--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014, 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * 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>
+#endif
+
+#include <assert.h>
+
+#include <sys/types.h>
+#include <math.h>
+#include "typedefs.h"
+#include "physics.h"
+#include "gromacs/utility/smalloc.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "vec.h"
+#include "coulomb.h"
+#include "calc_verletbuf.h"
+#include "../mdlib/nbnxn_consts.h"
+
+#ifdef GMX_NBNXN_SIMD
+/* The include below sets the SIMD instruction type (precision+width)
+ * for all nbnxn SIMD search and non-bonded kernel code.
+ */
+#ifdef GMX_NBNXN_HALF_WIDTH_SIMD
+#define GMX_USE_HALF_WIDTH_SIMD_HERE
+#endif
+#include "gromacs/simd/simd.h"
+#endif
+
+
+/* The code in this file estimates a pairlist buffer length
+ * given a target energy drift per atom per picosecond.
+ * This is done by estimating the drift given a buffer length.
+ * Ideally we would like to have a tight overestimate of the drift,
+ * but that can be difficult to achieve.
+ *
+ * Significant approximations used:
+ *
+ * Uniform particle density. UNDERESTIMATES the drift by rho_global/rho_local.
+ *
+ * Interactions don't affect particle motion. OVERESTIMATES the drift on longer
+ * time scales. This approximation probably introduces the largest errors.
+ *
+ * Only take one constraint per particle into account: OVERESTIMATES the drift.
+ *
+ * For rotating constraints assume the same functional shape for time scales
+ * where the constraints rotate significantly as the exact expression for
+ * short time scales. OVERESTIMATES the drift on long time scales.
+ *
+ * For non-linear virtual sites use the mass of the lightest constructing atom
+ * to determine the displacement. OVER/UNDERESTIMATES the drift, depending on
+ * the geometry and masses of constructing atoms.
+ *
+ * Note that the formulas for normal atoms and linear virtual sites are exact,
+ * apart from the first two approximations.
+ *
+ * Note that apart from the effect of the above approximations, the actual
+ * drift of the total energy of a system can be order of magnitude smaller
+ * due to cancellation of positive and negative drift for different pairs.
+ */
+
+
+/* Struct for unique atom type for calculating the energy drift.
+ * The atom displacement depends on mass and constraints.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+typedef struct
+{
+ real mass; /* mass */
+ int type; /* type (used for LJ parameters) */
+ real q; /* charge */
+ gmx_bool bConstr; /* constrained, if TRUE, use #DOF=2 iso 3 */
+ real con_mass; /* mass of heaviest atom connected by constraints */
+ real con_len; /* constraint length to the heaviest atom */
+} atom_nonbonded_kinetic_prop_t;
+
+/* Struct for unique atom type for calculating the energy drift.
+ * The atom displacement depends on mass and constraints.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+typedef struct
+{
+ atom_nonbonded_kinetic_prop_t prop; /* non-bonded and kinetic atom prop. */
+ int n; /* #atoms of this type in the system */
+} verletbuf_atomtype_t;
+
+void verletbuf_get_list_setup(gmx_bool bGPU,
+ verletbuf_list_setup_t *list_setup)
+{
+ list_setup->cluster_size_i = NBNXN_CPU_CLUSTER_I_SIZE;
+
+ if (bGPU)
+ {
+ list_setup->cluster_size_j = NBNXN_GPU_CLUSTER_SIZE;
+ }
+ else
+ {
+#ifndef GMX_NBNXN_SIMD
+ list_setup->cluster_size_j = NBNXN_CPU_CLUSTER_I_SIZE;
+#else
+ list_setup->cluster_size_j = GMX_SIMD_REAL_WIDTH;
+#ifdef GMX_NBNXN_SIMD_2XNN
+ /* We assume the smallest cluster size to be on the safe side */
+ list_setup->cluster_size_j /= 2;
+#endif
+#endif
+ }
+}
+
+static gmx_bool
+atom_nonbonded_kinetic_prop_equal(const atom_nonbonded_kinetic_prop_t *prop1,
+ const atom_nonbonded_kinetic_prop_t *prop2)
+{
+ return (prop1->mass == prop2->mass &&
+ prop1->type == prop2->type &&
+ prop1->q == prop2->q &&
