t);
}
if (fr->n_tpi == 0)
{
Vcorr += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
- &dvdl, fr->vir_el_recip);
+ &dvdl_long_range_correction,
+ fr->vir_el_recip);
}
- PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr, dvdl);
- enerd->dvdl_lin[efptCOUL] += dvdl;
+ PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr,
+ dvdl_long_range_correction);
+ enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction;
}
- status = 0;
- Vlr = 0;
- dvdl = 0;
switch (fr->eeltype)
{
case eelPME:
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
fr->vir_el_recip, fr->ewaldcoeff,
- &Vlr, lambda[efptCOUL], &dvdl,
+ &Vlr, lambda[efptCOUL], &dvdl_long_range,
pme_flags);
*cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
md->chargeA + md->homenr - fr->n_tpi,
&Vlr);
}
- PRINT_SEPDVDL("PME mesh", Vlr, dvdl);
+ PRINT_SEPDVDL("PME mesh", Vlr, dvdl_long_range);
}
break;
case eelEWALD:
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff,
- lambda[efptCOUL], &dvdl, fr->ewald_table);
- PRINT_SEPDVDL("Ewald long-range", Vlr, dvdl);
+ lambda[efptCOUL], &dvdl_long_range, fr->ewald_table);
+ PRINT_SEPDVDL("Ewald long-range", Vlr, dvdl_long_range);
break;
default:
gmx_fatal(FARGS, "No such electrostatics method implemented %s",
status, EELTYPE(fr->eeltype));
}
/* Note that with separate PME nodes we get the real energies later */
- enerd->dvdl_lin[efptCOUL] += dvdl;
+ enerd->dvdl_lin[efptCOUL] += dvdl_long_range;
enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
if (debug)
{
}
else
{
- if (EEL_RF(fr->eeltype))
+ /* Is there a reaction-field exclusion correction needed? */
+ if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
{
- /* With the Verlet scheme exclusion forces are calculated
+ /* With the Verlet scheme, exclusion forces are calculated
* in the non-bonded kernel.
*/
- if (ir->cutoff_scheme != ecutsVERLET && fr->eeltype != eelRF_NEC)
+ if (ir->cutoff_scheme != ecutsVERLET)
{
- dvdl = 0;
+ real dvdl_rf_excl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fr, graph, md, excl, x, f,
- fr->fshift, &pbc, lambda[efptCOUL], &dvdl);
- }
+ fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
- enerd->dvdl_lin[efptCOUL] += dvdl;
- PRINT_SEPDVDL("RF exclusion correction",
- enerd->term[F_RF_EXCL], dvdl);
+ enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
+ PRINT_SEPDVDL("RF exclusion correction",
+ enerd->term[F_RF_EXCL], dvdl_rf_excl);
+ }
}
}
where();
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff