/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, 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.
#include <cstdio>
+#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
+#include "gromacs/mdlib/rf_util.h"
+#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/pleasecite.h"
interaction_const_t::SoftCoreParameters::SoftCoreParameters(const t_lambda& fepvals) :
alphaVdw(fepvals.sc_alpha),
// This is checked during tpr reading, so we can assert here
GMX_RELEASE_ASSERT(fepvals.sc_r_power == 6.0, "We only support soft-core r-power 6");
}
+
+/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
+static void initCoulombEwaldParameters(FILE* fp,
+ const t_inputrec& ir,
+ bool systemHasNetCharge,
+ interaction_const_t* ic)
+{
+ if (!EEL_PME_EWALD(ir.coulombtype))
+ {
+ return;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
+
+ if (ir.coulombtype == CoulombInteractionType::P3mAD)
+ {
+ please_cite(fp, "Hockney1988");
+ please_cite(fp, "Ballenegger2012");
+ }
+ else
+ {
+ please_cite(fp, "Essmann95a");
+ }
+
+ if (ir.ewald_geometry == EwaldGeometry::ThreeDC)
+ {
+ if (fp)
+ {
+ fprintf(fp,
+ "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
+ systemHasNetCharge ? " and net charge" : "");
+ }
+ please_cite(fp, "In-Chul99a");
+ if (systemHasNetCharge)
+ {
+ please_cite(fp, "Ballenegger2009");
+ }
+ }
+ }
+
+ ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir.rcoulomb, ir.ewald_rtol);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
+ }
+
+ if (ic->coulomb_modifier == InteractionModifiers::PotShift)
+ {
+ GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
+ }
+ else
+ {
+ ic->sh_ewald = 0;
+ }
+}
+
+/*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
+static void initVdwEwaldParameters(FILE* fp, const t_inputrec& ir, interaction_const_t* ic)
+{
+ if (!EVDW_PME(ir.vdwtype))
+ {
+ return;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
+ please_cite(fp, "Essmann95a");
+ }
+ ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir.rvdw, ir.ewald_rtol_lj);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
+ }
+
+ if (ic->vdw_modifier == InteractionModifiers::PotShift)
+ {
+ real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
+ ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
+ }
+ else
+ {
+ ic->sh_lj_ewald = 0;
+ }
+}
+
+static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t& mtop)
+{
+ const t_atoms *at1, *at2;
+ int i, j, tpi, tpj, ntypes;
+ real b, bmin;
+
+ if (fplog)
+ {
+ fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
+ }
+ ntypes = mtop.ffparams.atnr;
+
+ bmin = -1;
+ real bham_b_max = 0;
+ for (size_t mt1 = 0; mt1 < mtop.moltype.size(); mt1++)
+ {
+ at1 = &mtop.moltype[mt1].atoms;
+ for (i = 0; (i < at1->nr); i++)
+ {
+ tpi = at1->atom[i].type;
+ if (tpi >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
+ }
+
+ for (size_t mt2 = mt1; mt2 < mtop.moltype.size(); mt2++)
+ {
+ at2 = &mtop.moltype[mt2].atoms;
+ for (j = 0; (j < at2->nr); j++)
+ {
+ tpj = at2->atom[j].type;
+ if (tpj >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
+ }
+ b = mtop.ffparams.iparams[tpi * ntypes + tpj].bham.b;
+ if (b > bham_b_max)
+ {
+ bham_b_max = b;
+ }
+ if ((b < bmin) || (bmin == -1))
+ {
+ bmin = b;
+ }
+ }
+ }
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
+ }
+
+ return bham_b_max;
+}
+
+static void clear_force_switch_constants(shift_consts_t* sc)
+{
+ sc->c2 = 0;
+ sc->c3 = 0;
+ sc->cpot = 0;
+}
+
+static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
+{
+ /* Here we determine the coefficient for shifting the force to zero
+ * between distance rsw and the cut-off rc.
+ * For a potential of r^-p, we have force p*r^-(p+1).
+ * But to save flops we absorb p in the coefficient.
+ * Thus we get:
+ * force/p = r^-(p+1) + c2*r^2 + c3*r^3
+ * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
+ */
+ sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
+ sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
+ sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
+ + p * sc->c3 / 4 * gmx::power4(rc - rsw);
+}
+
+static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
+{
+ /* The switch function is 1 at rsw and 0 at rc.
+ * The derivative and second derivate are zero at both ends.