+ prop1->bConstr == prop2->bConstr &&
+ prop1->con_mass == prop2->con_mass &&
+ prop1->con_len == prop2->con_len);
+}
+
+static void add_at(verletbuf_atomtype_t **att_p, int *natt_p,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ int nmol)
+{
+ verletbuf_atomtype_t *att;
+ int natt, i;
+
+ if (prop->mass == 0)
+ {
+ /* Ignore massless particles */
+ return;
+ }
+
+ att = *att_p;
+ natt = *natt_p;
+
+ i = 0;
+ while (i < natt && !atom_nonbonded_kinetic_prop_equal(prop, &att[i].prop))
+ {
+ i++;
+ }
+
+ if (i < natt)
+ {
+ att[i].n += nmol;
+ }
+ else
+ {
+ (*natt_p)++;
+ srenew(*att_p, *natt_p);
+ (*att_p)[i].prop = *prop;
+ (*att_p)[i].n = nmol;
+ }
+}
+
+static void get_vsite_masses(const gmx_moltype_t *moltype,
+ const gmx_ffparams_t *ffparams,
+ real *vsite_m,
+ int *n_nonlin_vsite)
+{
+ int ft, i;
+ const t_ilist *il;
+
+ *n_nonlin_vsite = 0;
+
+ /* Check for virtual sites, determine mass from constructing atoms */
+ for (ft = 0; ft < F_NRE; ft++)
+ {
+ if (IS_VSITE(ft))
+ {
+ il = &moltype->ilist[ft];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(ft))
+ {
+ const t_iparams *ip;
+ real cam[5], inv_mass, m_aj;
+ int a1, j, aj, coeff;
+
+ ip = &ffparams->iparams[il->iatoms[i]];
+
+ a1 = il->iatoms[i+1];
+
+ if (ft != F_VSITEN)
+ {
+ for (j = 1; j < NRAL(ft); j++)
+ {
+ cam[j] = moltype->atoms.atom[il->iatoms[i+1+j]].m;
+ if (cam[j] == 0)
+ {
+ cam[j] = vsite_m[il->iatoms[i+1+j]];
+ }
+ if (cam[j] == 0)
+ {
+ gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
+ *moltype->name,
+ interaction_function[ft].longname,
+ il->iatoms[i+1+j]+1);
+ }
+ }
+ }
+
+ switch (ft)
+ {
+ case F_VSITE2:
+ /* Exact */
+ vsite_m[a1] = (cam[1]*cam[2])/(cam[2]*sqr(1-ip->vsite.a) + cam[1]*sqr(ip->vsite.a));
+ break;
+ case F_VSITE3:
+ /* Exact */
+ vsite_m[a1] = (cam[1]*cam[2]*cam[3])/(cam[2]*cam[3]*sqr(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*sqr(ip->vsite.a) + cam[1]*cam[2]*sqr(ip->vsite.b));
+ break;
+ case F_VSITEN:
+ /* Exact */
+ inv_mass = 0;
+ for (j = 0; j < 3*ip->vsiten.n; j += 3)
+ {
+ aj = il->iatoms[i+j+2];
+ coeff = ip[il->iatoms[i+j]].vsiten.a;
+ if (moltype->atoms.atom[aj].ptype == eptVSite)
+ {
+ m_aj = vsite_m[aj];
+ }
+ else
+ {
+ m_aj = moltype->atoms.atom[aj].m;
+ }
+ if (m_aj <= 0)
+ {
+ gmx_incons("The mass of a vsiten constructing atom is <= 0");
+ }
+ inv_mass += coeff*coeff/m_aj;
+ }
+ vsite_m[a1] = 1/inv_mass;
++ /* Correct for loop increment of i */
++ i += j - 1 - NRAL(ft);
+ break;
+ default:
+ /* Use the mass of the lightest constructing atom.
+ * This is an approximation.
+ * If the distance of the virtual site to the
+ * constructing atom is less than all distances
+ * between constructing atoms, this is a safe
+ * over-estimate of the displacement of the vsite.
+ * This condition holds for all H mass replacement
+ * vsite constructions, except for SP2/3 groups.
+ * In SP3 groups one H will have a F_VSITE3
+ * construction, so even there the total drift
+ * estimate shouldn't be far off.
+ */
+ assert(j >= 1);
+ vsite_m[a1] = cam[1];
+ for (j = 2; j < NRAL(ft); j++)
+ {
+ vsite_m[a1] = min(vsite_m[a1], cam[j]);
+ }
+ (*n_nonlin_vsite)++;
+ break;
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "atom %4d %-20s mass %6.3f\n",
+ a1, interaction_function[ft].longname, vsite_m[a1]);
+ }
+ }
+ }
+ }
+}
+
+static void get_verlet_buffer_atomtypes(const gmx_mtop_t *mtop,
+ verletbuf_atomtype_t **att_p,
+ int *natt_p,
+ int *n_nonlin_vsite)
+{
+ verletbuf_atomtype_t *att;
+ int natt;
+ int mb, nmol, ft, i, a1, a2, a3, a;
+ const t_atoms *atoms;
+ const t_ilist *il;
+ const t_iparams *ip;
+ atom_nonbonded_kinetic_prop_t *prop;
+ real *vsite_m;
+ int n_nonlin_vsite_mol;
+
+ att = NULL;
+ natt = 0;
+
+ if (n_nonlin_vsite != NULL)
+ {
+ *n_nonlin_vsite = 0;
+ }
+
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+
+ /* Check for constraints, as they affect the kinetic energy.
