Arguments of the submit script

Note

One can load, modify, and export the input file by using our effective web-based tool DP-GUI online or hosted using the command line interface dpgen2 gui. All parameters below can be set in DP-GUI. By clicking “SAVE JSON”, one can download the input file.

dflow_config:

type: dict | NoneType, optional, default: None

argument path: dflow_config

The configuration passed to dflow

dflow_s3_config:

type: dict | NoneType, optional, default: None

argument path: dflow_s3_config

The S3 configuration passed to dflow

default_step_config:

type: dict, optional, default: {}

argument path: default_step_config

The default step configuration.

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: default_step_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: default_step_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: default_step_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: default_step_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: default_step_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: default_step_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: default_step_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: default_step_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: default_step_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: default_step_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: default_step_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: default_step_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: default_step_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: default_step_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: default_step_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

bohrium_config:

type: dict | NoneType, optional, default: None

argument path: bohrium_config

Configurations for the Bohrium platform.

username:

type: str

argument path: bohrium_config/username

The username of the Bohrium platform

password:

type: str

argument path: bohrium_config/password

The password of the Bohrium platform

project_id:

type: int

argument path: bohrium_config/project_id

The project ID of the Bohrium platform

host:

type: str, optional, default: https://workflows.deepmodeling.com

argument path: bohrium_config/host

The host name of the Bohrium platform. Will overwrite dflow_config[‘host’]

k8s_api_server:

type: str, optional, default: https://workflows.deepmodeling.com

argument path: bohrium_config/k8s_api_server

The k8s server of the Bohrium platform. Will overwrite dflow_config[‘k8s_api_server’]

repo_key:

type: str, optional, default: oss-bohrium

argument path: bohrium_config/repo_key

The repo key of the Bohrium platform. Will overwrite dflow_s3_config[‘repo_key’]

storage_client:

type: str, optional, default: dflow.plugins.bohrium.TiefblueClient

argument path: bohrium_config/storage_client

The storage client of the Bohrium platform. Will overwrite dflow_s3_config[‘storage_client’]

step_configs:

type: dict, optional, default: {}

argument path: step_configs

Configurations for executing dflow steps

prep_train_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/prep_train_config

Configuration for prepare train

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/prep_train_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/prep_train_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/prep_train_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_train_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/prep_train_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/prep_train_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/prep_train_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_train_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_train_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/prep_train_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

run_train_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/run_train_config

Configuration for run train

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/run_train_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/run_train_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/run_train_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_train_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/run_train_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/run_train_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/run_train_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/run_train_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_train_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/run_train_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

prep_explore_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/prep_explore_config

Configuration for prepare exploration

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/prep_explore_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/prep_explore_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/prep_explore_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_explore_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/prep_explore_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/prep_explore_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/prep_explore_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_explore_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_explore_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/prep_explore_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

run_explore_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/run_explore_config

Configuration for run exploration

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/run_explore_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/run_explore_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/run_explore_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_explore_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/run_explore_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/run_explore_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/run_explore_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/run_explore_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_explore_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/run_explore_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

prep_fp_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/prep_fp_config

Configuration for prepare fp

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/prep_fp_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/prep_fp_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/prep_fp_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_fp_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/prep_fp_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/prep_fp_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/prep_fp_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/prep_fp_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/prep_fp_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/prep_fp_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

run_fp_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/run_fp_config

Configuration for run fp

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/run_fp_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/run_fp_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/run_fp_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_fp_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/run_fp_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/run_fp_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/run_fp_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/run_fp_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/run_fp_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/run_fp_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

select_confs_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/select_confs_config

Configuration for the select confs

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/select_confs_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/select_confs_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/select_confs_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/select_confs_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/select_confs_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/select_confs_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/select_confs_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/select_confs_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/select_confs_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/select_confs_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

collect_data_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/collect_data_config

Configuration for the collect data

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/collect_data_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/collect_data_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/collect_data_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/collect_data_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/collect_data_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/collect_data_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/collect_data_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/collect_data_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/collect_data_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/collect_data_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

cl_step_config:

type: dict, optional, default: {'template_config': {'image': 'dptechnology/dpgen2:latest', 'timeout': None, 'retry_on_transient_error': None, 'timeout_as_transient_error': False, 'envs': None}, 'continue_on_failed': False, 'continue_on_num_success': None, 'continue_on_success_ratio': None, 'parallelism': None, 'executor': None}

argument path: step_configs/cl_step_config

Configuration for the concurrent learning step

template_config:

type: dict, optional, default: {'image': 'dptechnology/dpgen2:latest'}

argument path: step_configs/cl_step_config/template_config

The configs passed to the PythonOPTemplate.

image:

type: str, optional, default: dptechnology/dpgen2:latest

argument path: step_configs/cl_step_config/template_config/image

The image to run the step.

timeout:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/template_config/timeout

The time limit of the OP. Unit is second.

retry_on_transient_error:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/template_config/retry_on_transient_error

The number of retry times if a TransientError is raised.

timeout_as_transient_error:

type: bool, optional, default: False

argument path: step_configs/cl_step_config/template_config/timeout_as_transient_error

Treat the timeout as TransientError.

envs:

type: dict | NoneType, optional, default: None

argument path: step_configs/cl_step_config/template_config/envs

The environmental variables.

template_slice_config:

type: dict, optional

argument path: step_configs/cl_step_config/template_slice_config

The configs passed to the Slices.

group_size:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/template_slice_config/group_size

The number of tasks running on a single node. It is efficient for a large number of short tasks.

pool_size:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/template_slice_config/pool_size

The number of tasks running at the same time on one node.

continue_on_failed:

type: bool, optional, default: False

argument path: step_configs/cl_step_config/continue_on_failed

If continue the the step is failed (FatalError, TransientError, A certain number of retrial is reached…).

continue_on_num_success:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/continue_on_num_success

Only in the sliced OP case. Continue the workflow if a certain number of the sliced jobs are successful.

continue_on_success_ratio:

type: NoneType | float, optional, default: None

argument path: step_configs/cl_step_config/continue_on_success_ratio

Only in the sliced OP case. Continue the workflow if a certain ratio of the sliced jobs are successful.

parallelism:

type: NoneType | int, optional, default: None

argument path: step_configs/cl_step_config/parallelism

The parallelism for the step

executor:

type: dict | NoneType, optional, default: None

argument path: step_configs/cl_step_config/executor

The executor of the step.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: step_configs/cl_step_config/executor/type

possible choices: dispatcher

The type of the executor.

When type is set to dispatcher:

upload_python_packages:

type: typing.List[str] | str | NoneType, optional, default: None, alias: upload_python_package

argument path: upload_python_packages

Upload python package, for debug purpose

inputs:

type: dict

argument path: inputs

The input parameter and artifacts for dpgen2

type_map:

type: typing.List[str]

argument path: inputs/type_map

The type map. e.g. [“Al”, “Mg”]. Al and Mg will have type 0 and 1, respectively.

mass_map:

type: typing.List[float]

argument path: inputs/mass_map

The mass map. e.g. [27., 24.]. Al and Mg will be set with mass 27. and 24. amu, respectively.

init_data_prefix:

type: str | NoneType, optional, default: None

argument path: inputs/init_data_prefix

The prefix of initial data systems

mixed_type:

type: bool, optional, default: False

argument path: inputs/mixed_type

Use deepmd/npy/mixed format for storing training data.

do_finetune:

type: bool, optional, default: False

argument path: inputs/do_finetune

Finetune the pretrained model during the first iteration. If it is set to True, then in the first iteration, the internal flag finetune_mode is set to “finetune”. In this step, we finetune the pretrained model in the train step. After that, in the following iterations, init_model_policy is forced to be “yes”, the flag finetune_mode is set as “no”, which means we use –init-frz-model or –init-model to train based on models from the previous iteration. The “do_finetune” flag is set to False by default, while the internal flag finetune_mode is set to “no”, which means anything related to finetuning will not be done.

init_data_sys:

type: typing.List[str] | str | NoneType, optional, default: None

argument path: inputs/init_data_sys

The inital data systems

init_data_uri:

type: str | NoneType, optional, default: None

argument path: inputs/init_data_uri

The URI of initial data

multitask:

type: bool, optional, default: False

argument path: inputs/multitask

Do multitask training

head:

type: str | NoneType, optional, default: None

argument path: inputs/head

Head to use in the multitask training

multi_init_data:

type: dict | NoneType, optional, default: None

argument path: inputs/multi_init_data

The inital data for multitask, it should be a dict, whose keys are task names and each value is a dictcontaining fields prefix and sys for initial data of each task

multi_init_data_uri:

type: str | NoneType, optional, default: None

argument path: inputs/multi_init_data_uri

The URI of initial data for multitask

valid_data_prefix:

type: str | NoneType, optional, default: None

argument path: inputs/valid_data_prefix

The prefix of validation data systems

valid_data_sys:

type: typing.List[str] | str | NoneType, optional, default: None

argument path: inputs/valid_data_sys

The validation data systems

valid_data_uri:

type: str | NoneType, optional, default: None

argument path: inputs/valid_data_uri

The URI of validation data

use_ele_temp:

type: int, optional, default: 0

argument path: inputs/use_ele_temp

Whether to use electronic temperature, 0 for no, 1 for frame temperature, and 2 for atomic temperature

multi_valid_data:

type: dict | NoneType, optional, default: None

argument path: inputs/multi_valid_data

The validation data for multitask, it should be a dict, whose keys are task names and each value is a dictcontaining fields prefix and sys for initial data of each task

multi_valid_data_uri:

type: str | NoneType, optional, default: None

argument path: inputs/multi_valid_data_uri

The URI of validation data for multitask

train:

type: dict

argument path: train

The configuration for training

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: train/type

possible choices: dp, dp-dist

the type of the training

When type is set to dp:

config:

type: dict, optional, default: {'command': 'dp', 'impl': 'tensorflow', 'init_model_policy': 'no', 'init_model_old_ratio': 0.9, 'init_model_numb_steps': 400000, 'init_model_start_lr': 0.0001, 'init_model_start_pref_e': 0.1, 'init_model_start_pref_f': 100, 'init_model_start_pref_v': 0.0, 'init_model_with_finetune': False, 'finetune_args': '', 'multitask': False, 'head': None, 'train_args': ''}

argument path: train[dp]/config

Number of models trained for evaluating the model deviation

command:

type: str, optional, default: dp

argument path: train[dp]/config/command

The command for DP, ‘dp’ for default

impl:

type: str, optional, default: tensorflow, alias: backend

argument path: train[dp]/config/impl

The implementation/backend of DP. It can be ‘tensorflow’ or ‘pytorch’. ‘tensorflow’ for default.

init_model_policy:

type: str, optional, default: no

argument path: train[dp]/config/init_model_policy

The policy of init-model training. It can be

• ‘no’: No init-model training. Traing from scratch.

