417 lines
11 KiB
C++
417 lines
11 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 DUMP_CLASS
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// clang-format off
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DumpStyle(custom,DumpCustom);
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// clang-format on
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#else
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#ifndef LMP_DUMP_CUSTOM_H
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#define LMP_DUMP_CUSTOM_H
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#include "dump.h"
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namespace LAMMPS_NS {
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class DumpCustom : public Dump {
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public:
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DumpCustom(class LAMMPS *, int, char **);
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~DumpCustom() override;
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const char *MAGIC_STRING = "DUMPCUSTOM";
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const int FORMAT_REVISION = 0x0002;
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const int ENDIAN = 0x0001;
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protected:
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int nevery; // dump frequency for output
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int iregion; // -1 if no region, else which region
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char *idregion; // region ID
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int nthresh; // # of defined thresholds
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int nthreshlast; // # of defined thresholds with value = LAST
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//
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int *thresh_array; // array to threshold on for each nthresh
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int *thresh_op; // threshold operation for each nthresh
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double *thresh_value; // threshold value for each nthresh
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int *thresh_last; // for threshold value = LAST,
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// index into thresh_fix
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// -1 if not LAST, value is numeric
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//
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class FixStore **thresh_fix; // stores values for each threshold LAST
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char **thresh_fixID; // IDs of thresh_fixes
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int *thresh_first; // 1 the first time a FixStore values accessed
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int expand; // flag for whether field args were expanded
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char **earg; // field names with wildcard expansion
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int nargnew; // size of earg
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//
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int *vtype; // type of each vector (INT, DOUBLE)
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char **vformat; // format string for each vector element
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//
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char *columns; // column labels
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//
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int nchoose; // # of selected atoms
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int maxlocal; // size of atom selection and variable arrays
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int *choose; // local indices of selected atoms
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double *dchoose; // value for each atom to threshold against
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int *clist; // compressed list of indices of selected atoms
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int nfield; // # of keywords listed by user
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int ioptional; // index of start of optional args
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//
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int *field2index; // which compute,fix,variable,custom calcs this field
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int *argindex; // index into compute,fix,custom per-atom data
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// 0 for per-atom vector, 1-N for cols of per-atom array
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//
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int ncompute; // # of Computes accessed by dump
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char **id_compute; // their IDs
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class Compute **compute; // list of ptrs to the Computes
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//
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int nfix; // # of Fixes used by dump
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char **id_fix; // their IDs
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class Fix **fix; // list of ptrs to the Fixes
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//
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int nvariable; // # of Variables used by dump
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char **id_variable; // their names
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int *variable; // list of Variable indices in Variable class
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double **vbuf; // local storage for variable evaluation
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//
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int ncustom; // # of Custom atom properties used by dump
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char **id_custom; // their names
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int *custom; // list of Custom indices in Atom class
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int *custom_flag; // list of IVEC,DVEC,IARRAY,DARRAY styles
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//
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int ntypes; // # of atom types
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char **typenames; // array of element names for each type
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// private methods
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void init_style() override;
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void write_header(bigint) override;
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int count() override;
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void pack(tagint *) override;
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int convert_string(int, double *) override;
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void write_data(int, double *) override;
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double memory_usage() override;
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int parse_fields(int, char **);
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int add_compute(const char *);
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int add_fix(const char *);
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int add_variable(const char *);
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int add_custom(const char *, int);
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int modify_param(int, char **) override;
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void header_format_binary();
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void header_unit_style_binary();
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void header_time_binary();
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void header_columns_binary();
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void format_magic_string_binary();
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void format_endian_binary();
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void format_revision_binary();
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typedef void (DumpCustom::*FnPtrHeader)(bigint);
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FnPtrHeader header_choice; // ptr to write header functions
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void header_binary(bigint);
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void header_binary_triclinic(bigint);
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void header_item(bigint);
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void header_item_triclinic(bigint);
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typedef int (DumpCustom::*FnPtrConvert)(int, double *);
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FnPtrConvert convert_choice; // ptr to convert data functions
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int convert_image(int, double *);
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int convert_noimage(int, double *);
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typedef void (DumpCustom::*FnPtrWrite)(int, double *);
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FnPtrWrite write_choice; // ptr to write data functions
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void write_binary(int, double *);
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void write_string(int, double *);
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void write_lines(int, double *);
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// customize by adding a method prototype
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typedef void (DumpCustom::*FnPtrPack)(int);
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FnPtrPack *pack_choice; // ptrs to pack functions
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void pack_compute(int);
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void pack_fix(int);
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void pack_variable(int);
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void pack_custom(int);
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void pack_id(int);
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void pack_molecule(int);
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void pack_proc(int);
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void pack_procp1(int);
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void pack_type(int);
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void pack_mass(int);
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void pack_x(int);
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void pack_y(int);
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void pack_z(int);
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void pack_xs(int);
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void pack_ys(int);
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void pack_zs(int);
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void pack_xs_triclinic(int);
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void pack_ys_triclinic(int);
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void pack_zs_triclinic(int);
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void pack_xu(int);
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void pack_yu(int);
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void pack_zu(int);
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void pack_xu_triclinic(int);
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void pack_yu_triclinic(int);
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void pack_zu_triclinic(int);
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void pack_xsu(int);
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void pack_ysu(int);
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void pack_zsu(int);
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void pack_xsu_triclinic(int);
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void pack_ysu_triclinic(int);
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void pack_zsu_triclinic(int);
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void pack_ix(int);
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void pack_iy(int);
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void pack_iz(int);
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void pack_vx(int);
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void pack_vy(int);
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void pack_vz(int);
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void pack_fx(int);
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void pack_fy(int);
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void pack_fz(int);
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void pack_q(int);
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void pack_mux(int);
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void pack_muy(int);
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void pack_muz(int);
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void pack_mu(int);
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void pack_radius(int);
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void pack_diameter(int);
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void pack_omegax(int);
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void pack_omegay(int);
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void pack_omegaz(int);
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void pack_angmomx(int);
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void pack_angmomy(int);
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void pack_angmomz(int);
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void pack_tqx(int);
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void pack_tqy(int);
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void pack_tqz(int);
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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: No dump custom arguments specified
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The dump custom command requires that atom quantities be specified to
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output to dump file.
