lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
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/* -*- c++ -*- ----------------------------------------------------------
   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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Lars Pastewka (University of Freiburg)
------------------------------------------------------------------------- */

#if defined(LMP_HAS_PNETCDF)

#ifdef DUMP_CLASS

DumpStyle(netcdf/mpiio,DumpNetCDFMPIIO)

#else

#ifndef LMP_DUMP_NETCDF_MPIIO_H
#define LMP_DUMP_NETCDF_MPIIO_H

#include "dump_custom.h"

namespace LAMMPS_NS {

const int NC_MPIIO_FIELD_NAME_MAX = 100;
const int DUMP_NC_MPIIO_MAX_DIMS  = 100;

class DumpNetCDFMPIIO : public DumpCustom {
 public:
  DumpNetCDFMPIIO(class LAMMPS *, int, char **);
  virtual ~DumpNetCDFMPIIO();
  virtual void write();

 private:
  // per-atoms quantities (positions, velocities, etc.)
  struct nc_perat_t {
    int dims;                           // number of dimensions
    int field[DUMP_NC_MPIIO_MAX_DIMS];  // field indices corresponding to the dim.
    char name[NC_MPIIO_FIELD_NAME_MAX]; // field name
    int var;                            // NetCDF variable
  };

  typedef void (DumpNetCDFMPIIO::*funcptr_t)(void *);

  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 *thermovar;                       // NetCDF variables for thermo output

  bool double_precision;                // write everything as double precision
  bool thermo;                          // write thermo output to netcdf file

  bigint n_buffer;                      // size of buffer
  bigint *int_buffer;                   // buffer for passing data to netcdf
  double *double_buffer;                // buffer for passing data to netcdf

  int ncid;

  int frame_dim;
  int vector_dim[DUMP_NC_MPIIO_MAX_DIMS];
  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();
  void write_time_and_cell();
  virtual void write_data(int, double *);
  void write_prmtop();

  virtual int modify_param(int, char **);

  void ncerr(int, const char *, int);
};

}

#endif
#endif
#endif /* defined(LMP_HAS_PNETCDF) */