• ‘yes’: Do init-model training.

• ‘old_data_larger_than:XXX’: Do init-model if the training data size of the previous model is larger than XXX. XXX is an int number.

init_model_old_ratio:

type: float, optional, default: 0.9

argument path: train[dp]/config/init_model_old_ratio

The frequency ratio of old data over new data

init_model_numb_steps:

type: int, optional, default: 400000, alias: init_model_stop_batch

argument path: train[dp]/config/init_model_numb_steps

The number of training steps when init-model

init_model_start_lr:

type: float, optional, default: 0.0001

argument path: train[dp]/config/init_model_start_lr

The start learning rate when init-model

init_model_start_pref_e:

type: float, optional, default: 0.1

argument path: train[dp]/config/init_model_start_pref_e

The start energy prefactor in loss when init-model

init_model_start_pref_f:

type: float, optional, default: 100

argument path: train[dp]/config/init_model_start_pref_f

The start force prefactor in loss when init-model

init_model_start_pref_v:

type: float, optional, default: 0.0

argument path: train[dp]/config/init_model_start_pref_v

The start virial prefactor in loss when init-model

init_model_with_finetune:

type: bool, optional, default: False

argument path: train[dp]/config/init_model_with_finetune

Use finetune for init model

finetune_args:

type: str, optional, default: (empty string)

argument path: train[dp]/config/finetune_args

Extra arguments for finetuning

multitask:

type: bool, optional, default: False

argument path: train[dp]/config/multitask

Do multitask training

head:

type: str | NoneType, optional, default: None

argument path: train[dp]/config/head

Head to use in the multitask training

train_args:

type: str, optional, default: (empty string)

argument path: train[dp]/config/train_args

Extra arguments for dp train

numb_models:

type: int, optional, default: 4

argument path: train[dp]/numb_models

Number of models trained for evaluating the model deviation

template_script:

type: typing.List[str] | str

argument path: train[dp]/template_script

File names of the template training script. It can be a List[str], the length of which is the same as numb_models. Each template script in the list is used to train a model. Can be a str, the models share the same template training script.

init_models_paths:

type: typing.List[str] | NoneType, optional, default: None, alias: training_iter0_model_path

argument path: train[dp]/init_models_paths

the paths to initial models

init_models_uri:

type: str | NoneType, optional, default: None

argument path: train[dp]/init_models_uri

The URI of initial models

optional_files:

type: list | NoneType, optional, default: None

argument path: train[dp]/optional_files

Optional files for training

When type is set to dp-dist:

config:

type: dict, optional, default: {'command': 'dp', 'impl': 'tensorflow', 'init_model_policy': 'no', 'init_model_old_ratio': 0.9, 'init_model_numb_steps': 400000, 'init_model_start_lr': 0.0001, 'init_model_start_pref_e': 0.1, 'init_model_start_pref_f': 100, 'init_model_start_pref_v': 0.0, 'init_model_with_finetune': False, 'finetune_args': '', 'multitask': False, 'head': None, 'train_args': ''}

argument path: train[dp-dist]/config

Configuration of training

command:

type: str, optional, default: dp

argument path: train[dp-dist]/config/command

The command for DP, ‘dp’ for default

impl:

type: str, optional, default: tensorflow, alias: backend

argument path: train[dp-dist]/config/impl

The implementation/backend of DP. It can be ‘tensorflow’ or ‘pytorch’. ‘tensorflow’ for default.

init_model_policy:

type: str, optional, default: no

argument path: train[dp-dist]/config/init_model_policy

The policy of init-model training. It can be

• ‘no’: No init-model training. Traing from scratch.

• ‘yes’: Do init-model training.

• ‘old_data_larger_than:XXX’: Do init-model if the training data size of the previous model is larger than XXX. XXX is an int number.

init_model_old_ratio:

type: float, optional, default: 0.9

argument path: train[dp-dist]/config/init_model_old_ratio

The frequency ratio of old data over new data

init_model_numb_steps:

type: int, optional, default: 400000, alias: init_model_stop_batch

argument path: train[dp-dist]/config/init_model_numb_steps

The number of training steps when init-model

init_model_start_lr:

type: float, optional, default: 0.0001

argument path: train[dp-dist]/config/init_model_start_lr

The start learning rate when init-model

init_model_start_pref_e:

type: float, optional, default: 0.1

argument path: train[dp-dist]/config/init_model_start_pref_e

The start energy prefactor in loss when init-model

init_model_start_pref_f:

type: float, optional, default: 100

argument path: train[dp-dist]/config/init_model_start_pref_f

The start force prefactor in loss when init-model

init_model_start_pref_v:

type: float, optional, default: 0.0

argument path: train[dp-dist]/config/init_model_start_pref_v

The start virial prefactor in loss when init-model

init_model_with_finetune:

type: bool, optional, default: False

argument path: train[dp-dist]/config/init_model_with_finetune

Use finetune for init model

finetune_args:

type: str, optional, default: (empty string)

argument path: train[dp-dist]/config/finetune_args

Extra arguments for finetuning

multitask:

type: bool, optional, default: False

argument path: train[dp-dist]/config/multitask

Do multitask training

head:

type: str | NoneType, optional, default: None

argument path: train[dp-dist]/config/head

Head to use in the multitask training

train_args:

type: str, optional, default: (empty string)

argument path: train[dp-dist]/config/train_args

Extra arguments for dp train

template_script:

type: typing.List[str] | str

argument path: train[dp-dist]/template_script

File names of the template training script. It can be a List[str], the length of which is the same as numb_models. Each template script in the list is used to train a model. Can be a str, the models share the same template training script.

student_model_path:

type: str, optional

argument path: train[dp-dist]/student_model_path

The path of student model

student_model_uri:

type: str | NoneType, optional, default: None

argument path: train[dp-dist]/student_model_uri

The URI of student model

optional_files:

type: list | NoneType, optional, default: None

argument path: train[dp-dist]/optional_files

Optional files for training

explore:

type: dict

argument path: explore

The configuration for exploration

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore/type

possible choices: lmp, calypso, calypso:default, calypso:merge, diffcsp

The type of the exploration

• lmp: The exploration by LAMMPS simulations

• calypso: The exploration by CALYPSO structure prediction

• calypso:default: The exploration by CALYPSO structure prediction

• calypso:merge: The exploration by CALYPSO structure prediction

• diffcsp: The exploration by DiffCSP

When type is set to lmp:

The exploration by LAMMPS simulations

config:

type: dict, optional, default: {'command': 'lmp', 'teacher_model_path': None, 'shuffle_models': False, 'head': None, 'use_ele_temp': 0, 'model_frozen_head': None, 'use_hdf5': False}

argument path: explore[lmp]/config

Configuration of lmp exploration

command:

type: str, optional, default: lmp

argument path: explore[lmp]/config/command

The command of LAMMPS

teacher_model_path:

type: BinaryFileInput | str | NoneType, optional, default: None

argument path: explore[lmp]/config/teacher_model_path

The teacher model in Knowledge Distillation

shuffle_models:

type: bool, optional, default: False

argument path: explore[lmp]/config/shuffle_models

Randomly pick a model from the group of models to drive theexploration MD simulation

head:

type: str | NoneType, optional, default: None

argument path: explore[lmp]/config/head

Select a head from multitask

use_ele_temp:

type: int, optional, default: 0

argument path: explore[lmp]/config/use_ele_temp

Whether to use electronic temperature, 0 for no, 1 for frame temperature, and 2 for atomic temperature

model_frozen_head:

type: str | NoneType, optional, default: None

argument path: explore[lmp]/config/model_frozen_head

Select a head from multitask

use_hdf5:

type: bool, optional, default: False

argument path: explore[lmp]/config/use_hdf5

Use HDF5 to store trajs and model_devis

max_numb_iter:

type: int, optional, default: 10

argument path: explore[lmp]/max_numb_iter

Maximum number of iterations per stage

fatal_at_max:

type: bool, optional, default: True

argument path: explore[lmp]/fatal_at_max

Fatal when the number of iteration per stage reaches the max_numb_iter

output_nopbc:

type: bool, optional, default: False

argument path: explore[lmp]/output_nopbc

Remove pbc of the output configurations

convergence:

type: dict

argument path: explore[lmp]/convergence

The method of convergence check.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[lmp]/convergence/type

possible choices: fixed-levels, fixed-levels-max-select, adaptive-lower

the type of the condidate selection and convergence check method.

• fixed-levels: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• fixed-levels-max-select: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• adaptive-lower: The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

When type is set to fixed-levels:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[lmp]/convergence[fixed-levels]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[lmp]/convergence[fixed-levels]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[lmp]/convergence[fixed-levels]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[lmp]/convergence[fixed-levels]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[lmp]/convergence[fixed-levels]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to fixed-levels-max-select:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[lmp]/convergence[fixed-levels-max-select]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[lmp]/convergence[fixed-levels-max-select]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[lmp]/convergence[fixed-levels-max-select]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[lmp]/convergence[fixed-levels-max-select]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[lmp]/convergence[fixed-levels-max-select]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to adaptive-lower:

The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

level_f_hi:

type: float, optional, default: 0.5

argument path: explore[lmp]/convergence[adaptive-lower]/level_f_hi

The higher trust level of force model deviation

numb_candi_f:

type: int, optional, default: 200

argument path: explore[lmp]/convergence[adaptive-lower]/numb_candi_f

The number of force frames that has a model deviation lower than level_f_hi treated as candidate.

rate_candi_f:

type: float, optional, default: 0.01

argument path: explore[lmp]/convergence[adaptive-lower]/rate_candi_f

The ratio of force frames that has a model deviation lower than level_f_hi treated as candidate.

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[lmp]/convergence[adaptive-lower]/level_v_hi

The higher trust level of virial model deviation

numb_candi_v:

type: int, optional, default: 0

argument path: explore[lmp]/convergence[adaptive-lower]/numb_candi_v

The number of virial frames that has a model deviation lower than level_v_hi treated as candidate.

rate_candi_v:

type: float, optional, default: 0.0

argument path: explore[lmp]/convergence[adaptive-lower]/rate_candi_v

The ratio of virial frames that has a model deviation lower than level_v_hi treated as candidate.

n_checked_steps:

type: int, optional, default: 2

argument path: explore[lmp]/convergence[adaptive-lower]/n_checked_steps

The number of steps to check the convergence.

conv_tolerance:

type: float, optional, default: 0.05

argument path: explore[lmp]/convergence[adaptive-lower]/conv_tolerance

The convergence tolerance.

candi_sel_prob:

type: str, optional, default: uniform

argument path: explore[lmp]/convergence[adaptive-lower]/candi_sel_prob

The method for selecting candidates. It can be ‘uniform’: all candidates are of the same probability. ‘inv_pop_f’ or ‘inv_pop_f:nhist’: the probability is inversely propotional to the population of a histogram between leven_f_lo and level_f_hi. The number of bins in the histogram is set by nhist, which should be an integer. The default is 10.

configurations:

type: list, alias: configuration

argument path: explore[lmp]/configurations

A list of initial configurations.

This argument takes a list with each element containing the following:

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[lmp]/configurations/type

possible choices: alloy, file

the type of the initial configuration generator.

• alloy: Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

• file: Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

When type is set to alloy:

Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

numb_confs:

type: int, optional, default: 1

argument path: explore[lmp]/configurations[alloy]/numb_confs

The number of configurations to generate

lattice:

type: list | tuple

argument path: explore[lmp]/configurations[alloy]/lattice

The lattice. Should be a list providing [ “lattice_type”, lattice_const ], or a list providing [ “/path/to/dpdata/system”, “fmt” ]. The two styles are distinguished by the type of the second element. Currently “lattice_type” can be “bcc”, “fcc”, “hcp”, “sc” or “diamond”.

replicate:

type: list | NoneType, optional, default: None

argument path: explore[lmp]/configurations[alloy]/replicate

The number of replicates in each direction

concentration:

type: list | NoneType, optional, default: None

argument path: explore[lmp]/configurations[alloy]/concentration

The concentration of each element. List[List[float]] or List[float] or None. If List[float], the concentrations of each element. The length of the list should be the same as the type_map. If List[List[float]], a list of concentrations (List[float]) is randomly picked from the List. If None, the elements are assumed to be of equal concentration.

cell_pert_frac:

type: float, optional, default: 0.0

argument path: explore[lmp]/configurations[alloy]/cell_pert_frac

The faction of cell perturbation

atom_pert_dist:

type: float, optional, default: 0.0

argument path: explore[lmp]/configurations[alloy]/atom_pert_dist

The distance of atomic position perturbation

When type is set to file:

Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

files:

type: str | list

argument path: explore[lmp]/configurations[file]/files

The paths to the configuration files. widecards are supported.

prefix:

type: str | NoneType, optional, default: None

argument path: explore[lmp]/configurations[file]/prefix

The prefix of file paths.

fmt:

type: str, optional, default: auto

argument path: explore[lmp]/configurations[file]/fmt

The format (dpdata accepted formats) of the files.

remove_pbc:

type: bool, optional, default: False

argument path: explore[lmp]/configurations[file]/remove_pbc

The remove the pbc of the data. shift the coords to the center of box so it can be used with lammps.

stages:

type: typing.List[typing.List[dict]]

argument path: explore[lmp]/stages

The definition of exploration stages of type List[List[ExplorationTaskGroup]. The outer list provides the enumeration of the exploration stages. Then each stage is defined by a list of exploration task groups. Each task group is described in the task group definition

filters:

type: list | dict, optional, default: []

argument path: explore[lmp]/filters

A list of configuration filters

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[lmp]/filters/type

possible choices: distance, box_skewness, box_length

the type of the configuration filter.

• distance: Configuration filter of type distance

• box_skewness: Configuration filter of type box_skewness

• box_length: Configuration filter of type box_length

When type is set to distance:

Configuration filter of type distance

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[lmp]/filters[distance]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

custom_safe_dist:

type: dict, optional, default: {}

argument path: explore[lmp]/filters[distance]/custom_safe_dist

Custom safe distance (in unit of bohr) for each element

safe_dist_ratio:

type: float, optional, default: 1.0

argument path: explore[lmp]/filters[distance]/safe_dist_ratio

The ratio multiplied to the safe distance

When type is set to box_skewness:

Configuration filter of type box_skewness

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[lmp]/filters[box_skewness]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

theta:

type: float, optional, default: 60.0

argument path: explore[lmp]/filters[box_skewness]/theta

The threshold for angles between the edges of the cell. If all angles are larger than this value the check is passed

When type is set to box_length:

Configuration filter of type box_length

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[lmp]/filters[box_length]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

length_ratio:

type: float, optional, default: 5.0

argument path: explore[lmp]/filters[box_length]/length_ratio

The threshold for the length ratio between the edges of the cell. If all length ratios are smaller than this value the check is passed

When type is set to calypso:

The exploration by CALYPSO structure prediction

config:

type: dict, optional, default: {'command': 'lmp', 'teacher_model_path': None, 'shuffle_models': False, 'head': None, 'use_ele_temp': 0, 'model_frozen_head': None, 'use_hdf5': False}

argument path: explore[calypso]/config

Configuration of calypso exploration

model_devi_group_size:

type: int, optional

argument path: explore[calypso]/config/model_devi_group_size

group size for model deviation.

run_calypso_command:

type: str, optional, default: calypso.x

argument path: explore[calypso]/config/run_calypso_command

command of running calypso.

run_opt_command:

type: str, optional

argument path: explore[calypso]/config/run_opt_command

command of running optimization with dp.

max_numb_iter:

type: int, optional, default: 10

argument path: explore[calypso]/max_numb_iter

Maximum number of iterations per stage

fatal_at_max:

type: bool, optional, default: True

argument path: explore[calypso]/fatal_at_max

Fatal when the number of iteration per stage reaches the max_numb_iter

output_nopbc:

type: bool, optional, default: False

argument path: explore[calypso]/output_nopbc

Remove pbc of the output configurations

convergence:

type: dict

argument path: explore[calypso]/convergence

The method of convergence check.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso]/convergence/type

possible choices: fixed-levels, fixed-levels-max-select, adaptive-lower

the type of the condidate selection and convergence check method.

• fixed-levels: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• fixed-levels-max-select: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• adaptive-lower: The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

When type is set to fixed-levels:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso]/convergence[fixed-levels]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso]/convergence[fixed-levels]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso]/convergence[fixed-levels]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso]/convergence[fixed-levels]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso]/convergence[fixed-levels]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to fixed-levels-max-select:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso]/convergence[fixed-levels-max-select]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso]/convergence[fixed-levels-max-select]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso]/convergence[fixed-levels-max-select]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso]/convergence[fixed-levels-max-select]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso]/convergence[fixed-levels-max-select]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to adaptive-lower:

The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

level_f_hi:

type: float, optional, default: 0.5

argument path: explore[calypso]/convergence[adaptive-lower]/level_f_hi

The higher trust level of force model deviation

numb_candi_f:

type: int, optional, default: 200

argument path: explore[calypso]/convergence[adaptive-lower]/numb_candi_f

The number of force frames that has a model deviation lower than level_f_hi treated as candidate.

rate_candi_f:

type: float, optional, default: 0.01

argument path: explore[calypso]/convergence[adaptive-lower]/rate_candi_f

The ratio of force frames that has a model deviation lower than level_f_hi treated as candidate.

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso]/convergence[adaptive-lower]/level_v_hi

The higher trust level of virial model deviation

numb_candi_v:

type: int, optional, default: 0

argument path: explore[calypso]/convergence[adaptive-lower]/numb_candi_v

The number of virial frames that has a model deviation lower than level_v_hi treated as candidate.

rate_candi_v:

type: float, optional, default: 0.0

argument path: explore[calypso]/convergence[adaptive-lower]/rate_candi_v

The ratio of virial frames that has a model deviation lower than level_v_hi treated as candidate.

n_checked_steps:

type: int, optional, default: 2

argument path: explore[calypso]/convergence[adaptive-lower]/n_checked_steps

The number of steps to check the convergence.

conv_tolerance:

type: float, optional, default: 0.05

argument path: explore[calypso]/convergence[adaptive-lower]/conv_tolerance

The convergence tolerance.

candi_sel_prob:

type: str, optional, default: uniform

argument path: explore[calypso]/convergence[adaptive-lower]/candi_sel_prob

The method for selecting candidates. It can be ‘uniform’: all candidates are of the same probability. ‘inv_pop_f’ or ‘inv_pop_f:nhist’: the probability is inversely propotional to the population of a histogram between leven_f_lo and level_f_hi. The number of bins in the histogram is set by nhist, which should be an integer. The default is 10.

configurations:

type: list, alias: configuration

argument path: explore[calypso]/configurations

A list of initial configurations.

