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lammps/src/USER-NC-DUMP/dump_nc.h
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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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