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enhancement.h
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enhancement.h
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/*
* Copyright 2018 Benjamin Santos <caos21@gmail.com>
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*/
#ifndef ENHANCEMENT_H
#define ENHANCEMENT_H
#include <algorithm>
#include <chrono>
#include <cstdlib>
#include <ctime>
#include <fstream>
#include <functional>
#include <iostream>
#include <memory>
#include <parallel/algorithm>
#include <vector>
#include <sstream>
#include <string>
#include <utility>
#include <omp.h>
#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
#include "array.h"
#include "constants.h"
#include "eint.h"
#include "log.h"
#include "utils.h"
#define MPC_ERROR 1.0 // 0.4
#define ETA_TOL 1.0e-16
using namespace utils;
typedef std::pair<short, short> pp;
typedef std::pair<pp, pp> pairs;
typedef std::vector<short> vs;
typedef std::vector<pp> vp;
typedef std::vector<pairs> vpairs;
namespace enhancement {
const boost::uintmax_t ROOT_MAXITER = 1000;
const tools::eps_tolerance<double> ROOT_TOL(30);
/*!
* class PairElement
*
* Represents a value for a particle pair combination (l,q)+(m,p)
*
*/
class PairElement {
public:
//
PairElement() {
l_ = 0;
q_ = 0;
m_ = 0;
p_ = 0;
value_ = 0.0;
}
PairElement(const short &l, const short &q, const short &m, const short &p,
const double &value)
: l_(l), q_(q), m_(m), p_(p), value_(value) {}
PairElement(const PairElement &pe) { assign(pe); }
short l_; //!< Index l of coalescing particle 1
short q_; //!< Index q of coalescing particle 1
short m_; //!< Index m of coalescing particle 2
short p_; //!< Index p of coalescing particle 2
double value_; //!< Value
void assign(const PairElement &pe) {
l_ = pe.l_;
q_ = pe.q_;
m_ = pe.m_;
p_ = pe.p_;
value_ = pe.value_;
}
friend void fill_pe(PairElement &pe, const short &l, const short &q,
const short &m, const short &p, const double &value);
friend void pairelement_tostream(const PairElement &pe, std::ostream &stream);
friend void pairelement_tostream(PairElement &pe, std::istringstream &stream);
void print(std::ostream &stream = std::cout) {
pairelement_tostream(*this, stream);
}
};
inline void get_pe(const PairElement &pe, short &l, short &q, short &m,
short &p, double &value) {
l = pe.l_;
q = pe.q_;
m = pe.m_;
p = pe.p_;
value = pe.value_;
}
inline void fill_pe(PairElement &pe, const short &l, const short &q,
const short &m, const short &p, const double &value) {
pe.l_ = l;
pe.q_ = q;
pe.m_ = m;
pe.p_ = p;
pe.value_ = value;
}
inline void pairelement_tostream(const PairElement &pe, std::ostream &stream) {
stream << pe.l_ << '\t' << pe.q_ << '\t' << pe.m_ << '\t' << pe.p_ << '\t'
<< pe.value_;
}
inline void pairelement_fromstream(PairElement &pe,
std::istringstream &stream) {
std::string sl_; //!< Index l of current volume section
std::string sq_; //!< Index q of current charge section
std::string sm_; //!< Index m of coalescing volume
std::string sp_; //!< Index p of coalescing charge
std::string svalue_;
short l_; //!< Index l of coalescing particle 1
