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reader_common.cpp
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Thu, Jun 13, 22:43 (1 d, 23 h)
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18246212
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rSPECMICP SpecMiCP / ReactMiCP
reader_common.cpp
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/*-------------------------------------------------------------------------------
Copyright (c) 2015 F. 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:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. 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.
3. Neither the name of the copyright holder 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 HOLDER 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.
-----------------------------------------------------------------------------*/
#include "reader_common.hpp"
#include "section_name.hpp"
#include "errors.hpp"
#include <iostream>
#include <boost/algorithm/string/split.hpp>
#include <boost/algorithm/string/trim_all.hpp>
#include <boost/algorithm/string/predicate.hpp>
#include <locale>
//#include <cctype>
namespace
specmicp
{
namespace
database
{
void
parse_equation
(
const
std
::
string
&
equation
,
std
::
map
<
std
::
string
,
scalar_t
>
&
compo
)
{
std
::
vector
<
std
::
string
>
list_compo
;
boost
::
split
(
list_compo
,
equation
,
[](
char
input
){
return
input
==
','
;},
boost
::
token_compress_on
);
for
(
auto
it
=
list_compo
.
begin
();
it
!=
list_compo
.
end
();
++
it
)
{
std
::
string
&
toparse
=
*
it
;
double
coeff
=
0
;
boost
::
trim_all
(
toparse
);
unsigned
int
pos_end
=
0
;
while
(
pos_end
<
toparse
.
size
())
{
if
(
std
::
isalpha
(
toparse
[
pos_end
]))
// or std::isblank(toparse[pos_end]))
{
break
;
}
++
pos_end
;
}
std
::
string
label
(
toparse
.
substr
(
pos_end
,
toparse
.
size
()
-
pos_end
));
boost
::
trim_all
(
label
);
if
(
pos_end
==
0
)
coeff
=
1
;
else
if
(
pos_end
==
1
and
toparse
[
0
]
==
'-'
)
coeff
=-
1
;
else
{
std
::
string
tofloat
=
toparse
.
substr
(
0
,
pos_end
);
while
(
pos_end
>
1
)
{
if
((
tofloat
[
0
]
==
'-'
or
tofloat
[
0
]
==
'+'
)
and
std
::
isspace
(
tofloat
[
1
]))
{
tofloat
=
tofloat
[
0
]
+
tofloat
.
substr
(
2
,
pos_end
-
2
);
--
pos_end
;
continue
;
}
else
{
break
;
}
}
if
(
tofloat
[
pos_end
-
1
]
==
'-'
)
{
coeff
=
-
1
;}
else
if
(
tofloat
[
pos_end
-
1
]
==
'+'
)
{
coeff
=
+
1
;}
else
{
coeff
=
std
::
stof
(
tofloat
);}
}
compo
[
label
]
=
coeff
;
}
}
scalar_t
charge_from_label
(
const
std
::
string
&
label
)
{
int
sign
=
1
;
auto
start
=
label
.
end
();
auto
stop
=
label
.
end
();
for
(
auto
it
=
label
.
begin
();
it
!=
label
.
end
();
++
it
)
{
if
(
*
it
==
INDB_OPEN_DELIMITER_CHARGE
)
{
start
=
it
;
}
}
if
(
start
==
label
.
end
())
{
return
0
;}
// no charge specified
for
(
auto
it
=
start
+
1
;
it
!=
label
.
end
();
++
it
)
{
if
(
*
it
==
INDB_CLOSE_DELIMITER_CHARGE
)
{
stop
=
it
;
}
}
if
(
stop
==
label
.
end
())
{
throw
db_invalid_syntax
(
"Charge : missing closing delimiter for species : "
+
label
+
"."
