Add support for "Dipoles" section in molecule file
This commit is contained in:
Axel Kohlmeyer
@ -188,7 +188,7 @@ internally.
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These are the allowed section keywords for the body of the file.
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* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
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* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
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* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
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* *Special Bond Counts, Special Bonds* = special neighbor info
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* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
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@ -303,6 +303,19 @@ not listed, the default diameter of each atom in the molecule is 1.0.
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----------
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*Dipoles* section:
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* one line per atom
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* line syntax: ID mux muy muz
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* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
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This section is only allowed for :doc:`atom styles <atom_style>` that
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support particles with point dipoles, e.g. atom_style dipole. If not
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listed, the default dipole component of each atom in the molecule is set
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to 0.0.
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----------
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*Masses* section:
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* one line per atom
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10
src/atom.cpp
10
src/atom.cpp
@ -26,6 +26,7 @@
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#include "input.h"
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#include "label_map.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "modify.h"
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#include "molecule.h"
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@ -2112,6 +2113,15 @@ std::vector<Molecule *>Atom::get_molecule_by_id(const std::string &id)
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void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint offset)
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{
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if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
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if (onemol->muflag && mu_flag) {
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double r[3], rotmat[3][3];
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MathExtra::quat_to_mat(onemol->quat_external, rotmat);
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MathExtra::matvec(rotmat, onemol->mu[iatom], r);
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mu[ilocal][0] = r[0];
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mu[ilocal][1] = r[1];
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mu[ilocal][2] = r[2];
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mu[ilocal][3] = sqrt(r[0] * r[0] + r[1] * r[1] + r[2] * r[2]);
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}
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if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
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if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
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else if (rmass_flag)
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@ -41,15 +41,16 @@ using namespace LAMMPS_NS;
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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),
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radius(nullptr), 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),
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num_improper(nullptr), 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),
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ibodyparams(nullptr), dbodyparams(nullptr), fragmentmask(nullptr), dx(nullptr), dxcom(nullptr),
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dxbody(nullptr), quat_external(nullptr), fp(nullptr), count(nullptr)
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radius(nullptr), rmass(nullptr), mu(nullptr), num_bond(nullptr), bond_type(nullptr),
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bond_atom(nullptr), num_angle(nullptr), angle_type(nullptr), angle_atom1(nullptr),
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angle_atom2(nullptr), angle_atom3(nullptr), num_dihedral(nullptr), dihedral_type(nullptr),
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dihedral_atom1(nullptr), dihedral_atom2(nullptr), dihedral_atom3(nullptr),
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dihedral_atom4(nullptr), num_improper(nullptr), improper_type(nullptr), improper_atom1(nullptr),
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improper_atom2(nullptr), improper_atom3(nullptr), improper_atom4(nullptr), nspecial(nullptr),
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special(nullptr), shake_flag(nullptr), shake_atom(nullptr), shake_type(nullptr),
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avec_body(nullptr), ibodyparams(nullptr), dbodyparams(nullptr), fragmentmask(nullptr),
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dx(nullptr), dxcom(nullptr), dxbody(nullptr), quat_external(nullptr), fp(nullptr),
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count(nullptr)
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{
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me = comm->me;
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@ -132,7 +133,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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// initialize all fields to empty
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initialize();
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Molecule::initialize();
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// scan file for sizes of all fields and allocate storage for them
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@ -141,14 +142,14 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
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if (fp == nullptr)
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error->one(FLERR, "Cannot open molecule file {}: {}", arg[ifile], utils::getsyserror());
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}
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read(0);
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Molecule::read(0);
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if (me == 0) fclose(fp);
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allocate();
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Molecule::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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Molecule::read(1);
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if (me == 0) fclose(fp);
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// stats
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@ -572,6 +573,12 @@ void Molecule::read(int flag)
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diameters(line);
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else
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skip_lines(natoms, line, keyword);
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} else if (keyword == "Dipoles") {
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muflag = 1;
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if (flag)
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dipoles(line);
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else
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skip_lines(natoms, line, keyword);
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} else if (keyword == "Masses") {
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rmassflag = 1;