+ * For virtual sites we need the masses and geometry of
+ * the constructing atoms to determine their velocity distribution.
+ */
+ snew(prop, atoms->nr);
+ snew(vsite_m, atoms->nr);
+
+ for (ft = F_CONSTR; ft <= F_CONSTRNC; ft++)
+ {
+ il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(ft))
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ a1 = il->iatoms[i+1];
+ a2 = il->iatoms[i+2];
+ if (atoms->atom[a2].m > prop[a1].con_mass)
+ {
+ prop[a1].con_mass = atoms->atom[a2].m;
+ prop[a1].con_len = ip->constr.dA;
+ }
+ if (atoms->atom[a1].m > prop[a2].con_mass)
+ {
+ prop[a2].con_mass = atoms->atom[a1].m;
+ prop[a2].con_len = ip->constr.dA;
+ }
+ }
+ }
+
+ il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(F_SETTLE))
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ a1 = il->iatoms[i+1];
+ a2 = il->iatoms[i+2];
+ a3 = il->iatoms[i+3];
+ /* Usually the mass of a1 (usually oxygen) is larger than a2/a3.
+ * If this is not the case, we overestimate the displacement,
+ * which leads to a larger buffer (ok since this is an exotic case).
+ */
+ prop[a1].con_mass = atoms->atom[a2].m;
+ prop[a1].con_len = ip->settle.doh;
+
+ prop[a2].con_mass = atoms->atom[a1].m;
+ prop[a2].con_len = ip->settle.doh;
+
+ prop[a3].con_mass = atoms->atom[a1].m;
+ prop[a3].con_len = ip->settle.doh;
+ }
+
+ get_vsite_masses(&mtop->moltype[mtop->molblock[mb].type],
+ &mtop->ffparams,
+ vsite_m,
+ &n_nonlin_vsite_mol);
+ if (n_nonlin_vsite != NULL)
+ {
+ *n_nonlin_vsite += nmol*n_nonlin_vsite_mol;
+ }
+
+ for (a = 0; a < atoms->nr; a++)
+ {
+ if (atoms->atom[a].ptype == eptVSite)
+ {
+ prop[a].mass = vsite_m[a];
+ }
+ else
+ {
+ prop[a].mass = atoms->atom[a].m;
+ }
+ prop[a].type = atoms->atom[a].type;
+ prop[a].q = atoms->atom[a].q;
+ /* We consider an atom constrained, #DOF=2, when it is
+ * connected with constraints to (at least one) atom with
+ * a mass of more than 0.4x its own mass. This is not a critical
+ * parameter, since with roughly equal masses the unconstrained
+ * and constrained displacement will not differ much (and both
+ * overestimate the displacement).
+ */
+ prop[a].bConstr = (prop[a].con_mass > 0.4*prop[a].mass);
+
+ add_at(&att, &natt, &prop[a], nmol);
+ }
+
+ sfree(vsite_m);
+ sfree(prop);
+ }
+
+ if (gmx_debug_at)
+ {
+ for (a = 0; a < natt; a++)
+ {
+ fprintf(debug, "type %d: m %5.2f t %d q %6.3f con %d con_m %5.3f con_l %5.3f n %d\n",
+ a, att[a].prop.mass, att[a].prop.type, att[a].prop.q,
+ att[a].prop.bConstr, att[a].prop.con_mass, att[a].prop.con_len,
+ att[a].n);
+ }
+ }
+
+ *att_p = att;
+ *natt_p = natt;
+}
+
+/* This function computes two components of the estimate of the variance
+ * in the displacement of one atom in a system of two constrained atoms.
+ * Returns in sigma2_2d the variance due to rotation of the constrained
+ * atom around the atom to which it constrained.
+ * Returns in sigma2_3d the variance due to displacement of the COM
+ * of the whole system of the two constrained atoms.
+ *
+ * Note that we only take a single constraint (the one to the heaviest atom)
+ * into account. If an atom has multiple constraints, this will result in
+ * an overestimate of the displacement, which gives a larger drift and buffer.
+ */
+static void constrained_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d)
+{
+ real sigma2_rot;
+ real com_dist;
+ real sigma2_rel;
+ real scale;
+
+ /* Here we decompose the motion of a constrained atom into two
+ * components: rotation around the COM and translation of the COM.
+ */
+
+ /* Determine the variance for the displacement of the rotational mode */
+ sigma2_rot = kT_fac/(prop->mass*(prop->mass + prop->con_mass)/prop->con_mass);
+
+ /* The distance from the atom to the COM, i.e. the rotational arm */
+ com_dist = prop->con_len*prop->con_mass/(prop->mass + prop->con_mass);
+
+ /* The variance relative to the arm */
+ sigma2_rel = sigma2_rot/(com_dist*com_dist);
+ /* At 6 the scaling formula has slope 0,
+ * so we keep sigma2_2d constant after that.
+ */
+ if (sigma2_rel < 6)
+ {
+ /* A constrained atom rotates around the atom it is constrained to.
+ * This results in a smaller linear displacement than for a free atom.
+ * For a perfectly circular displacement, this lowers the displacement
+ * by: 1/arcsin(arc_length)
+ * and arcsin(x) = 1 + x^2/6 + ...
+ * For sigma2_rel<<1 the displacement distribution is erfc
+ * (exact formula is provided below). For larger sigma, it is clear
+ * that the displacement can't be larger than 2*com_dist.
+ * It turns out that the distribution becomes nearly uniform.
+ * For intermediate sigma2_rel, scaling down sigma with the third
+ * order expansion of arcsin with argument sigma_rel turns out
+ * to give a very good approximation of the distribution and variance.
+ * Even for larger values, the variance is only slightly overestimated.
+ * Note that the most relevant displacements are in the long tail.
+ * This rotation approximation always overestimates the tail (which
+ * runs to infinity, whereas it should be <= 2*com_dist).
+ * Thus we always overestimate the drift and the buffer size.
+ */
+ scale = 1/(1 + sigma2_rel/6);
+ *sigma2_2d = sigma2_rot*scale*scale;
+ }
+ else
+ {
+ /* sigma_2d is set to the maximum given by the scaling above.
+ * For large sigma2 the real displacement distribution is close
+ * to uniform over -2*con_len to 2*com_dist.
+ * Our erfc with sigma_2d=sqrt(1.5)*com_dist (which means the sigma
+ * of the erfc output distribution is con_dist) overestimates
+ * the variance and additionally has a long tail. This means
+ * we have a (safe) overestimation of the drift.
+ */
+ *sigma2_2d = 1.5*com_dist*com_dist;
+ }
+
+ /* The constrained atom also moves (in 3D) with the COM of both atoms */
+ *sigma2_3d = kT_fac/(prop->mass + prop->con_mass);
+}
+
+static void get_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d)
+{
+ if (prop->bConstr)
+ {
+ /* Complicated constraint calculation in a separate function */
+ constrained_atom_sigma2(kT_fac, prop, sigma2_2d, sigma2_3d);
+ }
+ else
+ {
+ /* Unconstrained atom: trivial */
+ *sigma2_2d = 0;
+ *sigma2_3d = kT_fac/prop->mass;
+ }
+}
+
+static void approx_2dof(real s2, real x, real *shift, real *scale)
+{
+ /* A particle with 1 DOF constrained has 2 DOFs instead of 3.
+ * This code is also used for particles with multiple constraints,
+ * in which case we overestimate the displacement.
+ * The 2DOF distribution is sqrt(pi/2)*erfc(r/(sqrt(2)*s))/(2*s).
+ * We approximate this with scale*Gaussian(s,r+shift),
+ * by matching the distribution value and derivative at x.
+ * This is a tight overestimate for all r>=0 at any s and x.
+ */
+ real ex, er;
+
+ ex = exp(-x*x/(2*s2));
+ er = gmx_erfc(x/sqrt(2*s2));
+
+ *shift = -x + sqrt(2*s2/M_PI)*ex/er;
+ *scale = 0.5*M_PI*exp(ex*ex/(M_PI*er*er))*er;
+}
+
+static real ener_drift(const verletbuf_atomtype_t *att, int natt,
+ const gmx_ffparams_t *ffp,
+ real kT_fac,
+ real md1_ljd, real d2_ljd, real md3_ljd,
+ real md1_ljr, real d2_ljr, real md3_ljr,
+ real md1_el, real d2_el,
+ real r_buffer,
+ real rlist, real boxvol)
+{
+ double drift_tot, pot1, pot2, pot3, pot;
+ int i, j;
+ real s2i_2d, s2i_3d, s2j_2d, s2j_3d, s2, s;
+ int ti, tj;
+ real md1, d2, md3;
+ real sc_fac, rsh, rsh2;
+ double c_exp, c_erfc;
+
+ drift_tot = 0;
+
+ /* Loop over the different atom type pairs */
+ for (i = 0; i < natt; i++)
+ {
+ get_atom_sigma2(kT_fac, &att[i].prop, &s2i_2d, &s2i_3d);
+ ti = att[i].prop.type;
+
+ for (j = i; j < natt; j++)
+ {
+ get_atom_sigma2(kT_fac, &att[j].prop, &s2j_2d, &s2j_3d);
+ tj = att[j].prop.type;
+
+ /* Add up the up to four independent variances */
+ s2 = s2i_2d + s2i_3d + s2j_2d + s2j_3d;
+
+ /* Note that attractive and repulsive potentials for individual
+ * pairs will partially cancel.
+ */
+ /* -dV/dr at the cut-off for LJ + Coulomb */
+ md1 =
+ md1_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ md1_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12 +
+ md1_el*att[i].prop.q*att[j].prop.q;
+
+ /* d2V/dr2 at the cut-off for LJ + Coulomb */
+ d2 =
+ d2_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ d2_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12 +
+ d2_el*att[i].prop.q*att[j].prop.q;
+
+ /* -d3V/dr3 at the cut-off for LJ, we neglect Coulomb */
+ md3 =
+ md3_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ md3_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12;
+
+ rsh = r_buffer;
+ sc_fac = 1.0;
+ /* For constraints: adapt r and scaling for the Gaussian */
+ if (att[i].prop.bConstr)
+ {
+ real sh, sc;
+
+ approx_2dof(s2i_2d, r_buffer*s2i_2d/s2, &sh, &sc);
+ rsh += sh;
+ sc_fac *= sc;
+ }
+ if (att[j].prop.bConstr)
+ {
+ real sh, sc;
+
+ approx_2dof(s2j_2d, r_buffer*s2j_2d/s2, &sh, &sc);
+ rsh += sh;
+ sc_fac *= sc;
+ }
+
+ /* Exact contribution of an atom pair with Gaussian displacement
+ * with sigma s to the energy drift for a potential with
+ * derivative -md and second derivative dd at the cut-off.
+ * The only catch is that for potentials that change sign
+ * near the cut-off there could be an unlucky compensation
+ * of positive and negative energy drift.
+ * Such potentials are extremely rare though.
+ *
+ * Note that pot has unit energy*length, as the linear
+ * atom density still needs to be put in.
+ */
+ c_exp = exp(-rsh*rsh/(2*s2))/sqrt(2*M_PI);
+ c_erfc = 0.5*gmx_erfc(rsh/(sqrt(2*s2)));
+ s = sqrt(s2);
+ rsh2 = rsh*rsh;
+
+ pot1 = sc_fac*
+ md1/2*((rsh2 + s2)*c_erfc - rsh*s*c_exp);
+ pot2 = sc_fac*
+ d2/6*(s*(rsh2 + 2*s2)*c_exp - rsh*(rsh2 + 3*s2)*c_erfc);
+ pot3 =
+ md3/24*((rsh2*rsh2 + 6*rsh2*s2 + 3*s2*s2)*c_erfc - rsh*s*(rsh2 + 5*s2)*c_exp);
+ pot = pot1 + pot2 + pot3;
+
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "n %d %d d s %.3f %.3f %.3f %.3f con %d -d1 %8.1e d2 %8.1e -d3 %8.1e pot1 %8.1e pot2 %8.1e pot3 %8.1e pot %8.1e\n",
+ att[i].n, att[j].n,
+ sqrt(s2i_2d), sqrt(s2i_3d),
+ sqrt(s2j_2d), sqrt(s2j_3d),
+ att[i].prop.bConstr+att[j].prop.bConstr,
+ md1, d2, md3,
+ pot1, pot2, pot3, pot);
+ }
+
+ /* Multiply by the number of atom pairs */
+ if (j == i)
+ {
+ pot *= (double)att[i].n*(att[i].n - 1)/2;
+ }
+ else
+ {
+ pot *= (double)att[i].n*att[j].n;
+ }
+ /* We need the line density to get the energy drift of the system.
+ * The effective average r^2 is close to (rlist+sigma)^2.
+ */
+ pot *= 4*M_PI*sqr(rlist + s)/boxvol;
+
+ /* Add the unsigned drift to avoid cancellation of errors */
+ drift_tot += fabs(pot);
+ }
+ }
+
+ return drift_tot;
+}
+
+static real surface_frac(int cluster_size, real particle_distance, real rlist)
+{
+ real d, area_rel;
+
+ if (rlist < 0.5*particle_distance)
+ {
+ /* We have non overlapping spheres */
+ return 1.0;
+ }
+
+ /* Half the inter-particle distance relative to rlist */
+ d = 0.5*particle_distance/rlist;
+
+ /* Determine the area of the surface at distance rlist to the closest
+ * particle, relative to surface of a sphere of radius rlist.
+ * The formulas below assume close to cubic cells for the pair search grid,
+ * which the pair search code tries to achieve.
+ * Note that in practice particle distances will not be delta distributed,
+ * but have some spread, often involving shorter distances,
+ * as e.g. O-H bonds in a water molecule. Thus the estimates below will
+ * usually be slightly too high and thus conservative.
+ */
+ switch (cluster_size)
+ {
+ case 1:
+ /* One particle: trivial */
+ area_rel = 1.0;
+ break;
+ case 2:
+ /* Two particles: two spheres at fractional distance 2*a */
+ area_rel = 1.0 + d;
+ break;
+ case 4:
+ /* We assume a perfect, symmetric tetrahedron geometry.
+ * The surface around a tetrahedron is too complex for a full
+ * analytical solution, so we use a Taylor expansion.
+ */
+ area_rel = (1.0 + 1/M_PI*(6*acos(1/sqrt(3))*d +
+ sqrt(3)*d*d*(1.0 +
+ 5.0/18.0*d*d +
+ 7.0/45.0*d*d*d*d +
+ 83.0/756.0*d*d*d*d*d*d)));
+ break;
+ default:
+ gmx_incons("surface_frac called with unsupported cluster_size");
+ area_rel = 1.0;
+ }
+
+ return area_rel/cluster_size;
+}
+
+/* Returns the negative of the third derivative of a potential r^-p
+ * with a force-switch function, evaluated at the cut-off rc.
+ */
+static real md3_force_switch(real p, real rswitch, real rc)
+{
+ /* The switched force function is:
+ * p*r^-(p+1) + a*(r - rswitch)^2 + b*(r - rswitch)^3
+ */
+ real a, b;
+ real md3_pot, md3_sw;
+
+ a = -((p + 4)*rc - (p + 1)*rswitch)/(pow(rc, p+2)*pow(rc-rswitch, 2));
+ b = ((p + 3)*rc - (p + 1)*rswitch)/(pow(rc, p+2)*pow(rc-rswitch, 3));
+
+ md3_pot = (p + 2)*(p + 1)*p*pow(rc, p+3);
+ md3_sw = 2*a + 6*b*(rc - rswitch);
+
+ return md3_pot + md3_sw;
+}
+
+void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
+ const t_inputrec *ir,
+ real reference_temperature,
+ const verletbuf_list_setup_t *list_setup,
+ int *n_nonlin_vsite,
+ real *rlist)
+{
+ double resolution;
+ char *env;
+
+ real particle_distance;
+ real nb_clust_frac_pairs_not_in_list_at_cutoff;
+
+ verletbuf_atomtype_t *att = NULL;
+ int natt = -1, i;
+ double reppow;
+ real md1_ljd, d2_ljd, md3_ljd;
+ real md1_ljr, d2_ljr, md3_ljr;
+ real md1_el, d2_el;
+ real elfac;
+ real kT_fac, mass_min;
+ int ib0, ib1, ib;
+ real rb, rl;
+ real drift;
+
+ if (reference_temperature < 0)
+ {
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ /* This case should be handled outside calc_verlet_buffer_size */
+ gmx_incons("calc_verlet_buffer_size called with an NVE ensemble and reference_temperature < 0");
+ }
+
+ /* We use the maximum temperature with multiple T-coupl groups.
+ * We could use a per particle temperature, but since particles
+ * interact, this might underestimate the buffer size.
+ */
+ reference_temperature = 0;
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ if (ir->opts.tau_t[i] >= 0)
+ {
+ reference_temperature = max(reference_temperature,
+ ir->opts.ref_t[i]);
+ }
+ }
+ }
+
+ /* Resolution of the buffer size */
+ resolution = 0.001;
+
+ env = getenv("GMX_VERLET_BUFFER_RES");
+ if (env != NULL)
+ {
+ sscanf(env, "%lf", &resolution);
+ }
+
+ /* In an atom wise pair-list there would be no pairs in the list
+ * beyond the pair-list cut-off.
+ * However, we use a pair-list of groups vs groups of atoms.
+ * For groups of 4 atoms, the parallelism of SSE instructions, only
+ * 10% of the atoms pairs are not in the list just beyond the cut-off.
+ * As this percentage increases slowly compared to the decrease of the
+ * Gaussian displacement distribution over this range, we can simply
+ * reduce the drift by this fraction.
+ * For larger groups, e.g. of 8 atoms, this fraction will be lower,
+ * so then buffer size will be on the conservative (large) side.
+ *
+ * Note that the formulas used here do not take into account
+ * cancellation of errors which could occur by missing both
+ * attractive and repulsive interactions.
+ *
+ * The only major assumption is homogeneous particle distribution.
+ * For an inhomogeneous system, such as a liquid-vapor system,
+ * the buffer will be underestimated. The actual energy drift
+ * will be higher by the factor: local/homogeneous particle density.
+ *
+ * The results of this estimate have been checked againt simulations.
+ * In most cases the real drift differs by less than a factor 2.
+ */
+
+ /* Worst case assumption: HCP packing of particles gives largest distance */
+ particle_distance = pow(boxvol*sqrt(2)/mtop->natoms, 1.0/3.0);
+
+ get_verlet_buffer_atomtypes(mtop, &att, &natt, n_nonlin_vsite);
+ assert(att != NULL && natt >= 0);
+
+ if (debug)
+ {
+ fprintf(debug, "particle distance assuming HCP packing: %f nm\n",
+ particle_distance);
+ fprintf(debug, "energy drift atom types: %d\n", natt);
+ }
+
+ reppow = mtop->ffparams.reppow;
+ md1_ljd = 0;
+ d2_ljd = 0;
+ md3_ljd = 0;
+ md1_ljr = 0;
+ d2_ljr = 0;
+ md3_ljr = 0;
+ if (ir->vdwtype == evdwCUT)
+ {
+ real sw_range, md3_pswf;
+
+ switch (ir->vdw_modifier)
+ {
+ case eintmodNONE:
+ case eintmodPOTSHIFT:
+ /* -dV/dr of -r^-6 and r^-reppow */
+ md1_ljd = -6*pow(ir->rvdw, -7.0);
+ md1_ljr = reppow*pow(ir->rvdw, -(reppow+1));
+ /* The contribution of the higher derivatives is negligible */
+ break;
+ case eintmodFORCESWITCH:
+ /* At the cut-off: V=V'=V''=0, so we use only V''' */
+ md3_ljd = -md3_force_switch(6.0, ir->rvdw_switch, ir->rvdw);
+ md3_ljr = md3_force_switch(reppow, ir->rvdw_switch, ir->rvdw);
+ break;
+ case eintmodPOTSWITCH:
+ /* At the cut-off: V=V'=V''=0.
+ * V''' is given by the original potential times
+ * the third derivative of the switch function.
+ */
+ sw_range = ir->rvdw - ir->rvdw_switch;
+ md3_pswf = 60.0*pow(sw_range, -3.0);
+
+ md3_ljd = -pow(ir->rvdw, -6.0 )*md3_pswf;
+ md3_ljr = pow(ir->rvdw, -reppow)*md3_pswf;
+ break;
+ default:
+ gmx_incons("Unimplemented VdW modifier");
+ }
+ }
+ else if (EVDW_PME(ir->vdwtype))
+ {
+ real b, r, br, br2, br4, br6;
+ b = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
+ r = ir->rvdw;
+ br = b*r;
+ br2 = br*br;
+ br4 = br2*br2;
+ br6 = br4*br2;
+ /* -dV/dr of g(br)*r^-6 [where g(x) = exp(-x^2)(1+x^2+x^4/2), see LJ-PME equations in manual] and r^-reppow */
+ md1_ljd = -exp(-br2)*(br6 + 3.0*br4 + 6.0*br2 + 6.0)*pow(r, -7.0);
+ md1_ljr = reppow*pow(r, -(reppow+1));
+ /* The contribution of the higher derivatives is negligible */
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Energy drift calculation is only implemented for plain cut-off Lennard-Jones interactions");
+ }
+
+ elfac = ONE_4PI_EPS0/ir->epsilon_r;
+
+ /* Determine md=-dV/dr and dd=d^2V/dr^2 */
+ md1_el = 0;
+ d2_el = 0;
+ if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
+ {
+ real eps_rf, k_rf;
+
+ if (ir->coulombtype == eelCUT)
+ {
+ eps_rf = 1;
+ k_rf = 0;
+ }
+ else
+ {
+ eps_rf = ir->epsilon_rf/ir->epsilon_r;
+ if (eps_rf != 0)
+ {
+ k_rf = pow(ir->rcoulomb, -3.0)*(eps_rf - ir->epsilon_r)/(2*eps_rf + ir->epsilon_r);
+ }
+ else
+ {
+ /* epsilon_rf = infinity */
+ k_rf = 0.5*pow(ir->rcoulomb, -3.0);
+ }
+ }
+
+ if (eps_rf > 0)
+ {
+ md1_el = elfac*(pow(ir->rcoulomb, -2.0) - 2*k_rf*ir->rcoulomb);
+ }
+ d2_el = elfac*(2*pow(ir->rcoulomb, -3.0) + 2*k_rf);
+ }
+ else if (EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD)
+ {
+ real b, rc, br;
+
+ b = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
+ rc = ir->rcoulomb;
+ br = b*rc;
+ md1_el = elfac*(b*exp(-br*br)*M_2_SQRTPI/rc + gmx_erfc(br)/(rc*rc));
+ d2_el = elfac/(rc*rc)*(2*b*(1 + br*br)*exp(-br*br)*M_2_SQRTPI + 2*gmx_erfc(br)/rc);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Energy drift calculation is only implemented for Reaction-Field and Ewald electrostatics");
+ }
+
+ /* Determine the variance of the atomic displacement
+ * over nstlist-1 steps: kT_fac
+ * For inertial dynamics (not Brownian dynamics) the mass factor
+ * is not included in kT_fac, it is added later.