short q_; //!< Index q of coalescing particle 1
short m_; //!< Index m of coalescing particle 2
short p_; //!< Index p of coalescing particle 2
double value_; //!< Value
stream >> sl_ >> sq_ >> sm_ >> sp_ >> svalue_;
l_ = boost::lexical_cast<short>(sl_);
q_ = boost::lexical_cast<short>(sq_);
m_ = boost::lexical_cast<short>(sm_);
p_ = boost::lexical_cast<short>(sp_);
value_ = std::stod(svalue_);
fill_pe(pe, l_, q_, m_, p_, value_);
}
//
class ParticlePair {
public:
//
ParticlePair() {
// call fill to set 0 all the fields
// fill_ppair(*this, 0, 0, 0, 0, 0.0, 0.0, true);
id_ = 0;
l_ = 0;
q_ = 0;
m_ = 0;
p_ = 0;
r21_ = 0.0;
q21_ = 0.0;
notswapd_ = true;
}
ParticlePair(const unsigned long &id, const short &l, const short &q,
const short &m, const short &p, const double &r21,
const double &q21, const bool ¬swapd)
: id_(id),
l_(l),
q_(q),
m_(m),
p_(p),
r21_(r21),
q21_(q21),
notswapd_(notswapd) {
// call fill to set 0 all the fields
// fill_ppair(*this, 0, 0, 0, 0, 0.0, 0.0, true);
}
ParticlePair(const ParticlePair &pp) { assign(pp); }
unsigned long id_; //!< Index
short l_; //!< Index l of coalescing particle 1
short q_; //!< Index q of coalescing particle 1
short m_; //!< Index m of coalescing particle 2
short p_; //!< Index p of coalescing particle 2
double r21_; //!< Value for radius fraction r2/r1
double q21_; //!< Value for radius fraction r2/r1
bool notswapd_; //!< false if indices were swapped
void assign(const ParticlePair &pp) {
id_ = pp.id_;
l_ = pp.l_;
q_ = pp.q_;
m_ = pp.m_;
p_ = pp.p_;
r21_ = pp.r21_;
q21_ = pp.q21_;
notswapd_ = pp.notswapd_;
}
friend void fill_ppair(ParticlePair &pp, const unsigned long &id,
const short &l, const short &q, const short &m,
const short &p, const double &r21, const double &q21,
const bool ¬swapd);
friend void particlepair_tostream(const ParticlePair &pp,
std::ostream &stream);
friend void particlepair_fromstream(ParticlePair &pp,
std::istringstream &stream);
void print(std::ostream &stream = std::cout) {
particlepair_tostream(*this, stream);
}
};
inline void fill_ppair(ParticlePair &pp, const unsigned long &id,
const short &l, const short &q, const short &m,
const short &p, const double &r21, const double &q21,
const bool ¬swapd) {
pp.id_ = id;
pp.l_ = l;
pp.q_ = q;
pp.m_ = m;
pp.p_ = p;
pp.r21_ = r21;
pp.q21_ = q21;
pp.notswapd_ = notswapd;
}
inline void particlepair_tostream(const ParticlePair &pp,
std::ostream &stream) {
stream << pp.id_ << '\t' << pp.l_ << '\t' << pp.q_ << '\t' << pp.m_ << '\t'
<< pp.p_ << '\t' << pp.r21_ << '\t' << pp.q21_ << '\t' << pp.notswapd_;
}
inline void particlepair_fromstream(ParticlePair &pp,
std::istringstream &stream) {
std::string sid_; //!< Index l of current volume section
std::string sl_; //!< Index l of current volume section
std::string sq_; //!< Index q of current charge section
std::string sm_; //!< Index m of coalescing volume
std::string sp_; //!< Index p of coalescing charge
std::string sr21_;
std::string sq21_;
std::string snotswapd_;
unsigned long id_;
short l_; //!< Index l of coalescing particle 1
short q_; //!< Index q of coalescing particle 1
short m_; //!< Index m of coalescing particle 2
short p_; //!< Index p of coalescing particle 2
double r21_; //!< Value for radius fraction r2/r1
double q21_; //!< Value for radius fraction r2/r1
bool notswapd_; //!< false if indices were swapped
stream >> sid_ >> sl_ >> sq_ >> sm_ >> sp_ >> sr21_ >> sq21_ >> snotswapd_;
id_ = boost::lexical_cast<unsigned long>(sid_);
l_ = boost::lexical_cast<short>(sl_);
q_ = boost::lexical_cast<short>(sq_);
m_ = boost::lexical_cast<short>(sm_);
p_ = boost::lexical_cast<short>(sp_);
r21_ = std::stod(sr21_);
q21_ = std::stod(sq21_);
notswapd_ = boost::lexical_cast<bool>(snotswapd_);
fill_ppair(pp, id_, l_, q_, m_, p_, r21_, q21_, notswapd_);
}
class ReducedParticlePair {
public:
//
ReducedParticlePair() {
// call fill to set 0 all the fields
fill_rppair(*this, 0, 0.0, 0.0);
}
bool operator<(const ReducedParticlePair &rpp) const {
if (r21_ != rpp.r21_) {
return (r21_ < rpp.r21_);
} else {
return (q21_ < rpp.q21_);
}
}
inline bool operator==(const ReducedParticlePair &rpp) const {
if ((r21_ == rpp.r21_) && (q21_ == rpp.q21_)) {
return true;
} else {
return false;
}
}
// friend
// bool operator == (const ReducedParticlePair& lx,
// const ReducedParticlePair& rx);
unsigned long id_;
double r21_; //!< Value for radius fraction r2/r1
double q21_; //!< Value for radius fraction r2/r1
std::vector<long> repetitions_;
ReducedParticlePair(const ReducedParticlePair &rpp) { assign(rpp); }
void assign(const ReducedParticlePair &rpp) {
id_ = rpp.id_;
r21_ = rpp.r21_;
q21_ = rpp.q21_;
repetitions_ = rpp.repetitions_;
}
friend void reducedparticlepair_tostream(const ReducedParticlePair &rpp,
std::ostream &stream);
friend void reducedparticlepair_fromstream(ReducedParticlePair &rpp,
std::istream &stream);
void print(std::ostream &stream = std::cout) {
reducedparticlepair_tostream(*this, stream);
}
friend void fill_rppair(ReducedParticlePair &rpp, unsigned long id_,
double r21, double q21);
friend void fill_rppair(ReducedParticlePair &rpp, unsigned long id_,
double r21, double q21,
std::vector<long> repetitions);
friend void fill_rppair(ReducedParticlePair &rpp, unsigned long id_,
double r21, double q21, long irepeated);
void fill_repeated(long const &irepeated) {
repetitions_.push_back(irepeated);
}
};
// bool operator == (const ReducedParticlePair& lx,
// const ReducedParticlePair& rx) {
// // return ((lx.r21_==rx.r21_) && (lx.q21_==rx.q21_));
// if ((lx.r21_==rx.r21_) && (lx.q21_==rx.q21_)) {
// return true;
// }
// else {
// return false;
// }
// }
inline bool operator==(const ReducedParticlePair &lr, const ParticlePair &rp) {
// return ((lx.r21_==rx.r21_) && (lx.q21_==rx.q21_));
if ((lr.r21_ == rp.r21_) && (lr.q21_ == rp.q21_)) {
return true;
} else {
return false;
}
}
inline void fill_rppair(ReducedParticlePair &rpp, unsigned long id, double r21,
double q21) {
rpp.id_ = id;
rpp.r21_ = r21;
rpp.q21_ = q21;
}
inline void fill_rppair(ReducedParticlePair &rpp, unsigned long id, double r21,
double q21, std::vector<long> repetitions) {
rpp.id_ = id;
rpp.r21_ = r21;
rpp.q21_ = q21;
rpp.repetitions_ = repetitions;
}
inline void fill_rppair(ReducedParticlePair &rpp, unsigned long id, double r21,
