/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #ifdef COMMAND_CLASS CommandStyle(read_data,ReadData) #else #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H #include "pointers.h" namespace LAMMPS_NS { class ReadData : protected Pointers { public: ReadData(class LAMMPS *); ~ReadData(); void command(int, char **); private: int me,compressed; char *line,*keyword,*buffer,*style; FILE *fp; char **coeffarg; int ncoeffarg,maxcoeffarg; char argoffset1[8],argoffset2[8]; bigint id_offset, mol_offset; int nlocal_previous; bigint natoms; bigint nbonds,nangles,ndihedrals,nimpropers; int ntypes; int nbondtypes,nangletypes,ndihedraltypes,nimpropertypes; bigint nellipsoids; class AtomVecEllipsoid *avec_ellipsoid; bigint nlines; class AtomVecLine *avec_line; bigint ntris; class AtomVecTri *avec_tri; bigint nbodies; class AtomVecBody *avec_body; // box info double boxlo[3],boxhi[3]; double xy,xz,yz; int triclinic; // optional args int addflag,offsetflag,shiftflag,coeffflag; tagint addvalue; int toffset,boffset,aoffset,doffset,ioffset; double shift[3]; int extra_atom_types,extra_bond_types,extra_angle_types; int extra_dihedral_types,extra_improper_types; int groupbit; int nfix; int *fix_index; char **fix_header; char **fix_section; // methods void open(char *); void scan(int &, int &, int &, int &); int reallocate(int **, int, int); void header(int); void parse_keyword(int); void skip_lines(bigint); void parse_coeffs(char *, const char *, int, int, int); int style_match(const char *, const char *); void atoms(); void velocities(); void bonds(int); void bond_scan(int, char *, int *); void angles(int); void dihedrals(int); void impropers(int); void bonus(bigint, class AtomVec *, const char *); void bodies(int, class AtomVec *); void mass(); void paircoeffs(); void pairIJcoeffs(); void bondcoeffs(); void anglecoeffs(int); void dihedralcoeffs(int); void impropercoeffs(int); void fix(int, char *); }; } #endif #endif /* ERROR/WARNING messages: E: Illegal ... command Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. E: Read data add atomID offset is too big UNDOCUMENTED E: Read data add molID offset is too big UNDOCUMENTED E: Non-zero read_data shift z value for 2d simulation Self-explanatory. E: No bonds allowed with this atom style Self-explanatory. E: No angles allowed with this atom style Self-explanatory. E: No dihedrals allowed with this atom style Self-explanatory. E: No impropers allowed with this atom style Self-explanatory. E: No bonded interactions allowed with this atom style UNDOCUMENTED E: Fix ID for read_data does not exist Self-explanatory. E: Cannot run 2d simulation with non-periodic Z dimension Use the boundary command to make the z dimension periodic in order to run a 2d simulation. E: Cannot read_data without add keyword after simulation box is defined Self-explanatory. E: Cannot use read_data add before simulation box is defined Self-explanatory. E: Cannot use read_data offset without add flag Self-explanatory. E: Cannot use read_data shift without add flag Self-explanatory. E: Cannot use read_data extra with add flag Self-explanatory. W: Atom style in data file differs from currently defined atom style Self-explanatory. E: Must read Atoms before Velocities The Atoms section of a data file must come before a Velocities section. E: Invalid data file section: Bonds Atom style does not allow bonds. E: Must read Atoms before Bonds The Atoms section of a data file must come before a Bonds section. E: Invalid data file section: Angles Atom style does not allow angles. E: Must read Atoms before Angles The Atoms section of a data file must come before an Angles section. E: Invalid data file section: Dihedrals Atom style does not allow dihedrals. E: Must read Atoms before Dihedrals The Atoms section of a data file must come before a Dihedrals section. E: Invalid data file section: Impropers Atom style does not allow impropers. E: Must read Atoms before Impropers The Atoms section of a data file must come before an Impropers section. E: Invalid data file section: Ellipsoids Atom style does not allow ellipsoids. E: Must read Atoms before Ellipsoids The Atoms section of a data file must come before a Ellipsoids section. E: Invalid data file section: Lines Atom style does not allow lines. E: Must read Atoms before Lines The Atoms section of a data file must come before a Lines section. E: Invalid data file section: Triangles Atom style does not allow triangles. E: Must read Atoms before Triangles The Atoms section of a data file must come before a Triangles section. E: Invalid data file section: Bodies Atom style does not allow bodies. E: Must read Atoms before Bodies The Atoms section of a data file must come before a Bodies section. E: Must define pair_style before Pair Coeffs Must use a pair_style command before reading a data file that defines Pair Coeffs. W: Pair style in data file differs from currently defined pair style Self-explanatory. E: Must define pair_style before PairIJ Coeffs Must use a pair_style command before reading a data file that defines PairIJ Coeffs. E: Invalid data file section: Bond Coeffs Atom style does not allow bonds. E: Must define bond_style before Bond Coeffs Must use a bond_style command before reading a data file that defines Bond Coeffs. W: Bond style in data file differs from currently defined bond style Self-explanatory. E: Invalid data file section: Angle Coeffs Atom style does not allow angles. E: Must define angle_style before Angle Coeffs Must use an angle_style command before reading a data file that defines Angle Coeffs. W: Angle style in data file differs from currently defined angle style Self-explanatory. E: Invalid data file section: Dihedral Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before Dihedral Coeffs Must use a dihedral_style command before reading a data file that defines Dihedral Coeffs. W: Dihedral style in data file differs from currently defined dihedral style Self-explanatory. E: Invalid data file section: Improper Coeffs Atom style does not allow impropers. E: Must define improper_style before Improper Coeffs Must use an improper_style command before reading a data file that defines Improper Coeffs. W: Improper style in data file differs from currently defined improper style Self-explanatory. E: Invalid data file section: BondBond Coeffs Atom style does not allow angles. E: Must define angle_style before BondBond Coeffs Must use an angle_style command before reading