This argument takes a list with each element containing the following:

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso]/configurations/type

possible choices: alloy, file

the type of the initial configuration generator.

• alloy: Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

• file: Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

When type is set to alloy:

Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

numb_confs:

type: int, optional, default: 1

argument path: explore[calypso]/configurations[alloy]/numb_confs

The number of configurations to generate

lattice:

type: list | tuple

argument path: explore[calypso]/configurations[alloy]/lattice

The lattice. Should be a list providing [ “lattice_type”, lattice_const ], or a list providing [ “/path/to/dpdata/system”, “fmt” ]. The two styles are distinguished by the type of the second element. Currently “lattice_type” can be “bcc”, “fcc”, “hcp”, “sc” or “diamond”.

replicate:

type: list | NoneType, optional, default: None

argument path: explore[calypso]/configurations[alloy]/replicate

The number of replicates in each direction

concentration:

type: list | NoneType, optional, default: None

argument path: explore[calypso]/configurations[alloy]/concentration

The concentration of each element. List[List[float]] or List[float] or None. If List[float], the concentrations of each element. The length of the list should be the same as the type_map. If List[List[float]], a list of concentrations (List[float]) is randomly picked from the List. If None, the elements are assumed to be of equal concentration.

cell_pert_frac:

type: float, optional, default: 0.0

argument path: explore[calypso]/configurations[alloy]/cell_pert_frac

The faction of cell perturbation

atom_pert_dist:

type: float, optional, default: 0.0

argument path: explore[calypso]/configurations[alloy]/atom_pert_dist

The distance of atomic position perturbation

When type is set to file:

Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

files:

type: str | list

argument path: explore[calypso]/configurations[file]/files

The paths to the configuration files. widecards are supported.

prefix:

type: str | NoneType, optional, default: None

argument path: explore[calypso]/configurations[file]/prefix

The prefix of file paths.

fmt:

type: str, optional, default: auto

argument path: explore[calypso]/configurations[file]/fmt

The format (dpdata accepted formats) of the files.

remove_pbc:

type: bool, optional, default: False

argument path: explore[calypso]/configurations[file]/remove_pbc

The remove the pbc of the data. shift the coords to the center of box so it can be used with lammps.

stages:

type: typing.List[typing.List[dict]]

argument path: explore[calypso]/stages

The definition of exploration stages of type List[List[ExplorationTaskGroup]. The outer list provides the enumeration of the exploration stages. Then each stage is defined by a list of exploration task groups. Each task group is described in the task group definition

filters:

type: list | dict, optional, default: []

argument path: explore[calypso]/filters

A list of configuration filters

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso]/filters/type

possible choices: distance, box_skewness, box_length

the type of the configuration filter.

• distance: Configuration filter of type distance

• box_skewness: Configuration filter of type box_skewness

• box_length: Configuration filter of type box_length

When type is set to distance:

Configuration filter of type distance

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso]/filters[distance]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

custom_safe_dist:

type: dict, optional, default: {}

argument path: explore[calypso]/filters[distance]/custom_safe_dist

Custom safe distance (in unit of bohr) for each element

safe_dist_ratio:

type: float, optional, default: 1.0

argument path: explore[calypso]/filters[distance]/safe_dist_ratio

The ratio multiplied to the safe distance

When type is set to box_skewness:

Configuration filter of type box_skewness

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso]/filters[box_skewness]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

theta:

type: float, optional, default: 60.0

argument path: explore[calypso]/filters[box_skewness]/theta

The threshold for angles between the edges of the cell. If all angles are larger than this value the check is passed

When type is set to box_length:

Configuration filter of type box_length

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso]/filters[box_length]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

length_ratio:

type: float, optional, default: 5.0

argument path: explore[calypso]/filters[box_length]/length_ratio

The threshold for the length ratio between the edges of the cell. If all length ratios are smaller than this value the check is passed

When type is set to calypso:default:

The exploration by CALYPSO structure prediction

config:

type: dict, optional, default: {'command': 'lmp', 'teacher_model_path': None, 'shuffle_models': False, 'head': None, 'use_ele_temp': 0, 'model_frozen_head': None, 'use_hdf5': False}

argument path: explore[calypso:default]/config

Configuration of calypso exploration

model_devi_group_size:

type: int, optional

argument path: explore[calypso:default]/config/model_devi_group_size

group size for model deviation.

run_calypso_command:

type: str, optional, default: calypso.x

argument path: explore[calypso:default]/config/run_calypso_command

command of running calypso.

run_opt_command:

type: str, optional

argument path: explore[calypso:default]/config/run_opt_command

command of running optimization with dp.

max_numb_iter:

type: int, optional, default: 10

argument path: explore[calypso:default]/max_numb_iter

Maximum number of iterations per stage

fatal_at_max:

type: bool, optional, default: True

argument path: explore[calypso:default]/fatal_at_max

Fatal when the number of iteration per stage reaches the max_numb_iter

output_nopbc:

type: bool, optional, default: False

argument path: explore[calypso:default]/output_nopbc

Remove pbc of the output configurations

convergence:

type: dict

argument path: explore[calypso:default]/convergence

The method of convergence check.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:default]/convergence/type

possible choices: fixed-levels, fixed-levels-max-select, adaptive-lower

the type of the condidate selection and convergence check method.

• fixed-levels: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• fixed-levels-max-select: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• adaptive-lower: The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

When type is set to fixed-levels:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso:default]/convergence[fixed-levels]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso:default]/convergence[fixed-levels]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso:default]/convergence[fixed-levels]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:default]/convergence[fixed-levels]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso:default]/convergence[fixed-levels]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to fixed-levels-max-select:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso:default]/convergence[fixed-levels-max-select]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso:default]/convergence[fixed-levels-max-select]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso:default]/convergence[fixed-levels-max-select]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:default]/convergence[fixed-levels-max-select]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso:default]/convergence[fixed-levels-max-select]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to adaptive-lower:

The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

level_f_hi:

type: float, optional, default: 0.5

argument path: explore[calypso:default]/convergence[adaptive-lower]/level_f_hi

The higher trust level of force model deviation

numb_candi_f:

type: int, optional, default: 200

argument path: explore[calypso:default]/convergence[adaptive-lower]/numb_candi_f

The number of force frames that has a model deviation lower than level_f_hi treated as candidate.

rate_candi_f:

type: float, optional, default: 0.01

argument path: explore[calypso:default]/convergence[adaptive-lower]/rate_candi_f

The ratio of force frames that has a model deviation lower than level_f_hi treated as candidate.

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:default]/convergence[adaptive-lower]/level_v_hi

The higher trust level of virial model deviation

numb_candi_v:

type: int, optional, default: 0

argument path: explore[calypso:default]/convergence[adaptive-lower]/numb_candi_v

The number of virial frames that has a model deviation lower than level_v_hi treated as candidate.

rate_candi_v:

type: float, optional, default: 0.0

argument path: explore[calypso:default]/convergence[adaptive-lower]/rate_candi_v

The ratio of virial frames that has a model deviation lower than level_v_hi treated as candidate.

n_checked_steps:

type: int, optional, default: 2

argument path: explore[calypso:default]/convergence[adaptive-lower]/n_checked_steps

The number of steps to check the convergence.

conv_tolerance:

type: float, optional, default: 0.05

argument path: explore[calypso:default]/convergence[adaptive-lower]/conv_tolerance

The convergence tolerance.

candi_sel_prob:

type: str, optional, default: uniform

argument path: explore[calypso:default]/convergence[adaptive-lower]/candi_sel_prob

The method for selecting candidates. It can be ‘uniform’: all candidates are of the same probability. ‘inv_pop_f’ or ‘inv_pop_f:nhist’: the probability is inversely propotional to the population of a histogram between leven_f_lo and level_f_hi. The number of bins in the histogram is set by nhist, which should be an integer. The default is 10.

configurations:

type: list, alias: configuration

argument path: explore[calypso:default]/configurations

A list of initial configurations.

This argument takes a list with each element containing the following:

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:default]/configurations/type

possible choices: alloy, file

the type of the initial configuration generator.