double q21, long irepeated) {
rpp.id_ = id;
rpp.r21_ = r21;
rpp.q21_ = q21;
rpp.repetitions_.push_back(irepeated);
}
struct reducedPairsComparison {
bool operator()(const ReducedParticlePair &lx,
const ReducedParticlePair &rx) const {
if (lx.r21_ != rx.r21_) {
return (lx.r21_ < rx.r21_);
}
return (lx.q21_ < rx.q21_);
}
};
inline void reducedparticlepair_tostream(const ReducedParticlePair &rpp,
std::ostream &stream) {
stream << rpp.id_ << '\t' << rpp.r21_ << '\t' << rpp.q21_ << '\t';
// << "repeated = \t";
for (auto ir : rpp.repetitions_) {
stream << ir << ",";
}
}
inline void reducedparticlepair_fromstream(ReducedParticlePair &rpp,
std::istream &stream) {
std::string sid_;
std::string sr21_;
std::string sq21_;
std::string srep_;
unsigned long id_;
double r21_; //!< Value for radius fraction r2/r1
double q21_; //!< Value for radius fraction r2/r1
std::vector<long> repetitions_;
stream >> sid_ >> sr21_ >> sq21_ >> srep_;
id_ = boost::lexical_cast<unsigned long>(sid_);
r21_ = std::stod(sr21_);
q21_ = std::stod(sq21_);
// split line
std::vector<std::string> vssrep_;
boost::split(vssrep_, srep_, boost::is_any_of(","));
for (std::vector<std::string>::iterator it = vssrep_.begin();
it < vssrep_.end(); ++it) {
try {
long trep = (boost::lexical_cast<long>(*it));
repetitions_.push_back(trep);
} catch (const boost::bad_lexical_cast &) {
// std::cerr << "\n[ee] Error from lexical cast : " << *it;
break;
}
// std::cout << "\t" << *it;
}
fill_rppair(rpp, id_, r21_, q21_, repetitions_);
}
class ContactPotential {
public:
ContactPotential(const unsigned long &id = 0, const double &potential = 0,
const short &n = 0)
: id_(id), potential_(potential), n_(n) {}
friend void fill_contact_potential(ContactPotential &cpot,
const unsigned long &id,
const double &potential, const short &n);
void print(std::ostream &stream = std::cout) {
contactpotential_tostream(*this, stream);
}
friend void contactpotential_tostream(const ContactPotential &cpot,
std::ostream &stream);
unsigned long id_;
double potential_;
short n_;
};
inline void fill_contact_potential(ContactPotential &cpot,
const unsigned long &id,
const double &potential, const short &n) {
cpot.id_ = id;
cpot.potential_ = potential;
cpot.n_ = n;
}
inline void contactpotential_tostream(const ContactPotential &cpot,
std::ostream &stream) {
stream << '\n' << cpot.id_ << '\t' << cpot.potential_ << '\t' << cpot.n_;
}
struct find_id {
unsigned long id;
find_id(const unsigned long &id_) : id(id_) {}
bool operator()(const ContactPotential &cpot) const {
// return rpp.id_ = id
// std::vector<long> rptd = rpp.repetitions_;
// std::vector<long>::iterator it = std::find(rptd.begin(), rptd.end(), id);
// return std::find(rptd.begin(), rptd.end(), id) != rptd.end();
return (cpot.id_ == id);
}
};
typedef std::vector<ContactPotential>::iterator ContactPotentialIterator;
class Enhancement {
public:
// Enhancement() {
//}
Enhancement(const darray &rarray_, const darray &qarray_,
boost_array4d_ref efactor_, boost_array4d_ref cpotentials_,
boost_array4d_ref bpotentials_, boost_array4d_ref rbarriers_,
