atomgraph_analysis.h

// -*-c++-*-
#ifndef STORMM_ATOMGRAPH_ANALYSIS_H
#define STORMM_ATOMGRAPH_ANALYSIS_H
 
#include <cmath>
#include <vector>
#include "copyright.h"
#include "Accelerator/hybrid.h"
#include "Constants/behavior.h"
#include "Constants/scaling.h"
#include "Potential/energy_enumerators.h"
#include "Reporting/error_format.h"
#include "atomgraph.h"
#include "atomgraph_abstracts.h"
#include "lennard_jones_analysis.h"
 
namespace stormm {
namespace topology {
 
using card::Hybrid;
using constants::ExceptionResponse;
using energy::VdwCombiningRule;

WaterModel identifyWaterModel(const AtomGraph &ag);

std::string listVirtualSiteFrameTypes(const AtomGraph &ag);
 
std::string listVirtualSiteFrameTypes(const AtomGraph *ag);
 
std::string listVirtualSiteFrameTypes(const int* vs_types, int nsite);

int colorConnectivity(const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,
                      int atom_i, int atom_j, std::vector<uint> *marked, bool *ring_report);
  
std::vector<int> mapRotatingGroup(const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,
                                  const int atom_i, const int atom_j, const std::string &filename,
                                  ExceptionResponse policy = ExceptionResponse::WARN);
  
std::vector<int> selectRotatingAtoms(const AtomGraph &ag, int atom_i, int atom_j,
                                     ExceptionResponse policy = ExceptionResponse::WARN);
 
std::vector<int> selectRotatingAtoms(const AtomGraph *ag, int atom_i, int atom_j,
                                     ExceptionResponse policy = ExceptionResponse::WARN);

VdwCombiningRule inferCombiningRule(const AtomGraph *ag,
                                    ExceptionResponse policy = ExceptionResponse::WARN,
                                    bool seek_prevalent = false);
 
VdwCombiningRule inferCombiningRule(const AtomGraph &ag,
                                    ExceptionResponse policy = ExceptionResponse::WARN,
                                    bool seek_prevalent = false);

int getConstrainedDegreesOfFreedom(const AtomGraph *ag, int low_atom_index = 0,
                                   int high_atom_index = 0);
 
int getConstrainedDegreesOfFreedom(const AtomGraph &ag, int low_atom_index = 0,
                                   int high_atom_index = 0);
 
} // namespace topology
} // namespace stormm
 
#endif