/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2014, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief This file defines functions for "pair" interactions
+ * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
#include "gmxpre.h"
#include "pairs.h"
-#include <math.h>
+#include <cmath>
#include "gromacs/legacyheaders/types/group.h"
-#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
-static void
-nb_listed_warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
+#include "listed-internal.h"
+
+namespace
+{
+
+/*! \brief Issue a warning if a listed interaction is beyond a table limit */
+void
+warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
{
gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
"at distance %.3f which is larger than the table limit %.3f nm.\n\n"
}
}
-
-
-/* This might logically belong better in the nb_generic.c module, but it is only
- * used in do_nonbonded_listed(), and we want it to be inlined there to avoid an
- * extra functional call for every single pair listed in the topology.
- */
-static real
-nb_evaluate_single(real r2, real tabscale, real *vftab,
- real qq, real c6, real c12, real *velec, real *vvdw)
+/*! \brief Compute the energy and force for a single pair interaction */
+real
+evaluate_single(real r2, real tabscale, real *vftab,
+ real qq, real c6, real c12, real *velec, real *vvdw)
{
real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
int ntab;
rinv = gmx_invsqrt(r2);
r = r2*rinv;
rtab = r*tabscale;
- ntab = rtab;
+ ntab = static_cast<int>(rtab);
eps = rtab-ntab;
eps2 = eps*eps;
ntab = 12*ntab;
return fscal;
}
-static real
-nb_free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul, real alpha_vdw,
- real tabscale, real *vftab,
- real qqA, real c6A, real c12A, real qqB, real c6B, real c12B,
- real LFC[2], real LFV[2], real DLF[2],
- real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2], real dlfac_vdw[2],
- real sigma6_def, real sigma6_min, real sigma2_def, real sigma2_min,
- real *velectot, real *vvdwtot, real *dvdl)
+/*! \brief Compute the energy and force for a single pair interaction under FEP */
+real
+free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul,
+ real alpha_vdw, real tabscale, real *vftab,
+ real qqA, real c6A, real c12A, real qqB,
+ real c6B, real c12B, real LFC[2], real LFV[2], real DLF[2],
+ real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2],
+ real dlfac_vdw[2], real sigma6_def, real sigma6_min,
+ real sigma2_def, real sigma2_min,
+ real *velectot, real *vvdwtot, real *dvdl)
{
- real r, rp, rpm2, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
- real qq[2], c6[2], c12[2], sigma6[2], sigma2[2], sigma_pow[2], sigma_powm2[2];
+ real rp, rpm2, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
+ real qq[2], c6[2], c12[2], sigma6[2], sigma2[2], sigma_pow[2];
real alpha_coul_eff, alpha_vdw_eff, dvdl_coul, dvdl_vdw;
real rpinv, r_coul, r_vdw, velecsum, vvdwsum;
real fscal_vdw[2], fscal_elec[2];
real velec[2], vvdw[2];
int i, ntab;
-
const real half = 0.5;
+ const real minusOne = -1.0;
+ const real oneThird = 1.0 / 3.0;
const real one = 1.0;
const real two = 2.0;
const real six = 6.0;
}
else
{
- rp = pow(r2, half*sc_r_power); /* not currently supported as input, but can handle it */
+ rp = std::pow(r2, half * sc_r_power); /* not currently supported as input, but can handle it */
rpm2 = rp/r2;
}
* Correct for this by multiplying with (1/12.0)/(1/6.0)=6.0/12.0=0.5.
