2.1.1. moha.system package

2.1.1.1. Subpackages

• 2.1.1.1.1. moha.system.basis package
  • 2.1.1.1.1.1. Submodules
  • 2.1.1.1.1.2. moha.system.basis.basis_set module
  • 2.1.1.1.1.3. moha.system.basis.gaussian_orbital module
  • 2.1.1.1.1.4. Module contents
• 2.1.1.1.2. moha.system.hamiltonian package
  • 2.1.1.1.2.1. Submodules
  • 2.1.1.1.2.2. moha.system.hamiltonian.abc module
  • 2.1.1.1.2.3. moha.system.hamiltonian.base module
  • 2.1.1.1.2.4. moha.system.hamiltonian.chemical_hamiltonian module
  • 2.1.1.1.2.5. Module contents
• 2.1.1.1.3. moha.system.integral package
  • 2.1.1.1.3.1. Submodules
  • 2.1.1.1.3.2. moha.system.integral.angular_momentum module
  • 2.1.1.1.3.3. moha.system.integral.differential module
  • 2.1.1.1.3.4. moha.system.integral.electron_repulsion module
  • 2.1.1.1.3.5. moha.system.integral.kinetic module
  • 2.1.1.1.3.6. moha.system.integral.linear_momentum module
  • 2.1.1.1.3.7. moha.system.integral.multipole_moment module
  • 2.1.1.1.3.8. moha.system.integral.nuclear_attraction module
  • 2.1.1.1.3.9. moha.system.integral.overlap module
  • 2.1.1.1.3.10. Module contents
• 2.1.1.1.4. moha.system.operator package
  • 2.1.1.1.4.1. Submodules
  • 2.1.1.1.4.2. moha.system.operator.base module
  • 2.1.1.1.4.3. moha.system.operator.one_electron module
  • 2.1.1.1.4.4. moha.system.operator.two_electron module
  • 2.1.1.1.4.5. moha.system.operator.zero_electron module
  • 2.1.1.1.4.6. Module contents
• 2.1.1.1.5. moha.system.wavefunction package
  • 2.1.1.1.5.1. Submodules
  • 2.1.1.1.5.2. moha.system.wavefunction.abc module
  • 2.1.1.1.5.3. moha.system.wavefunction.base module
  • 2.1.1.1.5.4. Module contents

2.1.1.2. Submodules

2.1.1.3. moha.system.atom module

class moha.system.atom.Atom(element, coordinate)

Bases: object

Class for atom.

namestr

Name of the atom.

valueint

Atomic number of the atom

coordinate3-list

Coordinate of the atom.

__init__(self,element,coordinate)

Initialize the instance.

2.1.1.4. moha.system.auxiliary module

moha.system.auxiliary.boys(n, t)

Boys function for the calculation of coulombic integrals.

nint

Order of boys function

tfloat

Varible for boys function.

TypeError

If boys function order is not an integer.

ValueError

If boys function order n is not a none negative number.

moha.system.auxiliary.eint(a, b, c, d)

moha.system.auxiliary.gaussian_product_center(a, A, b, B)

2.1.1.5. moha.system.molecule module

class moha.system.molecule.Molecule(title, size, symmetry='C1')

Bases: list

Molecular Class.

titlestr

Title of the system.

sizeint

Number of atoms.

symmetrystr

Point group of the molecule.

center_of_mass(self)

Calculate the center of mass for molecular.

bond_length(self,i,j)

bond_angle(i, j, k)

Calculate the bond angle between atoms i,j,k.

Where atom j is the central atom.

iint

Index of first atom.

jint

Index of second atom.

kint

Index of third atom.

TypeError

If index of atom is not int.

ValueError

If index of atom is not zero or positive number. If index of atom is not samller than number of atoms.

bond_length(i, j)

Calculate the the distances between atom i and j.

iint

Index of first atom.

jint

Index of second atom.

TypeError

If index of atom is not int.

ValueError

If index of atom is not zero or positive number. If index of atom is not samller than number of atoms.

dihedral_angle(A, B, C, D)

Calculate dihedral angle for atom connectivit A,B,C,D.

iint

Index of first atom.

jint

Index of second atom.

kint

Index of third atom.

lint

Index of fourth atom.

TypeError

If index of atom is not int.

ValueError

If index of atom is not zero or positive number. If index of atom is not samller than number of atoms.

classmethod from_file(filename)

Generate N electron basis set.

truncationlist

A list of truncation degree.

TypeError

If truncation is not a list.

out_of_plane_angle(i, j, k, l)

Calculate out of plane angle, which is for atom A

out of the plane consist by atoms B C D

iint

Index of first atom.

jint

Index of second atom.

kint

Index of third atom.

lint

Index of fourth atom.

TypeError

If index of atom is not int.

ValueError

If index of atom is not zero or positive number. If index of atom is not samller than number of atoms.

property center_of_mass

Calculate the center of mass for molecular.

2.1.1.6. moha.system.periodic module

class moha.system.periodic.Element(number=None, symbol=None, **kwargs)

Bases: object

Represents an element from the periodic table.

numberint

The atomic number.

symbolstr

A string with the symbol of the element.

namestr

The full element name.

groupint

The group of the element (not for actinides and lanthanides).

class moha.system.periodic.Periodic(elements)

Bases: object

A periodic table data structure.

moha.system.periodic.load_periodic()

Load the periodic table data.

radius_calculated: pm

periodic_table:

An instance of Periodic.

2.1.1.7. Module contents