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base_wrapper.hpp
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rSPECMICP SpecMiCP / ReactMiCP
base_wrapper.hpp
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/*-------------------------------------------------------
Copyright (c) 2014,2015 Fabien Georget <fabieng@princeton.edu>, Princeton University
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the Princeton University nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
---------------------------------------------------------*/
#ifndef SPECMICP_DATABASE_BASEWRAPPER_HPP
#define SPECMICP_DATABASE_BASEWRAPPER_HPP
#include "common.hpp"
//! \file base_wrapper.hpp
//!
//! \brief Base wrapper around vectors and matrices
//!
//! These classes encapsulate an Eigen Matrix (or vector)
//!
//! \defgroup database_species
namespace
specmicp
{
namespace
database
{
//! \class MatrixSpeciesWrapper
//! \brief A wrapper around a matrix, to be used by a SpeciesList (or a derived class) instance
//!
//! \ingroup database_species Describing the species in the database
class
MatrixSpeciesWrapper
{
public
:
//! \brief Default constructor
MatrixSpeciesWrapper
()
{}
//! \brief Constructor initializing the matrix
MatrixSpeciesWrapper
(
index_t
size
,
index_t
nb_cols
)
:
m_matrix
(
Matrix
::
Zero
(
size
,
nb_cols
))
{}
//! \name Size
// ============
//! \brief Return and set the size of the matrix
//! @{
//! \brief Return the number of rows in the matrix
index_t
size
()
const
{
return
m_matrix
.
rows
();}
//! \brief Resize the matrix
//! This is a resize only for the number of rows
void
resize
(
index_t
size
)
{
m_matrix
.
conservativeResize
(
size
,
Eigen
::
NoChange
);
}
//! \brief Resize the matrix (both rows and colums)
void
resize
(
index_t
rows
,
index_t
cols
)
{
m_matrix
.
conservativeResize
(
rows
,
cols
);
}
// @}
//! \name Getter
// =============
//! \brief Return the values
//! @{
//! \brief Return the element ['row', ['col']
const
scalar_t
&
operator
()(
index_t
row
,
index_t
col
)
const
{
return
m_matrix
(
row
,
col
);
}
//! \brief Return a const reference to the matrix
const
Matrix
&
get_matrix
()
const
{
return
m_matrix
;
}
//! \brief Return the row of a matrix
Eigen
::
MatrixBase
<
Matrix
>::
ConstRowXpr
get_row
(
index_t
k
)
const
{
return
m_matrix
.
row
(
k
);
}
//! \brief Return the element ['row','col']
const
scalar_t
&
get_value
(
index_t
row
,
index_t
col
)
const
{
return
m_matrix
(
row
,
col
);
}
//! @}
//! \name Setter
// =============
//! \brief Set the values
//! @{
//! \brief Add 'other' to row 'k'
template
<
typename
derived
>
void
add_to_row
(
index_t
k
,
const
Eigen
::
MatrixBase
<
derived
>&
other
)
{
m_matrix
.
row
(
k
)
+=
other
;
}
//! \brief Multiply row 'k' by 'multiplier'
template
<
typename
derived
>
void
multiply_by
(
const
Eigen
::
MatrixBase
<
derived
>&
multiplier
)
{
m_matrix
=
m_matrix
*
multiplier
;
}
//! \brief Set the value of the matrix by copying 'init_matrix'
template
<
typename
derived
>
void
set_matrix
(
const
Eigen
::
MatrixBase
<
derived
>&
init_matrix
)
{
m_matrix
=
init_matrix
;
}
//! \brief Set the element ['row','col'] to 'value'
void
set_value
(
index_t
row
,
index_t
col
,
scalar_t
value
)
{
m_matrix
(
row
,
col
)
=
value
;
}
//! \brief Reset row 'k'
void
reset_row
(
index_t
k
)
{
m_matrix
.
row
(
k
).
setZero
();
}
//! @}
//! \name Move
// ===========
//! \brief Move values inside, and outside, of the matrix
//! @{
//! \brief replace imformation of 'new_ind' by those contained in 'old_ind'
void
move_erase
(
index_t
old_ind
,
index_t
new_ind
)
{
m_matrix
.
row
(
new_ind
)
=
m_matrix
.
