File dataformat.hxx

Generic interface for file formats e.g. netCDF, HDF5.

Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu

Author

B.Dudson

Date

April 2009

Contact Ben Dudson, bd512@york.ac.uk

This file is part of BOUT++.

BOUT++ is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BOUT++ 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 Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with BOUT++. If not, see http://www.gnu.org/licenses/.

Functions

std::unique_ptr<DataFormat> data_format(const char *filename = nullptr)

class DataFormat

Subclassed by H5Format, NcFormat, Ncxx4, PncFormat

Public Functions

DataFormat(Mesh *mesh_in = nullptr)

virtual ~DataFormat()

virtual bool openr(const char *name) = 0

virtual bool openr(const std::string &name)

bool openr(const std::string &base, int mype)

virtual bool openw(const char *name, bool append = false) = 0

virtual bool openw(const std::string &name, bool append = false)

bool openw(const std::string &base, int mype, bool append = false)

virtual bool is_valid() = 0

virtual void close() = 0

virtual void flush() = 0

virtual const std::vector<int> getSize(const char *var) = 0

virtual const std::vector<int> getSize(const std::string &var) = 0

virtual bool setGlobalOrigin(int x = 0, int y = 0, int z = 0) = 0

bool setLocalOrigin(int x = 0, int y = 0, int z = 0, int offset_x = 0, int offset_y = 0, int offset_z = 0)

virtual bool setRecord(int t) = 0

virtual bool addVarInt(const std::string &name, bool repeat) = 0

virtual bool addVarBoutReal(const std::string &name, bool repeat) = 0

virtual bool addVarField2D(const std::string &name, bool repeat) = 0

virtual bool addVarField3D(const std::string &name, bool repeat) = 0

virtual bool addVarFieldPerp(const std::string &name, bool repeat) = 0

virtual bool read(int *var, const char *name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read(int *var, const std::string &name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read(BoutReal *var, const char *name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read(BoutReal *var, const std::string &name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read_perp(BoutReal *var, const std::string &name, int lx = 1, int lz = 0) = 0

virtual bool write(int *var, const char *name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write(int *var, const std::string &name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write(BoutReal *var, const char *name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write(BoutReal *var, const std::string &name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write_perp(BoutReal *var, const std::string &name, int lx = 0, int lz = 0) = 0

virtual bool read_rec(int *var, const char *name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read_rec(int *var, const std::string &name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read_rec(BoutReal *var, const char *name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read_rec(BoutReal *var, const std::string &name, int lx = 1, int ly = 0, int lz = 0) = 0

virtual bool read_rec_perp(BoutReal *var, const std::string &name, int lx = 1, int lz = 0) = 0

virtual bool write_rec(int *var, const char *name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write_rec(int *var, const std::string &name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write_rec(BoutReal *var, const char *name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write_rec(BoutReal *var, const std::string &name, int lx = 0, int ly = 0, int lz = 0) = 0

virtual bool write_rec_perp(BoutReal *var, const std::string &name, int lx = 0, int lz = 0) = 0

virtual void setLowPrecision()

virtual void setAttribute(const std::string &varname, const std::string &attrname, const std::string &text) = 0

Sets a string attribute

Inputs

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then the attribute will be added to the file instead of to a variable.
• attrname: Attribute name
• text: A string attribute to attach to the variable

virtual void setAttribute(const std::string &varname, const std::string &attrname, int value) = 0

Sets an integer attribute

Inputs

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then the attribute will be added to the file instead of to a variable.
• attrname: Attribute name
• value: An int attribute to attach to the variable

virtual void setAttribute(const std::string &varname, const std::string &attrname, BoutReal value) = 0

Sets a BoutReal attribute

Inputs

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then the attribute will be added to the file instead of to a variable.
• attrname: Attribute name
• value: A BoutReal attribute to attach to the variable

virtual bool getAttribute(const std::string &varname, const std::string &attrname, std::string &text) = 0

Gets a string attribute

Inputs

Returns

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then get the attribute from the top-level of the file instead of from a variable.
• attrname: Attribute name

text A string attribute of the variable

virtual bool getAttribute(const std::string &varname, const std::string &attrname, int &value) = 0

Gets an integer attribute

Inputs

Returns

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then get the attribute from the top-level of the file instead of from a variable.
• attrname: Attribute name

value An int attribute of the variable

virtual bool getAttribute(const std::string &varname, const std::string &attrname, BoutReal &value) = 0

Gets a BoutReal attribute

Inputs

Returns

Parameters

• varname: Variable name. The variable must already exist. If varname is the empty string “” then get the attribute from the top-level of the file instead of from a variable.
• attrname: Attribute name

value A BoutReal attribute of the variable

void writeFieldAttributes(const std::string &name, const Field &f)

Write out the meta-data of a field as attributes of the variable.

void writeFieldAttributes(const std::string &name, const FieldPerp &f)

Overload for FieldPerp so we can also write ‘yindex’.

void readFieldAttributes(const std::string &name, Field &f)

Read the attributes of a field.

void readFieldAttributes(const std::string &name, FieldPerp &f)

Overload for FieldPerp so we can also read ‘yindex’.

Protected Attributes

Mesh *mesh