322 lines
8.2 KiB
C++
322 lines
8.2 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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This file initially came from LIGGGHTS (www.liggghts.com)
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Copyright (2014) DCS Computing GmbH, Linz
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Copyright (2015) Johannes Kepler University Linz
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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(vtk,DumpVTK);
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// clang-format on
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#else
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#ifndef LMP_DUMP_VTK_H
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#define LMP_DUMP_VTK_H
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#include "dump_custom.h"
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#include <map>
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#include <set>
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#include <vtkCellArray.h>
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#include <vtkPoints.h>
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#include <vtkSmartPointer.h>
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class vtkAbstractArray;
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class vtkRectilinearGrid;
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class vtkUnstructuredGrid;
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namespace LAMMPS_NS {
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/**
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* @brief DumpVTK class
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* write atom data to vtk files.
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*
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* Similar to the DumpCustom class but uses the vtk library to write data to vtk simple
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* legacy or xml format depending on the filename extension specified. (Since this
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* conflicts with the way binary output is specified, dump_modify allows to set the
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* binary flag for this dump command explicitly).
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* In contrast to DumpCustom class the attributes to be packed are stored in a std::map
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* to avoid duplicate entries and enforce correct ordering of vector components (except
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* for computes and fixes - these have to be given in the right order in the input script).
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* (Note: std::map elements are sorted by their keys.)
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* This dump command does not support compressed files, buffering or custom format strings,
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* multiproc is only supported by the xml formats, multifile option has to be used.
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*/
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class DumpVTK : public DumpCustom {
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public:
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DumpVTK(class LAMMPS *, int, char **);
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~DumpVTK() override;
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void write() override;
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protected:
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char *label; // string for dump file header
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int vtk_file_format; // which vtk file format to write (vtk, vtp, vtu ...)
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std::map<int, int> field2index; // which compute,fix,variable calcs this field
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std::map<int, int> argindex; // index into compute,fix scalar_atom,vector_atom
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// 0 for scalar_atom, 1-N for vector_atom values
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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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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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void identify_vectors();
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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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typedef void (DumpVTK::*FnPtrHeader)(bigint);
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FnPtrHeader header_choice; // ptr to write header functions
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void header_vtk(bigint);
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typedef void (DumpVTK::*FnPtrWrite)(int, double *);
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FnPtrWrite write_choice; // ptr to write data functions
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void write_vtk(int, double *);
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void write_vtp(int, double *);
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void write_vtu(int, double *);
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void prepare_domain_data(vtkRectilinearGrid *);
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void prepare_domain_data_triclinic(vtkUnstructuredGrid *);
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void write_domain_vtk();
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void write_domain_vtk_triclinic();
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void write_domain_vtr();
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void write_domain_vtu_triclinic();
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typedef void (DumpVTK::*FnPtrPack)(int);
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std::map<int, FnPtrPack> pack_choice; // ptrs to pack functions
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std::map<int, int> vtype; // data type
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std::map<int, std::string> name; // attribute labels
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std::set<int> vector_set; // set of vector attributes
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int current_pack_choice_key;
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// vtk data containers
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vtkSmartPointer<vtkPoints> points;
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vtkSmartPointer<vtkCellArray> pointsCells;
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std::map<int, vtkSmartPointer<vtkAbstractArray>> myarrays;
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int n_calls_;
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double (*boxcorners)[3]; // corners of triclinic domain box
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char *filecurrent;
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char *domainfilecurrent;
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char *parallelfilecurrent;
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char *multiname_ex;
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void setFileCurrent();
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void buf2arrays(int, double *); // transfer data from buf array to vtk arrays
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void reset_vtk_data_containers();
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// customize by adding a method prototype
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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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};
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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: Invalid attribute in dump custom command
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Self-explanatory.
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E: 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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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: 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: Dump_modify region ID does not exist
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Self-explanatory.
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E: 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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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 threshold operator
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Operator keyword used for threshold specification in not recognized.
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*/
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