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dump_custom_vtk.h
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dump_custom_vtk.h
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/* ----------------------------------------------------------------------
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.
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Daniel Queteschiner (DCS, JKU)
Christoph Kloss (DCS)
Richard Berger (JKU)
------------------------------------------------------------------------- */
#ifdef DUMP_CLASS
DumpStyle(custom/vtk,DumpCustomVTK)
#else
#ifndef LMP_DUMP_CUSTOM_VTK_H
#define LMP_DUMP_CUSTOM_VTK_H
#include "dump.h"
#include <map>
#include <set>
#include <string>
#include <vtkSmartPointer.h>
#include <vtkPoints.h>
#include <vtkCellArray.h>
class vtkAbstractArray;
class vtkRectilinearGrid;
class vtkUnstructuredGrid;
namespace LAMMPS_NS {
/**
* @brief DumpCustomVTK 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 DumpCustomVTK : public Dump {
public:
DumpCustomVTK(class LAMMPS *, int, char **);
virtual ~DumpCustomVTK();
virtual void write();
protected:
int nevery; // dump frequency for output
char *label; // string for dump file header
int iregion; // -1 if no region, else which region
char *idregion; // region ID
int nthresh; // # of defined thresholds
int *thresh_array; // array to threshold on for each nthresh
int *thresh_op; // threshold operation for each nthresh
double *thresh_value; // threshold value for each nthresh
int vtk_file_format; // which vtk file format to write (vtk, vtp, vtu ...)
int nchoose; // # of selected atoms
int maxlocal; // size of atom selection and variable arrays
int *choose; // local indices of selected atoms
double *dchoose; // value for each atom to threshhold against
int *clist; // compressed list of indices of selected atoms
int nfield; // # of keywords listed by user
int ioptional; // index of start of optional args
std::map<int, int> field2index; // which compute,fix,variable calcs this field
std::map<int, int> argindex; // index into compute,fix scalar_atom,vector_atom
// 0 for scalar_atom, 1-N for vector_atom values
int ncompute; // # of Compute objects used by dump
char **id_compute; // their IDs
class Compute **compute; // list of ptrs to the Compute objects
int nfix; // # of Fix objects used by dump
char **id_fix; // their IDs
class Fix **fix; // list of ptrs to the Fix objects
int nvariable; // # of Variables used by dump
char **id_variable; // their names
int *variable; // list of indices for the Variables
double **vbuf; // local storage for variable evaluation
int ncustom; // # of custom atom properties
char **id_custom; // their names
int *flag_custom; // their data type
int ntypes; // # of atom types
char **typenames; // array of element names for each type
// private methods
virtual void init_style();
virtual void write_header(bigint);
int count();
void pack(int *);
virtual void write_data(int, double *);
bigint memory_usage();
int parse_fields(int, char **);
void identify_vectors();
int add_compute(char *);
int add_fix(char *);
int add_variable(char *);
int add_custom(char *, int);
virtual int modify_param(int, char **);
typedef void (DumpCustomVTK::*FnPtrHeader)(bigint);
FnPtrHeader header_choice; // ptr to write header functions
void header_vtk(bigint);
typedef void (DumpCustomVTK::*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 (DumpCustomVTK::*FnPtrPack)(int);
std::map<int, FnPtrPack> pack_choice; // ptrs to pack functions
std::map<int, int> vtype; // data type
std::map<int, std::string> name; // attribute labels
std::set<int> vector_set; // set of vector attributes
int current_pack_choice_key;
// vtk data containers
vtkSmartPointer<vtkPoints> points;
vtkSmartPointer<vtkCellArray> pointsCells;
std::map<int, vtkSmartPointer<vtkAbstractArray> > 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);
void pack_id(int);
void pack_molecule(int);
void pack_type(int);
void pack_mass(int);
void pack_x(int);
void pack_y(int);
void pack_z(int);
void pack_xs(int);
void pack_ys(int);
void pack_zs(int);
void pack_xs_triclinic(int);
void pack_ys_triclinic(int);
void pack_zs_triclinic(int);
void pack_xu(int);
void pack_yu(int);
void pack_zu(int);
void pack_xu_triclinic(int);
void pack_yu_triclinic(int);
void pack_zu_triclinic(int);
void pack_xsu(int);
void pack_ysu(int);
void pack_zsu(int);
void pack_xsu_triclinic(int);
void pack_ysu_triclinic(int);
void pack_zsu_triclinic(int);
void pack_ix(int);
void pack_iy(int);
void pack_iz(int);
void pack_vx(int);
void pack_vy(int);
void pack_vz(int);
void pack_fx(int);
void pack_fy(int);
void pack_fz(int);
void pack_q(int);
void pack_mux(int);
void pack_muy(int);
void pack_muz(int);
void pack_mu(int);
void pack_radius(int);
void pack_diameter(int);
void pack_omegax(int);
void pack_omegay(int);
void pack_omegaz(int);
void pack_angmomx(int);
void pack_angmomy(int);
void pack_angmomz(int);
void pack_tqx(int);
void pack_tqy(int);
void pack_tqz(int);
};
}
#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-explantory.
E: Could not find dump custom compute ID
The compute ID needed by dump custom to compute a per-atom quantity
does not exist.
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: Region ID for dump custom does not exist
Self-explanatory.
E: Threshhold for an atom property that isn't allocated
A dump threshhold 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: Dumping an atom quantity that isn't allocated
Only per-atom quantities that are defined for the atom style being
used are allowed.
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: 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-explantory.
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: Invalid dump_modify threshhold operator
Operator keyword used for threshold specification in not recognized.
*/

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