• alloy: Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

• file: Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

When type is set to alloy:

Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

numb_confs:

type: int, optional, default: 1

argument path: explore[calypso:default]/configurations[alloy]/numb_confs

The number of configurations to generate

lattice:

type: list | tuple

argument path: explore[calypso:default]/configurations[alloy]/lattice

The lattice. Should be a list providing [ “lattice_type”, lattice_const ], or a list providing [ “/path/to/dpdata/system”, “fmt” ]. The two styles are distinguished by the type of the second element. Currently “lattice_type” can be “bcc”, “fcc”, “hcp”, “sc” or “diamond”.

replicate:

type: list | NoneType, optional, default: None

argument path: explore[calypso:default]/configurations[alloy]/replicate

The number of replicates in each direction

concentration:

type: list | NoneType, optional, default: None

argument path: explore[calypso:default]/configurations[alloy]/concentration

The concentration of each element. List[List[float]] or List[float] or None. If List[float], the concentrations of each element. The length of the list should be the same as the type_map. If List[List[float]], a list of concentrations (List[float]) is randomly picked from the List. If None, the elements are assumed to be of equal concentration.

cell_pert_frac:

type: float, optional, default: 0.0

argument path: explore[calypso:default]/configurations[alloy]/cell_pert_frac

The faction of cell perturbation

atom_pert_dist:

type: float, optional, default: 0.0

argument path: explore[calypso:default]/configurations[alloy]/atom_pert_dist

The distance of atomic position perturbation

When type is set to file:

Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

files:

type: str | list

argument path: explore[calypso:default]/configurations[file]/files

The paths to the configuration files. widecards are supported.

prefix:

type: str | NoneType, optional, default: None

argument path: explore[calypso:default]/configurations[file]/prefix

The prefix of file paths.

fmt:

type: str, optional, default: auto

argument path: explore[calypso:default]/configurations[file]/fmt

The format (dpdata accepted formats) of the files.

remove_pbc:

type: bool, optional, default: False

argument path: explore[calypso:default]/configurations[file]/remove_pbc

The remove the pbc of the data. shift the coords to the center of box so it can be used with lammps.

stages:

type: typing.List[typing.List[dict]]

argument path: explore[calypso:default]/stages

The definition of exploration stages of type List[List[ExplorationTaskGroup]. The outer list provides the enumeration of the exploration stages. Then each stage is defined by a list of exploration task groups. Each task group is described in the task group definition

filters:

type: list | dict, optional, default: []

argument path: explore[calypso:default]/filters

A list of configuration filters

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:default]/filters/type

possible choices: distance, box_skewness, box_length

the type of the configuration filter.

• distance: Configuration filter of type distance

• box_skewness: Configuration filter of type box_skewness

• box_length: Configuration filter of type box_length

When type is set to distance:

Configuration filter of type distance

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:default]/filters[distance]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

custom_safe_dist:

type: dict, optional, default: {}

argument path: explore[calypso:default]/filters[distance]/custom_safe_dist

Custom safe distance (in unit of bohr) for each element

safe_dist_ratio:

type: float, optional, default: 1.0

argument path: explore[calypso:default]/filters[distance]/safe_dist_ratio

The ratio multiplied to the safe distance

When type is set to box_skewness:

Configuration filter of type box_skewness

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:default]/filters[box_skewness]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

theta:

type: float, optional, default: 60.0

argument path: explore[calypso:default]/filters[box_skewness]/theta

The threshold for angles between the edges of the cell. If all angles are larger than this value the check is passed

When type is set to box_length:

Configuration filter of type box_length

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:default]/filters[box_length]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

length_ratio:

type: float, optional, default: 5.0

argument path: explore[calypso:default]/filters[box_length]/length_ratio

The threshold for the length ratio between the edges of the cell. If all length ratios are smaller than this value the check is passed

When type is set to calypso:merge:

The exploration by CALYPSO structure prediction

config:

type: dict, optional, default: {'command': 'lmp', 'teacher_model_path': None, 'shuffle_models': False, 'head': None, 'use_ele_temp': 0, 'model_frozen_head': None, 'use_hdf5': False}

argument path: explore[calypso:merge]/config

Configuration of calypso exploration

model_devi_group_size:

type: int, optional

argument path: explore[calypso:merge]/config/model_devi_group_size

group size for model deviation.

run_calypso_command:

type: str, optional, default: calypso.x

argument path: explore[calypso:merge]/config/run_calypso_command

command of running calypso.

run_opt_command:

type: str, optional

argument path: explore[calypso:merge]/config/run_opt_command

command of running optimization with dp.

max_numb_iter:

type: int, optional, default: 10

argument path: explore[calypso:merge]/max_numb_iter

Maximum number of iterations per stage

fatal_at_max:

type: bool, optional, default: True

argument path: explore[calypso:merge]/fatal_at_max

Fatal when the number of iteration per stage reaches the max_numb_iter

output_nopbc:

type: bool, optional, default: False

argument path: explore[calypso:merge]/output_nopbc

Remove pbc of the output configurations

convergence:

type: dict

argument path: explore[calypso:merge]/convergence

The method of convergence check.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:merge]/convergence/type

possible choices: fixed-levels, fixed-levels-max-select, adaptive-lower

the type of the condidate selection and convergence check method.

• fixed-levels: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• fixed-levels-max-select: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• adaptive-lower: The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

When type is set to fixed-levels:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso:merge]/convergence[fixed-levels]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso:merge]/convergence[fixed-levels]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso:merge]/convergence[fixed-levels]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:merge]/convergence[fixed-levels]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso:merge]/convergence[fixed-levels]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to fixed-levels-max-select:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[calypso:merge]/convergence[fixed-levels-max-select]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[calypso:merge]/convergence[fixed-levels-max-select]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[calypso:merge]/convergence[fixed-levels-max-select]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:merge]/convergence[fixed-levels-max-select]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[calypso:merge]/convergence[fixed-levels-max-select]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to adaptive-lower:

The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

level_f_hi:

type: float, optional, default: 0.5

argument path: explore[calypso:merge]/convergence[adaptive-lower]/level_f_hi

The higher trust level of force model deviation

numb_candi_f:

type: int, optional, default: 200

argument path: explore[calypso:merge]/convergence[adaptive-lower]/numb_candi_f

The number of force frames that has a model deviation lower than level_f_hi treated as candidate.

rate_candi_f:

type: float, optional, default: 0.01

argument path: explore[calypso:merge]/convergence[adaptive-lower]/rate_candi_f

The ratio of force frames that has a model deviation lower than level_f_hi treated as candidate.

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[calypso:merge]/convergence[adaptive-lower]/level_v_hi

The higher trust level of virial model deviation

numb_candi_v:

type: int, optional, default: 0

argument path: explore[calypso:merge]/convergence[adaptive-lower]/numb_candi_v

The number of virial frames that has a model deviation lower than level_v_hi treated as candidate.

rate_candi_v:

type: float, optional, default: 0.0

argument path: explore[calypso:merge]/convergence[adaptive-lower]/rate_candi_v

The ratio of virial frames that has a model deviation lower than level_v_hi treated as candidate.

n_checked_steps:

type: int, optional, default: 2

argument path: explore[calypso:merge]/convergence[adaptive-lower]/n_checked_steps

The number of steps to check the convergence.

conv_tolerance:

type: float, optional, default: 0.05

argument path: explore[calypso:merge]/convergence[adaptive-lower]/conv_tolerance

The convergence tolerance.

candi_sel_prob:

type: str, optional, default: uniform

argument path: explore[calypso:merge]/convergence[adaptive-lower]/candi_sel_prob

The method for selecting candidates. It can be ‘uniform’: all candidates are of the same probability. ‘inv_pop_f’ or ‘inv_pop_f:nhist’: the probability is inversely propotional to the population of a histogram between leven_f_lo and level_f_hi. The number of bins in the histogram is set by nhist, which should be an integer. The default is 10.

configurations:

type: list, alias: configuration

argument path: explore[calypso:merge]/configurations

A list of initial configurations.

This argument takes a list with each element containing the following:

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:merge]/configurations/type

possible choices: alloy, file

the type of the initial configuration generator.

• alloy: Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

• file: Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

When type is set to alloy:

Generate alloys with a certain lattice or user proided structure, the elements randomly occuping the lattice with user provided probability .

numb_confs:

type: int, optional, default: 1

argument path: explore[calypso:merge]/configurations[alloy]/numb_confs

The number of configurations to generate

lattice:

type: list | tuple

argument path: explore[calypso:merge]/configurations[alloy]/lattice

The lattice. Should be a list providing [ “lattice_type”, lattice_const ], or a list providing [ “/path/to/dpdata/system”, “fmt” ]. The two styles are distinguished by the type of the second element. Currently “lattice_type” can be “bcc”, “fcc”, “hcp”, “sc” or “diamond”.

replicate:

type: list | NoneType, optional, default: None

argument path: explore[calypso:merge]/configurations[alloy]/replicate

The number of replicates in each direction

concentration:

type: list | NoneType, optional, default: None

argument path: explore[calypso:merge]/configurations[alloy]/concentration

The concentration of each element. List[List[float]] or List[float] or None. If List[float], the concentrations of each element. The length of the list should be the same as the type_map. If List[List[float]], a list of concentrations (List[float]) is randomly picked from the List. If None, the elements are assumed to be of equal concentration.

cell_pert_frac:

type: float, optional, default: 0.0

argument path: explore[calypso:merge]/configurations[alloy]/cell_pert_frac

The faction of cell perturbation

atom_pert_dist:

type: float, optional, default: 0.0

argument path: explore[calypso:merge]/configurations[alloy]/atom_pert_dist

The distance of atomic position perturbation

When type is set to file:

Generate alloys from user provided file(s). The file(s) are assume to be load by dpdata.

files:

type: str | list

argument path: explore[calypso:merge]/configurations[file]/files

The paths to the configuration files. widecards are supported.

prefix:

type: str | NoneType, optional, default: None

argument path: explore[calypso:merge]/configurations[file]/prefix

The prefix of file paths.

fmt:

type: str, optional, default: auto

argument path: explore[calypso:merge]/configurations[file]/fmt

The format (dpdata accepted formats) of the files.

remove_pbc:

type: bool, optional, default: False

argument path: explore[calypso:merge]/configurations[file]/remove_pbc

The remove the pbc of the data. shift the coords to the center of box so it can be used with lammps.

stages:

type: typing.List[typing.List[dict]]

argument path: explore[calypso:merge]/stages

The definition of exploration stages of type List[List[ExplorationTaskGroup]. The outer list provides the enumeration of the exploration stages. Then each stage is defined by a list of exploration task groups. Each task group is described in the task group definition

filters:

type: list | dict, optional, default: []

argument path: explore[calypso:merge]/filters

A list of configuration filters

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[calypso:merge]/filters/type

possible choices: distance, box_skewness, box_length

the type of the configuration filter.