double eps_, src::severity_logger<severity_level> lg_)
: rarray(rarray_),
qarray(qarray_),
efactor(efactor_),
cpotentials(cpotentials_),
bpotentials(bpotentials_),
rbarriers(rbarriers_),
eps(eps_),
lg(lg_) {
rarray_size = static_cast<unsigned short>(rarray.size());
qarray_size = static_cast<unsigned short>(qarray.size());
ncombs =
((rarray_size * qarray_size) * (rarray_size * qarray_size + 1)) / 2;
particle_pairs.reserve(ncombs);
potential_threshold = 0.0;
nmin = 25;
nmax = 2000;
nstep = 5;
AH = 20e-20;
}
Enhancement(const darray &rarray_, const darray &qarray_, double eps_,
src::severity_logger<severity_level> lg_)
: rarray(rarray_),
qarray(qarray_),
efactor(dummy), // Hack, references must belong to an actual object
cpotentials(dummy),
bpotentials(dummy),
rbarriers(dummy),
eps(eps_),
lg(lg_) {
rarray_size = static_cast<unsigned short>(rarray.size());
qarray_size = static_cast<unsigned short>(qarray.size());
ncombs =
((rarray_size * qarray_size) * (rarray_size * qarray_size + 1)) / 2;
particle_pairs.reserve(ncombs);
potential_threshold = 0.0;
nmin = 25;
nmax = 2000;
nstep = 5;
}
Enhancement(const darray &rarray_, const darray &qarray_,
boost_array4d_ref efactor_, double eps_,
src::severity_logger<severity_level> lg_)
: rarray(rarray_),
qarray(qarray_),
efactor(efactor_), // Hack, references must belong to an actual object
cpotentials(dummy),
bpotentials(dummy),
rbarriers(dummy),
eps(eps_),
lg(lg_) {
rarray_size = static_cast<unsigned short>(rarray.size());
qarray_size = static_cast<unsigned short>(qarray.size());
ncombs =
((rarray_size * qarray_size) * (rarray_size * qarray_size + 1)) / 2;
particle_pairs.reserve(ncombs);
potential_threshold = 0.0;
nmin = 25;
nmax = 2000;
nstep = 5;
}
inline int write_particlepairs(std::string ppfilename) {
std::ofstream ppstream(std::string(ppfilename + "_pp.dat"));
ppstream << "#id\tl\tq\tm\tp\tr21\tq21\tnotswapd";
// #pragma omp parallel for ordered//schedule(nonmonotonic:dynamic)
for (unsigned int i = 0; i < particle_pairs.size(); ++i) {
// #pragma omp ordered
// {
ppstream << '\n';
particlepair_tostream(particle_pairs[i], ppstream);
// }
}
ppstream.close();
// Neutral particles
std::ofstream npstream(std::string(ppfilename + "_np.dat"));
npstream << "#id\tl\tq\tm\tp\tr21\tq21\tnotswapd";
// #pragma omp parallel for ordered//schedule(nonmonotonic:dynamic)
for (unsigned int i = 0; i < neutral_pairs.size(); ++i) {
// #pragma omp ordered
// {
npstream << '\n';
particlepair_tostream(neutral_pairs[i], npstream);
// }
}
npstream.close();
// Reduced pairs
std::ofstream rpstream(std::string(ppfilename + "_rp.dat"));
rpstream << "#id\tr21\tq21\trepetitions";
// #pragma omp parallel for ordered//schedule(nonmonotonic:dynamic)
for (unsigned int i = 0; i < reduced_pairs.size(); ++i) {
// #pragma omp ordered
// {
rpstream << '\n';
reducedparticlepair_tostream(reduced_pairs[i], rpstream);
// }
}
rpstream.close();
return 0;
}
inline int read_particlepairs(std::string ppfilename) {
// Read particle pairs
{
// Clear vector
particle_pairs.clear();
std::ifstream ppstream(std::string(ppfilename + "_pp.dat"));
std::string line;
unsigned int nlines = 0;