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if (flag)
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@ -948,6 +955,40 @@ void Molecule::diameters(char *line)
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}
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}
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/* ----------------------------------------------------------------------
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read charges from file
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------------------------------------------------------------------------- */
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void Molecule::dipoles(char *line)
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{
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for (int i = 0; i < natoms; i++) count[i] = 0;
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try {
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for (int i = 0; i < natoms; i++) {
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readline(line);
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ValueTokenizer values(utils::trim_comment(line));
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if ((int) values.count() != 4)
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error->all(FLERR, "Invalid line in Dipoles section of molecule file: {}", line);
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int iatom = values.next_int() - 1;
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if (iatom < 0 || iatom >= natoms)
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error->all(FLERR, "Invalid atom index in Dipoles section of molecule file");
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count[iatom]++;
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mu[iatom][0] = values.next_double();
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mu[iatom][1] = values.next_double();
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mu[iatom][2] = values.next_double();
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}
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} catch (TokenizerException &e) {
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error->all(FLERR, "Invalid line in Dipoles section of molecule file: {}\n{}", e.what(), line);
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}
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for (int i = 0; i < natoms; i++) {
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if (count[i] == 0)
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error->all(FLERR, "Atom {} missing in Dipoles section of molecule file", i + 1);
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}
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}
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/* ----------------------------------------------------------------------
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read masses from file
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------------------------------------------------------------------------- */
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@ -1828,6 +1869,7 @@ void Molecule::check_attributes()
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int mismatch = 0;
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if (qflag && !atom->q_flag) mismatch = 1;
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if (muflag && !atom->mu_flag) mismatch = 1;
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if (radiusflag && !atom->radius_flag) mismatch = 1;
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if (rmassflag && !atom->rmass_flag) mismatch = 1;
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@ -1880,7 +1922,7 @@ void Molecule::initialize()
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bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
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maxspecial = 0;
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xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = rmassflag = 0;
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xflag = typeflag = moleculeflag = fragmentflag = qflag = radiusflag = muflag = rmassflag = 0;
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bondflag = angleflag = dihedralflag = improperflag = 0;
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nspecialflag = specialflag = 0;
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shakeflag = shakeflagflag = shakeatomflag = shaketypeflag = 0;
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@ -1943,6 +1985,7 @@ void Molecule::allocate()
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for (int j = 0; j < natoms; j++) fragmentmask[i][j] = 0;
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}
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if (qflag) memory->create(q, natoms, "molecule:q");
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if (muflag) memory->create(mu, natoms, 3, "molecule:mu");
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if (radiusflag) memory->create(radius, natoms, "molecule:radius");
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if (rmassflag) memory->create(rmass, natoms, "molecule:rmass");
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@ -2167,6 +2210,11 @@ void Molecule::print()
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for (int i = 0; i < natoms; i++)
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printf(" %d %g\n",i+1,radius[i]);
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}
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if (muflag) {
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printf( "Dipoles:\n");
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for (int i = 0; i < natoms; i++)
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printf(" %d %g %g %g\n",i+1,mu[i][0],mu[i][1],mu[i][2]);
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}
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if (rmassflag) {
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printf( "Masses:\n");
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for (int i = 0; i < natoms; i++)
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@ -41,7 +41,7 @@ class Molecule : protected Pointers {
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// 1 if attribute defined in file, 0 if not
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int xflag, typeflag, moleculeflag, fragmentflag, qflag, radiusflag, rmassflag;
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int xflag, typeflag, moleculeflag, fragmentflag, qflag, radiusflag, muflag, rmassflag;
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int bondflag, angleflag, dihedralflag, improperflag;
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int nspecialflag, specialflag;
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int shakeflag, shakeflagflag, shakeatomflag, shaketypeflag;
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@ -63,6 +63,7 @@ class Molecule : protected Pointers {
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double *q; // charge on each atom
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double *radius; // radius of each atom
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double *rmass; // mass of each atom
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double **mu; // dipole vector of each atom
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int *num_bond; // bonds, angles, dihedrals, impropers for each atom
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int **bond_type;
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@ -142,6 +143,7 @@ class Molecule : protected Pointers {
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void fragments(char *);
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void charges(char *);
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void diameters(char *);
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void dipoles(char *);
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void masses(char *);
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void bonds(int, char *);
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void angles(int, char *);
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