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Molecules

Loading Molecule Files

Molecule input files are stored in PorousMaterials.PATH_TO_MOLECULES. Each molecule possesses its own directory containing two files: charges.csv and atoms.csv, comma-separated-value files, which describe the point charges and Lennard Jones spheres, respectively, that compose the molecule. Only rigid molecules are currently supported. Units of length are in Angstroms ($\AA$); units of charges are electrons.

molecule = Molecule("CO2")
# output
Molecule species: CO2
Center of mass (fractional coords): Cart([0.0; 0.0; 0.0])
Atoms:

	atom = C_CO2, x = [0.000, 0.000, 0.000]
	atom = O_CO2, x = [-1.160, 0.000, 0.000]
	atom = O_CO2, x = [1.160, 0.000, 0.000]
Point charges:
	charge = 0.700000, x = [0.000, 0.000, 0.000]
	charge = -0.350000, x = [-1.160, 0.000, 0.000]
	charge = -0.350000, x = [1.160, 0.000, 0.000]

Building Blocks of PorousMaterials: Molecules

# access the attributes that comprise the molecule object
molecule.species   # molecule species
molecule.com       # center-of-mass
molecule.atoms     # Lennard-Jones spheres
molecule.charges   # point charges

To see specific information about the atoms and charges attributes of the molecule see Atoms and Charges.

Moving Molecules

We can translate and roatate a molecule:

# convert to Molecule{Frac}
molecule = Frac(molecule, unit_cube())

# translate center-of-mass to [1.0, 2.0, 3.0] in fractional coordinates
x = Cart([1.0, 2.0, 3.0])
translate_to!(molecule, x, unit_cube())

# translate by [0.1, 0.0, 0.0] in fractional coordinates
dx = Cart([0.1, 0.0, 0.0])
translate_by!(molecule, dx, unit_cube())

# conduct a uniform random rotation about the center-of-mass
random_rotation!(molecule, unit_cube())

detailed docs

Molecules

PorousMaterials.Molecule — Type

Data structure for a molecule/adsorbate.

Attributes

  • species::Symbol: Species of molecule, e.g. :CO2
  • atoms::Atoms: array of Lennard-Jones spheres comprising the molecule
  • charges::Charges: array of point charges comprising the molecule
  • com::Coords: center of mass
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PorousMaterials.translate_to! — Function
translate_to!(molecule, xf)
translate_to!(molecule, x)
translate_to!(molecule, xf, box)
translate_to!(molecule, x, box)

Translate a molecule so that its center of masss is at a point xf in fractional coordinate space or at x in Cartesian coordinate space. For the latter, a unit cell box is required for context.

source
PorousMaterials.random_rotation_matrix — Method
r = random_rotation_matrix() # rotation matrix in cartesian coords

Generate a 3x3 random rotation matrix r such that when a point x is rotated using this rotation matrix via r * x, this point x is placed at a uniform random distributed position on the surface of a sphere of radius norm(x). the point x is in Cartesian coordinates here. See James Arvo. Fast Random Rotation Matrices.

https://pdfs.semanticscholar.org/04f3/beeee1ce89b9adf17a6fabde1221a328dbad.pdf

Returns

  • r::Array{Float64, 2}: A 3x3 random rotation matrix
source
PorousMaterials.ion — Function
molecule = ion(q, coords)

Facilitate constructing a point charge by constructing a molecule: Molecule(:ion, Atoms{Frac}(0), Charges(q, coords), coords)

Arguments

  • q::Float64: value of point charge, units: electrons
  • coords::Frac: fractional coordinates of the charge

Returns

  • molecule::Molecule{Frac}: the ion as a molecule with Fractional coordinates
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PorousMaterials.distortion — Function
is_distorted = distortion(molecule, ref_molecule, box; 
                          atol=1e-12, throw_warning=true)

Determine whether a molecule has distortion w.r.t. a reference molecule via pairwise distance comparison of the atoms and charges coordinates.

Arguments

  • molecule::Molecule{Frac}: molecule you want to compare
  • ref_molecule::Molecule{Frac}: reference molecule
  • box::Box: box used for the fractional coordinates
  • atol::Float64=1e-12: absolute tolerance for distance comparison
  • throw_warning::Bool=true: issue a warning if there is distortion

Returns

  • is_distorted::Bool: true if there is distortion w.r.t. reference molecule
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Molecular Movement

PorousMaterials.apply_periodic_boundary_condition! — Function
apply_periodic_boundary_condition!(molecule::Molecule{Frac})

Check if each of a molecule's center-of-mass coordinates is within the bounds (0.0, 1.0) in fractional coordinates, and translate if needed.

Arguments

  • molecule::Molecule{Frac}: the molecule to be checked

Returns

  • nothing, if the molecule is within the boundary; ohterwise, the coordinates of the input molecule will be modified
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PorousMaterials.random_insertion! — Function
random_insertion!(molecules::Array{Molecule{Frac}, 1}, box::Box, template::Molecule{Cart})

Insert a molecule into the simulation box and perform a random rotation if needed.

Arguments

  • molecules::Array{Molecule{Frac}, 1}: array containing the molecules in the simulation
  • box::Box: the box used for fractional coordinats
  • template::Molecule{Cart}: reference molecule of the type inserted
source
PorousMaterials.remove_molecule! — Function
remove_molecule!(molecule_id, molecules)

Remove a molecule from the array of molecules.

Arguments

  • molecule_id::Int: the ID of the molecule to be removed
  • molecules::Array{<:Molecule, 1}: array of molecules to be modified
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PorousMaterials.random_translation! — Function
random_reinsertion!(molecule, box)

Perform a translational perturbation in Cartesian coordinates on a molecule, apply the periodic boundry conditions, and keep a copy of the original in case it needs to be restored.

Arguements

  • molecule::Molecule{Frac}: molecule to be translated
  • box::Box: the box used in rotation

Returns

  • old_molecule::Molecule{Frac}: a copy of the original molecule
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PorousMaterials.random_reinsertion! — Function
random_reinsertion!(molecule, box)

Perform a translation and rotated (if needed) on a molecule, and keep a copy of the original in case it needs to be restored.

Arguements

  • molecule::Molecule{Frac}: molecule to be translated and rotated (if needed)
  • box::Box: the box used in rotation

Returns

  • old_molecule::Molecule{Frac}: a copy of the original molecule
source
PorousMaterials.needs_rotations — Function
needs_rotations(molecule) # true or false

Determine whether a molecule needs to undergo rotation.

`true` if molecule.atoms.n + molecule.charges.n > 1
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