orbitals_base Module Reference

Procedures for creating and manipulating atomic and hybrid orbitals. More...

Data Types
interface	addhybridorbital
type	angularpart
	Angular parts of orbitals. More...
type	angularpart_ptr
interface	changehybridcoefficients
type	hybridatomicorbital
interface	makehybridatomicorbital
type	orbital
	All the data fields necessary for orbitals. More...
type	orbital_ptr
type	orbitalbasis
type	orbitalexpansioncoefficient
	Orbital and its expansion coefficient. More...
type	slaterradialpart
	Radial parts of orbitals. More...
type	spinorbital
type	spinorbital_ptr
type	spinorbitalbasis
interface	trfmd_hybs_same
interface	trfmd_hybs_same_ordered

Functions/Subroutines
type(angularpart) function, pointer	pangularpart (l, m)
integer function	l_and_m_index_sp (l, m)
	Returns an array index corresponding to the order s, px, py, pz, starting from 0. More...
subroutine	createatomicorbital (atom, idnum, n, l, m, set_of_primitives, ao)
	Function to make atomic orbital. More...
subroutine	setatomicorbitalexpansion (set_of_primitives, ao)
	Adds an orbital expansion to a basis in an atomic basis set based on the provided set_of_primitives More...
subroutine	addcreatedatomicorbital_ptr (atom, orb_ptr)
	Supplementary procedure to add an already created atomic orbital (given as a pointer to an orbital_ptr) to the hybrid list of the atom. More...
recursive subroutine	createsameorbitalattachedtonewatom (old, new, newAtom)
	Copies all of the data of the given orbital to the new orbital, changing the pAtom pointer. All coefficient pointers in the orbital expansions point to the location of the old expansion coefficients. More...
subroutine	createsameatomicorbitalsattachedtonewatom (old_orbitals_list, new_atom)
	Copies all orbitals in the list to the new atom, changing the pAtom pointer. All coefficient pointers in the orbital expansions point to the location of the old expansion coefficients. More...
recursive real function	eval_orbital_radial_part (orbital1, r)
	Find the value of the radial part of an orbital at given r value. More...
subroutine	getsizeofbasis (part, sizeOfBasis)
	Function which allows to get size of basis of AOs for some polyatomic particles in valence approximation. More...
subroutine	getatomicvalenceorbitals (atom, shell)
	Returns an array of orbitals of atoms lighter than Na. More...
subroutine	makeorbitalexpansioncoefficient (someOrbital, coef, oec)
	Generates a variable of type orbitalExpansionCoefficient. More...
subroutine	makemolecularorbital (id, orbitals, coefficients, mo)
	Creates a molecular orbital with an expansion over input orbitals with their coefficients. More...
subroutine	makespinorbitalwithspinalpha (num, someOrbital, AlphaSpinOrbital)
subroutine	makespinorbitalwithspinbeta (num, someOrbital, BetaSpinOrbital)
subroutine	generatespinorbitalsfrombasis (basis, spinOrbitals)
	Assigns every odd orbital in the basis spin alpha, and every even one - beta. More...
subroutine	sortorbitalarraybynumbers (orbitals)
	Sorts array of orbitals by ID's in ascending order. More...
subroutine	sortorbitallistbynumbers (orbitals)
	Sorts linked list of orbitals by ID's in ascending order. More...
logical function	sortkeyfororbitals (x1, x2)
	Returns TRUE of the ID of x1 is less than the ID of x2. More...
logical function	sortkeyfororbitalpointers (x1, x2)
	Returns TRUE of the ID of x1 is less than the ID of x2. More...
logical function	sortkeyforspinorbitals (x1, x2)
logical function	sortkeyforexpansioncoefficients (x1, x2)
subroutine	whatisorbitaltype (someOrbital, typeName)
logical function	isatomicorbital (someOrbital)
	If pAtom and pY pointers are associated, returns true. More...
logical function	ismolecularorbital (someOrbital)
	If pAtom pointer is not associated, but the orbital expansion is, returns true. More...
logical function	ishybridatomicorbital (someOrbital)
	Is the pAtom and orbital exoansion pointers are associated, but the pY is not, returns true. More...
subroutine	whatisspinorbitaltype (someSpinOrbital, typeName)
logical function	isspinatomicorbital (someSpinOrbital)
logical function	isspinmolecularorbital (someSpinOrbital)
logical function	issameorbitals (orbital1, orbital2)
logical function	issamespinorbitals (spinOrbital1, spinOrbital2)
logical function	do_aos_belong_to_same_particle (orbital1, orbital2)
	Checks if atomic orbitals belong to the same particles or different. More...
subroutine	orbitallisttoarrayptr (orbital_list, orbital_array)
	Converts list of orbitals to allocatable array of type orbital_ptr. More...
subroutine	orbitallisttoarray (orbital_list, orbital_array)
	Converts list of orbitals to type orbitalsBasis. More...
subroutine	orbitalarrayptrtolist (orbital_array, orbital_list)
	Converts array of type orbital_ptr to list. More...
subroutine	orbitalarraytolist (orbital_array, orbital_list)
	Converts orbitalBasis to list of orbitals. More...
type(orbital) function, pointer	orbital_from_polymorphic (x)
	Converts a polymorphic pointer to an orbital pointer if possible, else returns a null-pointer. More...
type(orbital_ptr) function, pointer	orbital_ptr_from_polymorphic (x)
	Converts a polymorphic pointer to an orbital_ptr pointer if possible, else returns a null-pointer. More...
type(orbitalexpansioncoefficient) function, pointer	orbital_expansion_coef_from_polymorphic (x)
	Converts a polymorphic pointer to an OrbitalExpansionCoefficient pointer if possible, else returns a null-pointer. More...
logical function	isorbitalprimitive (orb)
	Checks if orbital is atomic primitive (not a linear combination of STOs or others). More...
type(list) function, pointer	getorbitals (someParticle)
	Returns the particle's orbitals contained in AttributeList. More...
type(list) function, pointer	getorbitalswithangularnumber (someParticle, l)
	From the list returned by GetOrbitals, creates a list of orbitals with given angular number l. More...
type(orbital) function, pointer	getorbitalwithquantumnumbers (someParticle, n, l, m)
type(list) function, pointer	getsorbitals (someParticle)
	From the list returned by GetOrbitals, creates a list of orbitals with angular number zero. More...
type(list) function, pointer	getporbitals (someParticle)
	From the list returned by GetOrbitals, creates a list of orbitals with angular number one. More...
type(list) function, pointer	getdorbitals (someParticle)
	From the list returned by GetOrbitals, creates a list of orbitals with angular number two. More...
type(list) function, pointer	getforbitals (someParticle)
	From the list returned by GetOrbitals, creates a list of orbitals with angular number three. More...
