/* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, 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. This file initially came from LIGGGHTS (www.liggghts.com) Copyright (2014) DCS Computing GmbH, Linz Copyright (2015) Johannes Kepler University Linz See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #ifdef DUMP_CLASS // clang-format off DumpStyle(vtk,DumpVTK); // clang-format on #else #ifndef LMP_DUMP_VTK_H #define LMP_DUMP_VTK_H #include "dump_custom.h" #include #include #include #include #include class vtkAbstractArray; class vtkRectilinearGrid; class vtkUnstructuredGrid; namespace LAMMPS_NS { /** * @brief DumpVTK class * write atom data to vtk files. * * Similar to the DumpCustom class but uses the vtk library to write data to vtk simple * legacy or xml format depending on the filename extension specified. (Since this * conflicts with the way binary output is specified, dump_modify allows to set the * binary flag for this dump command explicitly). * In contrast to DumpCustom class the attributes to be packed are stored in a std::map * to avoid duplicate entries and enforce correct ordering of vector components (except * for computes and fixes - these have to be given in the right order in the input script). * (Note: std::map elements are sorted by their keys.) * This dump command does not support compressed files, buffering or custom format strings, * multiproc is only supported by the xml formats, multifile option has to be used. */ class DumpVTK : public DumpCustom { public: DumpVTK(class LAMMPS *, int, char **); ~DumpVTK() override; void write() override; protected: char *label; // string for dump file header int vtk_file_format; // which vtk file format to write (vtk, vtp, vtu ...) std::map field2index; // which compute,fix,variable calcs this field std::map argindex; // index into compute,fix scalar_atom,vector_atom // 0 for scalar_atom, 1-N for vector_atom values // private methods void init_style() override; void write_header(bigint) override; int count() override; void pack(tagint *) override; void write_data(int, double *) override; double memory_usage() override; int parse_fields(int, char **); void identify_vectors(); int add_compute(const char *); int add_fix(const char *); int add_variable(const char *); int add_custom(const char *, int); int modify_param(int, char **) override; typedef void (DumpVTK::*FnPtrHeader)(bigint); FnPtrHeader header_choice; // ptr to write header functions void header_vtk(bigint); typedef void (DumpVTK::*FnPtrWrite)(int, double *); FnPtrWrite write_choice; // ptr to write data functions void write_vtk(int, double *); void write_vtp(int, double *); void write_vtu(int, double *); void prepare_domain_data(vtkRectilinearGrid *); void prepare_domain_data_triclinic(vtkUnstructuredGrid *); void write_domain_vtk(); void write_domain_vtk_triclinic(); void write_domain_vtr(); void write_domain_vtu_triclinic(); typedef void (DumpVTK::*FnPtrPack)(int); std::map pack_choice; // ptrs to pack functions std::map vtype; // data type std::map name; // attribute labels std::set vector_set; // set of vector attributes int current_pack_choice_key; // vtk data containers vtkSmartPointer points; vtkSmartPointer pointsCells; std::map> myarrays; int n_calls_; double (*boxcorners)[3]; // corners of triclinic domain box char *filecurrent; char *domainfilecurrent; char *parallelfilecurrent; char *multiname_ex; void setFileCurrent(); void buf2arrays(int, double *); // transfer data from buf array to vtk arrays void reset_vtk_data_containers(); // customize by adding a method prototype void pack_compute(int); void pack_fix(int); void pack_variable(int); void pack_custom(int); }; } // namespace LAMMPS_NS #endif #endif /* ERROR/WARNING messages: E: No dump custom arguments specified The dump custom command requires that atom quantities be specified to output to dump file. E: Invalid attribute in dump custom command Self-explanatory. E: Dump_modify format string is too short There are more fields to be dumped in a line of output than your format string specifies. E: Could not find dump custom compute ID Self-explanatory. E: Could not find dump custom fix ID Self-explanatory. E: Dump custom and fix not computed at compatible times The fix must produce per-atom quantities on timesteps that dump custom needs them. E: Could not find dump custom variable name Self-explanatory. E: Could not find custom per-atom property ID Self-explanatory. E: Region ID for dump custom does not exist Self-explanatory. E: Compute used in dump between runs is not current The compute was not invoked on the current timestep, therefore it cannot be used in a dump between runs. E: Threshold for an atom property that isn't allocated A dump threshold has been requested on a quantity that is not defined by the atom style used in this simulation. E: Dumping an atom property that isn't allocated The chosen atom style does not define the per-atom quantity being dumped. E: Dump custom compute does not compute per-atom info Self-explanatory. E: Dump custom compute does not calculate per-atom vector Self-explanatory. E: Dump custom compute does not calculate per-atom array Self-explanatory. E: Dump custom compute vector is accessed out-of-range Self-explanatory. E: Dump custom fix does not compute per-atom info Self-explanatory. E: Dump custom fix does not compute per-atom vector Self-explanatory. E: Dump custom fix does not compute per-atom array Self-explanatory. E: Dump custom fix vector is accessed out-of-range Self-explanatory. E: Dump custom variable is not atom-style variable Only atom-style variables generate per-atom quantities, needed for dump output. E: Custom per-atom property ID is not floating point Self-explanatory. E: Custom per-atom property ID is not integer Self-explanatory. 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: Dump_modify region ID does not exist Self-explanatory. E: Dump modify element names do not match atom types Number of element names must equal number of atom types. E: Invalid attribute in dump modify command Self-explanatory. E: Could not find dump modify compute ID Self-explanatory. E: Dump modify compute ID does not compute per-atom info Self-explanatory. E: Dump modify compute ID does not compute per-atom vector Self-explanatory. E: Dump modify compute ID does not compute per-atom array Self-explanatory. E: Dump modify compute ID vector is not large enough Self-explanatory. E: Could not find dump modify fix ID Self-explanatory. E: Dump modify fix ID does not compute per-atom info Self-explanatory. E: Dump modify fix ID does not compute per-atom vector Self-explanatory. E: Dump modify fix ID does not compute per-atom array Self-explanatory. E: Dump modify fix ID vector is not large enough Self-explanatory. E: Could not find dump modify variable name Self-explanatory. E: Dump modify variable is not atom-style variable Self-explanatory. E: Could not find dump modify custom atom floating point property ID Self-explanatory. E: Could not find dump modify custom atom integer property ID Self-explanatory. E: Invalid dump_modify threshold operator Operator keyword used for threshold specification in not recognized. */