2163 lines
69 KiB
C++
2163 lines
69 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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Steve Plimpton, sjplimp@sandia.gov
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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 "molecule.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "atom_vec_body.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "math_extra.h"
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#include "math_eigen.h"
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#include "memory.h"
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#include "tokenizer.h"
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#include <cctype>
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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#define MAXLINE 256
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#define EPSILON 1.0e-7
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#define BIG 1.0e20
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#define SINERTIA 0.4 // moment of inertia prefactor for sphere
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/* ---------------------------------------------------------------------- */
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Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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Pointers(lmp), id(nullptr), x(nullptr), type(nullptr), molecule(nullptr), q(nullptr), radius(nullptr),
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rmass(nullptr), num_bond(nullptr), bond_type(nullptr), bond_atom(nullptr),
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num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr), angle_atom2(nullptr),
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angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr), dihedral_atom1(nullptr),
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dihedral_atom2(nullptr), dihedral_atom3(nullptr), dihedral_atom4(nullptr), num_improper(nullptr),
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improper_type(nullptr), improper_atom1(nullptr), improper_atom2(nullptr),
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improper_atom3(nullptr), improper_atom4(nullptr), nspecial(nullptr), special(nullptr),
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shake_flag(nullptr), shake_atom(nullptr), shake_type(nullptr), avec_body(nullptr), ibodyparams(nullptr),
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dbodyparams(nullptr), fragmentmask(nullptr),
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dx(nullptr), dxcom(nullptr), dxbody(nullptr), quat_external(nullptr), fp(nullptr), count(nullptr)
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{
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me = comm->me;
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if (index >= narg) error->all(FLERR,"Illegal molecule command");
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id = utils::strdup(arg[0]);
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if (!utils::is_id(id))
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error->all(FLERR,"Molecule template ID must have only "
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"alphanumeric or underscore characters");
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// parse args until reach unknown arg (next file)
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toffset = 0;
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boffset = aoffset = doffset = ioffset = 0;
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sizescale = 1.0;
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int ifile = index;
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int iarg = ifile+1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"offset") == 0) {
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if (iarg+6 > narg) error->all(FLERR,"Illegal molecule command");
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toffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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boffset = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
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aoffset = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
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doffset = utils::inumeric(FLERR,arg[iarg+4],false,lmp);
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ioffset = utils::inumeric(FLERR,arg[iarg+5],false,lmp);
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if (toffset < 0 || boffset < 0 || aoffset < 0 ||
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doffset < 0 || ioffset < 0)
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error->all(FLERR,"Illegal molecule command");
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iarg += 6;
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} else if (strcmp(arg[iarg],"toff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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toffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (toffset < 0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"boff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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boffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (boffset < 0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"aoff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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aoffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (aoffset < 0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"doff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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doffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (doffset < 0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"ioff") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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ioffset = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if (ioffset < 0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"scale") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal molecule command");
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sizescale = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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if (sizescale <= 0.0) error->all(FLERR,"Illegal molecule command");
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iarg += 2;
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} else break;
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}
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index = iarg;
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// last molecule if have scanned all args
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if (iarg == narg) last = 1;
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else last = 0;
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// initialize all fields to empty
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initialize();
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// scan file for sizes of all fields and allocate storage for them
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if (me == 0) {
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fp = fopen(arg[ifile],"r");
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if (fp == nullptr)
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error->one(FLERR,"Cannot open molecule file {}: {}",
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arg[ifile], utils::getsyserror());
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}
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read(0);
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if (me == 0) fclose(fp);
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allocate();
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// read file again to populate all fields
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if (me == 0) fp = fopen(arg[ifile],"r");
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read(1);
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if (me == 0) fclose(fp);
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// stats
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if (me == 0)
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utils::logmesg(lmp,"Read molecule template {}:\n {} molecules\n"
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" {} fragments\n"
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" {} atoms with max type {}\n"
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" {} bonds with max type {}\n"
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" {} angles with max type {}\n"
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" {} dihedrals with max type {}\n"
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" {} impropers with max type {}\n", id,nmolecules,
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nfragments,natoms,ntypes,nbonds,nbondtypes,nangles,
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nangletypes,ndihedrals,ndihedraltypes,nimpropers,
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nimpropertypes);
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}
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/* ---------------------------------------------------------------------- */
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Molecule::~Molecule()
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{
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delete [] id;
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deallocate();
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}
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/* ----------------------------------------------------------------------
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compute center = geometric center of molecule