type(orbital_ptr) function, dimension(0:3)	getsandporbitals_array_fn (someParticle)
	Returns an array of orbital pointers to s, px, py, pz. If any of the orbitals are not present, the corresponding pointer is null. More...
type(list) function, pointer	gethybridorbitals (someParticle)
	Returns the hybrid orbitals of the atom in the form a list. More...
type(orbitalbasis) function	gethybridorbitalsarray (someParticle)
	Returns the hybrid orbitals of the atom in the form of an array (type orbitalBasis). More...
type(orbital) function, pointer	gethybridorbital_from_coeffs (someParticle, coeffs)
subroutine	makehybridatomicorbital_from_array_noid (coefs, atom, hybridOrbital)
	Creates a new hybrid orbital with the expansion coefficients (in an array). More...
subroutine	makehybridatomicorbital_from_array_ptr_noid (coefs, atom, hybridOrbital)
	Creates a new hybrid orbital with the expansion coefficients pointing to the given data locations. More...
subroutine	makehybridatomicorbital_from_array (id, coefs, atom, hybridOrbital)
	Creates a new hybrid orbital with the given expansion coefficients (in an array). Contains an id field for backwards compatibility. More...
subroutine	makehybridatomicorbital_from_vals (id, s, px, py, pz, atom, hybridOrbital)
	Creates a new hybrid orbital with the given expansion coefficients. Contains an id field for backwards compatibility. More...
subroutine	addhybridorbital_from_array (atom, coefs, outputHybrid)
	Creates a new hybrid with given coefficients (in an array) and adds it to the hybrid list of the atom. More...
subroutine	addhybridorbital_from_vals (atom, s, px, py, pz, outputHybrid)
	Creates a new hybrid with given coefficients and adds it to the hybrid list of the atom. More...
subroutine	addhybridorbital_from_array_ptr (atom, coefs, outputHybrid)
	Creates a new hyrbid with coefficients pointing to the given data locations and adds it to the hybrid list of the atom. More...
subroutine	addcreatedhybridorbital_ptr (atom, hybrid_ptr)
	Supplementary procedure to add an already created hybrid (given as a pointer to an orbital_ptr) to the hybrid list of the atom. More...
subroutine	createsamehybridorbitalsattachedtonewatom (old_hybrids_list, new_atom)
	Creates hybrids on the new atom with coefficients pointing to the old data locations. More...
real function, dimension(0:3)	gethybridorbitalcoeffs (hybrid)
	Returns an array of coefficients of the given hybrid. More...
type(real_ptr) function, dimension(0:3)	gethybridorbitalcoeffs_ptr (hybrid)
	Returns an array of pointers to the data locations of the coefficients of the given hybrid. More...
type(quaternion) function, pointer	gethybridorbitalquaternion (hybrid)
	Returns the coefficients of the hybrid in quaternion form. More...
subroutine	changehybridcoefficients_from_array (hybrid, new_coefs)
	Changes the coeffiecients of the given hybrid. More...
subroutine	changehybridcoefficients_from_array_ptr (hybrid, new_coefs)
	Changes the data location of the coeffiecients of the given hybrid. More...
subroutine	changehybridcoefficients_from_vals (hybrid, s, px, py, pz)
	Changes the coeffiecients of the given hybrid. More...
subroutine	deallocatehybridcoefficients (hybrid)
subroutine	normalize_hybrid_order (atom)
	If the determinant of the hybridization matrix is negative, rotates the order of hybrids, which changes the sign. More...
subroutine	set_image_hybrid_coeffs_explicit_list (trfm, pim_hybs, im_hybs)
subroutine	set_image_hybrid_coeffs_implicit (pim_atom, im_atom)
logical function	trfmd_hybs_same_explicit_list (trfm, pim_hyblist, im_hyblist)
	Given the explicit transformation matrix, returns true if the image hybrid list contains every image of the preimage hybrids (in any order) More...
logical function	trfmd_hybs_same_explicit (trfm, preim_atom, im_atom)
	Given the explicit transformation matrix, returns true if the image atom's hybrid list contains every image of the preimage atom's hybrids (in any order) More...
logical function	trfmd_hybs_same_implicit (preim_atom, im_atom)
	Same as above, but computes the transformation matrix from the spaceTree. More...
subroutine	reorder_hyblist_for_transform_list (trfm, pim_hyblist, im_hyblist)
	Reorders the elements of the image list so that applying the given transform to preimage hybrids results gives the image hybrids in the same order. More...
logical function	trfmd_hybs_same_ordered_explicit_list (trfm, pim_hyblist, im_hyblist)
	Given the explicit transformation matrix, returns true if the image hybrid list contains every image of the preimage hybrids (in the same order). More...
logical function	trfmd_hybs_same_ordered_explicit (trfm, preim_atom, im_atom)
	Given the explicit transformation matrix, returns true if the image atom's hybrid list contains every image of the preimage atom's hybrids (in the same order). More...
logical function	trfmd_hybs_same_ordered_implicit (preim_atom, im_atom)
	Same as above, but computes the transformation matrix from the spaceTree. More...
subroutine	writehybridstoatom (atom, hybridMatrix, carbonHybrids)
subroutine	rewritehybridscoefficients (atom, hyb)
	Changes all of the hybrid coefficients of this atom based on the given matrix. More...
subroutine	writehybridizationmatrixtoatom (atom)
	Adds the hybridization matrix (taken from the already present hybrid expansions) to the attribute list of the atom. More...
real function, dimension(4, 4)	gethybridizationmatrix_from_list (hybrids_list)
	Returns the hybridization matrix defined in the given hybrids list. More...
subroutine	getatomichybridizationmatrix (atom, hybMatrix)
	Returns the hybridization matrix of the atom. More...
subroutine	getatomichybridizationmatrix_lab (atom, hybMatrix)
	Returns the hybridization matrix in the laboratory frame. More...
recursive subroutine	deallocate_orbital (pOrbital)
	Deallocates a non-hybrid orbital or orbital_ptr. An orbital is assumed to be dependent only on primitives (or itself be a primitive), so its orbital expansion is completely deallocated. More...
subroutine	deallocate_hybrid (pOrbital)
	Deallocates a hybrid orbital. Does not deallocate its non-hybrid orbitals. More...
subroutine	deallocate_molecular_orbital (pOrbital)
	Deallocates a molecular orbital. Does not deallocate its consituent orbitals. More...
subroutine	deallocate_spinorbital (pSpinOrbital)
	Deallocates a spinOrbital or a spinOrbital_ptr. More...
subroutine	deallocate_orbitalexpansioncoefficient (pOEC)
	Deallocates an orbital expansion coefficient. Deallocation of the orbital it points to should be done on its own. More...

