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/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright 2020- The GROMACS Authors
* and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
* Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
*
* GROMACS 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 2.1
* of the License, or (at your option) any later version.
*
* GROMACS 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 GROMACS; if not, see
* https://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at https://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out https://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements nblib Topology helpers
*
* \author Victor Holanda <victor.holanda@cscs.ch>
* \author Joe Jordan <ejjordan@kth.se>
* \author Prashanth Kanduri <kanduri@cscs.ch>
* \author Sebastian Keller <keller@cscs.ch>
* \author Artem Zhmurov <zhmurov@gmail.com>
*/
#include "topologyhelpers.h"
#include <cassert>
#include <algorithm>
#include <iterator>
#include <utility>
#include "gromacs/topology/exclusionblocks.h"
namespace nblib
{
std::vector<gmx::ExclusionBlock> toGmxExclusionBlock(const std::vector<std::tuple<int, int>>& tupleList)
{
std::vector<gmx::ExclusionBlock> ret;
auto firstLowerThan = [](auto const& tup1, auto const& tup2)
{ return std::get<0>(tup1) < std::get<0>(tup2); };
// Note this is a programming error as all particles should exclude at least themselves and empty topologies are not allowed.
// Note also that this is also checked in the parent function with a more informative error message.
assert((!tupleList.empty() && "No exclusions found.\n"));
// initialize pair of iterators delimiting the range of exclusions for
// the first particle in the list
auto range = std::equal_range(std::begin(tupleList), std::end(tupleList), tupleList[0], firstLowerThan);
auto it1 = range.first;
auto it2 = range.second;
// loop over all exclusions in molecule, linear in tupleList.size()
while (it1 != std::end(tupleList))
{
gmx::ExclusionBlock localBlock;
// loop over all exclusions for current particle
for (; it1 != it2; ++it1)
{
localBlock.atomNumber.push_back(std::get<1>(*it1));
}
ret.push_back(localBlock);
// update the upper bound of the range for the next particle
if (it1 != end(tupleList))
{
it2 = std::upper_bound(it1, std::end(tupleList), *it1, firstLowerThan);
}
}
return ret;
}
std::vector<gmx::ExclusionBlock> offsetGmxBlock(std::vector<gmx::ExclusionBlock> inBlock, int offset)
{
// shift particle numbers by offset
for (auto& localBlock : inBlock)
{
std::transform(std::begin(localBlock.atomNumber),
std::end(localBlock.atomNumber),
std::begin(localBlock.atomNumber),
[offset](auto i) { return i + offset; });
}
return inBlock;
}
} // namespace nblib
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