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also compute:
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dx = displacement of each atom from center
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molradius = radius of molecule from center
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including finite-size particles or body particles
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------------------------------------------------------------------------- */
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void Molecule::compute_center()
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{
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if (centerflag) return;
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centerflag = 1;
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center[0] = center[1] = center[2] = 0.0;
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for (int i = 0; i < natoms; i++) {
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center[0] += x[i][0];
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center[1] += x[i][1];
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center[2] += x[i][2];
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}
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center[0] /= natoms;
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center[1] /= natoms;
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center[2] /= natoms;
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memory->destroy(dx);
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memory->create(dx,natoms,3,"molecule:dx");
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for (int i = 0; i < natoms; i++) {
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dx[i][0] = x[i][0] - center[0];
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dx[i][1] = x[i][1] - center[1];
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dx[i][2] = x[i][2] - center[2];
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}
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molradius = 0.0;
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for (int i = 0; i < natoms; i++) {
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double rad = MathExtra::len3(dx[i]);
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if (radiusflag) rad += radius[i];
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molradius = MAX(molradius,rad);
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}
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}
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/* ----------------------------------------------------------------------
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compute masstotal = total mass of molecule
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could have been set by user, otherwise calculate it
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------------------------------------------------------------------------- */
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void Molecule::compute_mass()
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{
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if (massflag) return;
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massflag = 1;
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atom->check_mass(FLERR);
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masstotal = 0.0;
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for (int i = 0; i < natoms; i++) {
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if (rmassflag) masstotal += rmass[i];
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else masstotal += atom->mass[type[i]];
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}
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}
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/* ----------------------------------------------------------------------
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compute com = center of mass of molecule
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could have been set by user, otherwise calculate it
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works for finite size particles assuming no overlap
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also compute:
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dxcom = displacement of each atom from COM
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comatom = which atom (1-Natom) is nearest the COM
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maxextent = furthest any atom in molecule is from comatom (not COM)
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------------------------------------------------------------------------- */
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void Molecule::compute_com()
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{
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if (!comflag) {
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comflag = 1;
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atom->check_mass(FLERR);
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double onemass;
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com[0] = com[1] = com[2] = 0.0;
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for (int i = 0; i < natoms; i++) {
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if (rmassflag) onemass = rmass[i];
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else onemass = atom->mass[type[i]];
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com[0] += x[i][0]*onemass;
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com[1] += x[i][1]*onemass;
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com[2] += x[i][2]*onemass;
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}
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if (masstotal > 0.0) {
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com[0] /= masstotal;
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com[1] /= masstotal;
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com[2] /= masstotal;
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}
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}
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memory->destroy(dxcom);
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memory->create(dxcom,natoms,3,"molecule:dxcom");
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for (int i = 0; i < natoms; i++) {
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dxcom[i][0] = x[i][0] - com[0];
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dxcom[i][1] = x[i][1] - com[1];
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dxcom[i][2] = x[i][2] - com[2];
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}
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double rsqmin = BIG;
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for (int i = 0; i < natoms; i++) {
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double rsq = MathExtra::lensq3(dxcom[i]);
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if (rsq < rsqmin) {
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comatom = i;
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rsqmin = rsq;
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}
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}
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double rsqmax = 0.0;
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for (int i = 0; i < natoms; i++) {
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double dx = x[comatom][0] - x[i][0];
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double dy = x[comatom][1] - x[i][1];
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double dz = x[comatom][2] - x[i][2];
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double rsq = dx*dx + dy*dy + dz*dz;
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rsqmax = MAX(rsqmax,rsq);
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}
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comatom++;
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maxextent = sqrt(rsqmax);
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}
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/* ----------------------------------------------------------------------
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compute itensor = 6 moments of inertia of molecule around xyz axes
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could have been set by user, otherwise calculate it
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accounts for finite size spheres, assuming no overlap
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also compute:
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inertia = 3 principal components of inertia
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ex,ey,ez = principal axes in space coords
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quat = quaternion for orientation of molecule
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dxbody = displacement of each atom from COM in body frame
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------------------------------------------------------------------------- */
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void Molecule::compute_inertia()
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{
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if (!inertiaflag) {
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inertiaflag = 1;
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atom->check_mass(FLERR);
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double onemass,dx,dy,dz;
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for (int i = 0; i < 6; i++) itensor[i] = 0.0;
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for (int i = 0; i < natoms; i++) {
