File StructuralCompletion.hΒΆ

Copyright

This code is licensed under the 3-clause BSD license.

Copyright ETH Zurich, Laboratory for Physical Chemistry, Reiher Group.

See LICENSE.txt for details.

namespace Scine

This header file contains functions that allow for common notation for common things that can be done at a different degree of derivatives.

This header contains alias definitions defining which classes to use for the different degrees of derivatives.

namespace Utils
class StructuralCompletion
#include <StructuralCompletion.h>

Contains function to generate positions from other positions.

F.i. to be applied to add hydrogen atoms to a carbon chain.

Public Functions

StructuralCompletion()

Static functions only.

Public Static Functions

static void generate3TetrahedronCornersFrom1Other(const Eigen::Ref<Eigen::Vector3d> v1, Eigen::Ref<Eigen::Vector3d> v2, Eigen::Ref<Eigen::Vector3d> v3, Eigen::Ref<Eigen::Vector3d> v4)

Generates three missing position in a tetrahedron.

Given a normalized vector v1 showing from the center of a tetrahedron to one of its corners, calculates three other normalized vectors to three other possible corners. Application example: -C -> -CH3.

Parameters

  • v1: A vector connecting the center and a known corner.

  • v2: A vector to be populated, then connecting the center and a corner.

  • v3: A vector to be populated, then connecting the center and a corner.

  • v4: A vector to be populated, then connecting the center and a corner.

static void generate2TetrahedronCornersFrom2Others(const Eigen::Ref<Eigen::Vector3d> v1, const Eigen::Ref<Eigen::Vector3d> v2, Eigen::Ref<Eigen::Vector3d> v3, Eigen::Ref<Eigen::Vector3d> v4)

Generates two missing position in a tetrahedron.

Given two normalized vectors v1 and v2, calculates two other normalized vectors in order to generate a tetrahedron (as well as possible). Does not work if v1 and v2 are collinear. Application example: -C- -> -CH2-.

Parameters

  • v1: A vector connecting the center and a known corner.

  • v2: A vector connecting the center and a known corner.

  • v3: A vector to be populated, then connecting the center and a corner.

  • v4: A vector to be populated, then connecting the center and a corner.

static void generate1TetrahedronCornerFrom3Others(const Eigen::Ref<Eigen::Vector3d> v1, const Eigen::Ref<Eigen::Vector3d> v2, const Eigen::Ref<Eigen::Vector3d> v3, Eigen::Ref<Eigen::Vector3d> v4)

Generates one missing position in a tetrahedron.

Given three normalized vectors, calculates another normalized vector in order to generate a tetrahedron (as well as possible). Does not work if v1, v2 and v3 are in the same plane. Application example: -C-R2 -> -CH-R2.

Parameters

  • v1: A vector connecting the center and a known corner.

  • v2: A vector connecting the center and a known corner.

  • v3: A vector connecting the center and a known corner.

  • v4: A vector to be populated, then connecting the center and a corner.

static void generate2TriangleCornersFrom1Other(const Eigen::Ref<Eigen::Vector3d> v1, Eigen::Ref<Eigen::Vector3d> v2, Eigen::Ref<Eigen::Vector3d> v3)

Generates two missing position in a triangle.

Given a normalized vector v1 showing from the center of a triangle to one of its corners, calculates two other normalized vectors to two other possible corners. Application example: -C -> -CH2.

Parameters

  • v1: A vector connecting the center and a known corner.

  • v2: A vector to be populated, then connecting the center and a corner.

  • v3: A vector to be populated, then connecting the center and a corner.

static void generate1TriangleCornerFrom2Others(const Eigen::Ref<Eigen::Vector3d> v1, const Eigen::Ref<Eigen::Vector3d> v2, Eigen::Ref<Eigen::Vector3d> v3)

Generates a missing position in a triangle.

Given two normalized vectors, calculates another normalized vector in order to generate a triangle (as well as possible). Does not work if v1 and v2 are collinear. Application example: -C- -> -CH-.

Parameters

  • v1: A vector connecting the center and a known corner.

  • v2: A vector connecting the center and a known corner.

  • v3: A vector to be populated, then connecting the center and a corner.

Public Static Attributes

constexpr double tetrahedronAngle = 109.4712 * Constants::rad_per_degree

The standard tetrahedral angel in rad.