*/
sigma6[i] = half*c12[i]/c6[i];
- sigma2[i] = pow(half*c12[i]/c6[i], 1.0/3.0);
+ sigma2[i] = std::pow(half*c12[i]/c6[i], oneThird);
/* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
what data to store externally. Can't be fixed without larger scale changes, so not 5.0 */
if (sigma6[i] < sigma6_min) /* for disappearing coul and vdw with soft core at the same time */
if (sc_r_power == six)
{
sigma_pow[i] = sigma6[i];
- sigma_powm2[i] = sigma6[i]/sigma2[i];
}
else if (sc_r_power == fourtyeight)
{
sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^48 */
- sigma_powm2[i] = sigma_pow[i]/sigma2[i];
}
else
- { /* not really supported as input, but in here for testing the general case*/
- sigma_pow[i] = pow(sigma2[i], sc_r_power/2);
- sigma_powm2[i] = sigma_pow[i]/(sigma2[i]);
+ { /* not really supported as input, but in here for testing the general case*/
+ sigma_pow[i] = std::pow(sigma2[i], sc_r_power/2);
}
}
{
/* Coulomb */
rpinv = one/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
- r_coul = pow(rpinv, -one/sc_r_power);
+ r_coul = std::pow(rpinv, minusOne / sc_r_power);
/* Electrostatics table lookup data */
rtab = r_coul*tabscale;
- ntab = rtab;
+ ntab = static_cast<int>(rtab);
eps = rtab-ntab;
eps2 = eps*eps;
ntab = 12*ntab;
/* Vdw */
rpinv = one/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
- r_vdw = pow(rpinv, -one/sc_r_power);
+ r_vdw = std::pow(rpinv, minusOne / sc_r_power);
/* Vdw table lookup data */
rtab = r_vdw*tabscale;
- ntab = rtab;
+ ntab = static_cast<int>(rtab);
eps = rtab-ntab;
eps2 = eps*eps;
ntab = 12*ntab;
return fscal;
}
+} // namespace
+
real
-do_nonbonded_listed(int ftype, int nbonds,
- const t_iatom iatoms[], const t_iparams iparams[],
- const rvec x[], rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
- real *lambda, real *dvdl,
- const t_mdatoms *md,
- const t_forcerec *fr, gmx_grppairener_t *grppener,
- int *global_atom_index)
+do_pairs(int ftype, int nbonds,
+ const t_iatom iatoms[], const t_iparams iparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real *lambda, real *dvdl,
+ const t_mdatoms *md,
+ const t_forcerec *fr, gmx_grppairener_t *grppener,
+ int *global_atom_index)
{
- int ielec, ivdw;
real qq, c6, c12;
rvec dx;
ivec dt;
- int i, j, itype, ai, aj, gid;
+ int i, itype, ai, aj, gid;
int fshift_index;
- real r2, rinv;
+ real r2;
real fscal, velec, vvdw;
real * energygrp_elec;
real * energygrp_vdw;
gmx_bool bFreeEnergy;
real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
real qqB, c6B, c12B, sigma2_def, sigma2_min;
-
+ const real oneThird = 1.0 / 3.0;
switch (ftype)
{
DLF[1] = 1;
/* precalculate */
- sigma2_def = pow(fr->sc_sigma6_def, 1.0/3.0);
- sigma2_min = pow(fr->sc_sigma6_min, 1.0/3.0);
+ sigma2_def = pow(fr->sc_sigma6_def, oneThird);
+ sigma2_min = pow(fr->sc_sigma6_min, oneThird);
for (i = 0; i < 2; i++)
{
* disadvantage is that the warning is printed twice */
if (warned_rlimit == FALSE)
{
- nb_listed_warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
+ warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
warned_rlimit = TRUE;
}
continue;
c6B = iparams[itype].lj14.c6B*6.0;
c12B = iparams[itype].lj14.c12B*12.0;
- fscal = nb_free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
- fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
- LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
- fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
+ fscal = free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
+ fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
+ LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
+ fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
}
else
{
/* Evaluate tabulated interaction without free energy */
- fscal = nb_evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
+ fscal = evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
}
energygrp_elec[gid] += velec;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2014, 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _pairs_h
-#define _pairs_h
+/*! \internal \file
+ *
+ * \brief This file declares functions for "pair" interactions
+ * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#ifndef GMX_LISTED_FORCES_PAIRS_H
+#define GMX_LISTED_FORCES_PAIRS_H
#include "gromacs/legacyheaders/types/forcerec.h"
#include "gromacs/legacyheaders/types/mdatom.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-} /* fixes auto-indentation problems */
-#endif
-
struct t_graph;
struct t_pbc;
-/* Calculate VdW/charge listed pair interactions (usually 1-4 interactions).
+/*! \brief Calculate VdW/charge listed pair interactions (usually 1-4
+ * interactions).
+ *
* global_atom_index is only passed for printing error messages.
*/
real
-do_nonbonded_listed(int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[],
- const rvec x[], rvec f[], rvec fshift[],
- const struct t_pbc *pbc, const struct t_graph *g,
- real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
- gmx_grppairener_t *grppener, int *global_atom_index);
-
-#ifdef __cplusplus
-}
-#endif
+do_pairs(int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
+ gmx_grppairener_t *grppener, int *global_atom_index);
#endif
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