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if (rmassflag) onemass = rmass[i];
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else onemass = atom->mass[type[i]];
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dx = dxcom[i][0];
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dy = dxcom[i][1];
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dz = dxcom[i][2];
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itensor[0] += onemass * (dy*dy + dz*dz);
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itensor[1] += onemass * (dx*dx + dz*dz);
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itensor[2] += onemass * (dx*dx + dy*dy);
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itensor[3] -= onemass * dy*dz;
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itensor[4] -= onemass * dx*dz;
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itensor[5] -= onemass * dx*dy;
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}
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if (radiusflag) {
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for (int i = 0; i < natoms; i++) {
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if (rmassflag) onemass = rmass[i];
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else onemass = atom->mass[type[i]];
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itensor[0] += SINERTIA*onemass * radius[i]*radius[i];
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itensor[1] += SINERTIA*onemass * radius[i]*radius[i];
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itensor[2] += SINERTIA*onemass * radius[i]*radius[i];
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}
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}
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}
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// diagonalize inertia tensor for each body via Jacobi rotations
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// inertia = 3 eigenvalues = principal moments of inertia
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// evectors and exzy = 3 evectors = principal axes of rigid body
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double cross[3];
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double tensor[3][3],evectors[3][3];
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tensor[0][0] = itensor[0];
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tensor[1][1] = itensor[1];
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tensor[2][2] = itensor[2];
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tensor[1][2] = tensor[2][1] = itensor[3];
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tensor[0][2] = tensor[2][0] = itensor[4];
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tensor[0][1] = tensor[1][0] = itensor[5];
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if (MathEigen::jacobi3(tensor,inertia,evectors))
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error->all(FLERR,"Insufficient Jacobi rotations for rigid molecule");
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ex[0] = evectors[0][0];
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ex[1] = evectors[1][0];
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ex[2] = evectors[2][0];
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ey[0] = evectors[0][1];
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ey[1] = evectors[1][1];
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ey[2] = evectors[2][1];
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ez[0] = evectors[0][2];
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ez[1] = evectors[1][2];
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ez[2] = evectors[2][2];
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// if any principal moment < scaled EPSILON, set to 0.0
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double max;
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max = MAX(inertia[0],inertia[1]);
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max = MAX(max,inertia[2]);
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if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
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if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
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if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
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// enforce 3 evectors as a right-handed coordinate system
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// flip 3rd vector if needed
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MathExtra::cross3(ex,ey,cross);
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if (MathExtra::dot3(cross,ez) < 0.0) MathExtra::negate3(ez);
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// create quaternion
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MathExtra::exyz_to_q(ex,ey,ez,quat);
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// compute displacements in body frame defined by quat
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memory->destroy(dxbody);
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memory->create(dxbody,natoms,3,"molecule:dxbody");
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for (int i = 0; i < natoms; i++)
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MathExtra::transpose_matvec(ex,ey,ez,dxcom[i],dxbody[i]);
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}
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/* ----------------------------------------------------------------------
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read molecule info from file
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flag = 0, just scan for sizes of fields
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flag = 1, read and store fields
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------------------------------------------------------------------------- */
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void Molecule::read(int flag)
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{
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char line[MAXLINE];
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char *eof;
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// skip 1st line of file
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if (me == 0) {
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eof = fgets(line,MAXLINE,fp);
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if (eof == nullptr) error->one(FLERR,"Unexpected end of molecule file");
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}
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// read header lines
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// skip blank lines or lines that start with "#"
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// stop when read an unrecognized line
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while (1) {
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readline(line);
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// trim comments. if line is blank, continue
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auto text = utils::trim(utils::trim_comment(line));
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if (text.empty()) continue;
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// search line for header keywords and set corresponding variable
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try {
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ValueTokenizer values(text);
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int nmatch = values.count();
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int nwant = 0;
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if (values.contains("atoms")) {
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natoms = values.next_int();
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nwant = 2;
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} else if (values.contains("bonds")) {
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nbonds = values.next_int();
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nwant = 2;
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} else if (values.contains("angles")) {
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nangles = values.next_int();
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nwant = 2;
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} else if (values.contains("dihedrals")) {
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ndihedrals = values.next_int();
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nwant = 2;
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} else if (values.contains("impropers")) {
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nimpropers = values.next_int();
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nwant = 2;
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} else if (values.contains("fragments")) {
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nfragments = values.next_int();
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nwant = 2;
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} else if (values.contains("mass")) {
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massflag = 1;
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masstotal = values.next_double();
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nwant = 2;
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masstotal *= sizescale*sizescale*sizescale;
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} else if (values.contains("com")) {
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comflag = 1;
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com[0] = values.next_double();
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com[1] = values.next_double();
