462 lines
16 KiB
C++
462 lines
16 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <catch2/catch_all.hpp>
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#include "../common/CrystalLattice.h"
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#include "../common/Coord.h"
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#include "../common/UnitCell.h"
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#include "../image_analysis/lattice_search/LatticeSearch.h"
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#include "gemmi/symmetry.hpp"
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// Helper: check near-equality of unit cell parameters
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static void check_uc(const UnitCell& uc, double a, double b, double c,
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double alpha, double beta, double gamma,
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double eps_len = 1e-6, double eps_ang = 1e-4) {
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CHECK(uc.a == Catch::Approx(a).margin(eps_len));
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CHECK(uc.b == Catch::Approx(b).margin(eps_len));
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CHECK(uc.c == Catch::Approx(c).margin(eps_len));
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CHECK(uc.alpha == Catch::Approx(alpha).margin(eps_ang));
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CHECK(uc.beta == Catch::Approx(beta ).margin(eps_ang));
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CHECK(uc.gamma == Catch::Approx(gamma).margin(eps_ang));
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}
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TEST_CASE("LatticeSearch - cubic I") {
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// Build a body-centered cubic cell with a=40:
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// primitive basis vectors (conventional I cubic primitive):
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// p1 = (0, a/2, a/2), p2 = (a/2, 0, a/2), p3 = (a/2, a/2, 0)
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const double a = 40.0;
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CrystalLattice L(
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Coord(a, 0, 0),
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Coord(0, a, 0),
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Coord(0, 0, a)
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);
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L = L.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Cubic);
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CHECK(res.centering == 'I');
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// Conventional cubic I should have equal edges and 90° angles
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auto uc = res.conventional.GetUnitCell();
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CHECK(uc.a == Catch::Approx( a )); // In this construction, conventional a matches given a
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CHECK(uc.b == Catch::Approx( a ));
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CHECK(uc.c == Catch::Approx( a ));
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CHECK(uc.alpha == Catch::Approx(90.0));
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CHECK(uc.beta == Catch::Approx(90.0));
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CHECK(uc.gamma == Catch::Approx(90.0));
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}
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TEST_CASE("LatticeSearch - cubic F") {
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// Build a body-centered cubic cell with a=40:
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// primitive basis vectors (conventional I cubic primitive):
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// p1 = (0, a/2, a/2), p2 = (a/2, 0, a/2), p3 = (a/2, a/2, 0)
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const double a = 40.0;
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CrystalLattice L(
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Coord(a, 0, 0),
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Coord(0, a, 0),
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Coord(0, 0, a)
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);
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L = L.ToPrimitive('F');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Cubic);
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CHECK(res.centering == 'F');
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// Conventional cubic I should have equal edges and 90° angles
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auto uc = res.conventional.GetUnitCell();
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CHECK(uc.a == Catch::Approx( a )); // In this construction, conventional a matches given a
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CHECK(uc.b == Catch::Approx( a ));
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CHECK(uc.c == Catch::Approx( a ));
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CHECK(uc.alpha == Catch::Approx(90.0));
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CHECK(uc.beta == Catch::Approx(90.0));
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CHECK(uc.gamma == Catch::Approx(90.0));
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}
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TEST_CASE("LatticeSearch - cubic P") {
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// Simple cubic P, a=30
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const double a = 30.0;
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CrystalLattice L(
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Coord(a,0,0),
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Coord(0,a,0),
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Coord(0,0,a)
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);
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Cubic);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, a, a, 90.0, 90.0, 90.0, 1e-6, 1e-4);
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}
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TEST_CASE("LatticeSearch - tetragonal I") {
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// Build a body-centered cubic cell with a=40:
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// primitive basis vectors (conventional I cubic primitive):
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// p1 = (0, a/2, a/2), p2 = (a/2, 0, a/2), p3 = (a/2, a/2, 0)
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const double a = 40.0;
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const double b = 34.0;
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CrystalLattice L(
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Coord(a, 0, 0),
