adf1beea74
using this mechanism we can reject custom section names that will conflict with existing section names and thus avoid misleading errors. apply this also to fix property atom, where the section name is determined by the fix ID. in addition, allow to specify NULL as section name, which will use the fix ID.
573 lines
14 KiB
C++
573 lines
14 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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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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#ifdef COMMAND_CLASS
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// clang-format off
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CommandStyle(read_data,ReadData);
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// clang-format on
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#else
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#ifndef LMP_READ_DATA_H
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#define LMP_READ_DATA_H
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#include "command.h"
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namespace LAMMPS_NS {
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class ReadData : public Command {
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public:
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ReadData(class LAMMPS *);
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~ReadData();
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void command(int, char **);
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static bool is_data_section(const std::string &);
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private:
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int me, compressed;
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char *line, *keyword, *buffer, *style;
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FILE *fp;
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char **coeffarg;
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int ncoeffarg, maxcoeffarg;
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char argoffset1[8], argoffset2[8];
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bigint id_offset, mol_offset;
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int nlocal_previous;
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bigint natoms;
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bigint nbonds, nangles, ndihedrals, nimpropers;
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int ntypes;
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int nbondtypes, nangletypes, ndihedraltypes, nimpropertypes;
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bigint nellipsoids;
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class AtomVecEllipsoid *avec_ellipsoid;
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bigint nlines;
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class AtomVecLine *avec_line;
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bigint ntris;
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class AtomVecTri *avec_tri;
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bigint nbodies;
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class AtomVecBody *avec_body;
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// box info
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double boxlo[3], boxhi[3];
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double xy, xz, yz;
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int triclinic;
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// optional args
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int addflag, offsetflag, shiftflag, coeffflag;
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tagint addvalue;
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int toffset, boffset, aoffset, doffset, ioffset;
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double shift[3];
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int extra_atom_types, extra_bond_types, extra_angle_types;
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int extra_dihedral_types, extra_improper_types;
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int groupbit;
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int nfix;
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int *fix_index;
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char **fix_header;
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char **fix_section;
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// methods
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void open(const std::string &);
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void scan(int &, int &, int &, int &);
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int reallocate(int **, int, int);
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void header(int);
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void parse_keyword(int);
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void skip_lines(bigint);
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void parse_coeffs(char *, const char *, int, int, int);
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int style_match(const char *, const char *);
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void atoms();
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void velocities();
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void bonds(int);
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void bond_scan(int, char *, int *);
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void angles(int);
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void dihedrals(int);
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void impropers(int);
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void bonus(bigint, class AtomVec *, const char *);
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void bodies(int, class AtomVec *);
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void mass();
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void paircoeffs();
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void pairIJcoeffs();
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void bondcoeffs();
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void anglecoeffs(int);
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void dihedralcoeffs(int);
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void impropercoeffs(int);
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void fix(int, char *);
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Read data add atomID offset is too big
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UNDOCUMENTED
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E: Read data add molID offset is too big
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UNDOCUMENTED
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E: Non-zero read_data shift z value for 2d simulation
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Self-explanatory.
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E: No bonds allowed with this atom style
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Self-explanatory.
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E: No angles allowed with this atom style
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Self-explanatory.
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E: No dihedrals allowed with this atom style
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Self-explanatory.
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E: No impropers allowed with this atom style
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Self-explanatory.
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E: No bonded interactions allowed with this atom style
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UNDOCUMENTED
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E: Fix ID for read_data does not exist
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Self-explanatory.
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E: Cannot run 2d simulation with non-periodic Z dimension
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Use the boundary command to make the z dimension periodic in order to
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run a 2d simulation.
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E: Cannot read_data without add keyword after simulation box is defined
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Self-explanatory.
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E: Cannot use read_data add before simulation box is defined
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Self-explanatory.
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E: Cannot use read_data offset without add flag
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Self-explanatory.
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E: Cannot use read_data shift without add flag
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Self-explanatory.
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E: Cannot use read_data extra with add flag
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Self-explanatory.
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W: Atom style in data file differs from currently defined atom style
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Self-explanatory.
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E: Must read Atoms before Velocities
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The Atoms section of a data file must come before a Velocities
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section.
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E: Invalid data file section: Bonds
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Atom style does not allow bonds.
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E: Must read Atoms before Bonds
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The Atoms section of a data file must come before a Bonds section.
