forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14633 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
52ca6416a0
commit
53b3a4aec0
|
|
@ -50,11 +50,12 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
|
|||
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
|
||||
user-intel user-lb user-mgpt \
|
||||
user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
|
||||
user-quip user-reaxc user-smd user-smtbq user-sph user-tally
|
||||
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
|
||||
user-vtk
|
||||
|
||||
PACKLIB = compress gpu kim kokkos meam poems python reax voronoi \
|
||||
user-atc user-awpmd user-colvars user-cuda user-h5md user-molfile \
|
||||
user-qmmm user-quip
|
||||
user-qmmm user-quip user-vtk
|
||||
|
||||
PACKALL = $(PACKAGE) $(PACKUSER)
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,61 @@
|
|||
# Install/unInstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
|
||||
mode=$1
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
action $file
|
||||
done
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
if (test $1 = 1) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*vtk[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/vtk\/include |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/vtk |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(vtk_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(vtk_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(vtk_SYSPATH) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ..\/..\/lib\/vtk\/Makefile.lammps
|
||||
' ../Makefile.package.settings
|
||||
|
||||
fi
|
||||
|
||||
elif (test $1 = 0) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*vtk[^ \t]* //g' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*vtk.*$/d' ../Makefile.package.settings
|
||||
fi
|
||||
|
||||
fi
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
This package implements the "dump custom/vtk" command which can be used in a
|
||||
LAMMPS input script.
|
||||
|
||||
This dump allows to output atom data similar to dump custom, but directly into
|
||||
VTK files.
|
||||
|
||||
This package uses the VTK library (www.vtk.org) which must be installed on your
|
||||
system. See the lib/vtk/README file and the LAMMPS manual for information on
|
||||
building LAMMPS with external libraries. The settings in the Makefile.lammps
|
||||
file in that directory must be correct for LAMMPS to build correctly with this
|
||||
package installed.
|
||||
|
||||
This code was initially developed for LIGGGHTS by Daniel Queteschiner at DCS
|
||||
Computing. This is an effort to integrate it back to LAMMPS.
|
||||
|
||||
The person who created this package is Richard Berger at JKU
|
||||
(richard.berger@jku.at). Contact him directly if you have questions.
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,320 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
|
||||
DumpStyle(custom/vtk,DumpCustomVTK)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DUMP_CUSTOM_VTK_H
|
||||
#define LMP_DUMP_CUSTOM_VTK_H
|
||||
|
||||
#include "dump_custom.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 DumpCustom {
|
||||
public:
|
||||
DumpCustomVTK(class LAMMPS *, int, char **);
|
||||
virtual ~DumpCustomVTK();
|
||||
|
||||
virtual void write();
|
||||
protected:
|
||||
char *label; // string for dump file header
|
||||
|
||||
int vtk_file_format; // which vtk file format to write (vtk, vtp, vtu ...)
|
||||
|
||||
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
|
||||
|
||||
// private methods
|
||||
|
||||
virtual void init_style();
|
||||
virtual void write_header(bigint);
|
||||
int count();
|
||||
void pack(tagint *);
|
||||
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);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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: 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: 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: 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-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: 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 threshhold operator
|
||||
|
||||
Operator keyword used for threshold specification in not recognized.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue