#include "config.h"
-#include <cassert>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/listed_forces/pairs.h"
#include "gromacs/math/functions.h"
-#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/forcerec_threading.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
-#include "gromacs/mdlib/rf_util.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdlib/wholemoleculetransform.h"
#include "gromacs/mdtypes/commrec.h"
return (std::abs(fr->qsum[0]) > 1e-4 || std::abs(fr->qsum[1]) > 1e-4);
}
-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;
-}
-
/*!\brief If there's bonded interactions of type \c ftype1 or \c
* ftype2 present in the topology, build an array of the number of
* interactions present for each bonded interaction index found in the
}
}
-static real cutoff_inf(real cutoff)
-{
- if (cutoff == 0)
- {
- cutoff = GMX_CUTOFF_INF;
- }
-
- return cutoff;
-}
-
-/*! \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;
- }
-}
-
/* Generate Coulomb and/or Van der Waals Ewald long-range correction tables
*
* Tables are generated for one or both, depending on if the pointers
}
}
-static void clear_force_switch_constants(shift_consts_t* sc)
+real cutoff_inf(real cutoff)
{
- 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);
-}
-
-/*! \brief Construct interaction constants
- *
- * This data is used (particularly) by search and force code for
- * short-range interactions. Many of these are constant for the whole
- * simulation; some are constant only after PME tuning completes.
- */
-static 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)
+ if (cutoff == 0)
{
- GMX_RELEASE_ASSERT(ir.fepvals, "ir.fepvals should be set wth free-energy");
- interactionConst.softCoreParameters =
- std::make_unique<interaction_const_t::SoftCoreParameters>(*ir.fepvals);
+ cutoff = GMX_CUTOFF_INF;
}
- return interactionConst;
+ return cutoff;
}
void init_forcerec(FILE* fplog,
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