Variables
character(len=3), public	typeofbasis
type(angularpart), dimension(0:0), target, save, public	sangularparts = [AngularPart(0,0)]
type(angularpart), dimension(-1:1), target, save, public	pangularparts = [AngularPart(1,-1), AngularPart(1,0), AngularPart(1,1)]
type(angularpart), dimension(-2:2), target, save, public	dangularparts = [AngularPart(2,-2), AngularPart(2,-1), AngularPart(2,0), AngularPart(2,1), AngularPart(2,2)]
type(angularpart), dimension(-3:3), target, save, public	fangularparts = [AngularPart(3,-3), AngularPart(3,-2), AngularPart(3,-1), AngularPart(3,0), AngularPart(3,1), AngularPart(3,2), AngularPart(3,3)]
type(angularpart_ptr), dimension(:), allocatable, protected	allangularparts
integer, target, save, public	spinalpha = 1
integer, target, save, public	spinbeta = -1

Detailed Description

Procedures for creating and manipulating atomic and hybrid orbitals.

Author

Andrei Tchougreeff and Ilya Popov.

Function/Subroutine Documentation

addcreatedatomicorbital_ptr()

subroutine orbitals_base::addcreatedatomicorbital_ptr	(	type(particle), intent(inout)	atom,
		type(orbital_ptr), intent(in), pointer	orb_ptr
	)

Supplementary procedure to add an already created atomic orbital (given as a pointer to an orbital_ptr) to the hybrid list of the atom.