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com[2] = values.next_double();
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nwant = 4;
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com[0] *= sizescale;
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com[1] *= sizescale;
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com[2] *= sizescale;
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if (domain->dimension == 2 && com[2] != 0.0)
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error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
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} else if (values.contains("inertia")) {
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inertiaflag = 1;
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itensor[0] = values.next_double();
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itensor[1] = values.next_double();
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itensor[2] = values.next_double();
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itensor[3] = values.next_double();
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itensor[4] = values.next_double();
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itensor[5] = values.next_double();
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nwant = 7;
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const double scale5 = sizescale*sizescale*sizescale*sizescale*sizescale;
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itensor[0] *= scale5;
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itensor[1] *= scale5;
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itensor[2] *= scale5;
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itensor[3] *= scale5;
|
|
itensor[4] *= scale5;
|
|
itensor[5] *= scale5;
|
|
} else if (values.contains("body")) {
|
|
bodyflag = 1;
|
|
avec_body = (AtomVecBody *) atom->style_match("body");
|
|
if (!avec_body)
|
|
error->all(FLERR,"Molecule file requires atom style body");
|
|
nibody = values.next_int();
|
|
ndbody = values.next_int();
|
|
nwant = 3;
|
|
} else {
|
|
// unknown header keyword
|
|
if (utils::strmatch(text,"^\\d+\\s+\\S+")) {
|
|
values.next_int();
|
|
auto keyword = values.next_string();
|
|
error->one(FLERR,"Invalid header keyword: {}",keyword);
|
|
} else break;
|
|
}
|
|
if (nmatch != nwant)
|
|
error->one(FLERR,"Invalid header line format in molecule file");
|
|
} catch (TokenizerException &e) {
|
|
error->one(FLERR, "Invalid header in molecule file\n"
|
|
"{}", e.what());
|
|
}
|
|
}
|
|
|
|
// error checks
|
|
|
|
if (natoms < 1)
|
|
error->all(FLERR,"No atoms or invalid atom count in molecule file");
|
|
if (nbonds < 0) error->all(FLERR,"Invalid bond count in molecule file");
|
|
if (nangles < 0) error->all(FLERR,"Invalid angle count in molecule file");
|
|
if (ndihedrals < 0)
|
|
error->all(FLERR,"Invalid dihedral count in molecule file");
|
|
if (nimpropers < 0)
|
|
error->all(FLERR,"Invalid improper count in molecule file");
|
|
|
|
// count = vector for tallying bonds,angles,etc per atom
|
|
|
|
if (flag == 0) memory->create(count,natoms,"molecule:count");
|
|
|
|
// grab keyword and skip next line
|
|
|
|
std::string keyword = parse_keyword(0,line);
|
|
readline(line);
|
|
|
|
// loop over sections of molecule file
|
|
|
|
while (!keyword.empty()) {
|
|
if (keyword == "Coords") {
|
|
xflag = 1;
|
|
if (flag) coords(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Types") {
|
|
typeflag = 1;
|
|
if (flag) types(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Molecules") {
|
|
moleculeflag = 1;
|
|
if (flag) molecules(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Fragments") {
|
|
if (nfragments == 0)
|
|
error->all(FLERR,"Found Fragments section but no nfragments setting in header");
|
|
fragmentflag = 1;
|
|
if (flag) fragments(line);
|
|
else skip_lines(nfragments,line,keyword);
|
|
} else if (keyword == "Charges") {
|
|
qflag = 1;
|
|
if (flag) charges(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Diameters") {
|
|
radiusflag = 1;
|
|
if (flag) diameters(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Masses") {
|
|
rmassflag = 1;
|
|
if (flag) masses(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
|
|
} else if (keyword == "Bonds") {
|
|
if (nbonds == 0)
|
|
error->all(FLERR,"Found Bonds section but no nbonds setting in header");
|
|
bondflag = tag_require = 1;
|
|
bonds(flag,line);
|
|
} else if (keyword == "Angles") {
|
|
if (nangles == 0)
|
|
error->all(FLERR,"Found Angles section but no nangles setting in header");
|
|
angleflag = tag_require = 1;
|
|
angles(flag,line);
|
|
} else if (keyword == "Dihedrals") {
|
|
if (ndihedrals == 0) error->all(FLERR,"Found Dihedrals section"
|
|
"but no ndihedrals setting in header");
|
|
dihedralflag = tag_require = 1;
|
|
dihedrals(flag,line);
|
|
} else if (keyword == "Impropers") {
|
|
if (nimpropers == 0) error->all(FLERR,"Found Impropers section"
|
|
"but no nimpropers setting in header");
|
|
improperflag = tag_require = 1;
|
|
impropers(flag,line);
|
|
|
|
} else if (keyword == "Special Bond Counts") {
|
|
nspecialflag = 1;
|
|
nspecial_read(flag,line);
|
|
} else if (keyword == "Special Bonds") {
|
|
specialflag = tag_require = 1;
|
|
if (flag) special_read(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
|
|
} else if (keyword == "Shake Flags") {
|
|
shakeflagflag = 1;
|
|
if (flag) shakeflag_read(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Shake Atoms") {
|
|
shakeatomflag = tag_require = 1;
|
|
if (shaketypeflag) shakeflag = 1;
|
|
if (!shakeflagflag)
|
|
error->all(FLERR,"Shake Flags section must come before Shake Atoms section");
|
|
if (flag) shakeatom_read(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
} else if (keyword == "Shake Bond Types") {
|
|
shaketypeflag = 1;
|
|
if (shakeatomflag) shakeflag = 1;
|
|
if (!shakeflagflag)
|
|
error->all(FLERR,"Shake Flags section must come before Shake Bonds section");
|
|
if (flag) shaketype_read(line);
|
|
else skip_lines(natoms,line,keyword);
|
|
|
|
} else if (keyword == "Body Integers") {
|
|
if (bodyflag == 0 || nibody == 0)
|
|
error->all(FLERR,"Found Body Integers section but no setting in header");
|
|
ibodyflag = 1;
|
|
body(flag,0,line);
|
|
} else if (keyword == "Body Doubles") {
|
|
if (bodyflag == 0 || ndbody == 0)
|
|
error->all(FLERR,"Found Body Doubles section but no setting in header");
|
|
dbodyflag = 1;
|
|
body(flag,1,line);
|
|
} else {
|
|
|
|
// Error: Either a too long/short section or a typo in the keyword
|
|
|
|
if (utils::strmatch(keyword,"^[A-Za-z ]+$"))
|
|
error->one(FLERR,"Unknown section '{}' in molecule "
|
|
"file\n",keyword);
|
|
else error->one(FLERR,"Unexpected line in molecule file "
|
|
"while looking for the next "
|
|
"section:\n{}",line);
|
|
}
|
|
keyword = parse_keyword(1,line);
|
|
}
|
|
|
|
// error check
|
|
|
|
if (flag == 0) {
|
|
if ((nspecialflag && !specialflag) || (!nspecialflag && specialflag))
|
|
error->all(FLERR,"Molecule file needs both Special Bond sections");
|
|
if (specialflag && !bondflag)
|
|
error->all(FLERR,"Molecule file has special flags but no bonds");
|
|
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
|
|
error->all(FLERR,"Molecule file shake info is incomplete");
|
|
if (bodyflag && nibody && ibodyflag == 0)
|
|
error->all(FLERR,"Molecule file has no Body Integers section");
|
|
if (bodyflag && ndbody && dbodyflag == 0)
|
|
error->all(FLERR,"Molecule file has no Body Doubles section");
|
|
if (nfragments > 0 && !fragmentflag)
|
|
error->all(FLERR,"Molecule file has no Fragments section");
|
|
}
|
|
|
|
// auto-generate special bonds if needed and not in file
|
|
|
|
if (bondflag && specialflag == 0) {
|
|
if (domain->box_exist == 0)
|
|
error->all(FLERR,"Cannot auto-generate special bonds before "
|
|
"simulation box is defined");
|
|
|
|
if (flag) {
|
|
special_generate();
|
|
specialflag = 1;
|
|
nspecialflag = 1;
|
|
}
|
|
}
|
|
|
|
// body particle must have natom = 1
|
|
// set radius by having body class compute its own radius
|
|
|
|
if (bodyflag) {
|
|
radiusflag = 1;
|
|
if (natoms != 1)
|
|
error->all(FLERR,"Molecule natoms must be 1 for body particle");
|
|
if (sizescale != 1.0)
|
|
error->all(FLERR,"Molecule sizescale must be 1.0 for body particle");
|
|
if (flag) {
|
|
radius[0] = avec_body->radius_body(nibody,ndbody,ibodyparams,dbodyparams);
|
|
maxradius = radius[0];
|
|
}
|
|
}
|
|
|
|
// clean up
|
|
|
|
if (flag) memory->destroy(count);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read coords from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::coords(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 4)
|
|
error->all(FLERR,"Invalid line in Coords section of "
|
|
"molecule file: {}",line);
|
|
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Coords section of molecule file");
|
|
count[iatom]++;
|
|
x[iatom][0] = values.next_double();
|
|
x[iatom][1] = values.next_double();
|
|
x[iatom][2] = values.next_double();
|
|
|
|
x[iatom][0] *= sizescale;
|
|
x[iatom][1] *= sizescale;
|
|
x[iatom][2] *= sizescale;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR,"Invalid line in Coords section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Coords "
|
|
"section of molecule file",i+1);
|
|
|
|
if (domain->dimension == 2) {
|
|
for (int i = 0; i < natoms; i++)
|
|
if (x[i][2] != 0.0)
|
|
error->all(FLERR,"Z coord in molecule file for atom {} "
|
|
"must be 0.0 for 2d-simulation.",i+1);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read types from file
|
|
set ntypes = max of any atom type
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::types(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 2)
|
|
error->all(FLERR,"Invalid line in Types section of "
|
|
"molecule file: {}",line);
|
|
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Types section of molecule file");
|
|
count[iatom]++;
|
|
type[iatom] = values.next_int();
|
|
type[iatom] += toffset;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Types section of "