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Coord(0, a, 0),
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Coord(0, 0, b)
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);
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L = L.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Tetragonal);
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CHECK(res.centering == 'I');
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// Conventional cubic I should have equal edges and 90° angles
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auto uc = res.conventional.GetUnitCell();
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CHECK(uc.a == Catch::Approx( a )); // In this construction, conventional a matches given a
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CHECK(uc.b == Catch::Approx( a ));
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CHECK(uc.c == Catch::Approx( b ));
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CHECK(uc.alpha == Catch::Approx(90.0));
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CHECK(uc.beta == Catch::Approx(90.0));
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CHECK(uc.gamma == Catch::Approx(90.0));
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}
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TEST_CASE("LatticeSearch - tetragonal I - v2") {
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// Build a body-centered cubic cell with a=40:
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// primitive basis vectors (conventional I cubic primitive):
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// p1 = (0, a/2, a/2), p2 = (a/2, 0, a/2), p3 = (a/2, a/2, 0)
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const double a = 40.0;
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const double b = 54.0;
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CrystalLattice L(
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Coord(a, 0, 0),
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Coord(0, a, 0),
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Coord(0, 0, b)
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);
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L = L.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Tetragonal);
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CHECK(res.centering == 'I');
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// Conventional cubic I should have equal edges and 90° angles
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auto uc = res.conventional.GetUnitCell();
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CHECK(uc.a == Catch::Approx( a )); // In this construction, conventional a matches given a
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CHECK(uc.b == Catch::Approx( a ));
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CHECK(uc.c == Catch::Approx( b ));
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CHECK(uc.alpha == Catch::Approx(90.0));
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CHECK(uc.beta == Catch::Approx(90.0));
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CHECK(uc.gamma == Catch::Approx(90.0));
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}
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// Tetragonal P: a=b!=c, all angles 90, P-centering
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TEST_CASE("LatticeSearch - tetragonal P") {
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const double a = 37.0, c = 59.0;
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CrystalLattice L(
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Coord(a,0,0),
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Coord(0,a,0),
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Coord(0,0,c)
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);
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Tetragonal);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, a, c, 90.0, 90.0, 90.0, 1e-2, 1e-2);
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}
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// Orthorhombic F: all angles 90, unequal edges, F-centering
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TEST_CASE("LatticeSearch - orthorhombic F") {
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const double a = 35.0, b = 41.0, c = 57.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('F');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'F');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, b, c, 90.0, 90.0, 90.0, 1e-1, 1e-2);
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}
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TEST_CASE("LatticeSearch - orthorhombic F - permutation 1") {
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const double a = 41.0, b = 57.0, c = 35.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('F');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'F');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, c, a, b, 90.0, 90.0, 90.0, 1e-1, 1e-2);
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}
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// Orthorhombic C: all angles 90, unequal edges, C-centering
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TEST_CASE("LatticeSearch - orthorhombic C") {
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const double a = 35.0, b = 41.0, c = 57.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('C');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'C');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, b, c, 90.0, 90.0, 90.0, 1e-1, 1e-2);
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}
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TEST_CASE("LatticeSearch - orthorhombic I") {
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const double a = 35.0, b = 41.0, c = 57.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'I');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, b, c, 90.0, 90.0, 90.0, 1e-2, 1e-2);
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}
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TEST_CASE("LatticeSearch - orthorhombic I - permutation1") {
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const double a = 57.0, b = 41.0, c = 35.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'I');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, c, b, a, 90.0, 90.0, 90.0, 1e-2, 1e-2);
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}
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TEST_CASE("LatticeSearch - orthorhombic I - permutation2") {
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const double a = 41.0, b = 57.0, c = 35.0;
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CrystalLattice conv(a,b,c, 90.0,90.0,90.0);
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CrystalLattice L = conv.ToPrimitive('I');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'I');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, c, a, b, 90.0, 90.0, 90.0, 1e-2, 1e-2);