std::getline(ppstream, line);
// if a comment first line isnt found, rewind the file
if (line.find("#") == std::string::npos) {
ppstream.clear();
ppstream.seekg(0);
}
// read line by line
while (std::getline(ppstream, line)) {
ParticlePair pp;
std::istringstream iss(line);
particlepair_fromstream(pp, iss);
particle_pairs.push_back(pp);
++nlines;
}
ppstream.close();
BOOST_LOG_SEV(lg, info)
<< "Particle pair size = " << particle_pairs.size();
}
// Read particle pairs
{
// Clear vector
neutral_pairs.clear();
std::ifstream npstream(std::string(ppfilename + "_np.dat"));
std::string line;
unsigned int nlines = 0;
std::getline(npstream, line);
// if a comment first line isnt found, rewind the file
if (line.find("#") == std::string::npos) {
npstream.clear();
npstream.seekg(0);
}
// read line by line
while (std::getline(npstream, line)) {
ParticlePair np;
std::istringstream iss(line);
particlepair_fromstream(np, iss);
neutral_pairs.push_back(np);
++nlines;
}
npstream.close();
BOOST_LOG_SEV(lg, info) << "Neutral pair size = " << neutral_pairs.size();
}
// Read reduced pairs
{
// Clear vector
reduced_pairs.clear();
std::ifstream rpstream(std::string(ppfilename + "_rp.dat"));
std::string line;
unsigned int nlines = 0;
std::getline(rpstream, line);
// if a comment first line isnt found, rewind the file
if (line.find("#") == std::string::npos) {
rpstream.clear();
rpstream.seekg(0);
}
// read line by line
while (std::getline(rpstream, line)) {
ReducedParticlePair rp;
std::istringstream iss(line);
reducedparticlepair_fromstream(rp, iss);
reduced_pairs.push_back(rp);
++nlines;
}
rpstream.close();
BOOST_LOG_SEV(lg, info) << "Reduced pair size = " << reduced_pairs.size();
}
// for (auto rp: reduced_pairs){
// std::cout << std::endl;
// rp.print();
// }
if (reduced_pairs.size() > 0) {
contact_potentials.resize(reduced_pairs.size());
}
return 0;
}
inline void compute_reducedpairs() {
BOOST_LOG_SEV(lg, info) << "Computing particle pairs...";
auto start = std::chrono::system_clock::now();
//
unsigned long idpp = 0; // index for particle pairs
unsigned long idnp = 0; // index for neutral pairs
// #pragma omp parallel for collapse(4) schedule(auto)
for (unsigned int l = 0; l < rarray_size; ++l) {
// iterate in charges particle 1
for (unsigned int q = 0; q < qarray_size; ++q) {
// iterate in radii particle 2
for (unsigned int m = 0; m < rarray_size; ++m) {
// iterate in charges particle 2
for (unsigned int p = 0; p < qarray_size; ++p) {
unsigned int ip1 = q * rarray_size + l;
unsigned int ip2 = p * rarray_size + m;
// avoid repetitions
if ((p >= q) && (ip2 >= ip1)) {
double r1 = rarray[l];
double q1 = qarray[q];
double r2 = rarray[m];
double q2 = qarray[p];
unsigned int lp1 = l;
unsigned int qp1 = q;
unsigned int mp2 = m;
unsigned int pp2 = p;
bool notswapd = true;
// swap particles. We want to keep r21 < 1
if (r2 > r1) {
std::swap(r1, r2);
std::swap(q1, q2);
std::swap(lp1, mp2);
std::swap(qp1, pp2);
notswapd = false;
}
//double r21 = r2 / r1;
double q21 = q2 / q1;
// WARNING float comparison
if (q1 == 0.0) {
// q1=0, permute particle 1 with 2
std::swap(r1, r2);
std::swap(q1, q2);
