CHANGELOG.md

Change Logs

v0.12.9

• fix: wrong lammps template for fep training

v0.12.8

• improvement: optimize job running indicator

v0.12.7

• improvement: allow to override fix_statement and ensemble in artifact

v0.12.6

• fix: rsplit max should be 1
• improve: don't keep good and poor structures to save storage

v0.12.5

• feat: support max_decent_per_traj

v0.12.4

• fix: wrong softlink path

v0.12.3

• improvement: create softlink for dw_model

v0.12.2

• fix: wrong lammps template_vars

v0.12.1

• fix: fail to load config when it contains key starts with
• fix: wrong lammps template_vars

v0.12.0

• feat: support dpff training mode
• improvement: strict check of workflow configuration
• fix: wrong specorder of fep-pka mode
• breaking: mode move to general config section
• breaking: atom id of DELETE_ATOMS of fep mode now start from 1 instead of 0 (the same as lammps)
• breaking: require deepmd-kit when use dpff mode

v0.11.3

• fix: incomplete lammps template_vars

v0.11.2

• fix: pickle issue

v0.11.1

• fix: typo

v0.11.0

• feat: cll-training-workflow support fep-redox mode, details here
• feat: dpdata support set_fparam

v0.10.16

• fix: ensure no duplicate dataset in deepmd input

v0.10.15

• fix: lammps vars should also be template vars

v0.10.14

• improvement: plumed config support lammps template vars, e.g $$TEMP

v0.10.13

• feat: batch toolkit

v0.10.12

• fix: openpbs workdir

v0.10.11

• feat: support pbs job scheduler

v0.10.10

• fix: dpdata filter

v0.10.9

• refactor: aos-analysis options

v0.10.8

• fix: dp train should support restart

v0.10.7

• chore: update ai2cat default value

v0.10.6

• chore: update ai2cat workflow template

v0.10.5

• feat: Amorphous Oxides Structure Analysis toolkit, for more detail please check here

v0.10.4

• fix: scale factor of fep lammps template

v0.10.3

• feat: support customize fix statement

v0.10.2

• fix: formily schema

v0.10.1

• fix: ai2cat lammps template

v0.10.0

• feat: release of ai2cat notebook

v0.9.17

• fix: missing files

v0.9.16

• feat: interactive ui for generate lammps input

v0.9.15

• feat: yaml tool

v0.9.14

• feat: ai2cat notebook

v0.9.13

• chore: upgrade jupyter-formily

v0.9.12

• wip: ai2cat tool and notebook
• fix: asap log error

v0.9.11

• feat: ase tool support set_by_ref and limit method
• feat: integrate jupyter-formily
• wip: ai2cat tool and notebook

v0.9.10

• fix: deepmd data path

v0.9.9

• feat: deepmd option to group data by formula
• fix: fep lammps template
• fix: copy dataset in deepmd

v0.9.8

• fix: fep lammps template
• fix: cp2k potential/basic-set parser
• fix: lammps config validator

v0.9.7

• fix: fep lammps template

v0.9.6

• fix: squeue options

v0.9.5

• feat: support broadcast_vars in explore step, for more detail please check here

v0.9.4

• refactor: deprecate type_order for deepmd >= 2.2.4, more detail please check here
• fix: HPC executor resubmit error

v0.9.3

• fix: asap selector
• fix: doc typo

v0.9.2

• fix: inject locals to eval

v0.9.1

• fix: selector screening function

v0.9.0

• improvement: avoid unnecessary job submission

v0.8.10

• fix: plumed template

v0.8.9

• fix: deepmd template

v0.8.8

• fix: cache for py38

v0.8.7

• feat: new ai2-cat commands

v0.8.6

• fix: drop deepmd v1 config format support as it is not compatible with v2.2.5

v0.8.5

• feat: cll-workflow support sort structure by energy, for more detail please check here

v0.8.4

• feat: cll-workflow support screening by energy, for more detail please check here

v0.8.3

• feat: cll-workflow deepmd support fixture_models, for more detail please check here
• feat: ai2cat support gen plumed input.

v0.8.2

• feat: handle outlier data in deepmd training stage, for more detail please check here
• feat: dpdata tool support filter systems by lambda expression, for more detail please check here
• improvement: cll-workflow now allow user to change init_dataset in each iteration.

v0.8.1

• feat: ase toolkit support save atoms as cp2k-inc file, which can be used as @include coord_n_cell.inc macro in CP2K input file.

v0.8.0

• feat: ai4cat toolkit, for more detail please check here

v0.7.4

• improvement: sorted input files for dpdata and ase tools
  • You may need to quote the input file name or else the file expansion will be handled by shell. e.g. ai2-kit ase tool read './path/to/*.xyz'

v0.7.3

• fix: ase tool read data

v0.7.2

• improvement: ignore squeue error
• fix: upgrade dpdata to 0.2.16 to support CP2K 2023.1

v0.7.1

• fix: condition of selecting new explore systems

v0.7.0

• feat: update explore systems for each iteration，for more detail please check 1, 2
  • This version breaks the compatibility of checkpoint file, you may remove the checkpoint file before running this version.