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addcreatedhybridorbital_ptr()

subroutine orbitals_base::addcreatedhybridorbital_ptr	(	type(particle), intent(inout)	atom,
		type(orbital_ptr), intent(in), pointer	hybrid_ptr
	)

Supplementary procedure to add an already created hybrid (given as a pointer to an orbital_ptr) to the hybrid list of the atom.

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addhybridorbital_from_array()

subroutine orbitals_base::addhybridorbital_from_array	(	type (particle), intent(inout), target	atom,
		real, dimension(0:3), intent(in)	coefs,
		type(orbital_ptr), optional, pointer	outputHybrid
	)

Creates a new hybrid with given coefficients (in an array) and adds it to the hybrid list of the atom.

addhybridorbital_from_array_ptr()

subroutine orbitals_base::addhybridorbital_from_array_ptr	(	type (particle), intent(inout), target	atom,
		type(real_ptr), dimension(0:3), intent(in)	coefs,
		type(orbital_ptr), optional, pointer	outputHybrid
	)

Creates a new hyrbid with coefficients pointing to the given data locations and adds it to the hybrid list of the atom.

addhybridorbital_from_vals()

subroutine orbitals_base::addhybridorbital_from_vals	(	type (particle), intent(inout), target	atom,
		real, intent(in)	s,
		real, intent(in)	px,
		real, intent(in)	py,
		real, intent(in)	pz,
		type(orbital_ptr), optional, pointer	outputHybrid
	)

Creates a new hybrid with given coefficients and adds it to the hybrid list of the atom.

changehybridcoefficients_from_array()

subroutine orbitals_base::changehybridcoefficients_from_array	(	type(orbital), intent(inout), pointer	hybrid,
		real, dimension(0:3), intent(in)	new_coefs
	)

Changes the coeffiecients of the given hybrid.

changehybridcoefficients_from_array_ptr()

subroutine orbitals_base::changehybridcoefficients_from_array_ptr	(	type(orbital), intent(inout), pointer	hybrid,
		type(real_ptr), dimension(0:3), intent(in)	new_coefs
	)

Changes the data location of the coeffiecients of the given hybrid.

changehybridcoefficients_from_vals()

subroutine orbitals_base::changehybridcoefficients_from_vals	(	type(orbital), intent(inout), pointer	hybrid,
		real, intent(in)	s,
		real, intent(in)	px,
		real, intent(in)	py,
		real, intent(in)	pz
	)

Changes the coeffiecients of the given hybrid.

createatomicorbital()

subroutine orbitals_base::createatomicorbital	(	type(particle), intent(in), target	atom,
		integer, intent(in)	idnum,
		integer, intent(in)	n,
		integer, intent(in)	l,
		integer, intent(in)	m,
		type(primitive), dimension(:), intent(in)	set_of_primitives,
		type(orbital), intent(out), target	ao
	)

Function to make atomic orbital.

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createsameatomicorbitalsattachedtonewatom()

subroutine orbitals_base::createsameatomicorbitalsattachedtonewatom	(	type(list), intent(inout)	old_orbitals_list,
		type(particle), intent(inout), target	new_atom
	)

Copies all orbitals in the list to the new atom, changing the pAtom pointer. All coefficient pointers in the orbital expansions point to the location of the old expansion coefficients.

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createsamehybridorbitalsattachedtonewatom()

subroutine orbitals_base::createsamehybridorbitalsattachedtonewatom	(	type(list), intent(inout)	old_hybrids_list,
		type(particle), intent(inout), target	new_atom
	)

Creates hybrids on the new atom with coefficients pointing to the old data locations.

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createsameorbitalattachedtonewatom()

recursive subroutine orbitals_base::createsameorbitalattachedtonewatom	(	type(orbital), intent(inout)	old,
		type(orbital), intent(inout)	new,
		type(particle), intent(inout), target	newAtom
	)

Copies all of the data of the given orbital to the new orbital, changing the pAtom pointer. All coefficient pointers in the orbital expansions point to the location of the old expansion coefficients.

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deallocate_hybrid()

subroutine orbitals_base::deallocate_hybrid

(

class(*), intent(inout), pointer

pOrbital

)

Deallocates a hybrid orbital. Does not deallocate its non-hybrid orbitals.

deallocate_molecular_orbital()

subroutine orbitals_base::deallocate_molecular_orbital

(

class(*), intent(inout), pointer

pOrbital

)

Deallocates a molecular orbital. Does not deallocate its consituent orbitals.

deallocate_orbital()

recursive subroutine orbitals_base::deallocate_orbital

(

class(*), intent(inout), pointer

pOrbital

)

Deallocates a non-hybrid orbital or orbital_ptr. An orbital is assumed to be dependent only on primitives (or itself be a primitive), so its orbital expansion is completely deallocated.