• distance: Configuration filter of type distance

• box_skewness: Configuration filter of type box_skewness

• box_length: Configuration filter of type box_length

When type is set to distance:

Configuration filter of type distance

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:merge]/filters[distance]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

custom_safe_dist:

type: dict, optional, default: {}

argument path: explore[calypso:merge]/filters[distance]/custom_safe_dist

Custom safe distance (in unit of bohr) for each element

safe_dist_ratio:

type: float, optional, default: 1.0

argument path: explore[calypso:merge]/filters[distance]/safe_dist_ratio

The ratio multiplied to the safe distance

When type is set to box_skewness:

Configuration filter of type box_skewness

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:merge]/filters[box_skewness]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

theta:

type: float, optional, default: 60.0

argument path: explore[calypso:merge]/filters[box_skewness]/theta

The threshold for angles between the edges of the cell. If all angles are larger than this value the check is passed

When type is set to box_length:

Configuration filter of type box_length

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[calypso:merge]/filters[box_length]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

length_ratio:

type: float, optional, default: 5.0

argument path: explore[calypso:merge]/filters[box_length]/length_ratio

The threshold for the length ratio between the edges of the cell. If all length ratios are smaller than this value the check is passed

When type is set to diffcsp:

The exploration by DiffCSP

config:

type: dict

argument path: explore[diffcsp]/config

Configuration of DiffCSP exploration

gen_tasks:

type: int, optional, default: 1

argument path: explore[diffcsp]/config/gen_tasks

Number of DiffCSP generation tasks

gen_command:

type: str

argument path: explore[diffcsp]/config/gen_command

Command for DiffCSP generation

relax_group_size:

type: int, optional, default: 100

argument path: explore[diffcsp]/config/relax_group_size

Group size for relaxation

use_hdf5:

type: bool, optional, default: False

argument path: explore[diffcsp]/config/use_hdf5

Use HDF5 to store trajs and model_devis

max_numb_iter:

type: int, optional, default: 10

argument path: explore[diffcsp]/max_numb_iter

Maximum number of iterations per stage

fatal_at_max:

type: bool, optional, default: True

argument path: explore[diffcsp]/fatal_at_max

Fatal when the number of iteration per stage reaches the max_numb_iter

output_nopbc:

type: bool, optional, default: False

argument path: explore[diffcsp]/output_nopbc

Remove pbc of the output configurations

convergence:

type: dict

argument path: explore[diffcsp]/convergence

The method of convergence check.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[diffcsp]/convergence/type

possible choices: fixed-levels, fixed-levels-max-select, adaptive-lower

the type of the condidate selection and convergence check method.

• fixed-levels: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• fixed-levels-max-select: The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

• adaptive-lower: The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

When type is set to fixed-levels:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations will be randomly sampled from candidates for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[diffcsp]/convergence[fixed-levels]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[diffcsp]/convergence[fixed-levels]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[diffcsp]/convergence[fixed-levels]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[diffcsp]/convergence[fixed-levels]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[diffcsp]/convergence[fixed-levels]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to fixed-levels-max-select:

The configurations with force model deviation between level_f_lo, level_f_hi or virial model deviation between level_v_lo and level_v_hi are treated as candidates (The virial model deviation check is optional). The configurations with maximal model deviation in the candidates are sent for FP calculations. If the ratio of accurate (below level_f_lo and level_v_lo) is higher then conv_accuracy, the stage is treated as converged.

level_f_lo:

type: float

argument path: explore[diffcsp]/convergence[fixed-levels-max-select]/level_f_lo

The lower trust level of force model deviation

level_f_hi:

type: float

argument path: explore[diffcsp]/convergence[fixed-levels-max-select]/level_f_hi

The higher trust level of force model deviation

level_v_lo:

type: NoneType | float, optional, default: None

argument path: explore[diffcsp]/convergence[fixed-levels-max-select]/level_v_lo

The lower trust level of virial model deviation

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[diffcsp]/convergence[fixed-levels-max-select]/level_v_hi

The higher trust level of virial model deviation

conv_accuracy:

type: float, optional, default: 0.9

argument path: explore[diffcsp]/convergence[fixed-levels-max-select]/conv_accuracy

If the ratio of accurate frames is larger than this value, the stage is converged

When type is set to adaptive-lower:

The method of adaptive adjust the lower trust levels. In each step of iterations, a number (set by numb_candi_f or numb_candi_v) or a ratio (set by rate_candi_f or rate_candi_v) of configurations with a model deviation lower than the higher trust level (level_f_hi, level_v_hi) are treated as candidates. The lowest model deviation of the candidates are treated as the lower trust level. If the lower trust level does not change significant (controlled by conv_tolerance) in n_checked_steps, the stage is treated as converged.

level_f_hi:

type: float, optional, default: 0.5

argument path: explore[diffcsp]/convergence[adaptive-lower]/level_f_hi

The higher trust level of force model deviation

numb_candi_f:

type: int, optional, default: 200

argument path: explore[diffcsp]/convergence[adaptive-lower]/numb_candi_f

The number of force frames that has a model deviation lower than level_f_hi treated as candidate.

rate_candi_f:

type: float, optional, default: 0.01

argument path: explore[diffcsp]/convergence[adaptive-lower]/rate_candi_f

The ratio of force frames that has a model deviation lower than level_f_hi treated as candidate.

level_v_hi:

type: NoneType | float, optional, default: None

argument path: explore[diffcsp]/convergence[adaptive-lower]/level_v_hi

The higher trust level of virial model deviation

numb_candi_v:

type: int, optional, default: 0

argument path: explore[diffcsp]/convergence[adaptive-lower]/numb_candi_v

The number of virial frames that has a model deviation lower than level_v_hi treated as candidate.

rate_candi_v:

type: float, optional, default: 0.0

argument path: explore[diffcsp]/convergence[adaptive-lower]/rate_candi_v

The ratio of virial frames that has a model deviation lower than level_v_hi treated as candidate.

n_checked_steps:

type: int, optional, default: 2

argument path: explore[diffcsp]/convergence[adaptive-lower]/n_checked_steps

The number of steps to check the convergence.

conv_tolerance:

type: float, optional, default: 0.05

argument path: explore[diffcsp]/convergence[adaptive-lower]/conv_tolerance

The convergence tolerance.

candi_sel_prob:

type: str, optional, default: uniform

argument path: explore[diffcsp]/convergence[adaptive-lower]/candi_sel_prob

The method for selecting candidates. It can be ‘uniform’: all candidates are of the same probability. ‘inv_pop_f’ or ‘inv_pop_f:nhist’: the probability is inversely propotional to the population of a histogram between leven_f_lo and level_f_hi. The number of bins in the histogram is set by nhist, which should be an integer. The default is 10.

stages:

type: typing.List[typing.List[dict]]

argument path: explore[diffcsp]/stages

The definition of exploration stages of type List[List[ExplorationTaskGroup]. The outer list provides the enumeration of the exploration stages. Then each stage is defined by a list of exploration task groups. Each task group is described in the task group definition

filters:

type: list | dict, optional, default: []

argument path: explore[diffcsp]/filters

A list of configuration filters

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: explore[diffcsp]/filters/type

possible choices: distance, box_skewness, box_length

the type of the configuration filter.

• distance: Configuration filter of type distance

• box_skewness: Configuration filter of type box_skewness

• box_length: Configuration filter of type box_length

When type is set to distance:

Configuration filter of type distance

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[diffcsp]/filters[distance]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

custom_safe_dist:

type: dict, optional, default: {}

argument path: explore[diffcsp]/filters[distance]/custom_safe_dist

Custom safe distance (in unit of bohr) for each element

safe_dist_ratio:

type: float, optional, default: 1.0

argument path: explore[diffcsp]/filters[distance]/safe_dist_ratio

The ratio multiplied to the safe distance

When type is set to box_skewness:

Configuration filter of type box_skewness

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[diffcsp]/filters[box_skewness]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

theta:

type: float, optional, default: 60.0

argument path: explore[diffcsp]/filters[box_skewness]/theta

The threshold for angles between the edges of the cell. If all angles are larger than this value the check is passed

When type is set to box_length:

Configuration filter of type box_length

max_workers:

type: NoneType | int, optional, default: None

argument path: explore[diffcsp]/filters[box_length]/max_workers

The maximum number of processes used to filter configurations, None represents as many as the processors of the machine, and 1 for serial

length_ratio:

type: float, optional, default: 5.0

argument path: explore[diffcsp]/filters[box_length]/length_ratio

The threshold for the length ratio between the edges of the cell. If all length ratios are smaller than this value the check is passed

fp:

type: dict

argument path: fp

The configuration for FP

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: fp/type

possible choices: vasp, gaussian, deepmd, fpop_abacus, fpop_cp2k

the type of the fp

When type is set to vasp:

inputs_config:

type: dict

argument path: fp[vasp]/inputs_config

Configuration for preparing vasp inputs

incar:

type: str

argument path: fp[vasp]/inputs_config/incar

The path to the template incar file

pp_files:

type: dict

argument path: fp[vasp]/inputs_config/pp_files

The pseudopotential files set by a dict, e.g. {“Al” : “path/to/the/al/pp/file”, “Mg” : “path/to/the/mg/pp/file”}

kspacing:

type: float

argument path: fp[vasp]/inputs_config/kspacing

The spacing of k-point sampling. ksapcing will overwrite the incar template

kgamma:

type: bool, optional, default: True

argument path: fp[vasp]/inputs_config/kgamma

If the k-mesh includes the gamma point. kgamma will overwrite the incar template

run_config:

type: dict

argument path: fp[vasp]/run_config

Configuration for running vasp tasks

command:

type: str, optional, default: vasp

argument path: fp[vasp]/run_config/command

The command of VASP

out:

type: str, optional, default: data

argument path: fp[vasp]/run_config/out

The output dir name of labeled data. In deepmd/npy format provided by dpdata.

