buildparticle Module Reference

Data Types
interface	build_system
type	scfslg_group_line_data

Functions/Subroutines
subroutine	init_from_old_data_noalloc (system, filename, input_format, laboratory, system_name, stat)
	Allocates and returns a new particle tree "system" from the existing data in various formats. More...
subroutine	init_from_old_data (system, filename, input_format, laboratory, system_name, stat)
	allocates the polymorphic tree system and positions it in the origin of the laboratory frame. Next fills the the polymorphic tree system by data read from historical formats. If format is not supported deallocates system by this defining null system. 12.09.2021 ALT More...
procedure(build_system) function, pointer	select_system_initer (input_format)
subroutine	init_not_implemented (filename, system, stat)
subroutine	init_from_poscar_or_adamas (filename, system, stat)
subroutine	init_from_wxdragoninternal (filename, system, stat)
subroutine	init_from_simplexyzwrittenbywxdragon (filename, system, stat)
subroutine	init_from_ecf (filename, system, stat)
subroutine	init_from_molcryst (filename, system, stat)
subroutine	init_from_gaussianviewfragment (filename, system, stat)
subroutine	init_from_catal (filename, system, stat)
subroutine	init_from_geomo (filename, system, stat)
subroutine	init_from_bfscf (filename, system, stat)
subroutine	init_from_magiixtic (filename, system, stat)
subroutine	init_from_bfecf (filename, system, stat)
subroutine	init_from_mult (filename, system, stat)
subroutine	init_from_scfslg_file (filename, system, stat)
subroutine	read_cif (filename, atomicNumbers, atomicCoordinates, unit_cell)
subroutine	read_poscar (filename, atomicNumbers, atomicCoordinates, unit_cell)
integer function	getatomicnumberfromuppercasesymbol (Element_Identifier)
integer function	getatomicnumberfromsymbol (Element_Identifier)
subroutine	createatom (newAtom, NewAtomId, Atomic_Number, frame, shift)
	Function that creates an atom with given attributes and adds its location to the given frame's spaceTree. More...
subroutine	createandaddatomtosystem (system, ParentID, NewAtomId, Atomic_Number, frame, shift, new_atom)
	Creates an atom with given atomic number, weight, and position and adds it to tree of the molecule: More...
subroutine	displaceatom (atom, givenDisplacement)
subroutine	add_origin_unit_cell (system)
	Creates origin unit cell and adds it to the list of attribute. It is required when one has to save input unit cell before optimization. More...
subroutine	parse_sp_weights_bfscf (line, atoms_array, coefs, atom_ind, ios, sym_op)
	Parses the s- and p-weights and the corresponding atom from a *.bfscf-like line. More...

Variables
character(len=8), parameter, private	default_system_name = 'molecule'

Function/Subroutine Documentation

add_origin_unit_cell()

subroutine buildparticle::add_origin_unit_cell

(

type(node), intent(inout)

system

)

Creates origin unit cell and adds it to the list of attribute. It is required when one has to save input unit cell before optimization.

Note

Unit cell should be defined for the system.

createandaddatomtosystem()

subroutine buildparticle::createandaddatomtosystem	(	type(node), intent(inout), target	system,
		character(len=*), intent(in)	ParentID,
		character(len=*), intent(in)	NewAtomId,
		integer, intent(in)	Atomic_Number,
		type(point), intent(in), target	frame,
		type(vector), intent(in)	shift,
		type(particle), intent(out), optional, pointer	new_atom
	)

Creates an atom with given atomic number, weight, and position and adds it to tree of the molecule:

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createatom()

subroutine buildparticle::createatom	(	type(particle), intent(out), pointer	newAtom,
		character(len=*), intent(in)	NewAtomId,
		integer, intent(in)	Atomic_Number,
		type(point), intent(in), target	frame,
		type(vector), intent(in)	shift
	)

Function that creates an atom with given attributes and adds its location to the given frame's spaceTree.

Parameters

newAtom	Result of the procedure. atom of type particle.
NewAtomId	String with the ID of the atom.
Atomic_Number	The atomic number. It will be written, along with the corresponding weight, to the list of its properties.
frame	Laboratory, Atomic, etc. Specifies the frame within which the coordinates are given.
shift	Atom location within the local frame's coordinate system (explicitly assumed to be cartesian).

Attention

Creation of atoms currently assumes only one existing isotope for every atom.

displaceatom()

subroutine buildparticle::displaceatom	(	type(particle), intent(inout)	atom,
		class(*), intent(in)	givenDisplacement
	)

getatomicnumberfromsymbol()

integer function buildparticle::getatomicnumberfromsymbol

(

character(len=2), intent(in)

Element_Identifier

)

getatomicnumberfromuppercasesymbol()

integer function buildparticle::getatomicnumberfromuppercasesymbol

(

character(len=2), intent(in)

Element_Identifier

)

init_from_bfecf()

subroutine buildparticle::init_from_bfecf	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_bfscf()

subroutine buildparticle::init_from_bfscf	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

Warning

DR 27.04.2021 We might want to introduce a new naming system. It is hard to find an atom by its number after the file has been read.

