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watersystem.h
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watersystem.h
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#pragma once
#ifndef WATERSYSTEM_H_
#define WATERSYSTEM_H_
#include "mdsystem.h"
#include "ambersystem.h"
#include "xyzsystem.h"
#include "gmxsystem.h"
#include "utility.h"
#include <libconfig.h++>
#include <cstdlib>
#include <iomanip>
#include <algorithm>
#include <functional>
#include <numeric>
template<class T>
class WaterSystem {
public:
WaterSystem (const std::string configuration_filename);
virtual ~WaterSystem ();
static libconfig::Config * config_file; /* Configuration file */
static libconfig::Setting& SystemParameterLookup (std::string param) {
try {
return WaterSystem<T>::config_file->lookup(param);
}
catch(const libconfig::SettingTypeException &stex) {
std::cerr << "Something is wrong with the " << param << " setting in the system.cfg configuration file." << std::endl;
exit(EXIT_FAILURE);
}
catch(const libconfig::SettingNotFoundException &snfex) {
std::cerr << "Couldn't find the " << param << " setting in the system.cfg configuration file." << std::endl;
exit(EXIT_FAILURE);
}
}
T * System () { return sys; }
static double posmin, posmax;
static double pbcflip; // location to flip about periodic boundaries
static coord axis; // axis normal to the interface
static VecR ref_axis; // vector representation of the reference axis
static double int_low, int_high, middle; // the positions of analysis cutoffs
static Atom_ptr_vec sys_atoms; // all atoms/mols in the system
static Mol_ptr_vec sys_mols;
static Atom_ptr_vec int_atoms; // interfacial water atoms (or as above)
static Mol_ptr_vec int_mols;
static Mol_ptr_vec int_wats; // interfacial waters, or just all the waters in the system depending on the function call
void OpenFile ();
static double AxisPosition (const AtomPtr a) {
double pos = a->Position()[axis];
pos = (pos > pbcflip) ? pos : pos + MDSystem::Dimensions()[axis];
return pos;
}
typedef std::pair<double,double> Double_pair;
// quick way to make a pair for the oft-used extents std::pair defaulting to the posmin/posmax in the config file
Double_pair ExtentPair (
const double low = WaterSystem<T>::posmin,
const double high = WaterSystem<T>::posmax) const {
return std::make_pair<double,double> (low, high);
}
void LoadAll (); // Loads all the molecules and atoms in the system into the containers
void SliceWaterCoordination (const bondgraph::coordination c);
// predicate determines if an atom sits within a particular slice of the system
class AtomPositionInSlice : public std::binary_function<AtomPtr, Double_pair&, bool> {
public:
bool operator() (const AtomPtr atom, const Double_pair& extents) const
{
double pos = AxisPosition (atom);
return pos > extents.first && pos < extents.second;
}
};
// remove all the atoms in the defined slice (extents=(min,max)) of the slab
void RemoveAtomsInSlice (Atom_ptr_vec& atoms, Double_pair& extents) {
atoms.erase(
remove_if(atoms.begin(), atoms.end(), std::bind2nd(AtomPositionInSlice(), extents)), atoms.end());
return;
}
void KeepAtomsInSlice (Atom_ptr_vec& atoms, Double_pair& extents) {
atoms.erase(
remove_if(atoms.begin(), atoms.end(), std::not1(std::bind2nd(AtomPositionInSlice(), extents))), atoms.end());
return;
}
// predicate to find if a water molecule is within a region (based on the position of the oxygen atom)
template <typename U>
class WaterInSlice : public std::binary_function<U, Double_pair, bool> {
private:
AtomPositionInSlice apis;
public:
bool operator() (const U wat, const Double_pair& extents) const
{
return apis (wat->GetAtom("O"), extents);
}
};
// This slices the water molecules and leaves only those within a given location of the slab. However, it does not do any loading or unloading of the atoms from int_atoms or anything else...
template <typename U>
//static void SliceWaters (std::vector<U>& mols, Double_pair& extents) {
static void SliceWaters (Mol_ptr_vec& mols, Double_pair& extents) {
mols.erase(
remove_if(mols.begin(), mols.end(), std::not1(std::bind2nd(WaterInSlice<U>(), extents))), mols.end());
//this->UpdateAtoms(int_wats, int_atoms);
return;
}
/* loads the int_wats and int_atoms with only waters and water atoms */
void LoadWaters () {
LoadAll();
int_wats.clear();
// copy over all the water molecules into the int_wats container
algorithm_extra::copy_if (sys_mols.begin(), sys_mols.end(), std::back_inserter(int_wats), member_functional::mem_fun_eq(&Molecule::MolType, Molecule::H2O));
// load in the water atoms to int_atoms
this->UpdateAtoms (int_wats, int_atoms);
return;
}
// Predicate to test if a water molecule has a given coordination (H-bonding pattern)
class WaterCoordination_p : public std::binary_function<Water *, bondgraph::coordination, bool> {
public:
bool operator() (const Water * wat, const bondgraph::coordination c) const {
return sys->graph.WaterCoordination(wat) == c;
}
};
void KeepWaterByCoordination (Mol_ptr_vec& mols, const bondgraph::coordination c) {
mols.erase(