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}
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// Orthorhombic P: all angles 90, unequal edges, P-centering
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TEST_CASE("LatticeSearch - orthorhombic P") {
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const double a = 35.0, b = 41.0, c = 57.0;
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CrystalLattice L(a,b,c, 90.0,90.0,90.0);
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Orthorhombic);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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check_uc(uc, a, b, c, 90.0, 90.0, 90.0, 1e-6, 1e-4);
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}
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// Hexagonal P: a=b!=c, alpha=beta=90, gamma=120, P-centering
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TEST_CASE("LatticeSearch - hexagonal P") {
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const double a = 30.0, c = 48.0;
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CrystalLattice L(
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Coord(a, 0, 0),
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Coord(-a/2, a*std::sqrt(3)/2, 0),
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Coord(0, 0, c)
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);
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Hexagonal);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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CHECK(uc.a == Catch::Approx(a).margin(1e-2));
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CHECK(uc.b == Catch::Approx(a).margin(1e-2));
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CHECK(uc.c == Catch::Approx(c).margin(1e-2));
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CHECK(uc.alpha == Catch::Approx(90.0).margin(1e-2));
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CHECK(uc.beta == Catch::Approx(90.0).margin(1e-2));
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CHECK(uc.gamma == Catch::Approx(120.0).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - monoclinic C (unique b)") {
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const double a = 50.0, b = 60.0, c = 70.0;
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const double alpha = 90.0, beta = 96.0, gamma = 90.0;
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CrystalLattice conv(a,b,c, alpha,beta,gamma);
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auto L = conv.ToPrimitive('C');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Monoclinic);
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CHECK(res.centering == 'C');
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auto uc = res.conventional.GetUnitCell();
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// Check right angles at alpha,gamma and non-90 beta; lengths comparable
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CHECK(std::fabs(uc.alpha - 90.0) < 1e-3);
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CHECK(std::fabs(uc.gamma - 90.0) < 1e-3);
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CHECK(std::fabs(uc.beta - beta) < 1e-2);
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// Lengths should match within small tolerance
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CHECK(uc.a == Catch::Approx(a).margin(1e-2));
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CHECK(uc.b == Catch::Approx(b).margin(1e-2));
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CHECK(uc.c == Catch::Approx(c).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - monoclinic C (unique b) - v2") {
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const double a = 71.0, b = 35.0, c = 90.0;
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const double alpha = 90.0, beta = 96.0, gamma = 90.0;
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CrystalLattice conv(a,b,c, alpha,beta,gamma);
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auto L = conv.ToPrimitive('C');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Monoclinic);
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CHECK(res.centering == 'C');
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auto uc = res.conventional.GetUnitCell();
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// Check right angles at alpha,gamma and non-90 beta; lengths comparable
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CHECK(std::fabs(uc.alpha - 90.0) < 1e-3);
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CHECK(std::fabs(uc.gamma - 90.0) < 1e-3);
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CHECK(std::fabs(uc.beta - beta) < 1e-2);
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// Lengths should match within small tolerance
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CHECK(uc.a == Catch::Approx(a).margin(1e-2));
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CHECK(uc.b == Catch::Approx(b).margin(1e-2));
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CHECK(uc.c == Catch::Approx(c).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - monoclinic C (unique a)") {
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const double a = 60.0, b = 50.0, c = 70.0;
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const double alpha = 96.0, beta = 90.0, gamma = 90.0;
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CrystalLattice conv(a,b,c, alpha,beta,gamma);
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auto L = conv.ToPrimitive('C');
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Monoclinic);
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CHECK(res.centering == 'C');
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auto uc = res.conventional.GetUnitCell();
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// Check right angles at alpha,gamma and non-90 beta; lengths comparable
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CHECK(std::fabs(uc.alpha - 90.0) < 1e-3);
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CHECK(std::fabs(uc.gamma - 90.0) < 1e-3);
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CHECK(std::fabs(uc.beta - alpha) < 1e-2);
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// Lengths should match within small tolerance
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CHECK(uc.a == Catch::Approx(b).margin(1e-2));
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CHECK(uc.b == Catch::Approx(a).margin(1e-2));
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CHECK(uc.c == Catch::Approx(c).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - monoclinic P (unique b)") {
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const double a = 50.0, b = 60.0, c = 70.0;
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const double alpha = 90.0, beta = 96.0, gamma = 90.0;
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CrystalLattice conv(a,b,c, alpha,beta,gamma);
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auto res = LatticeSearch(conv, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Monoclinic);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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// Check right angles at alpha,gamma and non-90 beta; lengths comparable
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CHECK(std::fabs(uc.alpha - 90.0) < 1e-3);
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CHECK(std::fabs(uc.gamma - 90.0) < 1e-3);
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CHECK(std::fabs(uc.beta - beta) < 1e-2);
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// Lengths should match within small tolerance
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CHECK(uc.a == Catch::Approx(a).margin(1e-2));
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CHECK(uc.b == Catch::Approx(b).margin(1e-2));
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CHECK(uc.c == Catch::Approx(c).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - monoclinic P (unique b) - v2") {
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const double a = 90.0, b = 35.0, c = 71.0;
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const double alpha = 90.0, beta = 96.0, gamma = 90.0;
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CrystalLattice conv(a,b,c, alpha,beta,gamma);
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auto res = LatticeSearch(conv, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Monoclinic);
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CHECK(res.centering == 'P');
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auto uc = res.conventional.GetUnitCell();
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// Check right angles at alpha,gamma and non-90 beta; lengths comparable
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CHECK(std::fabs(uc.alpha - 90.0) < 1e-3);
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CHECK(std::fabs(uc.gamma - 90.0) < 1e-3);
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CHECK(std::fabs(uc.beta - beta) < 1e-2);
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// Lengths should match within small tolerance
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CHECK(uc.a == Catch::Approx(c).margin(1e-2));
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CHECK(uc.b == Catch::Approx(b).margin(1e-2));
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CHECK(uc.c == Catch::Approx(a).margin(1e-2));
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}
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TEST_CASE("LatticeSearch - triclinic P") {
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// General triclinic primitive cell
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CrystalLattice L(33.1, 41.7, 52.3, 89.1, 85.0, 76.3);
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auto res = LatticeSearch(L, 1e-6);
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// System should be triclinic, centering P, and conventional equals some standardized primitive
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CHECK(res.system == gemmi::CrystalSystem::Triclinic);
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CHECK(res.centering == 'P');
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// The conventional cell should be metric-equivalent to input. We verify only the system and centering here.
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// Reduced primitive must be non-singular
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auto uc_red = res.primitive_reduced.GetUnitCell();
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CHECK(uc_red.a > 0);
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CHECK(uc_red.b > 0);
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CHECK(uc_red.c > 0);
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}
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TEST_CASE("LatticeSearch - triclinic P - v2") {
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// General triclinic primitive cell
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CrystalLattice L(33.1, 41.7, 52.3, 100, 92, 115);
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auto res = LatticeSearch(L, 1e-6);
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// System should be triclinic, centering P, and conventional equals some standardized primitive
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CHECK(res.system == gemmi::CrystalSystem::Triclinic);
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CHECK(res.centering == 'P');
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// The conventional cell should be metric-equivalent to input. We verify only the system and centering here.
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// Reduced primitive must be non-singular
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auto uc_red = res.primitive_reduced.GetUnitCell();
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CHECK(uc_red.a > 0);
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CHECK(uc_red.b > 0);
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CHECK(uc_red.c > 0);
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}
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TEST_CASE("LatticeSearch - trigonal R") {
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const double a = 32.0;
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const double alpha = 80.0;
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// Build rhombohedral in rhombohedral setting (primitive axes a=b=c, alpha=beta=gamma)
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CrystalLattice L(a, a, a, alpha, alpha, alpha);
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auto res = LatticeSearch(L, 1e-6);
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CHECK(res.system == gemmi::CrystalSystem::Trigonal);
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CHECK(res.centering == 'R');
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auto uc_red = res.conventional.GetUnitCell();
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CHECK(uc_red.alpha == Catch::Approx(90).margin(1e-2));
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CHECK(uc_red.beta == Catch::Approx(90).margin(1e-2));
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CHECK(uc_red.gamma == Catch::Approx(120).margin(1e-2));
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auto uc_prim = res.primitive_reduced.GetUnitCell();
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CHECK(uc_prim.alpha == Catch::Approx(alpha).margin(1e-2));
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CHECK(uc_prim.beta == Catch::Approx(alpha).margin(1e-2));
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CHECK(uc_prim.gamma == Catch::Approx(alpha).margin(1e-2));
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}
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