|
|
"molecule file: {}\n{}", e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Types "
|
|
"section of molecule file",i+1);
|
|
|
|
if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
|
|
error->all(FLERR,"Invalid atom type {} for atom {} "
|
|
"in molecule file",type[i],i+1);
|
|
|
|
ntypes = MAX(ntypes,type[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read molecules from file
|
|
set nmolecules = max of any molecule type
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::molecules(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 2)
|
|
error->all(FLERR,"Invalid line in Molecules section of "
|
|
"molecule file: {}",line);
|
|
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Molecules section of molecule file");
|
|
count[iatom]++;
|
|
molecule[iatom] = values.next_tagint();
|
|
// molecule[iatom] += moffset; // placeholder for possible molecule offset
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Molecules section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Molecules "
|
|
"section of molecule file",i+1);
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
if (molecule[i] < 0)
|
|
error->all(FLERR,"Invalid molecule ID {} for atom {} "
|
|
"in molecule file",molecule[i],i+1);
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
nmolecules = MAX(nmolecules,molecule[i]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read fragments from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::fragments(char *line)
|
|
{
|
|
try {
|
|
for (int i = 0; i < nfragments; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
|
|
if ((int)values.count() > natoms+1)
|
|
error->all(FLERR,"Too many atoms per fragment in Fragments "
|
|
"section of molecule file");
|
|
|
|
fragmentnames[i] = values.next_string();
|
|
|
|
while (values.has_next()) {
|
|
int iatom = values.next_int()-1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom ID {} for fragment {} in "
|
|
"Fragments section of molecule file",
|
|
iatom+1, fragmentnames[i]);
|
|
fragmentmask[i][iatom] = 1;
|
|
}
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid atom ID in Fragments section of "
|
|
"molecule file: {}\n{}", e.what(),line);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read charges from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::charges(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if ((int)values.count() != 2)
|
|
error->all(FLERR,"Invalid line in Charges section of "
|
|
"molecule file: {}",line);
|
|
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Charges section of molecule file");
|
|
|
|
count[iatom]++;
|
|
q[iatom] = values.next_double();
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Charges section of "
|
|
"molecule file: {}.\n{}",e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Charges "
|
|
"section of molecule file",i+1);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read diameters from file and set radii
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::diameters(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
maxradius = 0.0;
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 2)
|
|
error->all(FLERR,"Invalid line in Diameters section of "
|
|
"molecule file: {}",line);
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Diameters section of molecule file");
|
|
count[iatom]++;
|
|
radius[iatom] = values.next_double();
|
|
radius[iatom] *= sizescale;
|
|
radius[iatom] *= 0.5;
|
|
maxradius = MAX(maxradius,radius[iatom]);
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Diameters section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Diameters "
|
|
"section of molecule file",i+1);
|
|
if (radius[i] < 0.0)
|
|
error->all(FLERR,"Invalid atom diameter {} for atom {} "
|
|
"in molecule file", radius[i], i+1);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read masses from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::masses(char *line)
|
|
{
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 2)
|
|
error->all(FLERR,"Invalid line in Masses section of "
|
|
"molecule file: {}",line);
|
|
|
|
int iatom = values.next_int() - 1;
|
|
if (iatom < 0 || iatom >= natoms)
|
|
error->all(FLERR,"Invalid atom index in Masses section of molecule file");
|
|
count[iatom]++;
|
|
rmass[iatom] = values.next_double();
|
|
rmass[iatom] *= sizescale*sizescale*sizescale;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Masses section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
if (count[i] == 0) error->all(FLERR,"Atom {} missing in Masses "
|
|
"section of molecule file",i+1);
|
|
if (rmass[i] <= 0.0)
|
|
error->all(FLERR,"Invalid atom mass {} for atom {} "
|
|
"in molecule file", radius[i], i+1);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read bonds from file
|
|
set nbondtypes = max type of any bond
|
|
store each with both atoms if newton_bond = 0
|
|
if flag = 0, just count bonds/atom
|
|
if flag = 1, store them with atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::bonds(int flag, char *line)
|
|
{
|
|
int itype;
|
|
tagint m,atom1,atom2;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
if (flag == 0)
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
else
|
|
for (int i = 0; i < natoms; i++) num_bond[i] = 0;
|
|
|
|
for (int i = 0; i < nbonds; i++) {
|
|
readline(line);
|
|
|
|
try {
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 4)
|
|
error->all(FLERR,"Invalid line in Bonds section of "
|
|
"molecule file: {}",line);
|
|
values.next_int();
|
|
itype = values.next_int();
|
|
atom1 = values.next_tagint();
|
|
atom2 = values.next_tagint();
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Bonds section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
itype += boffset;
|
|
|
|
if ((atom1 <= 0) || (atom1 > natoms) ||
|
|
(atom2 <= 0) || (atom2 > natoms) || (atom1 == atom2))
|
|
error->all(FLERR,"Invalid atom ID in Bonds section of molecule file");
|
|
if ((itype <= 0) || (domain->box_exist && (itype > atom->nbondtypes)))
|
|
error->all(FLERR,"Invalid bond type in Bonds section of molecule file");
|
|
|
|
if (flag) {
|
|
m = atom1-1;
|
|
nbondtypes = MAX(nbondtypes,itype);
|
|
bond_type[m][num_bond[m]] = itype;
|
|
bond_atom[m][num_bond[m]] = atom2;
|
|
num_bond[m]++;
|
|
if (newton_bond == 0) {
|
|
m = atom2-1;
|
|
bond_type[m][num_bond[m]] = itype;
|
|
bond_atom[m][num_bond[m]] = atom1;
|
|
num_bond[m]++;
|
|
}
|
|
} else {
|
|
count[atom1-1]++;
|
|
if (newton_bond == 0) count[atom2-1]++;
|
|
}
|
|
}
|
|
|
|
// bond_per_atom = max of count vector
|
|
|
|
if (flag == 0) {
|
|
bond_per_atom = 0;
|
|
for (int i = 0; i < natoms; i++)
|
|
bond_per_atom = MAX(bond_per_atom,count[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read angles from file
|
|
store each with all 3 atoms if newton_bond = 0
|
|
if flag = 0, just count angles/atom
|
|
if flag = 1, store them with atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::angles(int flag, char *line)
|
|
{
|
|
int itype;
|
|
tagint m,atom1,atom2,atom3;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
if (flag == 0)
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
else
|
|
for (int i = 0; i < natoms; i++) num_angle[i] = 0;
|
|
|
|
for (int i = 0; i < nangles; i++) {
|
|
readline(line);
|
|
|
|
try {
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 5)
|
|
error->all(FLERR,"Invalid line in Angles section of "
|
|
"molecule file: {}",line);
|
|
values.next_int();
|
|
itype = values.next_int();
|
|
atom1 = values.next_tagint();
|
|
atom2 = values.next_tagint();
|
|
atom3 = values.next_tagint();
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Angles section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
itype += aoffset;
|
|
|
|
if ((atom1 <= 0) || (atom1 > natoms) ||
|
|
(atom2 <= 0) || (atom2 > natoms) ||
|
|
(atom3 <= 0) || (atom3 > natoms) ||
|
|
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
|
|
error->all(FLERR,"Invalid atom ID in Angles section of molecule file");
|
|
if ((itype <= 0) || (domain->box_exist && (itype > atom->nangletypes)))
|
|
error->all(FLERR,"Invalid angle type in Angles section of molecule file");
|
|
|
|
if (flag) {
|
|
m = atom2-1;
|
|
nangletypes = MAX(nangletypes,itype);
|
|
angle_type[m][num_angle[m]] = itype;
|
|
angle_atom1[m][num_angle[m]] = atom1;
|
|
angle_atom2[m][num_angle[m]] = atom2;
|
|
angle_atom3[m][num_angle[m]] = atom3;
|
|
num_angle[m]++;
|
|
if (newton_bond == 0) {
|
|
m = atom1-1;
|
|
angle_type[m][num_angle[m]] = itype;
|
|
angle_atom1[m][num_angle[m]] = atom1;
|
|
angle_atom2[m][num_angle[m]] = atom2;
|
|
angle_atom3[m][num_angle[m]] = atom3;
|
|
num_angle[m]++;
|
|
m = atom3-1;
|
|
angle_type[m][num_angle[m]] = itype;
|
|
angle_atom1[m][num_angle[m]] = atom1;
|
|
angle_atom2[m][num_angle[m]] = atom2;
|
|
angle_atom3[m][num_angle[m]] = atom3;
|
|
num_angle[m]++;
|
|
}
|
|
} else {
|
|
count[atom2-1]++;
|
|
if (newton_bond == 0) {
|
|
count[atom1-1]++;
|
|
count[atom3-1]++;
|
|
}
|
|
}
|
|
}
|
|
|
|
// angle_per_atom = max of count vector
|
|
|
|
if (flag == 0) {
|
|
angle_per_atom = 0;
|
|
for (int i = 0; i < natoms; i++)
|
|
angle_per_atom = MAX(angle_per_atom,count[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read dihedrals from file
|
|
store each with all 4 atoms if newton_bond = 0
|
|
if flag = 0, just count dihedrals/atom
|
|
if flag = 1, store them with atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::dihedrals(int flag, char *line)
|
|
{
|
|
int itype;
|
|
tagint m,atom1,atom2,atom3,atom4;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
if (flag == 0)
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
else
|
|
for (int i = 0; i < natoms; i++) num_dihedral[i] = 0;
|
|
|
|
for (int i = 0; i < ndihedrals; i++) {
|
|
readline(line);
|
|
|
|
try {
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 6)
|
|
error->all(FLERR,"Invalid line in Dihedrals section of "
|
|
"molecule file: {}",line);
|
|
|
|
values.next_int();
|
|
itype = values.next_int();
|
|
atom1 = values.next_tagint();