a data file that defines Angle Coeffs. E: Invalid data file section: BondAngle Coeffs Atom style does not allow angles. E: Must define angle_style before BondAngle Coeffs Must use an angle_style command before reading a data file that defines Angle Coeffs. E: Invalid data file section: MiddleBondTorsion Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before MiddleBondTorsion Coeffs Must use a dihedral_style command before reading a data file that defines MiddleBondTorsion Coeffs. E: Invalid data file section: EndBondTorsion Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before EndBondTorsion Coeffs Must use a dihedral_style command before reading a data file that defines EndBondTorsion Coeffs. E: Invalid data file section: AngleTorsion Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before AngleTorsion Coeffs Must use a dihedral_style command before reading a data file that defines AngleTorsion Coeffs. E: Invalid data file section: AngleAngleTorsion Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before AngleAngleTorsion Coeffs Must use a dihedral_style command before reading a data file that defines AngleAngleTorsion Coeffs. E: Invalid data file section: BondBond13 Coeffs Atom style does not allow dihedrals. E: Must define dihedral_style before BondBond13 Coeffs Must use a dihedral_style command before reading a data file that defines BondBond13 Coeffs. E: Invalid data file section: AngleAngle Coeffs Atom style does not allow impropers. E: Must define improper_style before AngleAngle Coeffs Must use an improper_style command before reading a data file that defines AngleAngle Coeffs. E: Unknown identifier in data file: %s A section of the data file cannot be read by LAMMPS. E: No atoms in data file The header of the data file indicated that atoms would be included, but they are not present. E: Needed molecular topology not in data file The header of the data file indicated bonds, angles, etc would be included, but they are not present. E: Needed bonus data not in data file Some atom styles require bonus data. See the read_data doc page for details. E: Read_data shrink wrap did not assign all atoms correctly This is typically because the box-size specified in the data file is large compared to the actual extent of atoms in a shrink-wrapped dimension. When LAMMPS shrink-wraps the box atoms will be lost if the processor they are re-assigned to is too far away. Choose a box size closer to the actual extent of the atoms. E: Unexpected end of data file LAMMPS hit the end of the data file while attempting to read a section. Something is wrong with the format of the data file. E: No ellipsoids allowed with this atom style Self-explanatory. Check data file. E: No lines allowed with this atom style Self-explanatory. Check data file. E: No triangles allowed with this atom style Self-explanatory. Check data file. E: No bodies allowed with this atom style Self-explanatory. Check data file. E: System in data file is too big See the setting for bigint in the src/lmptype.h file. E: Bonds defined but no bond types The data file header lists bonds but no bond types. E: Angles defined but no angle types The data file header lists angles but no angle types. E: Dihedrals defined but no dihedral types The data file header lists dihedrals but no dihedral types. E: Impropers defined but no improper types The data file header lists improper but no improper types. E: No molecule topology allowed with atom style template The data file cannot specify the number of bonds, angles, etc, because this info if inferred from the molecule templates. E: Did not assign all atoms correctly Atoms read in from a data file were not assigned correctly to processors. This is likely due to some atom coordinates being outside a non-periodic simulation box. E: Subsequent read data induced too many bonds per atom See the extra/bond/per/atom keyword for the create_box or the read_data command to set this limit larger. E: Bonds assigned incorrectly Bonds read in from the data file were not assigned correctly to atoms. This means there is something invalid about the topology definitions. E: Subsequent read data induced too many angles per atom See the extra/angle/per/atom keyword for the create_box or the read_data command to set this limit larger. E: Angles assigned incorrectly Angles read in from the data file were not assigned correctly to atoms. This means there is something invalid about the topology definitions. E: Subsequent read data induced too many dihedrals per atom See the extra/dihedral/per/atom keyword for the create_box or the read_data command to set this limit larger. E: Dihedrals assigned incorrectly Dihedrals read in from the data file were not assigned correctly to atoms. This means there is something invalid about the topology definitions. E: Subsequent read data induced too many impropers per atom See the extra/improper/per/atom keyword for the create_box or the read_data command to set this limit larger. E: Impropers assigned incorrectly Impropers read in from the data file were not assigned correctly to atoms. This means there is something invalid about the topology definitions. E: Too few values in body lines in data file Self-explanatory. E: Too many values in body lines in data file Self-explanatory. E: Too many lines in one body in data file - boost MAXBODY MAXBODY is a setting at the top of the src/read_data.cpp file. Set it larger and re-compile the code. E: Unexpected empty line in PairCoeffs section Read a blank line where there should be coefficient data. E: Unexpected empty line in BondCoeffs section Read a blank line where there should be coefficient data. E: Unexpected empty line in AngleCoeffs section Read a blank line where there should be coefficient data. E: Unexpected empty line in DihedralCoeffs section Read a blank line where there should be coefficient data. E: Unexpected empty line in ImproperCoeffs section Read a blank line where there should be coefficient data. E: Cannot open gzipped file LAMMPS was compiled without support for reading and writing gzipped files through a pipeline to the gzip program with -DLAMMPS_GZIP. E: Cannot open file %s The specified file cannot be opened. Check that the path and name are correct. If the file is a compressed file, also check that the gzip executable can be found and run. U: Read data add offset is too big It cannot be larger than the size of atom IDs, e.g. the maximum 32-bit integer. */