log:

type: str, optional, default: fp.log

argument path: fp[vasp]/run_config/log

The log file name of VASP

task_max:

type: int, optional, default: 10

argument path: fp[vasp]/task_max

Maximum number of vasp tasks for each iteration

extra_output_files:

type: list, optional, default: []

argument path: fp[vasp]/extra_output_files

Extra output file names, support wildcards

When type is set to gaussian:

inputs_config:

type: dict

argument path: fp[gaussian]/inputs_config

Configuration for preparing vasp inputs

keywords:

type: str | list

argument path: fp[gaussian]/inputs_config/keywords

Gaussian keywords, e.g. force b3lyp/6-31g**. If a list, run multiple steps.

multiplicity:

type: str | int, optional, default: auto

argument path: fp[gaussian]/inputs_config/multiplicity

spin multiplicity state. It can be a number. If auto, multiplicity will be detected automatically, with the following rules:

fragment_guesses=True multiplicity will +1 for each radical, and +2 for each oxygen molecule

fragment_guesses=False multiplicity will be 1 or 2, but +2 for each oxygen molecule.

charge:

type: int, optional, default: 0

argument path: fp[gaussian]/inputs_config/charge

molecule charge. Only used when charge is not provided by the system

basis_set:

type: str, optional

argument path: fp[gaussian]/inputs_config/basis_set

custom basis set

keywords_high_multiplicity:

type: str, optional

argument path: fp[gaussian]/inputs_config/keywords_high_multiplicity

keywords for points with multiple raicals. multiplicity should be auto. If not set, fallback to normal keywords

fragment_guesses:

type: bool, optional, default: False

argument path: fp[gaussian]/inputs_config/fragment_guesses

initial guess generated from fragment guesses. If True, multiplicity should be auto

nproc:

type: int, optional, default: 1

argument path: fp[gaussian]/inputs_config/nproc

Number of CPUs to use

run_config:

type: dict

argument path: fp[gaussian]/run_config

Configuration for running vasp tasks

command:

type: str, optional, default: g16

argument path: fp[gaussian]/run_config/command

The command of Gaussian

out:

type: str, optional, default: data

argument path: fp[gaussian]/run_config/out

The output dir name of labeled data. In deepmd/npy format provided by dpdata.

post_command:

type: str | NoneType, optional, default: None

argument path: fp[gaussian]/run_config/post_command

The command after Gaussian

task_max:

type: int, optional, default: 10

argument path: fp[gaussian]/task_max

Maximum number of vasp tasks for each iteration

extra_output_files:

type: list, optional, default: []

argument path: fp[gaussian]/extra_output_files

Extra output file names, support wildcards

When type is set to deepmd:

inputs_config:

type: dict

argument path: fp[deepmd]/inputs_config

Configuration for preparing vasp inputs

run_config:

type: dict

argument path: fp[deepmd]/run_config

Configuration for running vasp tasks

teacher_model_path:

type: BinaryFileInput | str

argument path: fp[deepmd]/run_config/teacher_model_path

The path of teacher model, which can be loaded by deepmd.infer.DeepPot

out:

type: str, optional, default: data

argument path: fp[deepmd]/run_config/out

The output dir name of labeled data. In deepmd/npy format provided by dpdata.

log:

type: str, optional, default: fp.log

argument path: fp[deepmd]/run_config/log

The log file name of dp

task_max:

type: int, optional, default: 10

argument path: fp[deepmd]/task_max

Maximum number of vasp tasks for each iteration

extra_output_files:

type: list, optional, default: []

argument path: fp[deepmd]/extra_output_files

Extra output file names, support wildcards

When type is set to fpop_abacus:

inputs_config:

type: dict

argument path: fp[fpop_abacus]/inputs_config

Configuration for preparing vasp inputs

input_file:

type: str

argument path: fp[fpop_abacus]/inputs_config/input_file

A template INPUT file.

pp_files:

type: dict

argument path: fp[fpop_abacus]/inputs_config/pp_files

The pseudopotential files for the elements. For example: {“H”: “/path/to/H.upf”, “O”: “/path/to/O.upf”}.

element_mass:

type: dict | NoneType, optional, default: None

argument path: fp[fpop_abacus]/inputs_config/element_mass

Specify the mass of some elements. For example: {“H”: 1.0079, “O”: 15.9994}.

kpt_file:

type: str | NoneType, optional, default: None

argument path: fp[fpop_abacus]/inputs_config/kpt_file

The KPT file, by default None.

orb_files:

type: dict | NoneType, optional, default: None

argument path: fp[fpop_abacus]/inputs_config/orb_files

The numerical orbital fiels for the elements, by default None. For example: {“H”: “/path/to/H.orb”, “O”: “/path/to/O.orb”}.

deepks_descriptor:

type: str | NoneType, optional, default: None

argument path: fp[fpop_abacus]/inputs_config/deepks_descriptor

The deepks descriptor file, by default None.

deepks_model:

type: str | NoneType, optional, default: None

argument path: fp[fpop_abacus]/inputs_config/deepks_model

The deepks model file, by default None.

run_config:

type: dict

argument path: fp[fpop_abacus]/run_config

Configuration for running vasp tasks

command:

type: str, optional, default: abacus

argument path: fp[fpop_abacus]/run_config/command

The command of abacus

task_max:

type: int, optional, default: 10

argument path: fp[fpop_abacus]/task_max

Maximum number of vasp tasks for each iteration

extra_output_files:

type: list, optional, default: []

argument path: fp[fpop_abacus]/extra_output_files

Extra output file names, support wildcards

When type is set to fpop_cp2k:

inputs_config:

type: dict

argument path: fp[fpop_cp2k]/inputs_config

Configuration for preparing vasp inputs

inp_file:

type: str

argument path: fp[fpop_cp2k]/inputs_config/inp_file

The path to the user-submitted CP2K input file.

run_config:

type: dict

argument path: fp[fpop_cp2k]/run_config

Configuration for running vasp tasks

command:

type: str, optional, default: cp2k

argument path: fp[fpop_cp2k]/run_config/command

The command of cp2k

task_max:

type: int, optional, default: 10

argument path: fp[fpop_cp2k]/task_max

Maximum number of vasp tasks for each iteration

extra_output_files:

type: list, optional, default: []

argument path: fp[fpop_cp2k]/extra_output_files

Extra output file names, support wildcards

name:

type: str, optional, default: dpgen

argument path: name

The workflow name, ‘dpgen’ for default

parallelism:

type: NoneType | int, optional, default: None

argument path: parallelism

The parallelism for the workflow. Accept an int that stands for the maximum number of running pods for the workflow. None for default

Task group definition

LAMMPS task group

task_group:

type: dict

argument path: task_group

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)

argument path: task_group/type

possible choices: lmp-md, lmp-template, customized-lmp-template

the type of the task group

• lmp-md: Lammps MD tasks. DPGEN will generate the lammps input script

• lmp-template: Lammps MD tasks defined by templates. User provide lammps (and plumed) template for lammps tasks. The variables in templates are revised by the revisions key. Notice that the lines for pair style, dump and plumed are reserved for the revision of dpgen2, and the users should not write these lines by themselves. Rather, users notify dpgen2 the poistion of the line for pair_style by writting ‘pair_style deepmd’, the line for dump by writting ‘dump dpgen_dump’. If plumed is used, the line for fix plumed shouldbe written exactly as ‘fix dpgen_plm’.

• customized-lmp-template: Lammps MD tasks defined by user customized shell commands and templates. User provided shell script generates a series of folders, and each folder contains a lammps template task group.

When type is set to lmp-md (or its alias lmp-npt):

Lammps MD tasks. DPGEN will generate the lammps input script

conf_idx:

type: list, alias: sys_idx

argument path: task_group[lmp-md]/conf_idx

The configurations of configurations[conf_idx] will be used to generate the initial configurations of the tasks. This key provides the index of selected item in the configurations array.

n_sample:

type: NoneType | int, optional, default: None

argument path: task_group[lmp-md]/n_sample

Number of configurations. If this number is smaller than the number of configruations in configruations[conf_idx], then n_sample configruations are randomly sampled from configruations[conf_idx], otherwise all configruations in configruations[conf_idx] will be used. If not provided, all configruations in configruations[conf_idx] will be used.

temps:

type: list, alias: Ts

argument path: task_group[lmp-md]/temps

A list of temperatures in K. Also used to initialize the temperature

press:

type: list, optional, alias: Ps

argument path: task_group[lmp-md]/press

A list of pressures in bar.

ens:

type: str, optional, default: nve, alias: ensemble

argument path: task_group[lmp-md]/ens

The ensemble. Allowd options are ‘nve’, ‘nvt’, ‘npt’, ‘npt-a’, ‘npt-t’. ‘npt-a’ stands for anisotrpic box sampling and ‘npt-t’ stands for triclinic box sampling.