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deallocate_orbitalexpansioncoefficient()

subroutine orbitals_base::deallocate_orbitalexpansioncoefficient

(

class(*), intent(inout), pointer

pOEC

)

Deallocates an orbital expansion coefficient. Deallocation of the orbital it points to should be done on its own.

deallocate_spinorbital()

subroutine orbitals_base::deallocate_spinorbital

(

class(*), intent(inout), pointer

pSpinOrbital

)

Deallocates a spinOrbital or a spinOrbital_ptr.

Todo:

DR 14.10.1021 Don't know how to correctly deallocate this. Please someone check this.

deallocatehybridcoefficients()

subroutine orbitals_base::deallocatehybridcoefficients

(

type(orbital), intent(inout), pointer

hybrid

)

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do_aos_belong_to_same_particle()

logical function orbitals_base::do_aos_belong_to_same_particle	(	type(orbital), intent(inout)	orbital1,
		type(orbital), intent(inout)	orbital2
	)

Checks if atomic orbitals belong to the same particles or different.

eval_orbital_radial_part()

recursive real function orbitals_base::eval_orbital_radial_part	(	type(orbital), intent(in)	orbital1,
		real, intent(in)	r
	)

Find the value of the radial part of an orbital at given r value.

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generatespinorbitalsfrombasis()

subroutine orbitals_base::generatespinorbitalsfrombasis	(	type (orbitalbasis), intent(in)	basis,
		type(spinorbital), dimension(:), intent(inout), allocatable	spinOrbitals
	)

Assigns every odd orbital in the basis spin alpha, and every even one - beta.

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getatomichybridizationmatrix()

subroutine orbitals_base::getatomichybridizationmatrix	(	type(particle), intent(inout)	atom,
		real, dimension(4,4), intent(out)	hybMatrix
	)

Returns the hybridization matrix of the atom.

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getatomichybridizationmatrix_lab()

subroutine orbitals_base::getatomichybridizationmatrix_lab	(	type(particle), intent(inout)	atom,
		real, dimension(4,4), intent(out)	hybMatrix
	)

Returns the hybridization matrix in the laboratory frame.

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getatomicvalenceorbitals()

subroutine orbitals_base::getatomicvalenceorbitals	(	type(particle), intent(inout), target	atom,
		type(orbital), dimension(:), intent(out), allocatable	shell
	)

Returns an array of orbitals of atoms lighter than Na.

Warning

In the shell, the radial part is only allocated, but not assigned.

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getdorbitals()

type(list) function, pointer orbitals_base::getdorbitals

(

type(particle)

someParticle

)

From the list returned by GetOrbitals, creates a list of orbitals with angular number two.

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getforbitals()

type(list) function, pointer orbitals_base::getforbitals

(

type(particle)

someParticle

)

From the list returned by GetOrbitals, creates a list of orbitals with angular number three.

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gethybridizationmatrix_from_list()

real function, dimension(4,4) orbitals_base::gethybridizationmatrix_from_list

(

type(list), intent(inout)

hybrids_list

)

Returns the hybridization matrix defined in the given hybrids list.

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gethybridorbital_from_coeffs()

type(orbital) function, pointer orbitals_base::gethybridorbital_from_coeffs	(	type(particle), intent(in)	someParticle,
		real, dimension(4), intent(in)	coeffs
	)

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gethybridorbitalcoeffs()

real function, dimension(0:3) orbitals_base::gethybridorbitalcoeffs

(

type(orbital), intent(in)

hybrid

)

Returns an array of coefficients of the given hybrid.

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gethybridorbitalcoeffs_ptr()

type(real_ptr) function, dimension(0:3) orbitals_base::gethybridorbitalcoeffs_ptr

(

type(orbital), intent(in)

hybrid

)

Returns an array of pointers to the data locations of the coefficients of the given hybrid.

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gethybridorbitalquaternion()

type(quaternion) function, pointer orbitals_base::gethybridorbitalquaternion

(

type(orbital)

hybrid

)

Returns the coefficients of the hybrid in quaternion form.

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gethybridorbitals()

type(list) function, pointer orbitals_base::gethybridorbitals

(

type(particle)

someParticle

)

Returns the hybrid orbitals of the atom in the form a list.

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gethybridorbitalsarray()

type(orbitalbasis) function orbitals_base::gethybridorbitalsarray

(

type(particle)

someParticle

)

Returns the hybrid orbitals of the atom in the form of an array (type orbitalBasis).

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getorbitals()

type(list) function, pointer orbitals_base::getorbitals

(

type(particle)

someParticle

)

Returns the particle's orbitals contained in AttributeList.

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getorbitalswithangularnumber()

type(list) function, pointer orbitals_base::getorbitalswithangularnumber	(	type(particle), intent(in)	someParticle,
		integer, intent(in)	l
	)

From the list returned by GetOrbitals, creates a list of orbitals with given angular number l.

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getorbitalwithquantumnumbers()

type(orbital) function, pointer orbitals_base::getorbitalwithquantumnumbers	(	type(particle), intent(in)	someParticle,
		integer, intent(in)	n,
		integer, intent(in)	l,
		integer, intent(in)	m
	)

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getporbitals()

type(list) function, pointer orbitals_base::getporbitals

(

type(particle)

someParticle

)

From the list returned by GetOrbitals, creates a list of orbitals with angular number one.