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E: Invalid data file section: Angles
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Atom style does not allow angles.
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E: Must read Atoms before Angles
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The Atoms section of a data file must come before an Angles section.
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E: Invalid data file section: Dihedrals
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Atom style does not allow dihedrals.
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E: Must read Atoms before Dihedrals
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The Atoms section of a data file must come before a Dihedrals section.
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E: Invalid data file section: Impropers
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Atom style does not allow impropers.
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E: Must read Atoms before Impropers
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The Atoms section of a data file must come before an Impropers
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section.
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E: Invalid data file section: Ellipsoids
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Atom style does not allow ellipsoids.
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E: Must read Atoms before Ellipsoids
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The Atoms section of a data file must come before a Ellipsoids
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section.
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E: Invalid data file section: Lines
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Atom style does not allow lines.
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E: Must read Atoms before Lines
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The Atoms section of a data file must come before a Lines section.
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E: Invalid data file section: Triangles
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Atom style does not allow triangles.
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E: Must read Atoms before Triangles
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The Atoms section of a data file must come before a Triangles section.
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E: Invalid data file section: Bodies
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Atom style does not allow bodies.
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E: Must read Atoms before Bodies
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The Atoms section of a data file must come before a Bodies section.
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E: Must define pair_style before Pair Coeffs
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Must use a pair_style command before reading a data file that defines
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Pair Coeffs.
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W: Pair style in data file differs from currently defined pair style
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Self-explanatory.
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E: Must define pair_style before PairIJ Coeffs
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Must use a pair_style command before reading a data file that defines
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PairIJ Coeffs.
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E: Invalid data file section: Bond Coeffs
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Atom style does not allow bonds.
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E: Must define bond_style before Bond Coeffs
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Must use a bond_style command before reading a data file that
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defines Bond Coeffs.
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W: Bond style in data file differs from currently defined bond style
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Self-explanatory.
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E: Invalid data file section: Angle Coeffs
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Atom style does not allow angles.
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E: Must define angle_style before Angle Coeffs
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Must use an angle_style command before reading a data file that
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defines Angle Coeffs.
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W: Angle style in data file differs from currently defined angle style
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Self-explanatory.
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E: Invalid data file section: Dihedral Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before Dihedral Coeffs
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Must use a dihedral_style command before reading a data file that
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defines Dihedral Coeffs.
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W: Dihedral style in data file differs from currently defined dihedral style
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Self-explanatory.
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E: Invalid data file section: Improper Coeffs
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Atom style does not allow impropers.
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E: Must define improper_style before Improper Coeffs
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Must use an improper_style command before reading a data file that
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defines Improper Coeffs.
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W: Improper style in data file differs from currently defined improper style
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Self-explanatory.
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E: Invalid data file section: BondBond Coeffs
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Atom style does not allow angles.
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E: Must define angle_style before BondBond Coeffs
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Must use an angle_style command before reading a data file that
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defines Angle Coeffs.
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E: Invalid data file section: BondAngle Coeffs
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Atom style does not allow angles.
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E: Must define angle_style before BondAngle Coeffs
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Must use an angle_style command before reading a data file that
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defines Angle Coeffs.
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E: Invalid data file section: MiddleBondTorsion Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before MiddleBondTorsion Coeffs
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Must use a dihedral_style command before reading a data file that
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defines MiddleBondTorsion Coeffs.
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E: Invalid data file section: EndBondTorsion Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before EndBondTorsion Coeffs
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Must use a dihedral_style command before reading a data file that
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defines EndBondTorsion Coeffs.
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E: Invalid data file section: AngleTorsion Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before AngleTorsion Coeffs
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Must use a dihedral_style command before reading a data file that
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defines AngleTorsion Coeffs.
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E: Invalid data file section: AngleAngleTorsion Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before AngleAngleTorsion Coeffs
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Must use a dihedral_style command before reading a data file that
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defines AngleAngleTorsion Coeffs.
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E: Invalid data file section: BondBond13 Coeffs
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Atom style does not allow dihedrals.
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E: Must define dihedral_style before BondBond13 Coeffs
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Must use a dihedral_style command before reading a data file that
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defines BondBond13 Coeffs.
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E: Invalid data file section: AngleAngle Coeffs
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Atom style does not allow impropers.
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E: Must define improper_style before AngleAngle Coeffs
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Must use an improper_style command before reading a data file that
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defines AngleAngle Coeffs.
