v0.1.3

What's Changed

• implements ase velocity verlet dynamics by @Tetracarbonylnickel in #298
• added MD22 dataset node by @M-R-Schaefer in #247
• Mapped ase md and Flatten node by @Tetracarbonylnickel in #299
• Change PredictionMetrics from pred vs true to error vs true by @M-R-Schaefer in #305
• Reduce packages that ship with IPSuite by @PythonFZ in #309
• Disable broken test by @PythonFZ in #314
• update znh5md and apax by @PythonFZ in #310
• fix cwd patch in newer ASE version by @PythonFZ in #318
• Gromacs Node by @PythonFZ in #306
• save more data from the GMX run by @PythonFZ in #320
• Improve GMX node by @PythonFZ in #321
• Moved remaining Apax nodes to apax by @M-R-Schaefer in #324
• update to uncertainty metrics, fix for stability check by @M-R-Schaefer in #304
• orca single point fix by @Tetracarbonylnickel in #313
• updated batchconfigurationselection base class by @M-R-Schaefer in #326
• removed MACE and Nequip models by @M-R-Schaefer in #328
• Update publish.yaml by @PythonFZ in #329
• bump version by @PythonFZ in #331

Full Changelog: v0.1.2...v0.1.3

IPSuite v0.1.2

What's Changed

• Save an image of the selected configurations by @PythonFZ in #219
• Update dscribe by @PythonFZ in #221
• 213 forces uncertainty selection broken by @Tetracarbonylnickel in #215
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #180
• add seed to ASEMD by @PythonFZ in #225
• Update how Threshold plots are created by @PythonFZ in #228
• [WIP] Batch configuration selection by @M-R-Schaefer in #218
• add FilterOutlier by @PythonFZ in #229
• fix: PBC not supported by packmol by @PythonFZ in #232
• Multipackmol by @PythonFZ in #234
• Box oscillating ramp modifier ramp by @PythonFZ in #233
• fix IPS side of TL by @PythonFZ in #231
• density updates by @PythonFZ in #237
• fixed unit convention in ase_md.py for future mapping function by @Tetracarbonylnickel in #240
• add ReadData by @PythonFZ in #243
• ZnTrack, Mace, apax updates by @PythonFZ in #248
• implementation of constrains in asegeoopt by @Tetracarbonylnickel in #249
• D3 Correction through TorchD3 by @PythonFZ in #250
• add description about docker container by @PythonFZ in #251
• TorchD3 with NL reuse by @M-R-Schaefer in #258
• MixCalculator by @PythonFZ in #255
• Added isotropic strain option to NPTThermostat by @M-R-Schaefer in #257
• Fix import of jax.config by @Tetracarbonylnickel in #265
• Add Citation by @PythonFZ in #267
• Docs by @MrJulEnergy in #264
• update mace to mace-torch and update apax by @PythonFZ in #262
• use zntrack.<> instead of deprecated zntrack.zn/dvc modules by @PythonFZ in #270
• remove the usage of get_deps_if_node in all affected Nodes. by @PythonFZ in #271
• remove secret apax credentials by @PythonFZ in #276
• add URL and docs and pypi badge by @PythonFZ in #278
• support Python 3.11 by @PythonFZ in #274
• automatically publish to docker hub by @PythonFZ in #281
• add maxstep and remove unused BatchASEGeoOpt by @PythonFZ in #277
• try to cleanup disc space by @PythonFZ in #284
• Metrics cleanup by @M-R-Schaefer in #273
• updated docstrings by @M-R-Schaefer in #286
• Rename modifiers by @M-R-Schaefer in #282
• rename atoms / trajectory to structures.h5 by @PythonFZ in #283
• remove index.rst on root by @PythonFZ in #287
• update docker image by @PythonFZ in #288

Full Changelog: v0.1.1...v0.1.2

IPSuite v0.1.1

What's Changed

• update default dtype in mace models by @PythonFZ in #216
• add LammpsSimulator by @PythonFZ in #217