std::swap(lp1, mp2);
std::swap(qp1, pp2);
q21 = 0.0;
notswapd = notswapd | false;
}
double r21 = r2 / r1;
// if(q2==0.0){
// q21 = 0.0;
// }
// all neutrals case
if ((q1 == 0.0) && (q2 == 0.0)) {
// lp1 = l; qp1 = q;
// mp2 = m; pp2 = p;
// q21 = 0.0;
// r21 = rarray[m]/rarray[l];
ParticlePair neutralpair(idnp, lp1, qp1, mp2, pp2, r21, q21,
notswapd);
neutral_pairs.push_back(neutralpair);
++idnp;
continue; // break;
}
ParticlePair ppair(idpp, lp1, qp1, mp2, pp2, r21, q21, notswapd);
particle_pairs.push_back(ppair);
++idpp;
// write symmetric combination
}
}
}
}
}
auto end = std::chrono::system_clock::now();
std::chrono::duration<double> elapsed_seconds = end - start;
BOOST_LOG_SEV(lg, info) << "Elapsed time : " << elapsed_seconds.count();
BOOST_LOG_SEV(lg, info) << "Pairs size : " << particle_pairs.size();
BOOST_LOG_SEV(lg, info) << "Neutral pairs size : " << neutral_pairs.size();
BOOST_LOG_SEV(lg, info) << "Total pairs size : "
<< particle_pairs.size() + neutral_pairs.size();
BOOST_LOG_SEV(lg, info) << "Total combinations : " << ncombs;
BOOST_LOG_SEV(lg, info) << "Computing reduced pairs...";
reduced_pairs.resize(particle_pairs.size());
start = std::chrono::system_clock::now();
for (unsigned int i = 0; i < particle_pairs.size(); ++i) {
reduced_pairs[i].id_ = particle_pairs[i].id_;
reduced_pairs[i].r21_ = particle_pairs[i].r21_;
reduced_pairs[i].q21_ = particle_pairs[i].q21_;
}
end = std::chrono::system_clock::now();
elapsed_seconds = end - start;
BOOST_LOG_SEV(lg, info) << "Elapsed time : " << elapsed_seconds.count();
start = std::chrono::system_clock::now();
BOOST_LOG_SEV(lg, info) << "Sorting...";
//__gnu_parallel::sort(reduced_pairs.begin(), reduced_pairs.end(),
//reducedPairsComparison());
std::sort(reduced_pairs.begin(), reduced_pairs.end(),
reducedPairsComparison());
end = std::chrono::system_clock::now();
elapsed_seconds = end - start;
BOOST_LOG_SEV(lg, info) << "Elapsed time : " << elapsed_seconds.count();
// ******** new stuff
// vector sorted with repeated
std::vector<ReducedParticlePair> sorted_reducedpairs = reduced_pairs;
// ******** end new stuff
BOOST_LOG_SEV(lg, info) << "Erasing...";
reduced_pairs.erase(std::unique(reduced_pairs.begin(), reduced_pairs.end()),
reduced_pairs.end());
//__gnu_parallel::unique_copy(reduced_pairs.begin(), reduced_pairs.end(),
//reduced_pairs);
// resize in memory
std::vector<ReducedParticlePair> tmp = reduced_pairs;
reduced_pairs.swap(tmp);
// clear memory for tmp
std::vector<ReducedParticlePair>().swap(tmp);
//****************************************************************************
// Add indices of repeated to vector repetitions
//****************************************************************************
BOOST_LOG_SEV(lg, info) << "Reduced pairs size : " << reduced_pairs.size();
start = std::chrono::system_clock::now();
/// new stuff
// #pragma omp parallel for schedule(nonmonotonic:dynamic)// collapse(2)
long jstart = 0;
for (unsigned int irp = 0; irp < reduced_pairs.size(); ++irp) {
for (long jpp = jstart; jpp < sorted_reducedpairs.size(); ++jpp) {
if (reduced_pairs[irp] == sorted_reducedpairs[jpp]) {
