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dump_nc.h
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Tue, Jul 2, 15:48
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rLAMMPS lammps
dump_nc.h
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/* ======================================================================
LAMMPS NetCDF dump style
https://github.com/pastewka/lammps-netcdf
Lars Pastewka, lars.pastewka@kit.edu
Copyright (2011-2013) Fraunhofer IWM
Copyright (2014) Karlsruhe Institute of Technology
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
====================================================================== */
/* ----------------------------------------------------------------------
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#if defined(LMP_HAS_NETCDF)
#ifdef DUMP_CLASS
DumpStyle
(
nc
,
DumpNC
)
#else
#ifndef LMP_DUMP_NC_H
#define LMP_DUMP_NC_H
#include "dump_custom.h"
namespace
LAMMPS_NS
{
const
int
NC_FIELD_NAME_MAX
=
100
;
const
int
DUMP_NC_MAX_DIMS
=
100
;
class
DumpNC
:
public
DumpCustom
{
public:
DumpNC
(
class
LAMMPS
*
,
int
,
char
**
);
virtual
~
DumpNC
();
virtual
void
write
();
private:
// per-atoms quantities (positions, velocities, etc.)
struct
nc_perat_t
{
int
dims
;
// number of dimensions
int
field
[
DUMP_NC_MAX_DIMS
];
// field indices corresponding to the dim.
char
name
[
NC_FIELD_NAME_MAX
];
// field name
int
var
;
// NetCDF variable
bool
constant
;
// is this property per file (not per frame)
int
ndumped
;
// number of enties written for this prop.
};
typedef
void
(
DumpNC
::*
funcptr_t
)(
void
*
);
// per-frame quantities (variables, fixes or computes)
struct
nc_perframe_t
{
char
name
[
NC_FIELD_NAME_MAX
];
// field name
int
var
;
// NetCDF variable
int
type
;
// variable, fix, compute or callback
int
index
;
// index in fix/compute list
funcptr_t
compute
;
// compute function
int
dim
;
// dimension
char
id
[
NC_FIELD_NAME_MAX
];
// variable id
bigint
bigint_data
;
// actual data
double
double_data
;
// actual data
};
int
framei
;
// current frame index
int
blocki
;
// current block index
int
ndata
;
// number of data blocks to expect
bigint
ntotalgr
;
// # of atoms
int
n_perat
;
// # of netcdf per-atom properties
nc_perat_t
*
perat
;
// per-atom properties
int
n_perframe
;
// # of global netcdf (not per-atom) fix props
nc_perframe_t
*
perframe
;
// global properties
bool
double_precision
;
// write everything as double precision
bigint
n_buffer
;
// size of buffer
int
*
int_buffer
;
// buffer for passing data to netcdf
double
*
double_buffer
;
// buffer for passing data to netcdf
int
ncid
;
int
frame_dim
;
int
spatial_dim
;
int
Voigt_dim
;
int
atom_dim
;
int
cell_spatial_dim
;
int
cell_angular_dim
;
int
label_dim
;
int
spatial_var
;
int
cell_spatial_var
;
int
cell_angular_var
;
int
time_var
;
int
cell_origin_var
;
int
cell_lengths_var
;
int
cell_angles_var
;
virtual
void
openfile
();
void
closefile
();
virtual
void
write_header
(
bigint
);
virtual
void
write_data
(
int
,
double
*
);
void
write_prmtop
();
virtual
int
modify_param
(
int
,
char
**
);
void
ncerr
(
int
,
const
char
*
,
int
);
void
compute_step
(
void
*
);
void
compute_elapsed
(
void
*
);
void
compute_elapsed_long
(
void
*
);
};
}
#endif
#endif
#endif
/* defined(LMP_HAS_NETCDF) */
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