|
|
atom2 = values.next_tagint();
|
|
atom3 = values.next_tagint();
|
|
atom4 = values.next_tagint();
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Dihedrals section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
itype += doffset;
|
|
|
|
if ((atom1 <= 0) || (atom1 > natoms) ||
|
|
(atom2 <= 0) || (atom2 > natoms) ||
|
|
(atom3 <= 0) || (atom3 > natoms) ||
|
|
(atom4 <= 0) || (atom4 > natoms) ||
|
|
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
|
|
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
|
|
error->all(FLERR,
|
|
"Invalid atom ID in dihedrals section of molecule file");
|
|
if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes)))
|
|
error->all(FLERR,"Invalid dihedral type in Dihedrals section of molecule file");
|
|
|
|
if (flag) {
|
|
m = atom2-1;
|
|
ndihedraltypes = MAX(ndihedraltypes,itype);
|
|
dihedral_type[m][num_dihedral[m]] = itype;
|
|
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
|
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
|
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
|
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
|
num_dihedral[m]++;
|
|
if (newton_bond == 0) {
|
|
m = atom1-1;
|
|
dihedral_type[m][num_dihedral[m]] = itype;
|
|
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
|
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
|
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
|
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
|
num_dihedral[m]++;
|
|
m = atom3-1;
|
|
dihedral_type[m][num_dihedral[m]] = itype;
|
|
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
|
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
|
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
|
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
|
num_dihedral[m]++;
|
|
m = atom4-1;
|
|
dihedral_type[m][num_dihedral[m]] = itype;
|
|
dihedral_atom1[m][num_dihedral[m]] = atom1;
|
|
dihedral_atom2[m][num_dihedral[m]] = atom2;
|
|
dihedral_atom3[m][num_dihedral[m]] = atom3;
|
|
dihedral_atom4[m][num_dihedral[m]] = atom4;
|
|
num_dihedral[m]++;
|
|
}
|
|
} else {
|
|
count[atom2-1]++;
|
|
if (newton_bond == 0) {
|
|
count[atom1-1]++;
|
|
count[atom3-1]++;
|
|
count[atom4-1]++;
|
|
}
|
|
}
|
|
}
|
|
|
|
// dihedral_per_atom = max of count vector
|
|
|
|
if (flag == 0) {
|
|
dihedral_per_atom = 0;
|
|
for (int i = 0; i < natoms; i++)
|
|
dihedral_per_atom = MAX(dihedral_per_atom,count[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read impropers from file
|
|
store each with all 4 atoms if newton_bond = 0
|
|
if flag = 0, just count impropers/atom
|
|
if flag = 1, store them with atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::impropers(int flag, char *line)
|
|
{
|
|
int itype;
|
|
tagint m,atom1,atom2,atom3,atom4;
|
|
int newton_bond = force->newton_bond;
|
|
|
|
if (flag == 0)
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
else
|
|
for (int i = 0; i < natoms; i++) num_improper[i] = 0;
|
|
|
|
for (int i = 0; i < nimpropers; i++) {
|
|
readline(line);
|
|
|
|
try {
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 6)
|
|
error->all(FLERR,"Invalid line in Impropers section of "
|
|
"molecule file: {}",line);
|
|
values.next_int();
|
|
itype = values.next_int();
|
|
atom1 = values.next_tagint();
|
|
atom2 = values.next_tagint();
|
|
atom3 = values.next_tagint();
|
|
atom4 = values.next_tagint();
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Impropers section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
itype += ioffset;
|
|
|
|
if ((atom1 <= 0) || (atom1 > natoms) ||
|
|
(atom2 <= 0) || (atom2 > natoms) ||
|
|
(atom3 <= 0) || (atom3 > natoms) ||
|
|
(atom4 <= 0) || (atom4 > natoms) ||
|
|
(atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) ||
|
|
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
|
|
error->all(FLERR,
|
|
"Invalid atom ID in impropers section of molecule file");
|
|
if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes)))
|
|
error->all(FLERR,"Invalid improper type in Impropers section of molecule file");
|
|
|
|
if (flag) {
|
|
m = atom2-1;
|
|
nimpropertypes = MAX(nimpropertypes,itype);
|
|
improper_type[m][num_improper[m]] = itype;
|
|
improper_atom1[m][num_improper[m]] = atom1;
|
|
improper_atom2[m][num_improper[m]] = atom2;
|
|
improper_atom3[m][num_improper[m]] = atom3;
|
|
improper_atom4[m][num_improper[m]] = atom4;
|
|
num_improper[m]++;
|
|
if (newton_bond == 0) {
|
|
m = atom1-1;
|
|
improper_type[m][num_improper[m]] = itype;
|
|
improper_atom1[m][num_improper[m]] = atom1;
|
|
improper_atom2[m][num_improper[m]] = atom2;
|
|
improper_atom3[m][num_improper[m]] = atom3;
|
|
improper_atom4[m][num_improper[m]] = atom4;
|
|
num_improper[m]++;
|
|
m = atom3-1;
|
|
improper_type[m][num_improper[m]] = itype;
|
|
improper_atom1[m][num_improper[m]] = atom1;
|
|
improper_atom2[m][num_improper[m]] = atom2;
|
|
improper_atom3[m][num_improper[m]] = atom3;
|
|
improper_atom4[m][num_improper[m]] = atom4;
|
|
num_improper[m]++;
|
|
m = atom4-1;
|
|
improper_type[m][num_improper[m]] = itype;
|
|
improper_atom1[m][num_improper[m]] = atom1;
|
|
improper_atom2[m][num_improper[m]] = atom2;
|
|
improper_atom3[m][num_improper[m]] = atom3;
|
|
improper_atom4[m][num_improper[m]] = atom4;
|
|
num_improper[m]++;
|
|
}
|
|
} else {
|
|
count[atom2-1]++;
|
|
if (newton_bond == 0) {
|
|
count[atom1-1]++;
|
|
count[atom3-1]++;
|
|
count[atom4-1]++;
|
|
}
|
|
}
|
|
}
|
|
|
|
// improper_per_atom = max of count vector
|
|
|
|
if (flag == 0) {
|
|
improper_per_atom = 0;
|
|
for (int i = 0; i < natoms; i++)
|
|
improper_per_atom = MAX(improper_per_atom,count[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read 3 special bonds counts from file
|
|
if flag = 0, just tally maxspecial
|
|
if flag = 1, store them with atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::nspecial_read(int flag, char *line)
|
|
{
|
|
if (flag == 0) maxspecial = 0;
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
int c1, c2, c3;
|
|
|
|
try {
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
if (values.count() != 4)
|
|
error->all(FLERR,"Invalid line in Special Bond Counts section of "
|
|
"molecule file: {}",line);
|
|
values.next_int();
|
|
c1 = values.next_tagint();
|
|
c2 = values.next_tagint();
|
|
c3 = values.next_tagint();
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Special Bond Counts section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
|
|
if (flag) {
|
|
nspecial[i][0] = c1;
|
|
nspecial[i][1] = c1+c2;
|
|
nspecial[i][2] = c1+c2+c3;
|
|
} else maxspecial = MAX(maxspecial,c1+c2+c3);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read special bond indices from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::special_read(char *line)
|
|
{
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
int nwords = values.count();
|
|
|
|
if (nwords != nspecial[i][2]+1)
|
|
error->all(FLERR,"Molecule file special list "
|
|
"does not match special count");
|
|
|
|
values.next_int(); // ignore
|
|
|
|
for (int m = 1; m < nwords; m++) {
|
|
special[i][m-1] = values.next_tagint();
|
|
if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
|
|
special[i][m-1] == i+1)
|
|
error->all(FLERR,"Invalid atom index in Special Bonds "
|
|
"section of molecule file");
|
|
}
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid line in Special Bonds section of "
|
|
"molecule file: {}\n{}",e.what(),line);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
auto generate special bond info
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::special_generate()
|
|
{
|
|
int newton_bond = force->newton_bond;
|
|
tagint atom1,atom2;
|
|
|
|
// temporary array for special atoms
|
|
|
|
tagint **tmpspecial;
|
|
memory->create(tmpspecial,natoms,atom->maxspecial,"molecule:tmpspecial");
|
|
memset(&tmpspecial[0][0],0,sizeof(tagint)*natoms*atom->maxspecial);
|
|
|
|
for (int i = 0; i < natoms; i++) count[i] = 0;
|
|
|
|
// 1-2 neighbors
|
|
|
|
if (newton_bond) {
|
|
for (int i = 0; i < natoms; i++) {
|
|
for (int j = 0; j < num_bond[i]; j++) {
|
|
atom1 = i;
|
|
atom2 = bond_atom[i][j]-1;
|
|
nspecial[i][0]++;
|
|
nspecial[atom2][0]++;
|
|
if (count[i] >= atom->maxspecial || count[atom2] >= atom->maxspecial)
|
|
error->all(FLERR,"Molecule auto special bond generation overflow");
|
|
tmpspecial[i][count[i]++] = atom2 + 1;
|
|
tmpspecial[atom2][count[atom2]++] = i + 1;
|
|
}
|
|
}
|
|
} else {
|
|
for (int i = 0; i < natoms; i++) {
|
|
nspecial[i][0] = num_bond[i];
|
|
for (int j = 0; j < num_bond[i]; j++) {
|
|
atom1 = i;
|
|
atom2 = bond_atom[i][j];
|
|
if (count[atom1] >= atom->maxspecial)
|
|
error->all(FLERR,"Molecule auto special bond generation overflow");
|
|
tmpspecial[i][count[atom1]++] = atom2;
|
|
}
|
|
}
|
|
}
|
|
|
|
// 1-3 neighbors with no duplicates
|
|
|
|
for (int i = 0; i < natoms; i++) nspecial[i][1] = nspecial[i][0];
|
|
|
|
int dedup;
|
|
for (int i = 0; i < natoms; i++) {
|
|
for (int m = 0; m < nspecial[i][0]; m++) {
|
|
for (int j = 0; j < nspecial[tmpspecial[i][m]-1][0]; j++) {
|
|
dedup = 0;
|
|
for (int k =0; k < count[i]; k++) {
|
|
if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] ||
|
|
tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
|
|
dedup = 1;
|
|
}
|
|
}
|
|
if (!dedup) {
|
|
if (count[i] >= atom->maxspecial)
|
|
error->all(FLERR,"Molecule auto special bond generation overflow");
|
|
tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
|
|
nspecial[i][1]++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
// 1-4 neighbors with no duplicates
|
|
|
|
for (int i = 0; i < natoms; i++) nspecial[i][2] = nspecial[i][1];
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
for (int m = nspecial[i][0]; m < nspecial[i][1]; m++) {
|
|
for (int j = 0; j < nspecial[tmpspecial[i][m]-1][0]; j++) {
|
|
dedup = 0;
|
|
for (int k =0; k < count[i]; k++) {
|
|
if (tmpspecial[tmpspecial[i][m]-1][j] == tmpspecial[i][k] ||
|
|
tmpspecial[tmpspecial[i][m]-1][j] == i+1) {
|
|
dedup = 1;
|
|
}
|
|
}
|
|
if (!dedup) {
|
|
