Program Listing for File symmetry.hpp

↰ Return to documentation for file (cif++/symmetry.hpp)

/*-
 * SPDX-License-Identifier: BSD-2-Clause
 *
 * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include "cif++/exports.hpp"
#include "cif++/matrix.hpp"
#include "cif++/point.hpp"

#include <array>
#include <cstdint>
#include <string>

#if defined(__cpp_impl_three_way_comparison)
#include <compare>
#endif

namespace cif
{

// --------------------------------------------------------------------

inline point operator*(const matrix3x3<float> &m, const point &pt)
{
    return {
        m(0, 0) * pt.m_x + m(0, 1) * pt.m_y + m(0, 2) * pt.m_z,
        m(1, 0) * pt.m_x + m(1, 1) * pt.m_y + m(1, 2) * pt.m_z,
        m(2, 0) * pt.m_x + m(2, 1) * pt.m_y + m(2, 2) * pt.m_z
    };
}

// --------------------------------------------------------------------

enum class space_group_name
{
    full,
    xHM,
    Hall
};

struct space_group
{
    const char *name;
    const char *xHM;
    const char *Hall;
    int nr;
};

extern CIFPP_EXPORT const space_group kSpaceGroups[];

extern CIFPP_EXPORT const std::size_t kNrOfSpaceGroups;

// --------------------------------------------------------------------

struct symop_data
{
    constexpr symop_data(const std::array<int, 15> &data)
        : m_packed((data[0] bitand 0x03ULL) << 34 bitor
                   (data[1] bitand 0x03ULL) << 32 bitor
                   (data[2] bitand 0x03ULL) << 30 bitor
                   (data[3] bitand 0x03ULL) << 28 bitor
                   (data[4] bitand 0x03ULL) << 26 bitor
                   (data[5] bitand 0x03ULL) << 24 bitor
                   (data[6] bitand 0x03ULL) << 22 bitor
                   (data[7] bitand 0x03ULL) << 20 bitor
                   (data[8] bitand 0x03ULL) << 18 bitor
                   (data[9] bitand 0x07ULL) << 15 bitor
                   (data[10] bitand 0x07ULL) << 12 bitor
                   (data[11] bitand 0x07ULL) << 9 bitor
                   (data[12] bitand 0x07ULL) << 6 bitor
                   (data[13] bitand 0x07ULL) << 3 bitor
                   (data[14] bitand 0x07ULL) << 0)
    {
    }

    bool operator==(const symop_data &rhs) const
    {
        return m_packed == rhs.m_packed;
    }

    bool operator<(const symop_data &rhs) const
    {
        return m_packed < rhs.m_packed;
    }

    inline constexpr int unpack3(int offset) const
    {
        int result = (m_packed >> offset) bitand 0x03;
        return result == 3 ? -1 : result;
    }

    inline constexpr int unpack7(int offset) const
    {
        return (m_packed >> offset) bitand 0x07;
    }

    constexpr std::array<int, 15> data() const
    {
        return {
            unpack3(34),
            unpack3(32),
            unpack3(30),
            unpack3(28),
            unpack3(26),
            unpack3(24),
            unpack3(22),
            unpack3(20),
            unpack3(18),
            unpack7(15),
            unpack7(12),
            unpack7(9),
            unpack7(6),
            unpack7(3),
            unpack7(0)
        };
    }

  private:
    friend struct symop_datablock;

    const uint64_t kPackMask = (~0ULL >> (64 - 36));

    symop_data(uint64_t v)
        : m_packed(v bitand kPackMask)
    {
    }

    uint64_t m_packed;
};

struct symop_datablock
{
    constexpr symop_datablock(int spacegroup, int rotational_number, const std::array<int, 15> &rt_data)
        : m_v((spacegroup bitand 0xffffULL) << 48 bitor
              (rotational_number bitand 0xffULL) << 40 bitor
              symop_data(rt_data).m_packed)
    {
    }

    uint16_t spacegroup() const { return m_v >> 48; }
    symop_data symop() const { return symop_data(m_v); }
    uint8_t rotational_number() const { return (m_v >> 40) bitand 0xff; }

  private:
    uint64_t m_v;
};

static_assert(sizeof(symop_datablock) == sizeof(uint64_t), "Size of symop_data is wrong");

extern CIFPP_EXPORT const symop_datablock kSymopNrTable[];

extern CIFPP_EXPORT const std::size_t kSymopNrTableSize;

// --------------------------------------------------------------------
// Some more symmetry related stuff here.

class datablock;

class cell;
class spacegroup;
class rtop;
struct sym_op;

struct sym_op
{
  public:
    sym_op(uint8_t nr = 1, uint8_t ta = 5, uint8_t tb = 5, uint8_t tc = 5)
        : m_nr(nr)
        , m_ta(ta)
        , m_tb(tb)
        , m_tc(tc)
    {
    }

    explicit sym_op(std::string_view s);

    sym_op(const sym_op &) = default;
    sym_op(sym_op &&) = default;
    sym_op &operator=(const sym_op &) = default;
    sym_op &operator=(sym_op &&) = default;
    constexpr bool is_identity() const
    {
        return m_nr == 1 and m_ta == 5 and m_tb == 5 and m_tc == 5;
    }

    explicit constexpr operator bool() const
    {
        return not is_identity();
    }

    std::string string() const;