Full Changelog: v0.1.0...v0.1.1

IPSuite v0.1.0

What's Changed

• Fix ramp by @PythonFZ in #132
• Npt and pressure, volume modifiers by @M-R-Schaefer in #138
• update to params by @PythonFZ in #139
• Uncertainty for volume scans by @PythonFZ in #144
• Ensemble stress by @M-R-Schaefer in #147
• Geoopt h5 by @M-R-Schaefer in #146
• use different atomic numbers for different mapping fragments by @PythonFZ in #148
• add logo by @PythonFZ in #151
• use DVCFileSystem to load H5MD files by @PythonFZ in #150
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #116
• poetry update & new version by @PythonFZ in #160
• Add Histrograms for Energy/Force Uncertainty by @PythonFZ in #157
• Unwrap fix by @M-R-Schaefer in #162
• add orca by @PythonFZ in #65
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #165
• frozen mapping + endcell update by @PythonFZ in #166
• Apax ensemble by @M-R-Schaefer in #149
• add ncols to each tqdm bar by @PythonFZ in #167
• SmilesToConformers by @PythonFZ in #169
• ASEMD refactor by @Tetracarbonylnickel in #168
• Update fixed sphere by @PythonFZ in #173
• Bugfix: sphere constraint was not using PBC by @PythonFZ in #174
• fix lables for energy and force plots by @PythonFZ in #181
• fix AnalyseSingleForceSensitivity by @PythonFZ in #178
• get forces from results dict by @PythonFZ in #185
• fix PredictionMetrics with different input sizes by @PythonFZ in #186
• Updates for zntrack.from_rev by @PythonFZ in #129
• add mse by @PythonFZ in #191
• Improve Force plots by @PythonFZ in #192
• small fix for nequip calc by @PythonFZ in #193
• use cp2k input tools from src by @PythonFZ in #203
• Transfer learning implemented for Apax. by @robert-toews in #172
• move from zntrack.zn.<field deps/node> to zntrack.deps by @PythonFZ in #205
• Asemd refactor2 by @Tetracarbonylnickel in #188
• cleanup package by @PythonFZ in #206
• allow loading cp2k_shell from enviroment variable by @PythonFZ in #207
• add optional model deps to bootstrap by @PythonFZ in #208
• Surface bootstrap and analysis by @Tetracarbonylnickel in #211
• Update cp2kyaml by @PythonFZ in #212

New Contributors

• @robert-toews made their first contribution in #172

Full Changelog: v0.1.0a3...v0.1.0

IPSuite v0.1.0a3

What's Changed

• add extras to IPS by @PythonFZ in #2
• use znh5md instead of ase.db.connect (no lazy sequence) by @PythonFZ in #5
• Improve base by @PythonFZ in #7
• Pre release by @PythonFZ in #8
• update zntrack version by @PythonFZ in #12
• update zntrack by @PythonFZ in #13
• xTB Calculator by @M-R-Schaefer in #11
• Barycenter Mapping by @PythonFZ in #14
• RattleAtoms node for bootstrapping an initial dataset by @M-R-Schaefer in #15
• add tqdm bar by @PythonFZ in #18
• update znh5md by @PythonFZ in #28
• add AddDataH5MD by @PythonFZ in #29
• LJ SinglePoint by @M-R-Schaefer in #19
• Bootstrap translate/ rotate molecules by @M-R-Schaefer in #31
• add combine utils by @PythonFZ in #30
• fixed force histogram for structures with different amounts of atoms by @M-R-Schaefer in #33
• Add ForceAnalysis based on mapping and inter/intra forces by @PythonFZ in #23
• Add h5md save by @PythonFZ in #36
• update znh5md by @PythonFZ in #35
• Change how Atoms are passed around by @PythonFZ in #22
• add SplitSelection by @PythonFZ in #40
• GAP add export for environmental variables by @PythonFZ in #42
• test example notebooks by @PythonFZ in #41
• Batch MD Stability Analysis by @M-R-Schaefer in #26
• supress ValueError on Volume for stress by @PythonFZ in #44
• Data generation by @PythonFZ in #47
• clean up analysis module by @PythonFZ in #45
• add lazy_loader by @PythonFZ in #51
• Fix ase copy by @PythonFZ in #54
• add mace live plot by @PythonFZ in #55
• merge mlsuite #54 by @PythonFZ in #60
• Improve cp2k calculator by @PythonFZ in #63
• Box guess by @PythonFZ in #64
• Add force distribution plots by @PythonFZ in #46
• mace config file by @PythonFZ in #69
• remove Prediction dataclass by @PythonFZ in #72
• Update cp2k.py by @PythonFZ in #75
• Generic MD by @Tetracarbonylnickel in #43
• add uncertainty selection node by @PythonFZ in #74
• add hash to ConfigurationSelection by @PythonFZ in #82
• add exclude to ConfigurationSelection by @PythonFZ in #86
• Update calc by @PythonFZ in #83
• bugfix calculator by @PythonFZ in #92
• replace lint ci with pre-commit.ci by @PythonFZ in #99
• Add Standard Deviation Check by @PythonFZ in #91
• Apax nodes by @Tetracarbonylnickel in #81
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #101
• use lazy loading by @PythonFZ in #102
• Apax lazy load by @Tetracarbonylnickel in #103
• Update README.md by @PythonFZ in #106
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #109
• update plot by @PythonFZ in #110
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #112
• Add ips.nodes by @PythonFZ in #78
• add data_ids to packmol by @PythonFZ in #117
• add min_distance by @PythonFZ in #118
• Add RescaleBoxModifier and TemperatureRampModifier by @PythonFZ in #119
• use plots template by @PythonFZ in #121
• Update binder setup by @PythonFZ in #52
• fix #123 by @PythonFZ in #124
• [MACE] default device to None by @PythonFZ in #125
• add gap output files by @PythonFZ in #126
• use DVC Filesystem to open files by @PythonFZ in #120
• rename to RattleAnalysis by @PythonFZ in #128
• bump version by @PythonFZ in #127

New Contributors

• @PythonFZ made their first contribution in #2
• @M-R-Schaefer made their first contribution in #11
• @Tetracarbonylnickel made their first contribution in #43
• @pre-commit-ci made their first contribution in #101

Full Changelog: https://github.com/zincware/IPSuite/commits/v0.1.0a3