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featomic::systems::read_from_file
This allow to disable the chemfiles dependency by default for the rust crate. This makes examples in C and C++ a bit more complex, but also a lot closer to how someone would actually use the code from these languages.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,9 @@ | ||
| Defining systems | ||
| ================ | ||
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| There are two ways you can define systems to pass to a | ||
| :cpp:class:`featomic::Calculator`. The easy way is to use | ||
| :cpp:class:`featomic::BasicSystems` to read all systems defined in a file, and | ||
| run the calculation on all these systems. The more complex but also more | ||
| flexible way is to define a new child class of :cpp:class:`featomic::System` | ||
| implementing all required functions; and then passing a vector of pointers to | ||
| the child class instances to your :cpp:class:`featomic::Calculator`. | ||
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| .. doxygenclass:: featomic::System | ||
| :members: | ||
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| .. doxygenclass:: featomic::BasicSystems | ||
| .. doxygenclass:: featomic::SimpleSystem | ||
| :members: |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -4,6 +4,7 @@ version = "0.1.0" | |
| authors = ["Guillaume Fraux <[email protected]>"] | ||
| edition = "2021" | ||
| rust-version = "1.74" | ||
| publish = false | ||
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| [lib] | ||
| # when https://github.com/rust-lang/cargo/pull/8789 lands, use it here! | ||
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@@ -12,10 +13,6 @@ name = "featomic" | |
| crate-type = ["cdylib", "staticlib"] | ||
| bench = false | ||
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| [features] | ||
| default = ["chemfiles"] | ||
| chemfiles = ["featomic/chemfiles"] | ||
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| [dependencies] | ||
| featomic = {path = "../featomic", version = "0.1.0", default-features = false} | ||
| metatensor = "0.2" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,186 @@ | ||
| #include <stdio.h> | ||
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| #include <chemfiles.h> | ||
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| #include "systems.h" | ||
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| // This file shows an example on how to define a custom `featomic_system_t`, | ||
| // based on chemfiles (https://chemfiles.org). | ||
| // | ||
| // The core idea is to define a set of functions to communicate data (atomic | ||
| // types, positions, periodic cell, …) between your code and featomic. Each | ||
| // function takes a `void* user_data` parameter, which you can set to anything | ||
| // relevant. | ||
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| typedef struct { | ||
| uint64_t size; | ||
| CHFL_FRAME* frame; | ||
| int32_t* atom_types; | ||
| } chemfiles_system_t; | ||
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| static featomic_status_t chemfiles_system_size(const void* system, uintptr_t* size) { | ||
| *size = ((const chemfiles_system_t*)system)->size; | ||
| return FEATOMIC_SUCCESS; | ||
| } | ||
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| static featomic_status_t chemfiles_system_cell(const void* system, double cell[9]) { | ||
| CHFL_CELL* chemfiles_cell = chfl_cell_from_frame(((const chemfiles_system_t*)system)->frame); | ||
| if (chemfiles_cell == NULL) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| return -1; | ||
| } | ||
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| chfl_status status = chfl_cell_matrix(chemfiles_cell, (chfl_vector3d*)cell); | ||
| chfl_free(chemfiles_cell); | ||
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| if (status == CHFL_SUCCESS) { | ||
| return FEATOMIC_SUCCESS; | ||
| } else { | ||
| printf("Error: %s", chfl_last_error()); | ||
| return -2; | ||
| } | ||
| } | ||
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| static featomic_status_t chemfiles_system_positions(const void* system, const double** positions) { | ||
| chfl_vector3d* chemfiles_positions = NULL; | ||
| uint64_t size = 0; | ||
| chfl_status status = chfl_frame_positions( | ||
| ((const chemfiles_system_t*)system)->frame, | ||
| &chemfiles_positions, | ||
| &size | ||
| ); | ||
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| if (status == CHFL_SUCCESS) { | ||
| *positions = (const double*)chemfiles_positions; | ||
| return FEATOMIC_SUCCESS; | ||
| } else { | ||
| return -1; | ||
| } | ||
| } | ||
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| static featomic_status_t chemfiles_system_types(const void* system, const int32_t** types) { | ||
| *types = ((const chemfiles_system_t*)system)->atom_types; | ||
| return FEATOMIC_SUCCESS; | ||
| } | ||
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| static featomic_status_t chemfiles_system_neighbors(void* system, double cutoff) { | ||
| // this system does not have a neighbor list, and needs to use the one | ||
| // inside featomic with `use_native_system=true` | ||
| return -1; | ||
| } | ||
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| int read_systems_example(const char* path, featomic_system_t** systems, uintptr_t* n_systems) { | ||
| CHFL_TRAJECTORY* trajectory = NULL; | ||
| CHFL_ATOM* atom = NULL; | ||
| chemfiles_system_t* system = NULL; | ||
| chfl_status status; | ||
| uint64_t step = 0; | ||
| uint64_t n_steps = 0; | ||
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| trajectory = chfl_trajectory_open(path, 'r'); | ||
| if (trajectory == NULL) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| status = chfl_trajectory_nsteps(trajectory, &n_steps); | ||
| if (status != CHFL_SUCCESS) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| *systems = calloc(n_steps, sizeof(featomic_system_t)); | ||
| if (*systems == NULL) { | ||
| printf("Error: Failed to allocate systems"); | ||
| goto error; | ||
| } | ||
| *n_systems = (uintptr_t)n_steps; | ||
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| for (step=0; step<n_steps; step++) { | ||
| system = calloc(1, sizeof(chemfiles_system_t)); | ||
| if (system == NULL) { | ||
| printf("Error: failed to allocate single system"); | ||
| goto error; | ||
| } | ||
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| system->frame = chfl_frame(); | ||
| if (system->frame == NULL) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| status = chfl_trajectory_read_step(trajectory, step, system->frame); | ||
| if (status != CHFL_SUCCESS) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| // extract atomic types from the frame | ||
| chfl_frame_atoms_count(system->frame, &system->size); | ||
| if (status != CHFL_SUCCESS) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| system->atom_types = calloc(system->size, sizeof(int32_t)); | ||
| if (system->atom_types == NULL) { | ||
| printf("Error: failed to allocate atom_types"); | ||
| goto error; | ||
| } | ||
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| for (uint64_t i=0; i<system->size; i++) { | ||
| atom = chfl_atom_from_frame(system->frame, i); | ||
| if (atom == NULL) { | ||
| printf("Error: %s", chfl_last_error()); | ||
| goto error; | ||
| } | ||
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| uint64_t number = 0; | ||
| chfl_atom_atomic_number(atom, &number); | ||
| system->atom_types[i] = (int32_t)(number); | ||
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| chfl_free(atom); | ||
| } | ||
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| // setup all the data and functions for the system | ||
| (*systems)[step].user_data = system; | ||
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| (*systems)[step].size = chemfiles_system_size; | ||
| (*systems)[step].cell = chemfiles_system_cell; | ||
| (*systems)[step].positions = chemfiles_system_positions; | ||
| (*systems)[step].types = chemfiles_system_types; | ||
| (*systems)[step].compute_neighbors = chemfiles_system_neighbors; | ||
| (*systems)[step].pairs = NULL; | ||
| (*systems)[step].pairs_containing = NULL; | ||
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| system = NULL; | ||
| } | ||
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| chfl_free(trajectory); | ||
| return 0; | ||
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| error: | ||
| chfl_free(trajectory); | ||
| chfl_free(atom); | ||
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| // cleanup any sucesfully allocated frames | ||
| free_systems_example(*systems, step); | ||
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| *systems = NULL; | ||
| *n_systems = 0; | ||
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| return 1; | ||
| } | ||
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| void free_systems_example(featomic_system_t* systems, uintptr_t n_systems) { | ||
| for (size_t i=0; i<n_systems; i++) { | ||
| chemfiles_system_t* system = systems[i].user_data; | ||
| chfl_free(system->frame); | ||
| free(system->atom_types); | ||
| free(system); | ||
| } | ||
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| free(systems); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| #ifndef FEATOMIC_EXAMPLE_SYSTEMS_H | ||
| #define FEATOMIC_EXAMPLE_SYSTEMS_H | ||
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| #include <featomic.h> | ||
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| int read_systems_example(const char* path, featomic_system_t** systems, uintptr_t* n_systems); | ||
| void free_systems_example(featomic_system_t* systems, uintptr_t n_systems); | ||
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| #endif |
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