v0.6.8

• improvement: allow user to ignore lammps error

v0.6.7

• fix: itemgetter bug: https://stackoverflow.com/a/48988896/3099733

v0.6.6

• BREAKING CHANGE: cp2k input template no longer support dict, system data should be loaded via @include coord_n_cell.inc macro. More detail here

v0.6.5

• fix: cp2k input file generation bug

v0.6.4

• feat: [cll-workflow] support wave function warmup for cp2k, more detail here
• improvement: [cll-workflow] raise invalid artifact error earlier

v0.6.3

• fix: ase tool arguments

v0.6.2

• improvement: [cll-workflow] save good/decent/poor structures in xyz file.
• feat: implement dpdata tool, more details here

v0.6.1

• fix: data handling bug

v0.6.0

• feat: Support training DP model for FEP simulation
• feat: ase tool support delete_atoms
• BREAKING CHANGE: [cll-workflow] LAMMPS configuration has been change, see example

v0.5.5

• improvement: change the squeue polling command
• feat: support load_text and load_yaml tag in yaml parser
• doc: config samples for cll-mlp-training workflow

v0.5.4

• fix: model_devi_decent.xyz not created when no dumps are selected

v0.5.3

• fix: atoms from lammps-dump-text not ordered by id

v0.5.2

• fix: sort atoms before exporting as POSCAR

v0.5.1

• improvement: suppress numba warning
• improvement: checkpoint rm support exclude pattern

v0.5.0

• BREAKING CHANGE: [cll-workflow] checkpoint file may not compatible with < v0.5.0
• feat: select distinct structures by global descriptor grouping

v0.4.0

• BREAKING CHANGE: [cll-workflow] checkpoint file may not compatible with < v0.4.0
• BREAKING CHANGE: [cll-workflow] config file change: select.by_threshold => select.model_devi
• feat: [cll-workflow] support explore with LASP
• refactor: [cll-workflow] data conversion system
• chore: asap tool integration

v0.3.33

• refactor: list_sample method
• fix: use len(dp_system) > 0 to filter broken data

v0.3.32

• fix: ignore data merge when SCF is not converged

v0.3.31

• refactor: simplify data handling

v0.3.30

• fix: slurm job checkpoint key

v0.3.29

• fix: cp2k command line

v0.3.28

• fix: use override instead of append for cp2k output

v0.3.26

• improvement: checkpoint tool command line
• fix: slurm job checkpoint key

v0.3.25

• improvement: pretty table output

v0.3.24

• fix: create missing dir

v0.3.23

• fix: cpk2 command

v0.3.22

• improvement: cp2k support post_cp2k_cmd option
• improvement: selector will save result in csv format

v0.3.21

• fix: dp empty validation data error

v0.3.20

• doc: generate online doc
• chore: github workflow
• improvement: support random sampling if selected structures hit limitation
• fix: add type_map when converting data to deepmd/npy

v0.3.19

• feat: distance analysis for proton transfer

v0.3.18

• fix: convert vasp data for deepmd

v0.3.17

• improvement: sample list evenly instead of truncate when selecting new structures

v0.3.16

• fix: use max_devi_f instead of avg_devi_f to select structures

v0.3.15

• fix: label all init data

v0.3.14

• feat: label all init data

v0.3.13

• feat: support specify deepmd validation data

v0.3.12

• fix: model deviation selection rules
• improvement: cll: stop workflow if no more data is generated
• refactor module names

v0.3.11

• fix: pass down ancestor attributes to child artifacts

v0.3.10

• chore: remove cp2k-input-tools
• feat: implement cpk2 parse module

v0.3.9

• fix: raise error on job failure

v0.3.8

• feat: ase tool support set_cell and set_pbc commands

v0.3.7

• feat: support VASP in cll training workflow
• feat: support compress_model option in deepmd step

v0.3.6

• feat: implement read tag for yaml parser

v0.3.5

• feat: support plumed config in cll workflow
• feat: support artifacts attributes inheritance in workflow
• feat: implement join tag for yaml parser

v0.3.4

• feat: apply checkpoint to all workflows and job submission steps
• feat: add checkpoint command line interface

v0.3.3

• refactor: using async.io to implement tasks and workflows

v0.3.2

• improvement: support relative work_dir

v0.3.1

• feat: async job polling

v0.3.0

• feat: ase toolkit
• fix: fep training workflow
• improvement: speed up command line interface with lazy import

v0.2.0

• feat: proton transfer analysis toolkit

v0.1.0

• feat: cll-mlp-training workflow
• feat: fep-mlp-training workflow

v0.0.2

• feat: support providing initial structures for label task at first iteration.
• feat: support dynamic configuration update for each iterations.
• improvement: reduce size of remote python script by compressing it with bz2.
• fix: ssh connection closed when running large remote python script.
• refactor: design common interface for CLL workflow.
• refactor: use ase.Atoms as the universal in-memory data structure.
• refactor: use ResourceManager to manage executors and artifacts.

v0.0.1

• feat: utilities to execute and manage jobs in local or remote HPC job scheduler.
• feat: utilities to run python functions in remote machines directly.
• feat: utilities to simplified automated workflows development with reusable components.
• feat: fundamental CLL & FEP workflows.