+ * rsw = max(r - r_switch, 0)
+ * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
+ * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
+ * force = force*dsw - potential*sw
+ * potential *= sw
+ */
+ sc->c3 = -10 / gmx::power3(rc - rsw);
+ sc->c4 = 15 / gmx::power4(rc - rsw);
+ sc->c5 = -6 / gmx::power5(rc - rsw);
+}
+
+
+interaction_const_t init_interaction_const(FILE* fp, const t_inputrec& ir, const gmx_mtop_t& mtop, bool systemHasNetCharge)
+{
+ interaction_const_t interactionConst;
+
+ interactionConst.coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
+ interactionConst.vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
+
+ /* Lennard-Jones */
+ interactionConst.vdwtype = ir.vdwtype;
+ interactionConst.vdw_modifier = ir.vdw_modifier;
+ interactionConst.reppow = mtop.ffparams.reppow;
+ interactionConst.rvdw = cutoff_inf(ir.rvdw);
+ interactionConst.rvdw_switch = ir.rvdw_switch;
+ interactionConst.ljpme_comb_rule = ir.ljpme_combination_rule;
+ interactionConst.useBuckingham = (mtop.ffparams.functype[0] == F_BHAM);
+ if (interactionConst.useBuckingham)
+ {
+ interactionConst.buckinghamBMax = calcBuckinghamBMax(fp, mtop);
+ }
+
+ initVdwEwaldParameters(fp, ir, &interactionConst);
+
+ clear_force_switch_constants(&interactionConst.dispersion_shift);
+ clear_force_switch_constants(&interactionConst.repulsion_shift);
+
+ switch (interactionConst.vdw_modifier)
+ {
+ case InteractionModifiers::PotShift:
+ /* Only shift the potential, don't touch the force */
+ interactionConst.dispersion_shift.cpot = -1.0 / gmx::power6(interactionConst.rvdw);
+ interactionConst.repulsion_shift.cpot = -1.0 / gmx::power12(interactionConst.rvdw);
+ break;
+ case InteractionModifiers::ForceSwitch:
+ /* Switch the force, switch and shift the potential */
+ force_switch_constants(
+ 6.0, interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.dispersion_shift);
+ force_switch_constants(
+ 12.0, interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.repulsion_shift);
+ break;
+ case InteractionModifiers::PotSwitch:
+ /* Switch the potential and force */
+ potential_switch_constants(
+ interactionConst.rvdw_switch, interactionConst.rvdw, &interactionConst.vdw_switch);
+ break;
+ case InteractionModifiers::None:
+ case InteractionModifiers::ExactCutoff:
+ /* Nothing to do here */
+ break;
+ default: gmx_incons("unimplemented potential modifier");
+ }
+
+ /* Electrostatics */
+ interactionConst.eeltype = ir.coulombtype;
+ interactionConst.coulomb_modifier = ir.coulomb_modifier;
+ interactionConst.rcoulomb = cutoff_inf(ir.rcoulomb);
+ interactionConst.rcoulomb_switch = ir.rcoulomb_switch;
+ interactionConst.epsilon_r = ir.epsilon_r;
+
+ /* Set the Coulomb energy conversion factor */
+ if (interactionConst.epsilon_r != 0)
+ {
+ interactionConst.epsfac = gmx::c_one4PiEps0 / interactionConst.epsilon_r;
+ }
+ else
+ {
+ /* eps = 0 is infinite dieletric: no Coulomb interactions */
+ interactionConst.epsfac = 0;
+ }
+
+ /* Reaction-field */
+ if (EEL_RF(interactionConst.eeltype))
+ {
+ GMX_RELEASE_ASSERT(interactionConst.eeltype != CoulombInteractionType::GRFNotused,
+ "GRF is no longer supported");
+ interactionConst.reactionFieldPermitivity = ir.epsilon_rf;
+ calc_rffac(fp,
+ interactionConst.epsilon_r,
+ interactionConst.reactionFieldPermitivity,
+ interactionConst.rcoulomb,
+ &interactionConst.reactionFieldCoefficient,
+ &interactionConst.reactionFieldShift);
+ }
+ else
+ {
+ /* For plain cut-off we might use the reaction-field kernels */
+ interactionConst.reactionFieldPermitivity = interactionConst.epsilon_r;
+ interactionConst.reactionFieldCoefficient = 0;
+ if (ir.coulomb_modifier == InteractionModifiers::PotShift)
+ {
+ interactionConst.reactionFieldShift = 1 / interactionConst.rcoulomb;
+ }
+ else
+ {
+ interactionConst.reactionFieldShift = 0;
+ }
+ }
+
+ initCoulombEwaldParameters(fp, ir, systemHasNetCharge, &interactionConst);
+
+ if (fp != nullptr)
+ {
+ real dispersion_shift;
+
+ dispersion_shift = interactionConst.dispersion_shift.cpot;
+ if (EVDW_PME(interactionConst.vdwtype))
+ {
+ dispersion_shift -= interactionConst.sh_lj_ewald;
+ }
+ fprintf(fp,
+ "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
+ interactionConst.repulsion_shift.cpot,
+ dispersion_shift);
+
+ if (interactionConst.eeltype == CoulombInteractionType::Cut)
+ {
+ fprintf(fp, ", Coulomb %.e", -interactionConst.reactionFieldShift);
+ }
+ else if (EEL_PME(interactionConst.eeltype))
+ {
+ fprintf(fp, ", Ewald %.3e", -interactionConst.sh_ewald);
+ }
+ fprintf(fp, "\n");
+ }
+
+ if (ir.efep != FreeEnergyPerturbationType::No)
+ {
+ GMX_RELEASE_ASSERT(ir.fepvals, "ir.fepvals should be set wth free-energy");
+ interactionConst.softCoreParameters =
+ std::make_unique<interaction_const_t::SoftCoreParameters>(*ir.fepvals);
+ }
+
+ return interactionConst;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff