670 lines
20 KiB
C++
670 lines
20 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_sna_atom.h"
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#include "sna.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "force.h"
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#include "pair.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), sna(nullptr),
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radelem(nullptr), wjelem(nullptr), sinnerelem(nullptr), dinnerelem(nullptr)
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{
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// begin code common to all SNAP computes
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
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int ntypes = atom->ntypes;
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int nargmin = 6 + 2 * ntypes;
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if (narg < nargmin) error->all(FLERR, "Illegal compute {} command", style);
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// default values
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rmin0 = 0.0;
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switchflag = 1;
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bzeroflag = 1;
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quadraticflag = 0;
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chemflag = 0;
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bnormflag = 0;
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wselfallflag = 0;
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switchinnerflag = 0;
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nelements = 1;
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nnn = 12;
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wmode = 0;
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delta = 1.e-3;
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nearest_neighbors_mode = false;
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// process required arguments
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memory->create(radelem, ntypes + 1, "sna/atom:radelem"); // offset by 1 to match up with types
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memory->create(wjelem, ntypes + 1, "sna/atom:wjelem");
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rcutfac = utils::numeric(FLERR, arg[3], false, lmp);
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rfac0 = utils::numeric(FLERR, arg[4], false, lmp);
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twojmax = utils::inumeric(FLERR, arg[5], false, lmp);
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for (int i = 0; i < ntypes; i++)
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radelem[i + 1] =
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utils::numeric(FLERR, arg[6 + i], false, lmp);
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for (int i = 0; i < ntypes; i++)
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wjelem[i + 1] =
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utils::numeric(FLERR, arg[6 + ntypes + i], false, lmp);
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// construct cutsq
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double cut;
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cutmax = 0.0;
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memory->create(cutsq, ntypes + 1, ntypes + 1, "sna/atom:cutsq");
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for (int i = 1; i <= ntypes; i++) {
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cut = 2.0 * radelem[i] * rcutfac;
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if (cut > cutmax) cutmax = cut;
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cutsq[i][i] = cut * cut;
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for (int j = i + 1; j <= ntypes; j++) {
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cut = (radelem[i] + radelem[j]) * rcutfac;
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cutsq[i][j] = cutsq[j][i] = cut * cut;
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}
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}
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// set local input checks
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int sinnerflag = 0;
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int dinnerflag = 0;
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// process optional args
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int iarg = nargmin;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "rmin0") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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rmin0 = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "switchflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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switchflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "bzeroflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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bzeroflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "quadraticflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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quadraticflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg],"nnn") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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nnn = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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nearest_neighbors_mode = true;
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if (nnn <= 0) error->all(FLERR, "Illegal compute compute {} command", style);
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iarg += 2;
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} else if (strcmp(arg[iarg],"wmode") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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wmode = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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if (wmode < 0) error->all(FLERR, "Illegal compute compute {} command", style);
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iarg += 2;
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} else if (strcmp(arg[iarg],"delta") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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delta = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
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if (delta < 1.0e-3) error->all(FLERR, "Illegal compute compute {} command", style);
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iarg += 2;
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} else if (strcmp(arg[iarg], "chem") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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chemflag = 1;
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memory->create(map, ntypes + 1, "compute_sna_grid:map");
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nelements = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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for (int i = 0; i < ntypes; i++) {
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int jelem = utils::inumeric(FLERR, arg[iarg + 2 + i], false, lmp);
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if (jelem < 0 || jelem >= nelements) error->all(FLERR, "Illegal compute {} command", style);
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map[i + 1] = jelem;
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}
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iarg += 2 + ntypes;
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} else if (strcmp(arg[iarg], "bnormflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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bnormflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "wselfallflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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wselfallflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "switchinnerflag") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal compute {} command", style);
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switchinnerflag = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "sinner") == 0) {
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iarg++;
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if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
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memory->create(sinnerelem, ntypes + 1, "snap:sinnerelem");
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for (int i = 0; i < ntypes; i++)
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sinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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sinnerflag = 1;
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iarg += ntypes;
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} else if (strcmp(arg[iarg], "dinner") == 0) {
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iarg++;
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if (iarg + ntypes > narg) error->all(FLERR, "Illegal compute {} command", style);
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memory->create(dinnerelem, ntypes + 1, "snap:dinnerelem");
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for (int i = 0; i < ntypes; i++)
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dinnerelem[i + 1] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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dinnerflag = 1;
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iarg += ntypes;
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} else
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error->all(FLERR, "Illegal compute {} command", style);
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}
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if (switchinnerflag && !(sinnerflag && dinnerflag))
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error->all(
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FLERR,
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"Illegal compute {} command: switchinnerflag = 1, missing sinner/dinner keyword",
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style);
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if (!switchinnerflag && (sinnerflag || dinnerflag))
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error->all(
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FLERR,
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"Illegal compute {} command: switchinnerflag = 0, unexpected sinner/dinner keyword",
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style);
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snaptr = new SNA(lmp, rfac0, twojmax, rmin0, switchflag, bzeroflag, chemflag, bnormflag,
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wselfallflag, nelements, switchinnerflag);
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ncoeff = snaptr->ncoeff;
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nvalues = ncoeff;
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if (quadraticflag) nvalues += (ncoeff * (ncoeff + 1)) / 2;
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// end code common to all SNAP computes
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size_peratom_cols = nvalues;
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peratom_flag = 1;
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nmax = 0;
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sna = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSNAAtom::~ComputeSNAAtom()
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{
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memory->destroy(sna);
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memory->destroy(radelem);
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memory->destroy(wjelem);
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memory->destroy(cutsq);
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delete snaptr;
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if (chemflag) memory->destroy(map);
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if (switchinnerflag) {
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memory->destroy(sinnerelem);
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memory->destroy(dinnerelem);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAAtom::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute sna/atom requires a pair style be defined");
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rcutsq = force->pair->cutforce * force->pair->cutforce;
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if (cutmax > force->pair->cutforce)
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error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
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if (modify->get_compute_by_style("sna/atom").size() > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute sna/atom");
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snaptr->init();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAAtom::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAAtom::compute_peratom()
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{
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invoked_peratom = update->ntimestep;
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// grow sna array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(sna);
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nmax = atom->nmax;
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memory->create(sna,nmax,size_peratom_cols,"sna/atom:sna");
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array_atom = sna;
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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const int inum = list->inum;
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const int* const ilist = list->ilist;
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const int* const numneigh = list->numneigh;
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int** const firstneigh = list->firstneigh;
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int * const type = atom->type;
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// compute sna for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double** const x = atom->x;
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const int* const mask = atom->mask;
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for (int ii = 0; ii < inum; ii++) {
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const int i = ilist[ii];
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if (mask[i] & groupbit) {
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const double xtmp = x[i][0];
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const double ytmp = x[i][1];
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const double ztmp = x[i][2];
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const int itype = type[i];
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int ielem = 0;
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if (chemflag)
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ielem = map[itype];
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const double radi = radelem[itype];
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const int* const jlist = firstneigh[i];
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const int jnum = numneigh[i];
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// ############################################################################## //
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// ##### Start of section for computing bispectrum on nnn nearest neighbors ##### //
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// ############################################################################## //
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if (nearest_neighbors_mode) {
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// ##### 1) : consider full neighbor list in rlist
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memory->create(distsq, jnum, "snann/atom:distsq");
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memory->create(rlist, jnum, 3, "snann/atom:rlist");
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int ncount = 0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx * delx + dely * dely + delz * delz;
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if (rsq < rcutsq) {
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distsq[ncount] = rsq;
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rlist[ncount][0] = delx;
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rlist[ncount][1] = dely;
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rlist[ncount][2] = delz;
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ncount++;
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}
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}
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// ##### 2) : compute optimal cutoff such that sum weights S_target = nnn
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double S_target=1.*nnn;
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double rc_start=0.1;
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double rc_max=sqrt(rcutsq);
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double tol=1.e-8;
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double * sol_dich = dichotomie(S_target, rc_start, rc_max, tol, distsq, ncount, wmode, delta);
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memory->destroy(distsq);
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// ##### 3) : assign that optimal cutoff radius to bispectrum context using rcsol
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double rcsol = (sol_dich[0]+sol_dich[1])/2.;
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memory->destroy(sol_dich);
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snaptr->grow_rij(ncount);
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int ninside = 0;
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for (int jj = 0; jj < ncount; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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const double rsq = rlist[jj][0]*rlist[jj][0]+rlist[jj][1]*rlist[jj][1]+rlist[jj][2]*rlist[jj][2];
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int jtype = type[j];
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int jelem = 0;
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if (chemflag)
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jelem = map[jtype];
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if (rsq < rcsol*rcsol) {
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snaptr->rij[ninside][0] = rlist[jj][0];//rijmax;
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snaptr->rij[ninside][1] = rlist[jj][1];//rijmax;
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snaptr->rij[ninside][2] = rlist[jj][2];//rijmax;
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snaptr->inside[ninside] = j;
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snaptr->wj[ninside] = 1.;
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snaptr->rcutij[ninside] = rcsol;
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if (switchinnerflag) {
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snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]);
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snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]);
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}
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if (chemflag) snaptr->element[ninside] = jelem;
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ninside++;
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}
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}
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memory->destroy(rlist);
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// ############################################################################ //
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// ##### End of section for computing bispectrum on nnn nearest neighbors ##### //
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// ############################################################################ //
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snaptr->compute_ui(ninside, ielem);
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snaptr->compute_zi();
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snaptr->compute_bi(ielem);
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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sna[i][icoeff] = snaptr->blist[icoeff];
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if (quadraticflag) {
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int ncount = ncoeff;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bi = snaptr->blist[icoeff];
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// diagonal element of quadratic matrix
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sna[i][ncount++] = 0.5*bi*bi;
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// upper-triangular elements of quadratic matrix
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
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sna[i][ncount++] = bi*snaptr->blist[jcoeff];
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}
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}
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} else {
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// ensure rij, inside, and typej are of size jnum
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snaptr->grow_rij(jnum);
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// rij[][3] = displacements between atom I and those neighbors
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// inside = indices of neighbors of I within cutoff
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// typej = types of neighbors of I within cutoff
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int ninside = 0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx*delx + dely*dely + delz*delz;
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int jtype = type[j];
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int jelem = 0;
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if (chemflag)
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jelem = map[jtype];
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if (rsq < cutsq[itype][jtype] && rsq>1e-20) {
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snaptr->rij[ninside][0] = delx;
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snaptr->rij[ninside][1] = dely;
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snaptr->rij[ninside][2] = delz;
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snaptr->inside[ninside] = j;
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snaptr->wj[ninside] = wjelem[jtype];
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snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
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if (switchinnerflag) {
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snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]);
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snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]);
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}
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if (chemflag) snaptr->element[ninside] = jelem;
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ninside++;
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}
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}
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snaptr->compute_ui(ninside, ielem);
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snaptr->compute_zi();
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snaptr->compute_bi(ielem);
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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sna[i][icoeff] = snaptr->blist[icoeff];
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if (quadraticflag) {
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int ncount = ncoeff;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bi = snaptr->blist[icoeff];
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// diagonal element of quadratic matrix
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sna[i][ncount++] = 0.5*bi*bi;
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// upper-triangular elements of quadratic matrix
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
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sna[i][ncount++] = bi*snaptr->blist[jcoeff];
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|
}
|
|
}
|
|
|
|
}
|
|
|
|
} else {
|
|
for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
|
|
sna[i][icoeff] = 0.0;
|
|
}
|
|
}
|
|
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeSNAAtom::memory_usage()
|
|
{
|
|
double bytes = (double)nmax*size_peratom_cols * sizeof(double); // sna
|
|
bytes += snaptr->memory_usage(); // SNA object
|
|
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
select3 routine from Numerical Recipes (slightly modified)
|
|
find k smallest values in array of length n
|
|
sort auxiliary arrays at same time
|
|
------------------------------------------------------------------------- */
|
|
|
|
// Use no-op do while to create single statement
|
|
|
|
#define SWAP(a, b) \
|
|
do { \
|
|
tmp = a; \
|
|
(a) = b; \
|
|
(b) = tmp; \
|
|
} while (0)
|
|
|
|
#define ISWAP(a, b) \
|
|
do { \
|
|
itmp = a; \
|
|
(a) = b; \
|
|
(b) = itmp; \
|
|
} while (0)
|
|
|
|
#define SWAP3(a, b) \
|
|
do { \
|
|
tmp = (a)[0]; \
|
|
(a)[0] = (b)[0]; \
|
|
(b)[0] = tmp; \
|
|
tmp = (a)[1]; \
|
|
(a)[1] = (b)[1]; \
|
|
(b)[1] = tmp; \
|
|
tmp = (a)[2]; \
|
|
(a)[2] = (b)[2]; \
|
|
(b)[2] = tmp; \
|
|
} while (0)
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeSNAAtom::select3(int k, int n, double *arr, int *iarr, double **arr3)
|
|
{
|
|
int i, ir, j, l, mid, ia, itmp;
|
|
double a, tmp, a3[3];
|
|
|
|
arr--;
|
|
iarr--;
|
|
arr3--;
|
|
l = 1;
|
|
ir = n;
|
|
for (;;) {
|
|
if (ir <= l + 1) {
|
|
if (ir == l + 1 && arr[ir] < arr[l]) {
|
|
SWAP(arr[l], arr[ir]);
|
|
ISWAP(iarr[l], iarr[ir]);
|
|
SWAP3(arr3[l], arr3[ir]);
|
|
}
|
|
return;
|
|
} else {
|
|
mid = (l + ir) >> 1;
|
|
SWAP(arr[mid], arr[l + 1]);
|
|
ISWAP(iarr[mid], iarr[l + 1]);
|
|
SWAP3(arr3[mid], arr3[l + 1]);
|
|
if (arr[l] > arr[ir]) {
|
|
SWAP(arr[l], arr[ir]);
|
|
ISWAP(iarr[l], iarr[ir]);
|
|
SWAP3(arr3[l], arr3[ir]);
|
|
}
|
|
if (arr[l + 1] > arr[ir]) {
|
|
SWAP(arr[l + 1], arr[ir]);
|
|
ISWAP(iarr[l + 1], iarr[ir]);
|
|
SWAP3(arr3[l + 1], arr3[ir]);
|
|
}
|
|
if (arr[l] > arr[l + 1]) {
|
|
SWAP(arr[l], arr[l + 1]);
|
|
ISWAP(iarr[l], iarr[l + 1]);
|
|
SWAP3(arr3[l], arr3[l + 1]);
|
|
}
|
|
i = l + 1;
|
|
j = ir;
|
|
a = arr[l + 1];
|
|
ia = iarr[l + 1];
|
|
a3[0] = arr3[l + 1][0];
|
|
a3[1] = arr3[l + 1][1];
|
|
a3[2] = arr3[l + 1][2];
|
|
for (;;) {
|
|
do i++;
|
|
while (arr[i] < a);
|
|
do j--;
|
|
while (arr[j] > a);
|
|
if (j < i) break;
|
|
SWAP(arr[i], arr[j]);
|
|
ISWAP(iarr[i], iarr[j]);
|
|
SWAP3(arr3[i], arr3[j]);
|
|
}
|
|
arr[l + 1] = arr[j];
|
|
arr[j] = a;
|
|
iarr[l + 1] = iarr[j];
|
|
iarr[j] = ia;
|
|
arr3[l + 1][0] = arr3[j][0];
|
|
arr3[l + 1][1] = arr3[j][1];
|
|
arr3[l + 1][2] = arr3[j][2];
|
|
arr3[j][0] = a3[0];
|
|
arr3[j][1] = a3[1];
|
|
arr3[j][2] = a3[2];
|
|
if (j >= k) ir = j - 1;
|
|
if (j <= k) l = i;
|
|
}
|
|
}
|
|
}
|
|
|
|
double *ComputeSNAAtom::weights(double *rsq, double rcut, int ncounts)
|
|
{
|
|
double *w=nullptr;
|
|
memory->destroy(w);
|
|
memory->create(w, ncounts, "snann:gauss_weights");
|
|
double rloc=0.;
|
|
for (int i=0; i<ncounts; i++) {
|
|
rloc = sqrt(rsq[i]);
|
|
if (rloc > rcut){
|
|
w[i]=0.;
|
|
} else {
|
|
w[i]=1.;
|
|
}
|
|
}
|
|
return w;
|
|
}
|
|
|
|
double *ComputeSNAAtom::tanh_weights(double *rsq, double rcut, double delta, int ncounts)
|
|
{
|
|
double *w=nullptr;
|
|
memory->destroy(w);
|
|
memory->create(w, ncounts, "snann:gauss_weights");
|
|
double rloc=0.;
|
|
|
|
for (int i=0; i<ncounts; i++) {
|
|
rloc = sqrt(rsq[i]);
|
|
w[i] = 0.5*(1.-tanh((rloc-rcut)/delta));
|
|
}
|
|
return w;
|
|
}
|
|
|
|
double ComputeSNAAtom::sum_weights(double * /*rsq*/, double *w, int ncounts)
|
|
{
|
|
double S=0.0;
|
|
for (int i=0; i<ncounts; i++) {
|
|
S += w[i];
|
|
}
|
|
return S;
|
|
}
|
|
|
|
double ComputeSNAAtom::get_target_rcut(double S_target, double *rsq, double rcut, int ncounts,
|
|
int weightmode, double delta)
|
|
{
|
|
double S_sol = 0.0;
|
|
if (weightmode == 0) {
|
|
double *www = weights(rsq, rcut, ncounts);
|
|
S_sol = sum_weights(rsq, www, ncounts);
|
|
memory->destroy(www);
|
|
} else if (weightmode == 1) {
|
|
double *www = tanh_weights(rsq, rcut, delta, ncounts);
|
|
S_sol = sum_weights(rsq, www, ncounts);
|
|
memory->destroy(www);
|
|
}
|
|
double err = S_sol - S_target;
|
|
return err;
|
|
}
|
|
|
|
double *ComputeSNAAtom::dichotomie(double S_target, double a, double b, double e, double *rsq,
|
|
int ncounts, int weightmode, double delta)
|
|
{
|
|
|
|
double d=b-a;
|
|
double *sol = nullptr;
|
|
memory->destroy(sol);
|
|
memory->create(sol, 2, "snann:sol");
|
|
double m=0.0;
|
|
|
|
do {
|
|
m = (a + b) / 2.0;
|
|
d = fabs(b - a);
|
|
double f_ra = get_target_rcut(S_target, rsq, a, ncounts, weightmode, delta);
|
|
double f_rm = get_target_rcut(S_target, rsq, m, ncounts, weightmode, delta);
|
|
if (f_rm == 0.0) {
|
|
sol[0]=m;
|
|
sol[1]=m;
|
|
return sol;
|
|
} else if (f_rm*f_ra > 0.0) {
|
|
a = m;
|
|
} else {
|
|
b = m;
|
|
}
|
|
} while (d > e);
|
|
sol[0]=a;
|
|
sol[1]=b;
|
|
return sol;
|
|
}
|