+ */
+ if (ir->eI == eiBD)
+ {
+ /* Get the displacement distribution from the random component only.
+ * With accurate integration the systematic (force) displacement
+ * should be negligible (unless nstlist is extremely large, which
+ * you wouldn't do anyhow).
+ */
+ kT_fac = 2*BOLTZ*reference_temperature*(ir->nstlist-1)*ir->delta_t;
+ if (ir->bd_fric > 0)
+ {
+ /* This is directly sigma^2 of the displacement */
+ kT_fac /= ir->bd_fric;
+
+ /* Set the masses to 1 as kT_fac is the full sigma^2,
+ * but we divide by m in ener_drift().
+ */
+ for (i = 0; i < natt; i++)
+ {
+ att[i].prop.mass = 1;
+ }
+ }
+ else
+ {
+ real tau_t;
+
+ /* Per group tau_t is not implemented yet, use the maximum */
+ tau_t = ir->opts.tau_t[0];
+ for (i = 1; i < ir->opts.ngtc; i++)
+ {
+ tau_t = max(tau_t, ir->opts.tau_t[i]);
+ }
+
+ kT_fac *= tau_t;
+ /* This kT_fac needs to be divided by the mass to get sigma^2 */
+ }
+ }
+ else
+ {
+ kT_fac = BOLTZ*reference_temperature*sqr((ir->nstlist-1)*ir->delta_t);
+ }
+
+ mass_min = att[0].prop.mass;
+ for (i = 1; i < natt; i++)
+ {
+ mass_min = min(mass_min, att[i].prop.mass);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "md1_ljd %9.2e d2_ljd %9.2e md3_ljd %9.2e\n", md1_ljd, d2_ljd, md3_ljd);
+ fprintf(debug, "md1_ljr %9.2e d2_ljr %9.2e md3_ljr %9.2e\n", md1_ljr, d2_ljr, md3_ljr);
+ fprintf(debug, "md1_el %9.2e d2_el %9.2e\n", md1_el, d2_el);
+ fprintf(debug, "sqrt(kT_fac) %f\n", sqrt(kT_fac));
+ fprintf(debug, "mass_min %f\n", mass_min);
+ }
+
+ /* Search using bisection */
+ ib0 = -1;
+ /* The drift will be neglible at 5 times the max sigma */
+ ib1 = (int)(5*2*sqrt(kT_fac/mass_min)/resolution) + 1;
+ while (ib1 - ib0 > 1)
+ {
+ ib = (ib0 + ib1)/2;
+ rb = ib*resolution;
+ rl = max(ir->rvdw, ir->rcoulomb) + rb;
+
+ /* Calculate the average energy drift at the last step
+ * of the nstlist steps at which the pair-list is used.
+ */
+ drift = ener_drift(att, natt, &mtop->ffparams,
+ kT_fac,
+ md1_ljd, d2_ljd, md3_ljd,
+ md1_ljr, d2_ljr, md3_ljr,
+ md1_el, d2_el,
+ rb,
+ rl, boxvol);
+
+ /* Correct for the fact that we are using a Ni x Nj particle pair list
+ * and not a 1 x 1 particle pair list. This reduces the drift.
+ */
+ /* We don't have a formula for 8 (yet), use 4 which is conservative */
+ nb_clust_frac_pairs_not_in_list_at_cutoff =
+ surface_frac(min(list_setup->cluster_size_i, 4),
+ particle_distance, rl)*
+ surface_frac(min(list_setup->cluster_size_j, 4),
+ particle_distance, rl);
+ drift *= nb_clust_frac_pairs_not_in_list_at_cutoff;
+
+ /* Convert the drift to drift per unit time per atom */
+ drift /= ir->nstlist*ir->delta_t*mtop->natoms;
+
+ if (debug)
+ {
+ fprintf(debug, "ib %3d %3d %3d rb %.3f %dx%d fac %.3f drift %f\n",
+ ib0, ib, ib1, rb,
+ list_setup->cluster_size_i, list_setup->cluster_size_j,
+ nb_clust_frac_pairs_not_in_list_at_cutoff,
+ drift);
+ }
+
+ if (fabs(drift) > ir->verletbuf_tol)
+ {
+ ib0 = ib;
+ }
+ else
+ {
+ ib1 = ib;
+ }
+ }
+
+ sfree(att);
+
+ *rlist = max(ir->rvdw, ir->rcoulomb) + ib1*resolution;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff