lammps-sys 0.6.0

/*Copyright (c) 2016 PM Larsen

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

#include "ptm_alloy_types.h"
#include "ptm_constants.h"
#include "ptm_convex_hull_incremental.h"
#include "ptm_deformation_gradient.h"
#include "ptm_functions.h"
#include "ptm_initialize_data.h"
#include "ptm_neighbour_ordering.h"
#include "ptm_normalize_vertices.h"
#include "ptm_polar.h"
#include "ptm_quat.h"
#include "ptm_structure_matcher.h"
#include <cassert>
#include <cmath>
#include <cstdio>
#include <cstring>
#include <stdint.h>

static double calculate_interatomic_distance(int type, double scale) {
        assert(type >= 1 && type <= 8);

        // these values should be equal to norm(template[1])
        double c[9] = {0,
                       1,
                       1,
                       (7. - 3.5 * sqrt(3)),
                       1,
                       1,
                       sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)),
                       sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)),
                       -3. / 11 + 6 * sqrt(3) / 11};
        return c[type] / scale;
}

static double calculate_lattice_constant(int type,
                                         double interatomic_distance) {
        assert(type >= 1 && type <= 8);
        double c[9] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2),
                       1, 4 / sqrt(3), 4 / sqrt(3), sqrt(3)};
        return c[type] * interatomic_distance;
}

static int rotate_into_fundamental_zone(int type,
                                        bool output_conventional_orientation,
                                        double *q) {
        if (type == PTM_MATCH_SC)
                return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
        if (type == PTM_MATCH_FCC)
                return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
        if (type == PTM_MATCH_BCC)
                return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
        if (type == PTM_MATCH_ICO)
                return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q);

        if (type == PTM_MATCH_HCP || type == PTM_MATCH_GRAPHENE) {
                if (output_conventional_orientation) {
                        return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q);
                } else {
                        return ptm::rotate_quaternion_into_hcp_fundamental_zone(q);
                }
        }

        if (type == PTM_MATCH_DCUB) {
                if (output_conventional_orientation) {
                        return ptm::rotate_quaternion_into_cubic_fundamental_zone(q);
                } else {
                        return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
                }
        }

        if (type == PTM_MATCH_DHEX) {
                if (output_conventional_orientation) {
                        return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q);
                } else {
                        return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
                }
        }

        return -1;
}

static void output_data(ptm::result_t *res, double (*points)[3],
                        int32_t *numbers, size_t *ordering,
                        bool output_conventional_orientation, int32_t *p_type,
                        int32_t *p_alloy_type, double *p_scale, double *p_rmsd,
                        double *q, double *F, double *F_res, double *U,
                        double *P, double *p_interatomic_distance,
                        double *p_lattice_constant, size_t *output_indices) {
        const ptm::refdata_t *ref = res->ref_struct;
        if (ref == NULL)
                return;

        *p_type = ref->type;
        if (p_alloy_type != NULL)
                *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers);

        int8_t temp[PTM_MAX_POINTS];
        memset(temp, -1, PTM_MAX_POINTS * sizeof(int8_t));
        int bi = rotate_into_fundamental_zone(ref->type,
                                              output_conventional_orientation, res->q);
        //todo: return if bi == -1
        if (bi != -1)
        {
                if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX))
                {
                        for (int i = 0; i < ref->num_nbrs + 1; i++)
                                temp[ref->mapping_conventional[bi][i]] = res->mapping[i];
                }
                else
                {
                        for (int i = 0; i < ref->num_nbrs + 1; i++)
                                temp[ref->mapping[bi][i]] = res->mapping[i];
                }
        }

        memcpy(res->mapping, temp, (ref->num_nbrs + 1) * sizeof(int8_t));

        if (F != NULL && F_res != NULL) {
                double scaled_points[PTM_MAX_INPUT_POINTS][3];

                ptm::subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
                for (int i = 0; i < ref->num_nbrs + 1; i++) {
                        scaled_points[i][0] *= res->scale;
                        scaled_points[i][1] *= res->scale;
                        scaled_points[i][2] *= res->scale;
                }

                const double (*ref_template)[3] = ref->points;
                const double (*ref_penrose)[3] = ref->penrose;
                if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX))
                {
                        if (ref->template_indices[bi] == 1)
                        {
                                ref_template = ref->points_alt1;
                                ref_penrose = ref->penrose_alt1;
                        }
                        else if (ref->template_indices[bi] == 2)
                        {
                                ref_template = ref->points_alt2;
                                ref_penrose = ref->penrose_alt2;
                        }
                        else if (ref->template_indices[bi] == 3)
                        {
                                ref_template = ref->points_alt3;
                                ref_penrose = ref->penrose_alt3;
                        }
                }

                ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref_template,
                                                    res->mapping, scaled_points, ref_penrose,
                                                    F, F_res);
                if (ref->type == PTM_MATCH_GRAPHENE) // hack for pseudo-2d structures
                        F[8] = 1;

                if (P != NULL && U != NULL)
                        ptm::polar_decomposition_3x3(F, false, U, P);
        }

        if (output_indices != NULL)
                for (int i = 0; i < ref->num_nbrs + 1; i++)
                        output_indices[i] = ordering[res->mapping[i]];

        double interatomic_distance =
            calculate_interatomic_distance(ref->type, res->scale);
        double lattice_constant =
            calculate_lattice_constant(ref->type, interatomic_distance);

        if (p_interatomic_distance != NULL)
                *p_interatomic_distance = interatomic_distance;

        if (p_lattice_constant != NULL)
                *p_lattice_constant = lattice_constant;

        *p_rmsd = res->rmsd;
        *p_scale = res->scale;
        memcpy(q, res->q, 4 * sizeof(double));
}

extern bool ptm_initialized;

int ptm_index(ptm_local_handle_t local_handle, size_t atom_index,
              int(get_neighbours)(void *vdata, size_t central_index, size_t atom_index, int num,
                                  size_t *nbr_indices, int32_t *numbers,
                                  double (*nbr_pos)[3]),
              void *nbrlist, int32_t flags,
              bool output_conventional_orientation, int32_t *p_type,
              int32_t *p_alloy_type, double *p_scale, double *p_rmsd, double *q,
              double *F, double *F_res, double *U, double *P,
              double *p_interatomic_distance, double *p_lattice_constant,
              size_t *output_indices) {
        assert(ptm_initialized);

        int ret = 0;
        ptm::result_t res;
        res.ref_struct = NULL;
        res.rmsd = INFINITY;

        size_t ordering[PTM_MAX_INPUT_POINTS];
        int32_t numbers[PTM_MAX_INPUT_POINTS];
        double points[PTM_MAX_INPUT_POINTS][3];

        size_t dordering[PTM_MAX_INPUT_POINTS];
        int32_t dnumbers[PTM_MAX_INPUT_POINTS];
        double dpoints[PTM_MAX_INPUT_POINTS][3];

        size_t gordering[PTM_MAX_INPUT_POINTS];
        int32_t gnumbers[PTM_MAX_INPUT_POINTS];
        double gpoints[PTM_MAX_INPUT_POINTS][3];

        ptm::convexhull_t ch;
        double ch_points[PTM_MAX_INPUT_POINTS][3];
        int num_lpoints = 0;

        if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO |
                     PTM_CHECK_BCC)) {
                int min_points = PTM_NUM_POINTS_SC;
                if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
                        min_points = PTM_NUM_POINTS_FCC;
                if (flags & PTM_CHECK_BCC)
                        min_points = PTM_NUM_POINTS_BCC;

                num_lpoints = ptm::calculate_neighbour_ordering(
                    local_handle, atom_index, min_points, get_neighbours, nbrlist, false,
                    ordering, points, numbers);
                if (num_lpoints >= min_points) {
                        ptm::normalize_vertices(num_lpoints, points, ch_points);
                        ch.ok = false;

                        if (flags & PTM_CHECK_SC)
                                ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res);

                        if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO))
                                ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res);

                        if (flags & PTM_CHECK_BCC)
                                ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res);
                }
        }

        if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) {
                const int num_inner = 4, num_outer = 3, max_snbrs = 12;
                ret = ptm::calculate_two_shell_neighbour_ordering(
                    (void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner,
                    num_outer, max_snbrs, false, dordering, dpoints, dnumbers);
                if (ret == 0) {
                        ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
                        ch.ok = false;

                        ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
                }
        }

        if (flags & PTM_CHECK_GRAPHENE) {
                const int num_inner = 3, num_outer = 2, max_snbrs = 12;
                ret = ptm::calculate_two_shell_neighbour_ordering(
                    (void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner,
                    num_outer, max_snbrs, true, gordering, gpoints, gnumbers);
                if (ret == 0) {
                        ret = match_graphene(gpoints, &res);
                }
        }

        *p_type = PTM_MATCH_NONE;
        if (p_alloy_type != NULL)
                *p_alloy_type = PTM_ALLOY_NONE;

        if (output_indices != NULL)
                memset(output_indices, -1, PTM_MAX_INPUT_POINTS * sizeof(size_t));

        if (res.ref_struct == NULL)
                return PTM_NO_ERROR;

        if (res.ref_struct->type == PTM_MATCH_DCUB ||
            res.ref_struct->type == PTM_MATCH_DHEX) {
                output_data(&res, dpoints, dnumbers, dordering,
                            output_conventional_orientation, p_type, p_alloy_type, p_scale,
                            p_rmsd, q, F, F_res, U, P, p_interatomic_distance,
                            p_lattice_constant, output_indices);
        } else if (res.ref_struct->type == PTM_MATCH_GRAPHENE) {
                output_data(&res, gpoints, gnumbers, gordering,
                            output_conventional_orientation, p_type, p_alloy_type, p_scale,
                            p_rmsd, q, F, F_res, U, P, p_interatomic_distance,
                            p_lattice_constant, output_indices);
        } else {
                output_data(&res, points, numbers, ordering, output_conventional_orientation,
                            p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, U, P,
                            p_interatomic_distance, p_lattice_constant, output_indices);
        }

        return PTM_NO_ERROR;
}