Programs¶

Default Programs¶

SCINE: Database¶

class scine_puffin.programs.database.Database(settings: dict)[source]¶

Scine: Database API – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

SCINE: molassembler¶

class scine_puffin.programs.molassembler.Molassembler(settings: dict)[source]¶

Scine: Molassembler – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

SCINE: Readuct¶

class scine_puffin.programs.readuct.Readuct(settings: dict)[source]¶

Scine: Readuct – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

SCINE: Utils¶

class scine_puffin.programs.utils.Utils(settings: dict)[source]¶

Scine: Utils – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

Optional Extensions¶

SCINE: Sparrow¶

class scine_puffin.programs.sparrow.Sparrow(settings: dict)[source]¶

Scine: Sparrow – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

SCINE: Parrot¶

class scine_puffin.programs.parrot.Parrot(settings: dict)[source]¶

Parrot – Machine Learning Potentials for SCINE

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()[source]¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, _: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(_: Configuration, __: dict, ___: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

Serenity¶

class scine_puffin.programs.serenity.Serenity(settings: dict)[source]¶

Serenity – installation and verification class

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

Orca¶

class scine_puffin.programs.orca.Orca(settings: dict)[source]¶

Setup of the Orca program

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1

Gaussian¶

class scine_puffin.programs.gaussian.Gaussian(settings: dict)[source]¶

Setup of the Gaussian program

available_models() → List[str][source]¶

A small function returning the single point models available now with the given program loaded/installed.

Returns:

modelsList[str]: A list of names of models that are available if the program is available.

check_install()[source]¶: A small function checking if the program was installed/located correctly and does provide the expected features.

static initialize()¶: Executed at Puffin start, run once for each available program

install(repo_dir: str, install_dir: str, ncores: int)[source]¶

Installs or loads the given program. After the install, the check_install function should run through with out exceptions. The choice of installation/compilation or loading of the program is based on the settings given in the constructor.

Parameters:

repo_dirstr: The folder for all repositories, if a clone or download is required for the installation, this folder will be used.
install_dirstr: If the program is actually installed and not just loaded, this folder will be used as target directory for the install process.
ncoresint: The number of cores/threads to be used when compiling/installing the program.

pip_module_source_install(repo_dir: str, install_dir: str)¶

static pip_package_install(package: str, install_dir: str)¶

scine_module_install(repo_dir: str, install_dir: str, ncores: int, add_lib: bool = False, add_bin: bool = False)¶

setup_environment(config: Configuration, env_paths: dict, env_vars: dict)[source]¶

Appends the program specific environment variables to the given dictionaries.

Parameters:

configscine_puffin.config.Configuration: The current global configuration.
env_pathsdict: A dictionary for all the environment paths, such as PATH and LD_LIBRARY_PATH. The added settings will be appended to the existing paths, using export PATH=$PATH:....
env_varsdict: A dictionary for all fixed environment variables. All settings will replace existing variables such as export OMP_NUM_THREADS=1