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getsandporbitals_array_fn()

type(orbital_ptr) function, dimension(0:3) orbitals_base::getsandporbitals_array_fn

(

type(particle), intent(in)

someParticle

)

Returns an array of orbital pointers to s, px, py, pz. If any of the orbitals are not present, the corresponding pointer is null.

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getsizeofbasis()

subroutine orbitals_base::getsizeofbasis	(	type(node), intent(inout)	part,
		integer, intent(out)	sizeOfBasis
	)

Function which allows to get size of basis of AOs for some polyatomic particles in valence approximation.

getsorbitals()

type(list) function, pointer orbitals_base::getsorbitals

(

type(particle)

someParticle

)

From the list returned by GetOrbitals, creates a list of orbitals with angular number zero.

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isatomicorbital()

logical function orbitals_base::isatomicorbital

(

type(orbital)

someOrbital

)

If pAtom and pY pointers are associated, returns true.

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ishybridatomicorbital()

logical function orbitals_base::ishybridatomicorbital

(

type(orbital)

someOrbital

)

Is the pAtom and orbital exoansion pointers are associated, but the pY is not, returns true.

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ismolecularorbital()

logical function orbitals_base::ismolecularorbital

(

type(orbital)

someOrbital

)

If pAtom pointer is not associated, but the orbital expansion is, returns true.

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isorbitalprimitive()

logical function orbitals_base::isorbitalprimitive

(

type(orbital), intent(in)

orb

)

Checks if orbital is atomic primitive (not a linear combination of STOs or others).

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issameorbitals()

logical function orbitals_base::issameorbitals	(	type(orbital)	orbital1,
		type(orbital)	orbital2
	)

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issamespinorbitals()

logical function orbitals_base::issamespinorbitals	(	type(spinorbital)	spinOrbital1,
		type(spinorbital)	spinOrbital2
	)

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isspinatomicorbital()

logical function orbitals_base::isspinatomicorbital

(

type(spinorbital)

someSpinOrbital

)

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isspinmolecularorbital()

logical function orbitals_base::isspinmolecularorbital

(

type(spinorbital)

someSpinOrbital

)

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l_and_m_index_sp()

integer function orbitals_base::l_and_m_index_sp	(	integer, intent(in)	l,
		integer, intent(in)	m
	)

Returns an array index corresponding to the order s, px, py, pz, starting from 0.

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makehybridatomicorbital_from_array()

subroutine orbitals_base::makehybridatomicorbital_from_array	(	integer, intent(in)	id,
		real, dimension(0:3), intent(in)	coefs,
		type(particle), intent(in), target	atom,
		type(orbital), intent(out)	hybridOrbital
	)

Creates a new hybrid orbital with the given expansion coefficients (in an array). Contains an id field for backwards compatibility.

makehybridatomicorbital_from_array_noid()

subroutine orbitals_base::makehybridatomicorbital_from_array_noid	(	real, dimension(0:3), intent(in)	coefs,
		type(particle), intent(in), target	atom,
		type(orbital), intent(out)	hybridOrbital
	)

Creates a new hybrid orbital with the expansion coefficients (in an array).

makehybridatomicorbital_from_array_ptr_noid()

subroutine orbitals_base::makehybridatomicorbital_from_array_ptr_noid	(	type(real_ptr), dimension(0:3), intent(in)	coefs,
		type(particle), intent(in), target	atom,
		type(orbital), intent(out)	hybridOrbital
	)

Creates a new hybrid orbital with the expansion coefficients pointing to the given data locations.

makehybridatomicorbital_from_vals()

subroutine orbitals_base::makehybridatomicorbital_from_vals	(	integer, intent(in)	id,
		real, intent(in)	s,
		real, intent(in)	px,
		real, intent(in)	py,
		real, intent(in)	pz,
		type(particle), intent(in), target	atom,
		type(orbital), intent(out)	hybridOrbital
	)

Creates a new hybrid orbital with the given expansion coefficients. Contains an id field for backwards compatibility.

Todo:

Finish commenting for hybrid atomic orbitals.

makemolecularorbital()

subroutine orbitals_base::makemolecularorbital	(	integer, intent(in)	id,
		type (orbital_ptr), dimension(:), intent(in), target	orbitals,
		real, dimension(:), intent(in)	coefficients,
		type(orbital), intent(out)	mo
	)

Creates a molecular orbital with an expansion over input orbitals with their coefficients.

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makeorbitalexpansioncoefficient()

subroutine orbitals_base::makeorbitalexpansioncoefficient	(	class(*), intent(in), pointer	someOrbital,
		real, intent(in), optional	coef,
		type(orbitalexpansioncoefficient), intent(out)	oec
	)

Generates a variable of type orbitalExpansionCoefficient.

