diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp
index e14d06db999d99268944e64850ab2d2a54c8ab91..151de3e5b852438e93c977154d80c8da0b9e7199 100644
--- a/src/USER-PTM/ptm_alloy_types.cpp
+++ b/src/USER-PTM/ptm_alloy_types.cpp
@@ -2,6 +2,7 @@
#include "ptm_constants.h"
#include "ptm_initialize_data.h"
+namespace ptm {
#define NUM_ALLOY_TYPES 3
static uint32_t typedata[NUM_ALLOY_TYPES][3] = {
@@ -99,3 +100,5 @@ int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers)
return PTM_ALLOY_NONE;
}
+}
+
diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h
index 6ea6ed1b8aaa8b7b45f0b5b744b085bb16d3f802..559e0a749048651dfba7d9036e9b31b6b3281503 100644
--- a/src/USER-PTM/ptm_alloy_types.h
+++ b/src/USER-PTM/ptm_alloy_types.h
@@ -3,7 +3,11 @@
#include "ptm_initialize_data.h"
+namespace ptm {
+
int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp
index 551f52d7e4b985bccff16a1ec0feaf34ef734dc7..ade8f23b15f7cbb3023de9acba4afef8f17d9dca 100644
--- a/src/USER-PTM/ptm_canonical_coloured.cpp
+++ b/src/USER-PTM/ptm_canonical_coloured.cpp
@@ -4,6 +4,7 @@
#include "ptm_graph_tools.h"
#include "ptm_constants.h"
+namespace ptm {
static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b)
{
@@ -165,3 +166,5 @@ int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, i
return PTM_NO_ERROR;
}
+}
+
diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h
index e71bb08bfc605752fd559d0d68ea657ec55819f9..f8e2a7af5db08031ccafacfdc0d9244fb9e3fbdb 100644
--- a/src/USER-PTM/ptm_canonical_coloured.h
+++ b/src/USER-PTM/ptm_canonical_coloured.h
@@ -3,7 +3,10 @@
#include <stdint.h>
+namespace ptm {
+
int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash);
+}
#endif
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp
index c996b17b5886785bfc148614b1afa7d6508af1ee..7c79fd371a532f1c20b9d21767b011d60e4d0849 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.cpp
+++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp
@@ -6,6 +6,7 @@
#include "ptm_convex_hull_incremental.h"
#include "ptm_constants.h"
+namespace ptm {
#define VISIBLE 1
#define INVISIBLE 2
@@ -361,3 +362,5 @@ int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch,
return ret;
}
+}
+
diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h
index 563a0c436a0b612d7dd519790a88ecf05fd71447..6474723907086652d084d8914a63fbea799650e2 100644
--- a/src/USER-PTM/ptm_convex_hull_incremental.h
+++ b/src/USER-PTM/ptm_convex_hull_incremental.h
@@ -6,6 +6,7 @@
#include <stdbool.h>
#include "ptm_constants.h"
+namespace ptm {
typedef struct
{
@@ -23,5 +24,7 @@ typedef struct
void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre);
int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp
index d566d5ca1198f0425f855283feddefbcc5cadb24..fc851920a6854f8dfeeb7ae59215567644ba111c 100644
--- a/src/USER-PTM/ptm_deformation_gradient.cpp
+++ b/src/USER-PTM/ptm_deformation_gradient.cpp
@@ -1,5 +1,6 @@
#include "ptm_deformation_gradient.h"
+namespace ptm {
void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res)
{
@@ -35,3 +36,5 @@ void calculate_deformation_gradient(int num_points, const double (*ideal_points)
}
}
+}
+
diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h
index 7decab4b76144400b084dbac493a59bca6855557..32836da44d48dfa8791bbb56f43a8c29e4ffc1f2 100644
--- a/src/USER-PTM/ptm_deformation_gradient.h
+++ b/src/USER-PTM/ptm_deformation_gradient.h
@@ -4,6 +4,8 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
+
void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res);
//sc
@@ -137,6 +139,8 @@ const double penrose_dhex[PTM_NUM_POINTS_DHEX][3] = {
{ 0, 2 * kdcub, -2 * kdcub },
{ 2 * kdcub, 0, -2 * kdcub },
};
+}
+
#endif
diff --git a/src/USER-PTM/ptm_fundamental_mappings.h b/src/USER-PTM/ptm_fundamental_mappings.h
index 3dd7c39cbb30f0bd494a7376bb93be553c7b876e..35fae7f08834cd303065591e0a54ad83f0480d93 100644
--- a/src/USER-PTM/ptm_fundamental_mappings.h
+++ b/src/USER-PTM/ptm_fundamental_mappings.h
@@ -3,6 +3,8 @@
#include <stdint.h>
+namespace ptm {
+
#define NUM_CUBIC_MAPPINGS 24
#define NUM_ICO_MAPPINGS 60
#define NUM_HEX_MAPPINGS 6
@@ -175,6 +177,7 @@ const int8_t mapping_dhex[NUM_DHEX_MAPPINGS][PTM_MAX_POINTS] = {
{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{0, 1, 3, 4, 2, 6, 7, 5, 11, 13, 12, 14, 16, 15, 8, 9, 10},
{0, 1, 4, 2, 3, 7, 5, 6, 14, 15, 16, 8, 10, 9, 11, 13, 12} };
+}
#endif
diff --git a/src/USER-PTM/ptm_graph_data.cpp b/src/USER-PTM/ptm_graph_data.cpp
index a591dbf993a8af5affaa6740b7d440ea60fe81b2..a742c8b3398c7c7a7eeb5862d8507756043fb078 100644
--- a/src/USER-PTM/ptm_graph_data.cpp
+++ b/src/USER-PTM/ptm_graph_data.cpp
@@ -1,6 +1,8 @@
#include "ptm_graph_data.h"
+namespace ptm {
+
int8_t automorphisms[65][17] = {
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16},
{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, -1, -1, -1, -1},
@@ -2057,3 +2059,5 @@ graph_t graphs_dhex[NUM_DHEX_GRAPHS] = {
};
+}
+
diff --git a/src/USER-PTM/ptm_graph_data.h b/src/USER-PTM/ptm_graph_data.h
index 11f46a471fc2a9c347d6d580159656e99a863a56..251c82d2f5b2381a19188709bca6ae6cbc87ad4d 100644
--- a/src/USER-PTM/ptm_graph_data.h
+++ b/src/USER-PTM/ptm_graph_data.h
@@ -4,6 +4,7 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
typedef struct
{
@@ -33,5 +34,7 @@ extern graph_t graphs_bcc[NUM_BCC_GRAPHS];
extern graph_t graphs_dcub[NUM_DCUB_GRAPHS];
extern graph_t graphs_dhex[NUM_DHEX_GRAPHS];
+}
+
#endif
diff --git a/src/USER-PTM/ptm_graph_tools.cpp b/src/USER-PTM/ptm_graph_tools.cpp
index 89d07fc87a39439660db05b7b6d2be7b4798acbc..f6fd34d097a19167896615f442ec818adc650fe0 100644
--- a/src/USER-PTM/ptm_graph_tools.cpp
+++ b/src/USER-PTM/ptm_graph_tools.cpp
@@ -4,6 +4,8 @@
#include "ptm_constants.h"
+namespace ptm {
+
bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS])
{
memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS);
@@ -50,3 +52,5 @@ int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degr
return max_degree;
}
+}
+
diff --git a/src/USER-PTM/ptm_graph_tools.h b/src/USER-PTM/ptm_graph_tools.h
index 78934e87c1d21a7a1ee38fc1be6cc80d38db2da3..7befad526b4435253742372ccad85d8355005619 100644
--- a/src/USER-PTM/ptm_graph_tools.h
+++ b/src/USER-PTM/ptm_graph_tools.h
@@ -4,8 +4,12 @@
#include <stdint.h>
#include "ptm_constants.h"
+namespace ptm {
+
bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]);
int graph_degree(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_index.cpp b/src/USER-PTM/ptm_index.cpp
index 7b6618848e18989efc2040f8507034cd6c2537b9..24998dadd0a440048740cd2ff30fdbf9eb244e57 100644
--- a/src/USER-PTM/ptm_index.cpp
+++ b/src/USER-PTM/ptm_index.cpp
@@ -36,13 +36,13 @@ static double calculate_lattice_constant(int type, double interatomic_distance)
static int rotate_into_fundamental_zone(int type, double* q)
{
- if (type == PTM_MATCH_SC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_FCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_BCC) return rotate_quaternion_into_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_ICO) return rotate_quaternion_into_icosahedral_fundamental_zone(q);
- if (type == PTM_MATCH_HCP) return rotate_quaternion_into_hcp_fundamental_zone(q);
- if (type == PTM_MATCH_DCUB) return rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
- if (type == PTM_MATCH_DHEX) return rotate_quaternion_into_diamond_hexagonal_fundamental_zone(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) return ptm::rotate_quaternion_into_hcp_fundamental_zone(q);
+ if (type == PTM_MATCH_DCUB) return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q);
+ if (type == PTM_MATCH_DHEX) return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q);
return -1;
}
@@ -52,8 +52,8 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double
if (topological_ordering)
{
double normalized_points[PTM_MAX_INPUT_POINTS][3];
- normalize_vertices(num_points, unpermuted_points, normalized_points);
- int ret = calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
+ ptm::normalize_vertices(num_points, unpermuted_points, normalized_points);
+ int ret = ptm::calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering);
if (ret != 0)
topological_ordering = false;
}
@@ -71,7 +71,7 @@ static void order_points(ptm_local_handle_t local_handle, int num_points, double
}
}
-static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
+static void output_data(ptm::result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering,
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, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant)
{
@@ -82,13 +82,13 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe
if (mapping != NULL)
memset(mapping, -1, num_points * sizeof(int8_t));
- const refdata_t* ref = res->ref_struct;
+ const ptm::refdata_t* ref = res->ref_struct;
if (ref == NULL)
return;
*p_type = ref->type;
if (p_alloy_type != NULL && unpermuted_numbers != NULL)
- *p_alloy_type = find_alloy_type(ref, res->mapping, numbers);
+ *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers);
int bi = rotate_into_fundamental_zone(ref->type, res->q);
int8_t temp[PTM_MAX_POINTS];
@@ -101,17 +101,17 @@ static void output_data(result_t* res, int num_points, int32_t* unpermuted_numbe
{
double scaled_points[PTM_MAX_INPUT_POINTS][3];
- subtract_barycentre(ref->num_nbrs + 1, points, scaled_points);
+ 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;
}
- calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
+ ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res);
if (P != NULL && U != NULL)
- polar_decomposition_3x3(F, false, U, P);
+ ptm::polar_decomposition_3x3(F, false, U, P);
}
if (mapping != NULL)
@@ -156,7 +156,7 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
assert(num_points >= PTM_NUM_POINTS_DCUB);
int ret = 0;
- result_t res;
+ ptm::result_t res;
res.ref_struct = NULL;
res.rmsd = INFINITY;
@@ -168,32 +168,32 @@ int ptm_index( ptm_local_handle_t local_handle, int32_t flags,
double dpoints[PTM_MAX_POINTS][3];
int32_t dnumbers[PTM_MAX_POINTS];
- convexhull_t ch;
+ ptm::convexhull_t ch;
double ch_points[PTM_MAX_INPUT_POINTS][3];
if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC))
{
int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points);
order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers);
- normalize_vertices(num_lpoints, points, ch_points);
+ ptm::normalize_vertices(num_lpoints, points, ch_points);
ch.ok = false;
if (flags & PTM_CHECK_SC)
- ret = match_general(&structure_sc, ch_points, points, &ch, &res);
+ 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(&structure_bcc, ch_points, points, &ch, &res);
+ ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res);
}
if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX))
{
- ret = calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
+ ret = ptm::calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers);
if (ret == 0)
{
- normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
+ ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points);
ch.ok = false;
ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res);
diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp
index 6157ff862f92e2c2bf69a9ad7c26e97d0d926096..8d96e2a2b77b877cdc020213cc98dd5934596824 100644
--- a/src/USER-PTM/ptm_initialize_data.cpp
+++ b/src/USER-PTM/ptm_initialize_data.cpp
@@ -14,20 +14,20 @@ static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const dou
double origin[3] = {0, 0, 0};
for (int i = 0;i<num_facets;i++)
- add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
+ ptm::add_facet(points, facets[i][0], facets[i][1], facets[i][2], facets[i], plane_normal, origin);
}
-static int initialize_graphs(const refdata_t* s, int8_t* colours)
+static int initialize_graphs(const ptm::refdata_t* s, int8_t* colours)
{
for (int i = 0;i<s->num_graphs;i++)
{
int8_t code[2 * PTM_MAX_EDGES];
int8_t degree[PTM_MAX_NBRS];
- int _max_degree = graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
+ int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree);
assert(_max_degree <= s->max_degree);
make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]);
- int ret = canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
+ int ret = ptm::canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash);
if (ret != 0)
return ret;
}
@@ -44,13 +44,13 @@ int ptm_initialize_global()
int8_t colours[PTM_MAX_POINTS] = {0};
int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
- int ret = initialize_graphs(&structure_sc, colours);
- ret |= initialize_graphs(&structure_fcc, colours);
- ret |= initialize_graphs(&structure_hcp, colours);
- ret |= initialize_graphs(&structure_ico, colours);
- ret |= initialize_graphs(&structure_bcc, colours);
- ret |= initialize_graphs(&structure_dcub, dcolours);
- ret |= initialize_graphs(&structure_dhex, dcolours);
+ int ret = initialize_graphs(&ptm::structure_sc, colours);
+ ret |= initialize_graphs(&ptm::structure_fcc, colours);
+ ret |= initialize_graphs(&ptm::structure_hcp, colours);
+ ret |= initialize_graphs(&ptm::structure_ico, colours);
+ ret |= initialize_graphs(&ptm::structure_bcc, colours);
+ ret |= initialize_graphs(&ptm::structure_dcub, dcolours);
+ ret |= initialize_graphs(&ptm::structure_dhex, dcolours);
if (ret == PTM_NO_ERROR)
ptm_initialized = true;
@@ -61,11 +61,11 @@ int ptm_initialize_global()
ptm_local_handle_t ptm_initialize_local()
{
assert(ptm_initialized);
- return (ptm_local_handle_t)voronoi_initialize_local();
+ return (ptm_local_handle_t)ptm::voronoi_initialize_local();
}
void ptm_uninitialize_local(ptm_local_handle_t ptr)
{
- voronoi_uninitialize_local(ptr);
+ ptm::voronoi_uninitialize_local(ptr);
}
diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h
index f381dd864b34637e926b3ce5e3c4df5fb4044b7e..5374fbf7d0212ede7278c635e654d258680d650e 100644
--- a/src/USER-PTM/ptm_initialize_data.h
+++ b/src/USER-PTM/ptm_initialize_data.h
@@ -11,6 +11,8 @@
#include "ptm_convex_hull_incremental.h"
+namespace ptm {
+
typedef struct
{
int type;
@@ -35,6 +37,7 @@ const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, N
const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub };
const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex };
+}
#ifdef __cplusplus
extern "C" {
diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp
index 6b5ac9601a568e4634d63d87321a3f9529cf1b57..c77a779c6885fdaf435f955f0a156b35e6484134 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.cpp
+++ b/src/USER-PTM/ptm_neighbour_ordering.cpp
@@ -5,9 +5,9 @@
#include <algorithm>
#include "ptm_constants.h"
#include "ptm_voronoi_cell.h"
-using namespace voro;
+namespace ptm {
typedef struct
{
@@ -31,7 +31,7 @@ static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b)
}
//todo: change voronoi code to return errors rather than exiting
-static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
+static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, std::vector<int>& nbr_indices, std::vector<double>& face_areas)
{
const double k = 1000 * max_norm; //todo: reduce this constant
v->init(-k,k,-k,k,-k,k);
@@ -53,7 +53,7 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do
{
assert(num_points <= PTM_MAX_INPUT_POINTS);
- voronoicell_neighbor* voronoi_handle = (voronoicell_neighbor*)_voronoi_handle;
+ ptm_voro::voronoicell_neighbor* voronoi_handle = (ptm_voro::voronoicell_neighbor*)_voronoi_handle;
double max_norm = 0;
double points[PTM_MAX_INPUT_POINTS][3];
@@ -116,13 +116,13 @@ int calculate_neighbour_ordering(void* _voronoi_handle, int num_points, const do
void* voronoi_initialize_local()
{
- voronoicell_neighbor* ptr = new voronoicell_neighbor;
+ ptm_voro::voronoicell_neighbor* ptr = new ptm_voro::voronoicell_neighbor;
return (void*)ptr;
}
void voronoi_uninitialize_local(void* _ptr)
{
- voronoicell_neighbor* ptr = (voronoicell_neighbor*)_ptr;
+ ptm_voro::voronoicell_neighbor* ptr = (ptm_voro::voronoicell_neighbor*)_ptr;
delete ptr;
}
@@ -201,3 +201,5 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po
return 0;
}
+}
+
diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h
index ce4dfca2c00a05e701e5dc6e35dbc03bc83e667c..e43ced9fd513c21bfddbe24a71c964f5e160dcd3 100644
--- a/src/USER-PTM/ptm_neighbour_ordering.h
+++ b/src/USER-PTM/ptm_neighbour_ordering.h
@@ -1,6 +1,8 @@
#ifndef PTM_NEIGHBOUR_ORDERING_H
#define PTM_NEIGHBOUR_ORDERING_H
+namespace ptm {
+
int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering);
int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers,
@@ -9,5 +11,7 @@ int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_po
void* voronoi_initialize_local();
void voronoi_uninitialize_local(void* ptr);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp
index 61dca5006f6d8c8a47f96cc65e8e541d89fafe5e..22e3c1e6706cbb7f3b50811b5d29ac7ac826cfac 100644
--- a/src/USER-PTM/ptm_normalize_vertices.cpp
+++ b/src/USER-PTM/ptm_normalize_vertices.cpp
@@ -1,5 +1,6 @@
#include <cmath>
+namespace ptm {
void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3])
{
@@ -53,3 +54,5 @@ double normalize_vertices(int num, double (*points)[3], double (*normalized)[3])
return scale;
}
+}
+
diff --git a/src/USER-PTM/ptm_normalize_vertices.h b/src/USER-PTM/ptm_normalize_vertices.h
index 2c7b7227529659c6b8ecc7f02efefccb69224c66..dc93db94a3ae97372f0343f1331a7e82ae618a54 100644
--- a/src/USER-PTM/ptm_normalize_vertices.h
+++ b/src/USER-PTM/ptm_normalize_vertices.h
@@ -1,8 +1,12 @@
#ifndef PTM_NORMALIZE_VERTICES_H
#define PTM_NORMALIZE_VERTICES_H
+namespace ptm {
+
void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]);
double normalize_vertices(int num, double (*points)[3], double (*normalized)[3]);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp
index 9089b327b91da9a2eb9df80a9f34b628eae1443e..fa199ca6567a87affc0a75ca5e2981454a419c4f 100644
--- a/src/USER-PTM/ptm_polar.cpp
+++ b/src/USER-PTM/ptm_polar.cpp
@@ -91,6 +91,8 @@
#include "ptm_quat.h"
+namespace ptm {
+
static void matmul_3x3(double* A, double* x, double* b)
{
b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6];
@@ -335,3 +337,5 @@ int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q,
return 0;
}
+}
+
diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h
index d5aa3d9540646410273d52d20bc3e33962b977d2..15d1f185b77749bf2207a3d44f7382e57b38f057 100644
--- a/src/USER-PTM/ptm_polar.h
+++ b/src/USER-PTM/ptm_polar.h
@@ -4,9 +4,13 @@
#include <stdint.h>
#include <stdbool.h>
+namespace ptm {
+
int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P);
void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation);
int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp
index f55aff3d2b923d7ced41a49ee46140a13ce8613d..376cc749015ead94a7f1ce79a10438e0c1829e49 100644
--- a/src/USER-PTM/ptm_quat.cpp
+++ b/src/USER-PTM/ptm_quat.cpp
@@ -3,6 +3,8 @@
#include <cfloat>
+namespace ptm {
+
#define SIGN(x) (x >= 0 ? 1 : -1)
#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y))
#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y))
@@ -394,3 +396,5 @@ double quat_disorientation_icosahedral(double* q0, double* q1)
return acos(quat_quick_disorientation_icosahedral(q0, q1));
}
+}
+
diff --git a/src/USER-PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h
index 381c3ce876d606bc7a8ee868702245d46b20cf70..74caa2c62c3776eee0e3953438fa6ff2da6794f8 100644
--- a/src/USER-PTM/ptm_quat.h
+++ b/src/USER-PTM/ptm_quat.h
@@ -1,6 +1,8 @@
#ifndef PTM_QUAT_H
#define PTM_QUAT_H
+namespace ptm {
+
int rotate_quaternion_into_cubic_fundamental_zone(double* q);
int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q);
int rotate_quaternion_into_icosahedral_fundamental_zone(double* q);
@@ -25,8 +27,7 @@ double quat_disorientation_diamond_hexagonal(double* q0, double* q1);
double quat_quick_disorientation_icosahedral(double* q0, double* q1);
double quat_disorientation_icosahedral(double* q0, double* q1);
-#endif
-
-
+}
+#endif
diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp
index 7eb0a4414329b34f6ab742c3facde75fd09e049e..a86b3670cef6818da8386f5d250b721d9a75752d 100644
--- a/src/USER-PTM/ptm_structure_matcher.cpp
+++ b/src/USER-PTM/ptm_structure_matcher.cpp
@@ -15,6 +15,8 @@
#include "ptm_constants.h"
+namespace ptm {
+
static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping,
double G1, double G2, double E0, double* q, double* p_scale)
{
@@ -292,3 +294,5 @@ int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags,
return PTM_NO_ERROR;
}
+}
+
diff --git a/src/USER-PTM/ptm_structure_matcher.h b/src/USER-PTM/ptm_structure_matcher.h
index 4b6f969597cee7dc8a787ef52d24c17a80a4dec6..ffaed78e82dceae4ab29b52dbae77b8f936c7e33 100644
--- a/src/USER-PTM/ptm_structure_matcher.h
+++ b/src/USER-PTM/ptm_structure_matcher.h
@@ -4,6 +4,9 @@
#include "ptm_initialize_data.h"
#include "ptm_constants.h"
+
+namespace ptm {
+
typedef struct
{
double rmsd;
@@ -17,5 +20,7 @@ int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3
int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res);
+}
+
#endif
diff --git a/src/USER-PTM/ptm_voronoi_cell.cpp b/src/USER-PTM/ptm_voronoi_cell.cpp
index 6503ea16c6d9c9d9de81debdbb43e8658ad9bc28..ffd7a95ea2cb62850501e6cc702d649d5fc36eea 100644
--- a/src/USER-PTM/ptm_voronoi_cell.cpp
+++ b/src/USER-PTM/ptm_voronoi_cell.cpp
@@ -15,7 +15,7 @@
#include "ptm_voronoi_config.h"
#include "ptm_voronoi_cell.h"
-namespace voro {
+namespace ptm_voro {
inline void voro_fatal_error(const char *p,int status) {
fprintf(stderr,"voro++: %s\n",p);
diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h
index 80a0501b3cd7146749bb02643977b4353771d2a6..e0284bc56fa6c7a65c2a467e2283e8d3ed291479 100644
--- a/src/USER-PTM/ptm_voronoi_cell.h
+++ b/src/USER-PTM/ptm_voronoi_cell.h
@@ -17,7 +17,7 @@
#include "ptm_voronoi_config.h"
-namespace voro {
+namespace ptm_voro {
/** \brief A class representing a single Voronoi cell.
*
diff --git a/src/USER-PTM/ptm_voronoi_config.h b/src/USER-PTM/ptm_voronoi_config.h
index 86257e60cc74436556492371ee7d4cc65c20e931..46c5a4b9151965104fb987b3514832ac38407231 100644
--- a/src/USER-PTM/ptm_voronoi_config.h
+++ b/src/USER-PTM/ptm_voronoi_config.h
@@ -12,7 +12,7 @@
#ifndef PTM_VOROPP_CONFIG_HH
#define PTM_VOROPP_CONFIG_HH
-namespace voro {
+namespace ptm_voro {
// These constants set the initial memory allocation for the Voronoi cell
/** The initial memory allocation for the number of vertices. */