dt:

type: float, optional, default: 0.001

argument path: task_group[lmp-md]/dt

The time step

nsteps:

type: int, optional, default: 100

argument path: task_group[lmp-md]/nsteps

The number of steps

trj_freq:

type: int, optional, default: 10, aliases: t_freq, trj_freq, traj_freq

argument path: task_group[lmp-md]/trj_freq

The number of steps

tau_t:

type: float, optional, default: 0.05

argument path: task_group[lmp-md]/tau_t

The time scale of thermostat

tau_p:

type: float, optional, default: 0.5

argument path: task_group[lmp-md]/tau_p

The time scale of barostat

pka_e:

type: NoneType | float, optional, default: None

argument path: task_group[lmp-md]/pka_e

The energy of primary knock-on atom

neidelay:

type: NoneType | int, optional, default: None

argument path: task_group[lmp-md]/neidelay

The delay of updating the neighbor list

no_pbc:

type: bool, optional, default: False

argument path: task_group[lmp-md]/no_pbc

Not using the periodic boundary condition

use_clusters:

type: bool, optional, default: False

argument path: task_group[lmp-md]/use_clusters

Calculate atomic model deviation

relative_f_epsilon:

type: NoneType | float, optional, default: None

argument path: task_group[lmp-md]/relative_f_epsilon

Calculate relative force model deviation

relative_v_epsilon:

type: NoneType | float, optional, default: None

argument path: task_group[lmp-md]/relative_v_epsilon

Calculate relative virial model deviation

ele_temp_f:

type: NoneType | float, optional, default: None

argument path: task_group[lmp-md]/ele_temp_f

The electron temperature set by frame style

ele_temp_a:

type: NoneType | float, optional, default: None

argument path: task_group[lmp-md]/ele_temp_a

The electron temperature set by atomistic style

pimd_bead:

type: str | NoneType, optional, default: None

argument path: task_group[lmp-md]/pimd_bead

Bead index for PIMD, None for non-PIMD

When type is set to lmp-template:

Lammps MD tasks defined by templates. User provide lammps (and plumed) template for lammps tasks. The variables in templates are revised by the revisions key. Notice that the lines for pair style, dump and plumed are reserved for the revision of dpgen2, and the users should not write these lines by themselves. Rather, users notify dpgen2 the poistion of the line for pair_style by writting ‘pair_style deepmd’, the line for dump by writting ‘dump dpgen_dump’. If plumed is used, the line for fix plumed shouldbe written exactly as ‘fix dpgen_plm’.

conf_idx:

type: list, alias: sys_idx

argument path: task_group[lmp-template]/conf_idx

The configurations of configurations[conf_idx] will be used to generate the initial configurations of the tasks. This key provides the index of selected item in the configurations array.

n_sample:

type: NoneType | int, optional, default: None

argument path: task_group[lmp-template]/n_sample

Number of configurations. If this number is smaller than the number of configruations in configruations[conf_idx], then n_sample configruations are randomly sampled from configruations[conf_idx], otherwise all configruations in configruations[conf_idx] will be used. If not provided, all configruations in configruations[conf_idx] will be used.

lmp_template_fname:

type: str, aliases: lmp_template, lmp

argument path: task_group[lmp-template]/lmp_template_fname

The file name of lammps input template

plm_template_fname:

type: str | NoneType, optional, default: None, aliases: plm_template, plm

argument path: task_group[lmp-template]/plm_template_fname

The file name of plumed input template

revisions:

type: dict, optional, default: {}

argument path: task_group[lmp-template]/revisions

The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enmerated.

traj_freq:

type: int, optional, default: 10, aliases: t_freq, trj_freq, trj_freq

argument path: task_group[lmp-template]/traj_freq

The frequency of dumping configurations and thermodynamic states

extra_pair_style_args:

type: str, optional, default: (empty string)

argument path: task_group[lmp-template]/extra_pair_style_args

The extra arguments for pair_style

pimd_bead:

type: str | NoneType, optional, default: None

argument path: task_group[lmp-template]/pimd_bead

Bead index for PIMD, None for non-PIMD

When type is set to customized-lmp-template:

Lammps MD tasks defined by user customized shell commands and templates. User provided shell script generates a series of folders, and each folder contains a lammps template task group.

conf_idx:

type: list, alias: sys_idx

argument path: task_group[customized-lmp-template]/conf_idx

The configurations of configurations[conf_idx] will be used to generate the initial configurations of the tasks. This key provides the index of selected item in the configurations array.

n_sample:

type: NoneType | int, optional, default: None

argument path: task_group[customized-lmp-template]/n_sample

Number of configurations. If this number is smaller than the number of configruations in configruations[conf_idx], then n_sample configruations are randomly sampled from configruations[conf_idx], otherwise all configruations in configruations[conf_idx] will be used. If not provided, all configruations in configruations[conf_idx] will be used.

custom_shell_commands:

type: list

argument path: task_group[customized-lmp-template]/custom_shell_commands

Customized shell commands to be run for each configuration. The commands require input_lmp_conf_name as input conf file, input_lmp_tmpl_name and input_plm_tmpl_name as templates, and input_extra_files as extra input files. By running the commands a series folders in pattern output_dir_pattern are supposed to be generated, and each folder is supposed to contain a configuration file output_lmp_conf_name, a lammps template file output_lmp_tmpl_name and a plumed template file output_plm_tmpl_name.

revisions:

type: dict, optional, default: {}

argument path: task_group[customized-lmp-template]/revisions

The revisions. Should be a dict providing the key - list of desired values pair. Key is the word to be replaced in the templates, and it may appear in both the lammps and plumed input templates. All values in the value list will be enmerated.

traj_freq:

type: int, optional, default: 10, aliases: t_freq, trj_freq, trj_freq

argument path: task_group[customized-lmp-template]/traj_freq

The frequency of dumping configurations and thermodynamic states

input_lmp_conf_name:

type: str, optional, default: conf.lmp

argument path: task_group[customized-lmp-template]/input_lmp_conf_name

Input conf file name for the shell commands.

input_lmp_tmpl_name:

type: str, optional, default: in.lammps, aliases: lmp_template, lmp

argument path: task_group[customized-lmp-template]/input_lmp_tmpl_name

The file name of lammps input template

input_plm_tmpl_name:

type: str | NoneType, optional, default: None, aliases: plm_template, plm

argument path: task_group[customized-lmp-template]/input_plm_tmpl_name

The file name of plumed input template

input_extra_files:

type: list, optional, default: []

argument path: task_group[customized-lmp-template]/input_extra_files

Extra files that may be needed to execute the shell commands

output_dir_pattern:

type: str | list, optional, default: *

argument path: task_group[customized-lmp-template]/output_dir_pattern

Pattern of resultant folders generated by the shell commands.

output_lmp_conf_name:

type: str, optional, default: conf.lmp

argument path: task_group[customized-lmp-template]/output_lmp_conf_name

Generated conf file name.

output_lmp_tmpl_name:

type: str, optional, default: in.lammps

argument path: task_group[customized-lmp-template]/output_lmp_tmpl_name

Generated lmp input file name.

output_plm_tmpl_name:

type: str, optional, default: input.plumed

argument path: task_group[customized-lmp-template]/output_plm_tmpl_name

Generated plm input file name.

CALYPSO task group

task_group:

type: dict

argument path: task_group

CALYPSO structure prediction tasks. DPGEN will generate the calypso input script

numb_of_species:

type: int

argument path: task_group/numb_of_species

number of species.

name_of_atoms:

type: list

argument path: task_group/name_of_atoms

name of atoms.

atomic_number:

type: list, optional

argument path: task_group/atomic_number

atomic number of each element.

numb_of_atoms:

type: list

argument path: task_group/numb_of_atoms

number of each atom.

distance_of_ions:

type: list | dict, optional

argument path: task_group/distance_of_ions

the distance matrix between different elements.

pop_size:

type: int, optional, default: 30

argument path: task_group/pop_size

the number of structures would be generated in each step.

max_step:

type: int, optional, default: 5

argument path: task_group/max_step

the max iteration number of CALYPSO loop.

system_name:

type: str, optional, default: CALYPSO

argument path: task_group/system_name

system name.

numb_of_formula:

type: list, optional, default: [1, 1]

argument path: task_group/numb_of_formula

the formula range of simulation cell.

pressure:

type: float, optional, default: 0.001

argument path: task_group/pressure

the aim pressure (in Kbar) when using MLP to optimize structures.

fmax:

type: float, optional, default: 0.01

argument path: task_group/fmax

the converge criterion. The force on all individual atoms should be less than fmax.

opt_step:

type: float, optional, default: 1000

argument path: task_group/opt_step

the converge criterion. The force on all individual atoms should be less than fmax.

volume:

type: float, optional, default: 0

argument path: task_group/volume

the volume of simulation cell in one formula.

ialgo:

type: int, optional, default: 2

argument path: task_group/ialgo

the evolution algorithm of CALYPSO. 1: global pso, 2: local pso, 3: sabc.

pso_ratio:

type: float, optional, default: 0.6

argument path: task_group/pso_ratio

the ratio of structures generated by evolution algorithm in one step.

icode:

type: int, optional, default: 15

argument path: task_group/icode

the software of structure optimization. 1: VASP, 15: DP.

numb_of_lbest:

type: int, optional, default: 4

argument path: task_group/numb_of_lbest

the number of evolution direction when using LPSO.

numb_of_local_optim:

type: int, optional, default: 3

argument path: task_group/numb_of_local_optim

the number of making structure optimization when using dft.

command:

type: str, optional, default: sh submit.sh

argument path: task_group/command

the command of running structure optimization.

max_time:

type: int, optional, default: 9000

argument path: task_group/max_time

the max time (in second) of structure optimization.

pick_up:

type: bool, optional, default: False

argument path: task_group/pick_up

whether to continue the calculation.

pick_step:

type: int, optional, default: 0

argument path: task_group/pick_step

from which step to continue the calculation.

parallel:

type: bool, optional, default: False

argument path: task_group/parallel

whether to run calypso in parallel.

split:

type: bool, optional, default: True

argument path: task_group/split

sperate generating structures and structure optimizations. in dpgen2, split must be True.

spec_space_group:

type: list, optional, default: [2, 230]

argument path: task_group/spec_space_group

the range of spacegroup.

vsc:

type: bool, optional, default: False

argument path: task_group/vsc

whether to run calypso in variational stoichiometry way.

ctrl_range:

type: list, optional, default: [[1, 10]]

argument path: task_group/ctrl_range

the atom range of each atoms.

max_numb_atoms:

type: int, optional, default: 100

argument path: task_group/max_numb_atoms

the max number of atoms.