);}
start
=
start
+
1
;
if
(
stop
==
start
)
{
return
0
;}
// nothing inside bracket
// get the signs
if
(
*
(
stop
-
1
)
==
'-'
)
{
sign
=
-
1
;
stop
=
stop
-
1
;
}
else
if
(
*
(
stop
-
1
)
==
'+'
)
{
sign
=
+
1
;
stop
=
stop
-
1
;
}
if
(
stop
==
start
)
{
return
sign
;
// just the sign, |z|=1
}
scalar_t
charge
;
try
{
charge
=
sign
*
std
::
stof
(
std
::
string
(
start
,
stop
));
}
catch
(
std
::
invalid_argument
&
)
{
throw
db_invalid_syntax
(
"Charge : bad formatting for species :"
+
label
+
"."
);
}
return
charge
;
}
// find the next element
std
::
string
::
size_type
find_element
(
const
std
::
string
&
label
,
std
::
string
::
size_type
pos
,
element_map
&
element_coeff
);
// insert label in elem_map if it doesn't exist else add coeff to the value
void
insert_or_add
(
element_map
&
elem_map
,
const
std
::
string
&
label
,
scalar_t
coeff
);
// find the position of the matching parenthesis
std
::
string
::
size_type
find_matching_parenthesis
(
const
std
::
string
&
label
,
std
::
string
::
size_type
init_pos
);
// find a number, return 1 if it's not there
std
::
string
::
size_type
find_number
(
const
std
::
string
&
label
,
std
::
string
::
size_type
init_pos
,
scalar_t
&
number
);
// return true of the bit in paremnthesis is a phase qualifier (aq, g, s, am, mic)
bool
is_phase_qualifier
(
const
std
::
string
&
bit_in_parenthesis
);
// return true if it is an expected special character (not a number or a parenthesis)
bool
is_special
(
std
::
string
::
size_type
charac
);
void
element_composition_from_label
(
std
::
string
label
,
element_map
&
compo
)
{
boost
::
trim_all
(
label
);
compo
.
clear
();
std
::
string
::
size_type
pos
=
0
;
while
(
pos
<
label
.
size
())
{
if
(
label
[
pos
]
==
'('
)
// ex Al(OH)4
{
++
pos
;
// go into the parenthesis
// find composition in parenthesis
element_map
subcompo
;
std
::
string
::
size_type
final_pos
=
find_matching_parenthesis
(
label
,
pos
);
const
std
::
string
sublabel
=
label
.
substr
(
pos
,
final_pos
-
pos
);
if
(
is_phase_qualifier
(
sublabel
))
{
// skip that
pos
=
final_pos
;
break
;
}
element_composition_from_label
(
sublabel
,
subcompo
);
// find coefficient of parenthesis
scalar_t
coeff
;
final_pos
=
find_number
(
label
,
final_pos
+
1
,
coeff
);
// add the compo of parenthesis to the total compo
add_to_element_map
(
compo
,
subcompo
,
coeff
);
pos
=
final_pos
;
}
else
if
(
label
[
pos
]
==
':'
)
// ex CaSO3:0.5H2O
{
++
pos
;
// skip the semi-colon
// find coefficient
scalar_t
coeff
;
std
::
string
::
size_type
final_pos
=
find_number
(
label
,
pos
,
coeff
);
// find element
element_map
subcompo
;
element_composition_from_label
(
label
.
substr
(
final_pos
,
label
.
size
()
-
final_pos
),
subcompo
);
// add compo to total compo
add_to_element_map
(
compo
,
subcompo
,
coeff
);
pos
=
label
.
size
();
}
else
if
(
label
[
pos
]
==
'['
)
// charge AlO(OH)3[-]
{
// it's finished
break
;
}
else
{
pos
=
find_element
(
label
,
pos
,
compo
);
}
}
}
bool
is_special
(
std
::
string
::
size_type
charac
)
{
return
(
charac
==
'('
or
charac
==
':'
or
charac
==
')'
or
charac
==
'['
or
charac
==
']'
);
}
std
::
string
::
size_type
find_matching_parenthesis
(
const
std
::
string
&
label
,
std
::
string
::
size_type
init_pos
)
{
for
(
std
::
string
::
size_type
ind
=
init_pos
;
ind
<
label
.
size
();
++
ind
)
{
if
(
label
[
ind
]
==
'('
)
{
throw
std
::
invalid_argument
(
"Too many parenthesis in label : '"
+
label
+
"' ( pos : "
+
std
::
to_string
(
ind
)
+
" )."