#if defined(__cpp_impl_three_way_comparison)
    constexpr auto operator<=>(const sym_op &rhs) const = default;
#else
    constexpr bool operator==(const sym_op &rhs) const
    {
        return m_nr == rhs.m_nr and m_ta == rhs.m_ta and m_tb == rhs.m_tb and m_tc == rhs.m_tc;
    }

    constexpr bool operator!=(const sym_op &rhs) const
    {
        return not operator==(rhs);
    }
#endif

    uint8_t m_nr;
    uint8_t m_ta, m_tb, m_tc;
};

static_assert(sizeof(sym_op) == 4, "Sym_op should be four bytes");

namespace literals
{
    inline sym_op operator""_symop(const char *text, std::size_t length)
    {
        return sym_op({ text, length });
    }
} // namespace literals

// --------------------------------------------------------------------
// The transformation class

class transformation
{
  public:
    transformation(const symop_data &data);

    transformation(const matrix3x3<float> &r, const cif::point &t);

    transformation(const transformation &) = default;
    transformation(transformation &&) = default;
    transformation &operator=(const transformation &) = default;
    transformation &operator=(transformation &&) = default;
    point operator()(point pt) const
    {
        if (m_q)
            pt.rotate(m_q);
        else
            pt = m_rotation * pt;

        return pt + m_translation;
    }

    friend transformation operator*(const transformation &lhs, const transformation &rhs);

    friend transformation inverse(const transformation &t);

    transformation operator-() const
    {
        return inverse(*this);
    }

    friend class spacegroup;

  private:
    // Most rotation matrices provided by the International Tables
    // are really rotation matrices, in those cases we can construct
    // a quaternion. Unfortunately, that doesn't work for all of them

    void try_create_quaternion();

    matrix3x3<float> m_rotation;
    quaternion m_q;
    point m_translation;
};

// --------------------------------------------------------------------
// class cell

class cell
{
  public:
    cell(float a, float b, float c, float alpha = 90.f, float beta = 90.f, float gamma = 90.f);

    cell(const datablock &db);

    float get_a() const { return m_a; }
    float get_b() const { return m_b; }
    float get_c() const { return m_c; }

    float get_alpha() const { return m_alpha; }
    float get_beta() const { return m_beta; }
    float get_gamma() const { return m_gamma; }

    float get_volume() const;

    matrix3x3<float> get_orthogonal_matrix() const { return m_orthogonal; }
    matrix3x3<float> get_fractional_matrix() const { return m_fractional; }

  private:
    void init();

    float m_a, m_b, m_c, m_alpha, m_beta, m_gamma;
    matrix3x3<float> m_orthogonal, m_fractional;
};

// --------------------------------------------------------------------

int get_space_group_number(const datablock &db);

int get_space_group_number(std::string_view spacegroup);

int get_space_group_number(std::string_view spacegroup, space_group_name type);

class spacegroup : public std::vector<transformation>
{
  public:
    spacegroup(const datablock &db)
        : spacegroup(get_space_group_number(db))
    {
    }

    spacegroup(std::string_view name)
        : spacegroup(get_space_group_number(name))
    {
    }

    spacegroup(std::string_view name, space_group_name type)
        : spacegroup(get_space_group_number(name, type))
    {
    }

    spacegroup(int nr);

    int get_nr() const { return m_nr; }
    std::string get_name() const;

    point operator()(const point &pt, const cell &c, sym_op symop) const;

    point inverse(const point &pt, const cell &c, sym_op symop) const;

  private:
    int m_nr;
    std::size_t m_index;
};

// --------------------------------------------------------------------
class crystal
{
  public:
    crystal(const datablock &db)
        : m_cell(db)
        , m_spacegroup(db)
    {
    }

    crystal(const cell &c, const spacegroup &sg)
        : m_cell(c)
        , m_spacegroup(sg)
    {
    }

    crystal(const crystal &) = default;
    crystal(crystal &&) = default;
    crystal &operator=(const crystal &) = default;
    crystal &operator=(crystal &&) = default;
    const cell &get_cell() const { return m_cell; }
    const spacegroup &get_spacegroup() const { return m_spacegroup; }

    point symmetry_copy(const point &pt, sym_op symop) const
    {
        return m_spacegroup(pt, m_cell, symop);
    }

    point inverse_symmetry_copy(const point &pt, sym_op symop) const
    {
        return m_spacegroup.inverse(pt, m_cell, symop);
    }

    std::tuple<float, point, sym_op> closest_symmetry_copy(point a, point b) const;

  private:
    cell m_cell;
    spacegroup m_spacegroup;
};

// --------------------------------------------------------------------
// Symmetry operations on points

inline point orthogonal(const point &pt, const cell &c)
{
    return c.get_orthogonal_matrix() * pt;
}

inline point fractional(const point &pt, const cell &c)
{
    return c.get_fractional_matrix() * pt;
}

// --------------------------------------------------------------------

} // namespace cif