tools.hpp

/*
Copyright (c) 2015, Florian Sittel (www.lettis.net)
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.

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.
*/
#pragma once

#include "config.hpp"

#include <string>
#include <vector>
#include <map>
#include <tuple>
#include <memory>
#include <iostream>

#if defined(__INTEL_COMPILER)
 #include <malloc.h>
#else
 #include <mm_malloc.h>
#endif

#if defined(__INTEL_COMPILER)
  #define ASSUME_ALIGNED(c) __assume_aligned( (c), DC_MEM_ALIGNMENT)
#else
  #define ASSUME_ALIGNED(c) (c) = (float*) __builtin_assume_aligned( (c), DC_MEM_ALIGNMENT)
#endif

namespace Clustering {
namespace Tools {
  using Neighbor = std::pair<std::size_t, float>;
  using Neighborhood = std::map<std::size_t, Clustering::Tools::Neighbor>;
  void
  write_pops(std::string fname, std::vector<std::size_t> pops);
  void
  write_fes(std::string fname, std::vector<float> fes);
  std::vector<std::size_t>
  read_clustered_trajectory(std::string filename);
  void
  write_clustered_trajectory(std::string filename, std::vector<std::size_t> traj);
  template <typename NUM>
  std::vector<NUM>
  read_single_column(std::string filename);
  template <typename NUM>
  void
  write_single_column(std::string filename, std::vector<NUM> dat, bool with_scientific_format=false);
  template <typename KEY, typename VAL>
  void
  write_map(std::string filename, std::map<KEY, VAL> mapping);
  std::vector<float>
  read_free_energies(std::string filename);
  std::pair<Neighborhood, Neighborhood>
  read_neighborhood(const std::string fname);
  void
  write_neighborhood(const std::string fname,
                     const Neighborhood& nh,
                     const Neighborhood& nh_high_dens);
  std::map<std::size_t, std::size_t>
  microstate_populations(std::vector<std::size_t> traj);
  template <typename NUM>
  std::tuple<NUM*, std::size_t, std::size_t>
  read_coords(std::string filename,
              std::vector<std::size_t> usecols = std::vector<std::size_t>());
  template <typename NUM>
  void
  free_coords(NUM* coords);
  std::string
  stringprintf(const std::string& str, ...);
  template <typename NUM>
  NUM
  string_to_num(const std::string &s);
} // end namespace 'Tools'
} // end namespace 'Clustering'

// template implementations
#include "tools.hxx"