// #pragma omp critical
// {
// one thread a at time
reduced_pairs[irp].fill_repeated(sorted_reducedpairs[jpp].id_);
// }
} else {
jstart = jpp;
break;
}
}
}
/// end new stuff
end = std::chrono::system_clock::now();
elapsed_seconds = end - start;
BOOST_LOG_SEV(lg, info) << "Elapsed time : " << elapsed_seconds.count();
start = std::chrono::system_clock::now();
// resize contact potentials
if (reduced_pairs.size() > 0) {
contact_potentials.resize(reduced_pairs.size());
}
end = std::chrono::system_clock::now();
elapsed_seconds = end - start;
BOOST_LOG_SEV(lg, info) << "Elapsed time : " << elapsed_seconds.count();
BOOST_LOG_SEV(lg, info) << "Done computing pairs.";
}
inline
void compute_ipavdwpotential_contact(double cutoff, double vdw=1.0) {
BOOST_LOG_SEV(lg, info) << "Computing IPA+vdW at contact...";
auto start = std::chrono::system_clock::now();
//
unsigned long idpp = 0; // index for particle pairs
unsigned long idnp = 0; // index for neutral pairs
// #pragma omp parallel for collapse(4) schedule(auto)
for (unsigned int l = 0; l < rarray_size; ++l) {
// iterate in charges particle 1
for (unsigned int q = 0; q < qarray_size; ++q) {
// iterate in radii particle 2
for (unsigned int m = 0; m < rarray_size; ++m) {
// iterate in charges particle 2
for (unsigned int p = 0; p < qarray_size; ++p) {
double r1 = rarray[l];
double q1 = qarray[q];
double r2 = rarray[m];
double q2 = qarray[p];
double rt = r1+r2;
eint::potential_ipavdw_funct pipavdw(r1, q1, r2, q2, eps, AH, cutoff, 1.0, vdw);
cpotentials[l][q][m][p] = pipavdw(rt);
}
}
}
}
BOOST_LOG_SEV(lg, info) << "Done computing IPA+vdW potential contact.";
}
inline
short particle_number(short l, short q, short L) {
return l+L*q;
}
inline
void mpcvdwpotential_barrier(short l, short q,
short m, short p,
double cutoff) {
double r1 = rarray[l];
double q1 = qarray[q];
double r2 = rarray[m];
double q2 = qarray[p];
double rmin = r1+r2;
double rmax = 100.0*rmin;
double min = rmin;
double max = rmax;
short n = nterms4d[l][q][m][p];
eint::force_mpcvdw_funct fmpcvdwfunct(r1, q1, r2, q2, eps, n, AH, cutoff, 1.0/*mpc*/, 1.0/*vdw*/);
// force mpc at contact
double fmpcvdw_rmin = fmpcvdwfunct(rmin);
// Force at r max
double fmpcvdw_rmax = fmpcvdwfunct(rmax);
// checks if minimum exists
if (fmpcvdw_rmin * fmpcvdw_rmax < 0.0) {
// std::cerr << "\n[ii] Mixed phi_rt = " << fmpc_rmin << '\t' <<
// fmpc_rmax;
boost::uintmax_t bmax_iter = ROOT_MAXITER;
tools::eps_tolerance<double> tol = ROOT_TOL;
std::pair<double, double> pair_fmpcvdw;
// try {
pair_fmpcvdw = tools::toms748_solve(fmpcvdwfunct, min, max, fmpcvdw_rmin,
fmpcvdw_rmax, tol, bmax_iter);
if (bmax_iter > 990) {
std::cerr << "\n ERROR max iter " << bmax_iter << "\n\n";
std::terminate();
}
double rbarrier = 0.5 * (pair_fmpcvdw.first + pair_fmpcvdw.second);
if (rbarrier >= min) {
//*********************** USE SAME COEFFICIENTS OF FORCE
//#pragma omp critical
//{
// mpc functor
eint::potential_mpcvdw_funct pmpcvdwfunct(r1, q1, r2, q2, eps, n, AH, cutoff, 1.0/*mpc*/, 1.0/*vdw*/);
// mpc at contact
double pmpcvdw_rb = pmpcvdwfunct(rbarrier);
bpotentials[l][q][m][p] = pmpcvdw_rb;