remove_if(mols.begin(), mols.end(), std::not1(std::bind2nd(WaterCoordination_p(), c))), mols.end());
return;
}
// Sets the atom container to hold only the atoms of the set of molecules given
void UpdateAtoms (const Mol_ptr_vec& mols, Atom_ptr_vec& atoms) {
atoms.clear();
for (Mol_it it = mols.begin(); it != mols.end(); it++) {
std::copy ((*it)->begin(), (*it)->end(), std::back_inserter(atoms));
}
return;
}
void UpdateGraph () { sys->graph.UpdateGraph (int_atoms); }
void UpdateGraph (const Atom_ptr_vec& atoms) { sys->graph.UpdateGraph (atoms); }
bondgraph::BondGraph& Graph () const { return sys->graph; }
protected:
T * sys; /* System coordinate & files */
virtual void _InitializeSystem ();
};
template<typename T> libconfig::Config * WaterSystem<T>::config_file;
template<typename T> double WaterSystem<T>::posmin;
template<typename T> double WaterSystem<T>::posmax;
template<typename T> double WaterSystem<T>::pbcflip;
template<typename T> coord WaterSystem<T>::axis;
template<typename T> VecR WaterSystem<T>::ref_axis;
template<typename T> Atom_ptr_vec WaterSystem<T>::sys_atoms;
template<typename T> Mol_ptr_vec WaterSystem<T>::sys_mols;
template<typename T> Mol_ptr_vec WaterSystem<T>::int_wats;
template<typename T> Mol_ptr_vec WaterSystem<T>::int_mols;
template<typename T> Atom_ptr_vec WaterSystem<T>::int_atoms;
template <class T>
WaterSystem<T>::WaterSystem (const std::string configuration_filename)
{
try {
config_file = new libconfig::Config();
printf ("\nUsing configuration file: \"%s\"\n", configuration_filename.c_str());
config_file->readFile(configuration_filename.c_str());
posmin = SystemParameterLookup("analysis.position-range")[0];
posmax = SystemParameterLookup("analysis.position-range")[1];
axis = (coord)((int)SystemParameterLookup("analysis.reference-axis"));
ref_axis = VecR(
SystemParameterLookup("analysis.reference-vector")[0],
SystemParameterLookup("analysis.reference-vector")[1],
SystemParameterLookup("analysis.reference-vector")[2]);
pbcflip = SystemParameterLookup("analysis.PBC-flip");
}
catch(const libconfig::SettingTypeException &stex) {
std::cerr << "Something is wrong with the configuration parameters or file - check syntax\n(watersystem.h)" << std::endl;
exit(EXIT_FAILURE);
}
catch(const libconfig::SettingNotFoundException &snfex) {
std::cerr << "A setting is missing from the configuration file!" << std::endl;
exit(EXIT_FAILURE);
}
try {
this->_InitializeSystem();
}
catch (const libconfig::SettingTypeException &stex) {
std::cerr << "WaterSystem<T>::_InitializeSystem() -- Something wrong with initializing the system. Try checking filenames in the system.cfg" << std::endl;
exit(EXIT_FAILURE);
}
return;
}
template <class T>
WaterSystem<T>::~WaterSystem () {
delete config_file;
return;
}
template <>
void WaterSystem<AmberSystem>::_InitializeSystem () {
try {
bool periodic = this->SystemParameterLookup("system.periodic");
this->sys = new AmberSystem(
this->SystemParameterLookup("system.files.prmtop"),
this->SystemParameterLookup("system.files.mdcrd"),
periodic);
}
catch (const libconfig::SettingNotFoundException &snfex) {
std::cerr << "Couldn't find the Amber system filenames listed in the configuration file" << std::endl;
exit(EXIT_FAILURE);
}
return;
}
template <>
void WaterSystem<XYZSystem>::_InitializeSystem () {
try {
std::string filepath = this->SystemParameterLookup("system.files.xyzfile");
double a,b,c;
a = this->SystemParameterLookup("system.dimensions")[0];
b = this->SystemParameterLookup("system.dimensions")[1];
c = this->SystemParameterLookup("system.dimensions")[2];
std::string wanniers = SystemParameterLookup("system.files.wanniers");
VecR dims(a,b,c);
printf ("system dimensions are: ");
dims.Print();
this->sys = new XYZSystem(filepath, dims, wanniers);
}
catch (const libconfig::SettingNotFoundException &snfex) {
std::cerr << "Couldn't find the xyz system parameters in the configuration file" << std::endl;
exit(EXIT_FAILURE);
}
return;
}
template <>
void WaterSystem< gromacs::GMXSystem<gromacs::TRRFile> >::_InitializeSystem () {
std::string gro = this->SystemParameterLookup("system.files.gmx-grofile");
std::string trr = this->SystemParameterLookup("system.files.gmx-trrfile");
this->sys = new gromacs::GMXSystem< gromacs::TRRFile >(gro.c_str(), trr.c_str());
return;
}
template <>
void WaterSystem< gromacs::GMXSystem<gromacs::XTCFile> >::_InitializeSystem () {
std::string gro = this->SystemParameterLookup("system.files.gmx-grofile");
std::string xtc = this->SystemParameterLookup("system.files.gmx-xtcfile");
this->sys = new gromacs::GMXSystem< gromacs::XTCFile >(gro.c_str(), xtc.c_str());
return;
}
template <class T>
void WaterSystem<T>::LoadAll () {
sys_mols.clear();
sys_atoms.clear();
int_mols.clear();
int_atoms.clear();
// copy the molecules and atoms into each container
std::copy(sys->begin_mols(), sys->end_mols(), std::back_inserter(sys_mols));
std::copy(sys->begin_mols(), sys->end_mols(), std::back_inserter(int_mols));
std::copy(sys->begin(), sys->end(), std::back_inserter(sys_atoms));
std::copy(sys->begin(), sys->end(), std::back_inserter(int_atoms));
return;
}
#endif