Psi4
Namespaces | Macros | Enumerations | Functions | Variables
libmints/molecule.cc File Reference
#include "psi4/libpsio/psio.hpp"
#include "psi4/libmints/molecule.h"
#include "psi4/libmints/matrix.h"
#include "psi4/libmints/vector.h"
#include "psi4/libmints/pointgrp.h"
#include "psi4/libciomr/libciomr.h"
#include "psi4/libefp_solver/efp_solver.h"
#include "psi4/psi4-dec.h"
#include "psi4/libmints/vector3.h"
#include "psi4/libmints/coordentry.h"
#include "psi4/libmints/corrtab.h"
#include "psi4/libmints/petitelist.h"
#include "psi4/masses.h"
#include "psi4/physconst.h"
#include "psi4/libmints/element_to_Z.h"
#include <cmath>
#include <cstdio>
#include <fstream>
#include <locale>
#include <iostream>
#include <algorithm>
#include <vector>
#include <string>
#include <limits>
#include <sstream>
#include <regex>
#include "psi4/libparallel/ParallelPrinter.h"

Namespaces

 psi
 Rotate a set of vectors around an arbitrary axis Vectors are rows of input matrix.
 

Macros

#define ZERO   1.0E-14
 
#define NOISY_ZERO   1.0e-8
 

Enumerations

enum  psi::AxisName { psi::XAxis, psi::YAxis, psi::ZAxis }
 

Functions

std::regex psi::realNumber_ ("(?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+(?:[DdEe][-+]?\\d+)?)", std::regex_constants::icase)
 
std::regex psi::integerNumber_ ("(-?\\d+)", std::regex_constants::icase)
 
std::regex psi::atomSymbol_ ("(([A-Z]{1,3})(?:(_\\w+)|(\\d+))?(?:@(\\d+\\.\\d+))?)", std::regex_constants::icase)
 
std::regex psi::variableDefinition_ ("\\s*(\\w+)\\s*=\\s*((-?\\d+\\.\\d+)|(-?\\d+\\.)|(-?\\.\\d+)|(-?\\d+)|(tda))\\s*", std::regex_constants::icase)
 
std::regex psi::blankLine_ ("[\\s%]*", std::regex_constants::icase)
 
std::regex psi::commentLine_ ("\\s*[#%].*", std::regex_constants::icase)
 
std::regex psi::unitLabel_ ("(\\s*(?:units?)[\\s=]+)((angstrom)|(ang)|(bohr)|(au)|(a\\.u\\.))\\s*", std::regex_constants::icase)
 
std::regex psi::chargeAndMultiplicity_ ("\\s*(-?\\d+)\\s+(\\d+)\\s*")
 
std::regex psi::fragmentMarker_ ("\\s*--\\s*")
 
std::regex psi::orientCommand_ ("\\s*no_?reorient\\s*", std::regex_constants::icase)
 
std::regex psi::comCommand_ ("\\s*no_?com\\s*", std::regex_constants::icase)
 
std::regex psi::symmetry_ ("\\s*symmetry[\\s=]+(\\w+)\\s*", std::regex_constants::icase)
 
std::regex psi::pubchemError_ ("\\s*PubchemError\\s*", std::regex_constants::icase)
 
std::regex psi::pubchemInput_ ("\\s*PubchemInput\\s*", std::regex_constants::icase)
 
std::regex psi::ghostAtom_ ("@(.*)|Gh\\((.*)\\)", std::regex_constants::icase)
 
std::regex psi::efpFileMarker_ ("\\s*efp\\s*(\\w+)\\s*", std::regex_constants::icase)
 
std::regex psi::efpAtomSymbol_ ("A\\d*([A-Z]{1,2})\\d*", std::regex_constants::icase)
 
int psi::str_to_int (const std::string &s)
 
double psi::str_to_double (const std::string &s)
 
void psi::if_to_invert_axis (const Vector3 &v1, int &must_invert, int &should_invert, double &maxproj)
 
static AxisName psi::like_world_axis (Vector3 &axis, const Vector3 &worldxaxis, const Vector3 &worldyaxis, const Vector3 &worldzaxis)
 
int psi::matrix_3d_rotation_Cn (Matrix &coord, Vector3 axis, bool reflect, double TOL, int max_Cn_to_check=-1)
 
bool psi::atom_present_in_geom (Matrix &geom, Vector3 &b, double tol)
 

Variables

std::smatch psi::reMatches_
 

Macro Definition Documentation

#define NOISY_ZERO   1.0e-8
#define ZERO   1.0E-14