);
}
else
if
(
label
[
ind
]
==
')'
)
{
return
ind
;
}
}
throw
std
::
invalid_argument
(
"Unmatched parenthesis in label : '"
+
label
+
"' (pos : "
+
std
::
to_string
(
init_pos
)
+
" )."
);
}
std
::
string
::
size_type
find_number
(
const
std
::
string
&
label
,
std
::
string
::
size_type
init_pos
,
scalar_t
&
number
)
{
if
(
not
std
::
isdigit
(
label
[
init_pos
]))
{
number
=
1
;
return
init_pos
;
}
std
::
string
::
size_type
pos
=
init_pos
+
1
;
while
(
pos
<
label
.
size
())
{
const
std
::
string
::
value_type
chr
=
label
[
pos
];
if
(
not
(
chr
==
'.'
or
std
::
isdigit
(
chr
)))
{
break
;
}
++
pos
;
}
const
std
::
string
coeff_str
=
label
.
substr
(
init_pos
,
pos
);
number
=
std
::
stod
(
coeff_str
);
return
pos
;
}
void
insert_or_add
(
element_map
&
elem_map
,
const
std
::
string
&
label
,
scalar_t
coeff
)
{
auto
it
=
elem_map
.
find
(
label
);
if
(
it
!=
elem_map
.
end
())
{
it
->
second
+=
coeff
;
}
else
{
elem_map
.
insert
(
element_map
::
value_type
(
label
,
coeff
));
}
}
std
::
string
::
size_type
find_element
(
const
std
::
string
&
label
,
std
::
string
::
size_type
pos
,
element_map
&
compo
)
{
if
(
not
std
::
isupper
(
label
[
pos
]))
throw
std
::
invalid_argument
(
"Invalid label : "
+
label
+
" (Error detected at position "
+
std
::
to_string
(
pos
)
+
" )."
);
std
::
string
::
size_type
current_pos
=
pos
+
1
;
std
::
string
::
size_type
start_number_pos
=
std
::
string
::
npos
;
while
(
true
)
{
if
(
current_pos
==
label
.
size
()
or
is_special
(
label
[
current_pos
])
or
std
::
isupper
(
label
[
current_pos
])
)
{
if
(
start_number_pos
==
std
::
string
::
npos
)
{
insert_or_add
(
compo
,
label
.
substr
(
pos
,
current_pos
-
pos
),
1.0
);
}
else
{
const
std
::
string
coeff_str
=
label
.
substr
(
start_number_pos
,
current_pos
-
start_number_pos
);
insert_or_add
(
compo
,
label
.
substr
(
pos
,
start_number_pos
-
pos
),
std
::
stod
(
coeff_str
));
}
break
;
}
else
if
(
std
::
isdigit
(
label
[
current_pos
])
or
label
[
current_pos
]
==
'.'
)
{
if
(
start_number_pos
==
std
::
string
::
npos
)
start_number_pos
=
current_pos
;
}
++
current_pos
;
}
return
current_pos
;
}
bool
is_phase_qualifier
(
const
std
::
string
&
bit_in_parenthesis
)
{
if
(
bit_in_parenthesis
==
"aq"
or
bit_in_parenthesis
==
"g"
or
bit_in_parenthesis
==
"s"
or
bit_in_parenthesis
==
"am"
or
bit_in_parenthesis
==
"mic"
)
{
return
true
;
}
else
{
return
false
;
}
}
void
add_to_element_map
(
element_map
&
to_update
,
const
element_map
&
to_add
,
const
scalar_t
coeff
)
{
for
(
auto
&
it:
to_add
)
{
insert_or_add
(
to_update
,
it
.
first
,
coeff
*
it
.
second
);
}
}
}
//end namespace database
}
//end namespace specmicp
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