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E: Unknown identifier in data file: %s
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A section of the data file cannot be read by LAMMPS.
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E: No atoms in data file
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The header of the data file indicated that atoms would be included,
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but they are not present.
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E: Needed molecular topology not in data file
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The header of the data file indicated bonds, angles, etc would be
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included, but they are not present.
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E: Needed bonus data not in data file
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Some atom styles require bonus data. See the read_data doc page for
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details.
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E: Read_data shrink wrap did not assign all atoms correctly
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This is typically because the box-size specified in the data file is
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large compared to the actual extent of atoms in a shrink-wrapped
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dimension. When LAMMPS shrink-wraps the box atoms will be lost if the
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processor they are re-assigned to is too far away. Choose a box
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size closer to the actual extent of the atoms.
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E: Unexpected end of data file
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LAMMPS hit the end of the data file while attempting to read a
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section. Something is wrong with the format of the data file.
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E: No ellipsoids allowed with this atom style
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Self-explanatory. Check data file.
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E: No lines allowed with this atom style
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Self-explanatory. Check data file.
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E: No triangles allowed with this atom style
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Self-explanatory. Check data file.
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E: No bodies allowed with this atom style
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Self-explanatory. Check data file.
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E: System in data file is too big
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See the setting for bigint in the src/lmptype.h file.
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E: Bonds defined but no bond types
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The data file header lists bonds but no bond types.
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E: Angles defined but no angle types
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The data file header lists angles but no angle types.
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E: Dihedrals defined but no dihedral types
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The data file header lists dihedrals but no dihedral types.
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E: Impropers defined but no improper types
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The data file header lists improper but no improper types.
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E: No molecule topology allowed with atom style template
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The data file cannot specify the number of bonds, angles, etc,
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because this info if inferred from the molecule templates.
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E: Did not assign all atoms correctly
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Atoms read in from a data file were not assigned correctly to
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processors. This is likely due to some atom coordinates being
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outside a non-periodic simulation box.
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E: Subsequent read data induced too many bonds per atom
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See the extra/bond/per/atom keyword for the create_box
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or the read_data command to set this limit larger.
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E: Bonds assigned incorrectly
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Bonds read in from the data file were not assigned correctly to atoms.
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This means there is something invalid about the topology definitions.
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E: Subsequent read data induced too many angles per atom
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See the extra/angle/per/atom keyword for the create_box
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or the read_data command to set this limit larger.
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E: Angles assigned incorrectly
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Angles read in from the data file were not assigned correctly to
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atoms. This means there is something invalid about the topology
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definitions.
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E: Subsequent read data induced too many dihedrals per atom
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See the extra/dihedral/per/atom keyword for the create_box
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or the read_data command to set this limit larger.
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E: Dihedrals assigned incorrectly
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Dihedrals read in from the data file were not assigned correctly to
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atoms. This means there is something invalid about the topology
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definitions.
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E: Subsequent read data induced too many impropers per atom
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See the extra/improper/per/atom keyword for the create_box
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or the read_data command to set this limit larger.
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E: Impropers assigned incorrectly
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Impropers read in from the data file were not assigned correctly to
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atoms. This means there is something invalid about the topology
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definitions.
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E: Too few values in body lines in data file
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Self-explanatory.
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E: Too many values in body lines in data file
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Self-explanatory.
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E: Too many lines in one body in data file - boost MAXBODY
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MAXBODY is a setting at the top of the src/read_data.cpp file.
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Set it larger and re-compile the code.
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E: Unexpected empty line in PairCoeffs section
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Read a blank line where there should be coefficient data.
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E: Unexpected empty line in BondCoeffs section
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Read a blank line where there should be coefficient data.
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E: Unexpected empty line in AngleCoeffs section
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Read a blank line where there should be coefficient data.
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E: Unexpected empty line in DihedralCoeffs section
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Read a blank line where there should be coefficient data.
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E: Unexpected empty line in ImproperCoeffs section
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Read a blank line where there should be coefficient data.
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E: Cannot open gzipped file
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LAMMPS was compiled without support for reading and writing gzipped
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files through a pipeline to the gzip program with -DLAMMPS_GZIP.
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E: Cannot open file %s
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The specified file cannot be opened. Check that the path and name are
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correct. If the file is a compressed file, also check that the gzip
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executable can be found and run.
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U: Read data add offset is too big
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It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit
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integer.
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*/
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