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makespinorbitalwithspinalpha()

subroutine orbitals_base::makespinorbitalwithspinalpha	(	integer, intent(in), optional, target	num,
		type(orbital), intent(in), target	someOrbital,
		type(spinorbital), intent(out)	AlphaSpinOrbital
	)

makespinorbitalwithspinbeta()

subroutine orbitals_base::makespinorbitalwithspinbeta	(	integer, intent(in), optional, target	num,
		type(orbital), intent(in), target	someOrbital,
		type(spinorbital), intent(out)	BetaSpinOrbital
	)

normalize_hybrid_order()

subroutine orbitals_base::normalize_hybrid_order

(

type(particle), intent(inout)

atom

)

If the determinant of the hybridization matrix is negative, rotates the order of hybrids, which changes the sign.

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orbital_expansion_coef_from_polymorphic()

type(orbitalexpansioncoefficient) function, pointer orbitals_base::orbital_expansion_coef_from_polymorphic

(

class(*), intent(in), pointer

x

)

Converts a polymorphic pointer to an OrbitalExpansionCoefficient pointer if possible, else returns a null-pointer.

orbital_from_polymorphic()

type(orbital) function, pointer orbitals_base::orbital_from_polymorphic

(

class(*), intent(in), pointer

x

)

Converts a polymorphic pointer to an orbital pointer if possible, else returns a null-pointer.

orbital_ptr_from_polymorphic()

type(orbital_ptr) function, pointer orbitals_base::orbital_ptr_from_polymorphic

(

class(*), intent(in), pointer

x

)

Converts a polymorphic pointer to an orbital_ptr pointer if possible, else returns a null-pointer.

orbitalarrayptrtolist()

subroutine orbitals_base::orbitalarrayptrtolist	(	type(orbital_ptr), dimension(:), intent(in)	orbital_array,
		type(list), intent(out)	orbital_list
	)

Converts array of type orbital_ptr to list.

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orbitalarraytolist()

subroutine orbitals_base::orbitalarraytolist	(	type(orbitalbasis), intent(in)	orbital_array,
		type(list), intent(out)	orbital_list
	)

Converts orbitalBasis to list of orbitals.

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orbitallisttoarray()

subroutine orbitals_base::orbitallisttoarray	(	type(list), intent(inout)	orbital_list,
		type(orbitalbasis), intent(out)	orbital_array
	)

Converts list of orbitals to type orbitalsBasis.

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orbitallisttoarrayptr()

subroutine orbitals_base::orbitallisttoarrayptr	(	type(list), intent(inout)	orbital_list,
		type(orbital_ptr), dimension(:), intent(out), allocatable	orbital_array
	)

Converts list of orbitals to allocatable array of type orbital_ptr.

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pangularpart()

type(angularpart) function, pointer orbitals_base::pangularpart	(	integer, intent(in)	l,
		integer, intent(in)	m
	)

reorder_hyblist_for_transform_list()

subroutine orbitals_base::reorder_hyblist_for_transform_list	(	real, dimension(3,3), intent(in)	trfm,
		type(list), intent(inout)	pim_hyblist,
		type(list), intent(inout)	im_hyblist
	)

Reorders the elements of the image list so that applying the given transform to preimage hybrids results gives the image hybrids in the same order.

Warning

Does not check whether the the hybrids correspond to one another. Check that with trfmd_hybs_same_explicit_list.

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rewritehybridscoefficients()

subroutine orbitals_base::rewritehybridscoefficients	(	type(particle), intent(inout)	atom,
		real, dimension(4,4), intent(in)	hyb
	)

Changes all of the hybrid coefficients of this atom based on the given matrix.

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set_image_hybrid_coeffs_explicit_list()

subroutine orbitals_base::set_image_hybrid_coeffs_explicit_list	(	real, dimension(3,3), intent(in)	trfm,
		type(list), intent(inout)	pim_hybs,
		type(list), intent(inout)	im_hybs
	)

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set_image_hybrid_coeffs_implicit()

subroutine orbitals_base::set_image_hybrid_coeffs_implicit	(	type(particle), intent(inout)	pim_atom,
		type(particle), intent(inout)	im_atom
	)

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setatomicorbitalexpansion()

subroutine orbitals_base::setatomicorbitalexpansion	(	type(primitive), dimension(:), intent(in)	set_of_primitives,
		type(orbital), intent(inout), target	ao
	)

Adds an orbital expansion to a basis in an atomic basis set based on the provided set_of_primitives

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sortkeyforexpansioncoefficients()

logical function orbitals_base::sortkeyforexpansioncoefficients	(	class(*), pointer	x1,
		class(*), pointer	x2
	)

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sortkeyfororbitalpointers()

logical function orbitals_base::sortkeyfororbitalpointers	(	class(*), pointer	x1,
		class(*), pointer	x2
	)

Returns TRUE of the ID of x1 is less than the ID of x2.

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sortkeyfororbitals()

logical function orbitals_base::sortkeyfororbitals	(	class(*), pointer	x1,
		class(*), pointer	x2
	)

Returns TRUE of the ID of x1 is less than the ID of x2.

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sortkeyforspinorbitals()

logical function orbitals_base::sortkeyforspinorbitals	(	class(*), pointer	x1,
		class(*), pointer	x2
	)

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sortorbitalarraybynumbers()

subroutine orbitals_base::sortorbitalarraybynumbers

(

type (orbital_ptr), dimension(:), intent(inout)

orbitals

)

Sorts array of orbitals by ID's in ascending order.

Bug:

This sorting loop will not work.

sortorbitallistbynumbers()

subroutine orbitals_base::sortorbitallistbynumbers

(

type(list), intent(inout)

orbitals

)

Sorts linked list of orbitals by ID's in ascending order.

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trfmd_hybs_same_explicit()

logical function orbitals_base::trfmd_hybs_same_explicit	(	real, dimension(3,3), intent(in)	trfm,
		type(particle), intent(in)	preim_atom,
		type(particle), intent(in)	im_atom
	)

Given the explicit transformation matrix, returns true if the image atom's hybrid list contains every image of the preimage atom's hybrids (in any order)

trfmd_hybs_same_explicit_list()

logical function orbitals_base::trfmd_hybs_same_explicit_list	(	real, dimension(3,3), intent(in)	trfm,
		type(list), intent(inout)	pim_hyblist,
		type(list), intent(inout)	im_hyblist
	)

Given the explicit transformation matrix, returns true if the image hybrid list contains every image of the preimage hybrids (in any order)

trfmd_hybs_same_implicit()

logical function orbitals_base::trfmd_hybs_same_implicit	(	type(particle), intent(in)	preim_atom,
		type(particle), intent(in)	im_atom
	)

Same as above, but computes the transformation matrix from the spaceTree.

trfmd_hybs_same_ordered_explicit()

logical function orbitals_base::trfmd_hybs_same_ordered_explicit	(	real, dimension(3,3), intent(in)	trfm,
		type(particle), intent(in)	preim_atom,
		type(particle), intent(in)	im_atom
	)

Given the explicit transformation matrix, returns true if the image atom's hybrid list contains every image of the preimage atom's hybrids (in the same order).

trfmd_hybs_same_ordered_explicit_list()

logical function orbitals_base::trfmd_hybs_same_ordered_explicit_list	(	real, dimension(3,3), intent(in)	trfm,
		type(list), intent(inout)	pim_hyblist,
		type(list), intent(inout)	im_hyblist
	)

Given the explicit transformation matrix, returns true if the image hybrid list contains every image of the preimage hybrids (in the same order).

trfmd_hybs_same_ordered_implicit()

logical function orbitals_base::trfmd_hybs_same_ordered_implicit	(	type(particle), intent(in)	preim_atom,
		type(particle), intent(in)	im_atom
	)

Same as above, but computes the transformation matrix from the spaceTree.

whatisorbitaltype()

subroutine orbitals_base::whatisorbitaltype	(	type(orbital), intent(in)	someOrbital,
		character(len=*), intent(out)	typeName
	)

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whatisspinorbitaltype()

subroutine orbitals_base::whatisspinorbitaltype	(	type(spinorbital), intent(in)	someSpinOrbital,
		character(len=*), intent(out)	typeName
	)

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writehybridizationmatrixtoatom()

subroutine orbitals_base::writehybridizationmatrixtoatom

(

type(particle), intent(inout)

atom

)

Adds the hybridization matrix (taken from the already present hybrid expansions) to the attribute list of the atom.

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writehybridstoatom()

subroutine orbitals_base::writehybridstoatom	(	type(particle), intent(inout)	atom,
		real, dimension(4,4), intent(inout)	hybridMatrix,
		type(orbital_ptr), dimension(4), target	carbonHybrids
	)

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Variable Documentation

allangularparts

type(angularpart_ptr), dimension(:), allocatable, protected orbitals_base::allangularparts

dangularparts

type(angularpart), dimension(-2:2), target, save, public orbitals_base::dangularparts = [AngularPart(2,-2), AngularPart(2,-1), AngularPart(2,0), AngularPart(2,1), AngularPart(2,2)]

fangularparts

type(angularpart), dimension(-3:3), target, save, public orbitals_base::fangularparts = [AngularPart(3,-3), AngularPart(3,-2), AngularPart(3,-1), AngularPart(3,0), AngularPart(3,1), AngularPart(3,2), AngularPart(3,3)]

pangularparts

type(angularpart), dimension(-1:1), target, save, public orbitals_base::pangularparts = [AngularPart(1,-1), AngularPart(1,0), AngularPart(1,1)]

sangularparts

type(angularpart), dimension(0:0), target, save, public orbitals_base::sangularparts = [AngularPart(0,0)]

Warning

DR At some point, (SPDF)AngularParts will not be enough. We should discuss what to do when this happens.

spinalpha

integer, target, save, public orbitals_base::spinalpha = 1

spinbeta

integer, target, save, public orbitals_base::spinbeta = -1

typeofbasis

character(len=3), public orbitals_base::typeofbasis

Attention

Would it make sense to give the freedom to choose the basis for every atom?