if (count[i] >= atom->maxspecial)
|
|
error->all(FLERR,"Molecule auto special bond generation overflow");
|
|
tmpspecial[i][count[i]++] = tmpspecial[tmpspecial[i][m]-1][j];
|
|
nspecial[i][2]++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
maxspecial = 0;
|
|
for (int i = 0; i < natoms; i++)
|
|
maxspecial = MAX(maxspecial,nspecial[i][2]);
|
|
|
|
memory->create(special,natoms,maxspecial,"molecule:special");
|
|
for (int i = 0; i < natoms; i++)
|
|
for (int j = 0; j < nspecial[i][2]; j++)
|
|
special[i][j] = tmpspecial[i][j];
|
|
|
|
memory->destroy(tmpspecial);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read SHAKE flags from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::shakeflag_read(char *line)
|
|
{
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
|
|
if (values.count() != 2)
|
|
error->all(FLERR,"Invalid Shake Flags section in molecule file");
|
|
|
|
values.next_int();
|
|
shake_flag[i] = values.next_int();
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid Shake Flags section in molecule file\n"
|
|
"{}", e.what());
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++)
|
|
if (shake_flag[i] < 0 || shake_flag[i] > 4)
|
|
error->all(FLERR,"Invalid shake flag in molecule file");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read SHAKE atom info from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::shakeatom_read(char *line)
|
|
{
|
|
int nmatch=0, nwant=0;
|
|
try {
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
nmatch = values.count();
|
|
|
|
switch (shake_flag[i]) {
|
|
case 1:
|
|
values.next_int();
|
|
shake_atom[i][0] = values.next_tagint();
|
|
shake_atom[i][1] = values.next_tagint();
|
|
shake_atom[i][2] = values.next_tagint();
|
|
nwant = 4;
|
|
break;
|
|
|
|
case 2:
|
|
values.next_int();
|
|
shake_atom[i][0] = values.next_tagint();
|
|
shake_atom[i][1] = values.next_tagint();
|
|
nwant = 3;
|
|
break;
|
|
|
|
case 3:
|
|
values.next_int();
|
|
shake_atom[i][0] = values.next_tagint();
|
|
shake_atom[i][1] = values.next_tagint();
|
|
shake_atom[i][2] = values.next_tagint();
|
|
nwant = 4;
|
|
break;
|
|
|
|
case 4:
|
|
values.next_int();
|
|
shake_atom[i][0] = values.next_tagint();
|
|
shake_atom[i][1] = values.next_tagint();
|
|
shake_atom[i][2] = values.next_tagint();
|
|
shake_atom[i][3] = values.next_tagint();
|
|
nwant = 5;
|
|
break;
|
|
|
|
case 0:
|
|
values.next_int();
|
|
nwant = 1;
|
|
break;
|
|
|
|
default:
|
|
error->all(FLERR,"Invalid shake atom in molecule file");
|
|
}
|
|
|
|
if (nmatch != nwant)
|
|
error->all(FLERR,"Invalid shake atom in molecule file");
|
|
}
|
|
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR,"Invalid shake atom in molecule file\n"
|
|
"{}", e.what());
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
int m = shake_flag[i];
|
|
if (m == 1) m = 3;
|
|
for (int j = 0; j < m; j++)
|
|
if (shake_atom[i][j] <= 0 || shake_atom[i][j] > natoms)
|
|
error->all(FLERR,"Invalid shake atom in molecule file");
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read SHAKE bond type info from file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::shaketype_read(char *line)
|
|
{
|
|
try {
|
|
int nmatch=0, nwant=0;
|
|
for (int i = 0; i < natoms; i++) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
nmatch = values.count();
|
|
|
|
switch (shake_flag[i]) {
|
|
case 1:
|
|
values.next_int();
|
|
shake_type[i][0] = values.next_int();
|
|
shake_type[i][1] = values.next_int();
|
|
shake_type[i][2] = values.next_int();
|
|
nwant = 4;
|
|
break;
|
|
|
|
case 2:
|
|
values.next_int();
|
|
shake_type[i][0] = values.next_int();
|
|
nwant = 2;
|
|
break;
|
|
|
|
case 3:
|
|
values.next_int();
|
|
shake_type[i][0] = values.next_int();
|
|
shake_type[i][1] = values.next_int();
|
|
nwant = 3;
|
|
break;
|
|
|
|
case 4:
|
|
values.next_int();
|
|
shake_type[i][0] = values.next_int();
|
|
shake_type[i][1] = values.next_int();
|
|
shake_type[i][2] = values.next_int();
|
|
nwant = 4;
|
|
break;
|
|
|
|
case 0:
|
|
values.next_int();
|
|
nwant = 1;
|
|
break;
|
|
|
|
default:
|
|
error->all(FLERR,"Invalid shake type data in molecule file");
|
|
}
|
|
|
|
if (nmatch != nwant)
|
|
error->all(FLERR,"Invalid shake type data in molecule file");
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid shake type data in molecule file\n",
|
|
"{}", e.what());
|
|
}
|
|
|
|
for (int i = 0; i < natoms; i++) {
|
|
int m = shake_flag[i];
|
|
if (m == 1) m = 3;
|
|
for (int j = 0; j < m-1; j++)
|
|
if (shake_type[i][j] <= 0)
|
|
error->all(FLERR,"Invalid shake bond type in molecule file");
|
|
if (shake_flag[i] == 1)
|
|
if (shake_type[i][2] <= 0)
|
|
error->all(FLERR,"Invalid shake angle type in molecule file");
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read body params from file
|
|
pflag = 0/1 for integer/double params
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::body(int flag, int pflag, char *line)
|
|
{
|
|
int nparam = nibody;
|
|
if (pflag) nparam = ndbody;
|
|
|
|
int nword = 0;
|
|
|
|
try {
|
|
while (nword < nparam) {
|
|
readline(line);
|
|
|
|
ValueTokenizer values(utils::trim_comment(line));
|
|
int ncount = values.count();
|
|
|
|
if (ncount == 0)
|
|
error->all(FLERR,"Too few values in body section of molecule file");
|
|
if (nword+ncount > nparam)
|
|
error->all(FLERR,"Too many values in body section of molecule file");
|
|
|
|
if (flag) {
|
|
if (pflag == 0) {
|
|
while (values.has_next()) {
|
|
ibodyparams[nword++] = values.next_int();
|
|
}
|
|
} else {
|
|
while (values.has_next()) {
|
|
dbodyparams[nword++] = values.next_double();
|
|
}
|
|
}
|
|
} else nword += ncount;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->all(FLERR, "Invalid body params in molecule file\n",
|
|
"{}", e.what());
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return fragment index if name matches existing fragment, -1 if no such fragment
|
|
------------------------------------------------------------------------- */
|
|
|
|
int Molecule::findfragment(const char *name)
|
|
{
|
|
for (int i = 0; i < nfragments; i++)
|
|
if (fragmentnames[i] == name) return i;
|
|
return -1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
error check molecule attributes and topology against system settings
|
|
flag = 0, just check this molecule
|
|
flag = 1, check all molecules in set, this is 1st molecule in set
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::check_attributes(int flag)
|
|
{
|
|
int n = 1;
|
|
if (flag) n = nset;
|
|
int imol = atom->find_molecule(id);
|
|
|
|
for (int i = imol; i < imol+n; i++) {
|
|
Molecule *onemol = atom->molecules[imol];
|
|
|
|
// check per-atom attributes of molecule
|
|
// warn if not a match
|
|
|
|
int mismatch = 0;
|
|
if (onemol->qflag && !atom->q_flag) mismatch = 1;
|
|
if (onemol->radiusflag && !atom->radius_flag) mismatch = 1;
|
|
if (onemol->rmassflag && !atom->rmass_flag) mismatch = 1;
|
|
|
|
if (mismatch && me == 0)
|
|
error->warning(FLERR,
|
|
"Molecule attributes do not match system attributes");
|
|
|
|
// for all atom styles, check nbondtype,etc
|
|
|
|
mismatch = 0;
|
|
if (atom->nbondtypes < onemol->nbondtypes) mismatch = 1;
|
|
if (atom->nangletypes < onemol->nangletypes) mismatch = 1;
|
|
if (atom->ndihedraltypes < onemol->ndihedraltypes) mismatch = 1;
|
|
if (atom->nimpropertypes < onemol->nimpropertypes) mismatch = 1;
|
|
|
|
if (mismatch)
|
|
error->all(FLERR,"Molecule topology type exceeds system topology type");
|
|
|
|
// for molecular atom styles, check bond_per_atom,etc + maxspecial
|
|
// do not check for atom style template, since nothing stored per atom
|
|
|
|
if (atom->molecular == Atom::MOLECULAR) {
|
|
if (atom->avec->bonds_allow &&
|
|
atom->bond_per_atom < onemol->bond_per_atom) mismatch = 1;
|
|
if (atom->avec->angles_allow &&
|
|
atom->angle_per_atom < onemol->angle_per_atom) mismatch = 1;
|
|
if (atom->avec->dihedrals_allow &&
|
|
atom->dihedral_per_atom < onemol->dihedral_per_atom) mismatch = 1;
|
|
if (atom->avec->impropers_allow &&
|
|
atom->improper_per_atom < onemol->improper_per_atom) mismatch = 1;
|
|
if (atom->maxspecial < onemol->maxspecial) mismatch = 1;
|
|
|
|
if (mismatch)
|
|
error->all(FLERR,"Molecule topology/atom exceeds system topology/atom");
|
|
}
|
|
|
|
// warn if molecule topology defined but no special settings
|
|
|
|
if (onemol->bondflag && !onemol->specialflag)
|
|
if (me == 0) error->warning(FLERR,"Molecule has bond topology "
|
|
"but no special bond settings");
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init all data structures to empty
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::initialize()
|
|
{
|
|
natoms = 0;
|
|
nbonds = nangles = ndihedrals = nimpropers = 0;
|
|
ntypes = 0;
|
|
nmolecules = 1;
|
|
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
|
|
nibody = ndbody = 0;
|
|
nfragments = 0;
|
|
|
|
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
|
|
maxspecial = 0;
|
|
|
|
xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;
|
|
bondflag = angleflag = dihedralflag = improperflag = 0;
|
|
nspecialflag = specialflag = 0;
|
|
shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
|
|
bodyflag = ibodyflag = dbodyflag = 0;
|
|
|
|
centerflag = massflag = comflag = inertiaflag = 0;
|
|
tag_require = 0;
|
|
|
|
x = nullptr;
|
|
type = nullptr;
|
|
q = nullptr;
|
|
radius = nullptr;
|
|
rmass = nullptr;
|
|
|
|
num_bond = nullptr;
|
|
bond_type = nullptr;
|
|
bond_atom = nullptr;
|
|
|
|
num_angle = nullptr;
|
|
angle_type = nullptr;
|
|
angle_atom1 = angle_atom2 = angle_atom3 = nullptr;
|
|
|
|
num_dihedral = nullptr;
|
|
dihedral_type = nullptr;
|
|
dihedral_atom1 = dihedral_atom2 = dihedral_atom3 = dihedral_atom4 = nullptr;
|
|
|
|
num_improper = nullptr;
|
|
improper_type = nullptr;
|
|
improper_atom1 = improper_atom2 = improper_atom3 = improper_atom4 = nullptr;
|
|
|
|
nspecial = nullptr;
|
|
special = nullptr;
|
|
|
|
shake_flag = nullptr;
|
|
shake_atom = nullptr;
|
|
shake_type = nullptr;
|
|
|
|
ibodyparams = nullptr;
|
|
dbodyparams = nullptr;
|
|
|
|
dx = nullptr;
|
|
dxcom = nullptr;
|
|
dxbody = nullptr;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
allocate all data structures
|
|
also initialize values for data structures that are always allocated
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::allocate()
|
|
{
|
|
if (xflag) memory->create(x,natoms,3,"molecule:x");
|
|
if (typeflag) memory->create(type,natoms,"molecule:type");
|
|
if (moleculeflag) memory->create(molecule,natoms,"molecule:molecule");
|
|
if (fragmentflag) {
|
|
fragmentnames.resize(nfragments);
|
|
memory->create(fragmentmask,nfragments,natoms,"molecule:fragmentmask");
|
|
for (int i = 0; i < nfragments; i++)
|
|
for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;
|
|
}
|
|
if (qflag) memory->create(q,natoms,"molecule:q");
|
|
if (radiusflag) memory->create(radius,natoms,"molecule:radius");
|
|
if (rmassflag) memory->create(rmass,natoms,"molecule:rmass");
|
|
|
|
// always allocate num_bond,num_angle,etc and nspecial
|
|
// even if not in molecule file, initialize to 0
|
|
// this is so methods that use these arrays don't have to check they exist
|
|
|
|
memory->create(num_bond,natoms,"molecule:num_bond");
|
|
for (int i = 0; i < natoms; i++) num_bond[i] = 0;
|
|
memory->create(num_angle,natoms,"molecule:num_angle");
|
|
for (int i = 0; i < natoms; i++) num_angle[i] = 0;
|
|
memory->create(num_dihedral,natoms,"molecule:num_dihedral");
|
|
for (int i = 0; i < natoms; i++) num_dihedral[i] = 0;
|
|
memory->create(num_improper,natoms,"molecule:num_improper");
|
|
for (int i = 0; i < natoms; i++) num_improper[i] = 0;
|
|
memory->create(nspecial,natoms,3,"molecule:nspecial");
|
|
for (int i = 0; i < natoms; i++)
|
|
nspecial[i][0] = nspecial[i][1] = nspecial[i][2] = 0;
|
|
|
|
if (specialflag)
|
|
memory->create(special,natoms,maxspecial,"molecule:special");
|
|
|
|
if (bondflag) {
|
|
memory->create(bond_type,natoms,bond_per_atom,
|
|
"molecule:bond_type");
|
|
memory->create(bond_atom,natoms,bond_per_atom,
|
|
"molecule:bond_atom");
|
|
}
|
|
|
|
if (angleflag) {
|
|
memory->create(angle_type,natoms,angle_per_atom,
|
|
"molecule:angle_type");
|
|
memory->create(angle_atom1,natoms,angle_per_atom,
|
|
"molecule:angle_atom1");
|
|
memory->create(angle_atom2,natoms,angle_per_atom,
|
|
"molecule:angle_atom2");
|
|
memory->create(angle_atom3,natoms,angle_per_atom,
|
|
"molecule:angle_atom3");
|
|
}
|
|
|
|
if (dihedralflag) {
|
|
memory->create(dihedral_type,natoms,dihedral_per_atom,
|
|
"molecule:dihedral_type");
|
|
memory->create(dihedral_atom1,natoms,dihedral_per_atom,
|
|
"molecule:dihedral_atom1");
|
|
memory->create(dihedral_atom2,natoms,dihedral_per_atom,
|
|
"molecule:dihedral_atom2");
|
|
memory->create(dihedral_atom3,natoms,dihedral_per_atom,
|
|
"molecule:dihedral_atom3");
|
|
memory->create(dihedral_atom4,natoms,dihedral_per_atom,
|
|
"molecule:dihedral_atom4");
|
|
}
|
|
|
|
if (improperflag) {
|
|
memory->create(improper_type,natoms,improper_per_atom,
|
|
"molecule:improper_type");
|
|
memory->create(improper_atom1,natoms,improper_per_atom,
|
|
"molecule:improper_atom1");
|
|
memory->create(improper_atom2,natoms,improper_per_atom,
|
|
"molecule:improper_atom2");
|
|
memory->create(improper_atom3,natoms,improper_per_atom,
|
|
"molecule:improper_atom3");
|
|
memory->create(improper_atom4,natoms,improper_per_atom,
|
|
"molecule:improper_atom4");
|
|
}
|
|
|
|
if (shakeflag) {
|
|
memory->create(shake_flag,natoms,"molecule:shake_flag");
|
|
memory->create(shake_atom,natoms,4,"molecule:shake_flag");
|
|
memory->create(shake_type,natoms,3,"molecule:shake_flag");
|
|
}
|
|
|
|
if (bodyflag) {
|
|
if (nibody) memory->create(ibodyparams,nibody,"molecule:ibodyparams");
|
|
if (ndbody) memory->create(dbodyparams,ndbody,"molecule:dbodyparams");
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
deallocate all data structures
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::deallocate()
|
|
{
|
|
memory->destroy(x);
|
|
memory->destroy(type);
|
|
memory->destroy(molecule);
|
|
memory->destroy(q);
|
|
memory->destroy(radius);
|
|
memory->destroy(rmass);
|
|
|
|
memory->destroy(molecule);
|
|
memory->destroy(fragmentmask);
|
|
|
|
if (fragmentflag) {
|
|
fragmentnames.clear();
|
|
}
|
|
|
|
memory->destroy(num_bond);
|
|
memory->destroy(bond_type);
|
|
memory->destroy(bond_atom);
|
|
|
|
memory->destroy(num_angle);
|
|
memory->destroy(angle_type);
|
|
memory->destroy(angle_atom1);
|
|
memory->destroy(angle_atom2);
|
|
memory->destroy(angle_atom3);
|
|
|
|
memory->destroy(num_dihedral);
|
|
memory->destroy(dihedral_type);
|
|
memory->destroy(dihedral_atom1);
|
|
memory->destroy(dihedral_atom2);
|
|
memory->destroy(dihedral_atom3);
|
|
memory->destroy(dihedral_atom4);
|
|
|
|
memory->destroy(num_improper);
|
|
memory->destroy(improper_type);
|
|
memory->destroy(improper_atom1);
|
|
memory->destroy(improper_atom2);
|
|
memory->destroy(improper_atom3);
|
|
memory->destroy(improper_atom4);
|
|
|
|
memory->destroy(nspecial);
|
|
memory->destroy(special);
|
|
|
|
memory->destroy(shake_flag);
|
|
memory->destroy(shake_atom);
|
|
memory->destroy(shake_type);
|
|
|
|
memory->destroy(dx);
|
|
memory->destroy(dxcom);
|
|
memory->destroy(dxbody);
|
|
|
|
memory->destroy(ibodyparams);
|
|
memory->destroy(dbodyparams);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
read and bcast a line
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::readline(char *line)
|
|
{
|
|
int n;
|
|
if (me == 0) {
|
|
if (fgets(line,MAXLINE,fp) == nullptr) n = 0;
|
|
else n = strlen(line) + 1;
|
|
}
|
|
MPI_Bcast(&n,1,MPI_INT,0,world);
|
|
if (n == 0) error->all(FLERR,"Unexpected end of molecule file");
|
|
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
extract keyword from line
|
|
flag = 0, read and bcast line
|
|
flag = 1, line has already been read
|
|
------------------------------------------------------------------------- */
|
|
|
|
std::string Molecule::parse_keyword(int flag, char *line)
|
|
{
|
|
char line2[MAXLINE];
|
|
if (flag) {
|
|
|
|
// read upto non-blank line plus 1 following line
|
|
// eof is set to 1 if any read hits end-of-file
|
|
|
|
int eof = 0;
|
|
if (me == 0) {
|
|
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
|
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
|
|
if (fgets(line,MAXLINE,fp) == nullptr) eof = 1;
|
|
}
|
|
if (fgets(line2,MAXLINE,fp) == nullptr) eof = 1;
|
|
}
|
|
|
|
// if eof, set keyword empty and return
|
|
|
|
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
|
if (eof) {
|
|
return std::string("");
|
|
}
|
|
|
|
// bcast keyword line to all procs
|
|
|
|
MPI_Bcast(line,MAXLINE,MPI_CHAR,0,world);
|
|
}
|
|
|
|
// return non-whitespace and non-comment portion of line
|
|
|
|
return utils::trim(utils::trim_comment(line));
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
skip N lines of file. Check if non-numeric content (e.g. keyword).
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Molecule::skip_lines(int n, char *line, const std::string §ion)
|
|
{
|
|
for (int i = 0; i < n; i++) {
|
|
readline(line);
|
|
if (utils::strmatch(utils::trim(utils::trim_comment(line)),"^[A-Za-z ]+$"))
|
|
error->one(FLERR,"Unexpected line in molecule file while "
|
|
"skipping {} section:\n{}",section,line);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
proc 0 prints molecule params
|
|
------------------------------------------------------------------------- */
|
|
|
|
/*
|
|
|
|
void Molecule::print()
|
|
{
|
|
printf("MOLECULE %s\n",id);
|
|
printf(" %d natoms\n",natoms);
|
|
if (nbonds) printf(" %d nbonds\n",nbonds);
|
|
if (nangles) printf(" %d nangles\n",nangles);
|
|
if (ndihedrals) printf(" %d ndihedrals\n",ndihedrals);
|
|
if (nimpropers) printf(" %d nimpropers\n",nimpropers);
|
|
|
|
if (xflag) {
|
|
printf( "Coords:\n");
|
|
for (int i = 0; i < natoms; i++)
|
|
printf(" %d %g %g %g\n",i+1,x[i][0],x[i][1],x[i][2]);
|
|
}
|
|
if (typeflag) {
|
|
printf( "Types:\n");
|
|
for (int i = 0; i < natoms; i++)
|
|
printf(" %d %d\n",i+1,type[i]);
|
|
}
|
|
if (qflag) {
|
|
printf( "Charges:\n");
|
|
for (int i = 0; i < natoms; i++)
|
|
printf(" %d %g\n",i+1,q[i]);
|
|
}
|
|
if (radiusflag) {
|
|
printf( "Radii:\n");
|
|
for (int i = 0; i < natoms; i++)
|
|
printf(" %d %g\n",i+1,radius[i]);
|
|
}
|
|
if (rmassflag) {
|
|
printf( "Masses:\n");
|
|
for (int i = 0; i < natoms; i++)
|
|
printf(" %d %g\n",i+1,rmass[i]);
|
|
}
|
|
|
|
if (bondflag) {
|
|
printf( "Bonds:\n");
|
|
for (int i = 0; i < natoms; i++) {
|
|
printf(" %d %d\n",i+1,num_bond[i]);
|
|
for (int j = 0; j < num_bond[i]; j++)
|
|
printf(" %d %d %d %d\n",j+1,bond_type[i][j],i+1,bond_atom[i][j]);
|
|
}
|
|
}
|
|
if (angleflag) {
|
|
printf( "Angles:\n");
|
|
for (int i = 0; i < natoms; i++) {
|
|
printf(" %d %d\n",i+1,num_angle[i]);
|
|
for (int j = 0; j < num_angle[i]; j++)
|
|
printf(" %d %d %d %d %d\n",
|
|
j+1,angle_type[i][j],
|
|
angle_atom1[i][j],angle_atom2[i][j],angle_atom3[i][j]);
|
|
}
|
|
}
|
|
if (dihedralflag) {
|
|
printf( "Dihedrals:\n");
|
|
for (int i = 0; i < natoms; i++) {
|
|
printf(" %d %d\n",i+1,num_dihedral[i]);
|
|
for (int j = 0; j < num_dihedral[i]; j++)
|
|
printf(" %d %d %d %d %d %d\n",
|
|
j+1,dihedral_type[i][j],
|
|
dihedral_atom1[i][j],dihedral_atom2[i][j],
|
|
dihedral_atom3[i][j],dihedral_atom4[i][j]);
|
|
}
|
|
}
|
|
if (improperflag) {
|
|
printf( "Impropers:\n");
|
|
for (int i = 0; i < natoms; i++) {
|
|
printf(" %d %d\n",i+1,num_improper[i]);
|
|
for (int j = 0; j < num_improper[i]; j++)
|
|
printf(" %d %d %d %d %d %d\n",
|
|
j+1,improper_type[i][j],
|
|
improper_atom1[i][j],improper_atom2[i][j],
|
|
improper_atom3[i][j],improper_atom4[i][j]);
|
|
}
|
|
}
|
|
|
|
if (specialflag) {
|
|
printf( "Special neighs:\n");
|
|
for (int i = 0; i < natoms; i++) {
|
|
printf(" %d %d %d %d\n",i+1,
|
|
nspecial[i][0],nspecial[i][1]-nspecial[i][0],
|
|
nspecial[i][2]-nspecial[i][1]);
|
|
printf(" ");
|
|
for (int j = 0; j < nspecial[i][2]; j++)
|
|
printf(" %d",special[i][j]);
|
|
printf("\n");
|
|
}
|
|
}
|
|
}
|
|
|
|
*/
|