Note

For "*.bfscf" this currently adds all atoms as children of the whole system, since fragments are not implemented yet.

Why it is so? What id wrong with Multiplicity itself? Why not to define integer pElectronicGroupMultiplicity? 12.09.2021 ALT

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init_from_catal()

subroutine buildparticle::init_from_catal	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_ecf()

subroutine buildparticle::init_from_ecf	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_gaussianviewfragment()

subroutine buildparticle::init_from_gaussianviewfragment	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_geomo()

subroutine buildparticle::init_from_geomo	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_magiixtic()

subroutine buildparticle::init_from_magiixtic	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_molcryst()

subroutine buildparticle::init_from_molcryst	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

Todo:

Needs to be expanded up to forming the particle containing the unit cell of Molecular crystal 12.09.2021 ALT

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init_from_mult()

subroutine buildparticle::init_from_mult	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_old_data()

subroutine buildparticle::init_from_old_data	(	type(node), intent(out), allocatable, target	system,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	input_format,
		type(point), intent(inout), pointer	laboratory,
		character(len=*), intent(in), optional	system_name,
		integer, intent(out), optional	stat
	)

allocates the polymorphic tree system and positions it in the origin of the laboratory frame. Next fills the the polymorphic tree system by data read from historical formats. If format is not supported deallocates system by this defining null system. 12.09.2021 ALT

Note

Ilya, please have a look on the comments

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init_from_old_data_noalloc()

subroutine buildparticle::init_from_old_data_noalloc	(	type(node), intent(out), target	system,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	input_format,
		type(point), intent(inout), pointer	laboratory,
		character(len=*), intent(in), optional	system_name,
		integer, intent(out), optional	stat
	)

Allocates and returns a new particle tree "system" from the existing data in various formats.

Todo:

Break up the cases into individual subroutines to make cleaner code

@Attention About spaceTree, since every node in the spaceTree ends with 'point', I think it makes sense to rename the 'root' node to 'rootpoint' and make sure the laboratory point's id is the same, maybe (see comment right above). If the spaceTree root node name is changed, 'organicum' will not compile because of one line. it can be found by searching for 'DR 30.09.2021'. CreateAtom and CreateAndAddAtomToSystem will not break, but I didn't check others. Moreover, we might want to add a key for 'root' either in Attributes or in polymorphic_tree_mod.

Todo:

Add a property to rootParticle that would allow to identify it as a fragment.

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init_from_poscar_or_adamas()

subroutine buildparticle::init_from_poscar_or_adamas	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_scfslg_file()

subroutine buildparticle::init_from_scfslg_file	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

Todo:

Add check for correct geometry of unit cell for given space group

Todo:

Properly deallocate scfslg system in case of error during init.

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init_from_simplexyzwrittenbywxdragon()

subroutine buildparticle::init_from_simplexyzwrittenbywxdragon	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_from_wxdragoninternal()

subroutine buildparticle::init_from_wxdragoninternal	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

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init_not_implemented()

subroutine buildparticle::init_not_implemented	(	character(len=*), intent(in)	filename,
		type(node), intent(inout), target	system,
		integer, intent(out), optional	stat
	)

parse_sp_weights_bfscf()

subroutine buildparticle::parse_sp_weights_bfscf	(	character(len=*), intent(in)	line,
		type(particle_ptr), dimension(:), intent(in), allocatable	atoms_array,
		real, dimension(0:3), intent(out)	coefs,
		integer, intent(out)	atom_ind,
		integer, intent(out), optional	ios,
		type(point), intent(out), optional	sym_op
	)

Parses the s- and p-weights and the corresponding atom from a *.bfscf-like line.

Parameters

line	Character string to be parsed
fragment	The (sub)system in which the atom exists
cs,cpx,cpy,cpz	The s, px, py, pz coefficients
atom_ind	Index of the atom whose hybrid coefficients are being calculated
ios	(optional) The parsing state. 0 means normal calculation. 1, 2, 3 mean the corresponding atom's name has not been identified. 4 means the bfscf string was input incorrectly.

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read_cif()

subroutine buildparticle::read_cif	(	character(len=*), intent(in)	filename,
		integer, dimension(:), intent(out), allocatable	atomicNumbers,
		real, dimension(:,:), intent(out), allocatable	atomicCoordinates,
		type(unitcell), intent(inout)	unit_cell
	)

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read_poscar()

subroutine buildparticle::read_poscar	(	character(len=*), intent(in)	filename,
		integer, dimension(:), intent(out), allocatable	atomicNumbers,
		real, dimension(:,:), intent(out), allocatable	atomicCoordinates,
		type(unitcell), intent(inout)	unit_cell
	)

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select_system_initer()

procedure(build_system) function, pointer buildparticle::select_system_initer

(

character(len=*), intent(in)

input_format

)

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Variable Documentation

default_system_name

character(len=8), parameter, private buildparticle::default_system_name = 'molecule'

private