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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: Invalid attribute in dump custom command
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Self-explanatory.
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E: Dump_modify format line is too short
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UNDOCUMENTED
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E: Could not find dump custom compute ID
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Self-explanatory.
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E: Could not find dump custom fix ID
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Self-explanatory.
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E: Dump custom and fix not computed at compatible times
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The fix must produce per-atom quantities on timesteps that dump custom
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needs them.
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E: Could not find dump custom variable name
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Self-explanatory.
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E: Could not find custom per-atom property ID
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Self-explanatory.
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E: Region ID for dump custom does not exist
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Self-explanatory.
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E: Compute used in dump between runs is not current
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The compute was not invoked on the current timestep, therefore it
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cannot be used in a dump between runs.
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E: Threshold for an atom property that isn't allocated
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A dump threshold has been requested on a quantity that is
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not defined by the atom style used in this simulation.
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E: Dumping an atom property that isn't allocated
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The chosen atom style does not define the per-atom quantity being
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dumped.
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E: Dump custom compute does not compute per-atom info
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Self-explanatory.
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E: Dump custom compute does not calculate per-atom vector
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Self-explanatory.
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E: Dump custom compute does not calculate per-atom array
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Self-explanatory.
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E: Dump custom compute vector is accessed out-of-range
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Self-explanatory.
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E: Dump custom fix does not compute per-atom info
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Self-explanatory.
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E: Dump custom fix does not compute per-atom vector
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Self-explanatory.
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E: Dump custom fix does not compute per-atom array
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Self-explanatory.
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E: Dump custom fix vector is accessed out-of-range
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Self-explanatory.
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E: Dump custom variable is not atom-style variable
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Only atom-style variables generate per-atom quantities, needed for
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dump output.
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E: Custom per-atom property ID is not floating point
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Self-explanatory.
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E: Custom per-atom property ID is not integer
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Self-explanatory.
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E: Dump_modify region ID does not exist
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Self-explanatory.
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E: Dump_modify int format does not contain d character
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UNDOCUMENTED
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E: Dump_modify element names do not match atom types
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UNDOCUMENTED
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E: Dump modify can only have one refresh
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UNDOCUMENTED
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E: Invalid attribute in dump modify command
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Self-explanatory.
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E: Could not find dump modify compute ID
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Self-explanatory.
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E: Dump modify compute ID does not compute per-atom info
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Self-explanatory.
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E: Dump modify compute ID does not compute per-atom vector
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Self-explanatory.
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E: Dump modify compute ID does not compute per-atom array
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Self-explanatory.
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E: Dump modify compute ID vector is not large enough
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Self-explanatory.
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E: Could not find dump modify fix ID
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Self-explanatory.
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E: Dump modify fix ID does not compute per-atom info
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Self-explanatory.
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E: Dump modify fix ID does not compute per-atom vector
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Self-explanatory.
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E: Dump modify fix ID does not compute per-atom array
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Self-explanatory.
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E: Dump modify fix ID vector is not large enough
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Self-explanatory.
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E: Could not find dump modify variable name
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Self-explanatory.
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E: Dump modify variable is not atom-style variable
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Self-explanatory.
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E: Could not find dump modify custom atom floating point property ID
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Self-explanatory.
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E: Could not find dump modify custom atom integer property ID
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Self-explanatory.
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E: Invalid dump_modify thresh attribute
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UNDOCUMENTED
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E: Invalid dump_modify thresh operator
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UNDOCUMENTED
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U: Dump_modify format string is too short
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There are more fields to be dumped in a line of output than your
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format string specifies.
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U: Dump modify element names do not match atom types
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Number of element names must equal number of atom types.
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U: Invalid dump_modify threshold operator
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Operator keyword used for threshold specification in not recognized.
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*/
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