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BioFVM_vector.h
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/*
#############################################################################
# If you use BioFVM in your project, please cite BioFVM and the version #
# number, such as below: #
# #
# We solved the diffusion equations using BioFVM (Version 1.1.7) [1] #
# #
# [1] A. Ghaffarizadeh, S.H. Friedman, and P. Macklin, BioFVM: an efficient #
# parallelized diffusive transport solver for 3-D biological simulations,#
# Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 #
# #
#############################################################################
# #
# BSD 3-Clause License (see https://opensource.org/licenses/BSD-3-Clause) #
# #
# Copyright (c) 2015-2017, Paul Macklin and the BioFVM Project #
# 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. #
# #
#############################################################################
*/
#ifndef __BioFVM_vector_h__
#define __BioFVM_vector_h__
#include <iostream>
#include <cstdlib>
#include <vector>
#include <cmath>
#include <cstring>
namespace BioFVM{
/* faster operator overloading. multiplication and division are element-wise (Hadamard) */
std::vector<double> operator-( const std::vector<double>& v1 , const std::vector<double>& v2 );
std::vector<double> operator+( const std::vector<double>& v1 , const std::vector<double>& v2 );
std::vector<double> operator*( const std::vector<double>& v1 , const std::vector<double>& v2 );
std::vector<double> operator/( const std::vector<double>& v1 , const std::vector<double>& v2 );
std::vector<double> operator*( double d , const std::vector<double>& v1 );
std::vector<double> operator+( double d , const std::vector<double>& v1 );
std::vector<double> operator+( const std::vector<double>& v1 , double d );
std::vector<double> operator-( double d , const std::vector<double>& v1 );
std::vector<double> operator-( const std::vector<double>& v1 , double d );
void operator+=( std::vector<double>& v1, const std::vector<double>& v2 );
void operator-=( std::vector<double>& v1, const std::vector<double>& v2 );
void operator/=( std::vector<double>& v1, const std::vector<double>& v2 );
void operator*=( std::vector<double>& v1, const double& a );
void operator*=( std::vector<double>& v1, const std::vector<double>& v2 );
void operator/=( std::vector<double>& v1, const double& a );
/* other commonly needed operations on vectors */
std::ostream& operator<<(std::ostream& os, const std::vector<double>& v );
// this one returns a new vector that has been normalized
std::vector<double> normalize( std::vector<double>& v );
// this one normalizes v
void normalize( std::vector<double>* v );
double norm_squared( const std::vector<double>& v );
double norm( const std::vector<double>& v );
double maxabs( const std::vector<double>& v );
double max_abs_difference( const std::vector<double>& v1 , const std::vector<double>& v2 );
std::vector<double> exponentiate( const std::vector<double>& exponent );
// note that the PRNG must be replaced if you are serious about this function
void randomize( std::vector<double>* v );
/* axpy and related BLAS-type operations */
// y = y + a*x
void axpy( std::vector<double>* y, double& a , std::vector<double>& x );
// y = y + a.*x
void axpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x );
// y = y - a*x
void naxpy( std::vector<double>* y, double& a , std::vector<double>& x );
// y = y - a.*x
void naxpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x );
/* I may cut these from the final version */
/* CLEANUP BEFORE RELEASE */
//y = y + a.*x ; y = y ./ d
void axpy_div( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x , std::vector<double>& d );
// y = y + a1.*x1 + a2.*x2
void double_axpy( std::vector<double>* y, std::vector<double>& a1 , std::vector<double>& a2, std::vector<double>& x1 , std::vector<double>& x2 );
// y = y + a.*(x1 + x2)
void double_axpy( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x1 , std::vector<double>& x2 );
// y = y + a.*(x1 + x2) ; y = y./d
void double_axpy_div( std::vector<double>* y, std::vector<double>& a , std::vector<double>& x1 , std::vector<double>& x2 , std::vector<double>& d);
// y = y + a1.*x1 + a2.*x2 ; y = y./d
void double_axpy_div( std::vector<double>* y, std::vector<double>& a1 , std::vector<double>& a2, std::vector<double>& x1 , std::vector<double>& x2 , std::vector<double>& d);
// turn a delimited character array (e.g., csv) into a vector of doubles
void csv_to_vector( const char* buffer , std::vector<double>& vect );
char* vector_to_csv( const std::vector<double>& vect );
void vector_to_csv_safe( const std::vector<double>& vect , char*& buffer );
void vector_to_csv( const std::vector<double>& vect , char*& buffer );
void list_to_vector( const char* buffer , std::vector<double>& vect , char delim ); // can be same as csv
char* vector_to_list( const std::vector<double>& vect , char delim );
void vector_to_list_safe( const std::vector<double>& vect , char*& buffer , char delim );
void vector_to_list( const std::vector<double>& vect , char*& buffer , char delim );
void vector3_to_list( const std::vector<double>& vect , char*& buffer , char delim );
};
#endif