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specmicp/src/database/reader_common.cpp
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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 <boost/algorithm/string/split.hpp>
#include <boost/algorithm/string/trim_all.hpp>
#include <boost/algorithm/string/predicate.hpp>
#include <locale>
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;
}
} //end namespace database
} //end namespace specmicp
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