row
(
old_ind
);
}
//! \brief replace imformation of 'new_ind' by those contained in 'old_ind'
void
move_erase
(
index_t
old_ind
,
index_t
new_ind
,
const
std
::
vector
<
bool
>
is_col_to_remove
);
//! \brief Move the row to another matrix
void
move_erase_to
(
index_t
ind
,
MatrixSpeciesWrapper
&
other
,
index_t
other_ind
)
{
other
.
m_matrix
.
row
(
other_ind
)
=
m_matrix
.
row
(
ind
);
m_matrix
.
row
(
ind
).
setZero
();
}
//! \brief Swap two rows
void
swap
(
index_t
ind
,
MatrixSpeciesWrapper
&
other
,
index_t
other_ind
)
{
m_matrix
.
row
(
ind
).
swap
(
other
.
m_matrix
.
row
(
other_ind
));
}
//! @}
private
:
Matrix
m_matrix
;
};
//! \class VectorSpeciesWrapper
//! \brief A wrapper around a vector
//!
//! \ingroup database_species
class
VectorSpeciesWrapper
{
public
:
//! \brief Default constructor
VectorSpeciesWrapper
()
{}
//! \brief Initialise the vector
//! \param size initial size of the vector
VectorSpeciesWrapper
(
index_t
size
)
:
m_vector
(
Vector
::
Zero
(
size
))
{}
//! \name Size
// ============
//! \brief Return and set the size of the vector
//! @{
//! \brief Return the size of the vector
index_t
size
()
const
{
return
m_vector
.
rows
();}
//! \brief Resize the vector
void
resize
(
index_t
size
)
{
m_vector
.
conservativeResize
(
size
);
}
//! @}
//! \name Getter
// =============
//! \brief Return the values
//! @{
//! \brief return the value of index k
const
scalar_t
&
operator
()(
index_t
k
)
const
{
return
m_vector
(
k
);
}
//! \brief Return the inner product of the vector and 'other'
template
<
typename
derived
>
scalar_t
dot
(
const
Eigen
::
MatrixBase
<
derived
>&
other
)
const
{
return
m_vector
.
dot
(
other
);
}
//! \brief Return the value of index k
const
scalar_t
&
get_value
(
index_t
k
)
const
{
return
m_vector
(
k
);
}
//! \brief Return the vector
const
Vector
&
get_vector
()
const
{
return
m_vector
;
}
//! @}
//! \name Setter
// =============
//! \brief Set the values
//! @{
//! \brief add 'vector'
template
<
typename
derived
>
void
add
(
const
Eigen
::
MatrixBase
<
derived
>&
vector
)
{
m_vector
+=
vector
;
}
//! \brief Multiply the vector by 'multiplier'
template
<
typename
derived
>
void
multiply_by
(
const
Eigen
::
MatrixBase
<
derived
>&
multiplier
)
{
m_vector
=
m_vector
*
multiplier
;
}
//! \brief Set the value at index k
void
set_value
(
index_t
k
,
scalar_t
value
)
{
m_vector
(
k
)
=
value
;
}
//! \brief Copy 'vector' to the vector
template
<
typename
derived
>
void
set_vector
(
const
Eigen
::
MatrixBase
<
derived
>&
vector
)
{
m_vector
=
vector
;
}
//! \brief Apply a linear transformation to the vector
template
<
typename
derived
>
void
transform
(
const
Eigen
::
MatrixBase
<
derived
>&
transform_matrix
)
{
specmicp_assert
(
transform_matrix
.
rows
()
==
transform_matrix
.
cols
());
m_vector
=
transform_matrix
*
m_vector
;
}
//! @}
//! \name Move
// ===========
//! \brief Move values inside, and outside, of the matrix
//! @{
//! \brief Move value of old_ind at new_ind
void
move_erase
(
index_t
old_ind
,
index_t
new_ind
)
{
m_vector
(
new_ind
)
=
m_vector
(
old_ind
);
}
//! \brief Move row 'ind' to 'other' at row 'other_ind'
void
move_erase_to
(
index_t
ind
,
VectorSpeciesWrapper
&
other
,
index_t
other_ind
)
{
other
.
m_vector
(
other_ind
)
=
m_vector
(
ind
);
m_vector
(
ind
)
=
0
;
}
//! @}
private
:
Vector
m_vector
;
};
}
// end namespace database
}
// end namespace specmicp
#endif
// SPECMICP_DATABASE_BASEWRAPPER_HPP
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