LICENSE
README.md
pyproject.toml
src/gdpx/config.py
src/gdpx/main.py
src/gdpx.egg-info/PKG-INFO
src/gdpx.egg-info/SOURCES.txt
src/gdpx.egg-info/dependency_links.txt
src/gdpx.egg-info/entry_points.txt
src/gdpx.egg-info/requires.txt
src/gdpx.egg-info/top_level.txt
src/gdpx/backend/__init__.py
src/gdpx/backend/ase/__init__.py
src/gdpx/backend/ase/dummy.py
src/gdpx/backend/ase/mixer.py
src/gdpx/backend/cp2k/__init__.py
src/gdpx/backend/cp2k/band.py
src/gdpx/backend/cp2k/calculators.py
src/gdpx/backend/cp2k/parser.py
src/gdpx/backend/lammps/__init__.py
src/gdpx/backend/lammps/deviation.py
src/gdpx/backend/lammps/parser.py
src/gdpx/backend/lasp/__init__.py
src/gdpx/backend/lasp/parser.py
src/gdpx/backend/plumed/__init__.py
src/gdpx/backend/plumed/parser.py
src/gdpx/backend/plumed/utils.py
src/gdpx/backend/vasp/__init__.py
src/gdpx/backend/vasp/calculators.py
src/gdpx/backend/vasp/parser.py
src/gdpx/backend/vasp/writer.py
src/gdpx/bias/__init__.py
src/gdpx/bias/bias.py
src/gdpx/bias/bondboost.py
src/gdpx/bias/nuclei.py
src/gdpx/bias/timeio.py
src/gdpx/bias/afir/__init__.py
src/gdpx/bias/afir/afir.py
src/gdpx/bias/gaussian/__init__.py
src/gdpx/bias/gaussian/bond.py
src/gdpx/bias/gaussian/com.py
src/gdpx/bias/gaussian/distance.py
src/gdpx/bias/gaussian/gaussian.py
src/gdpx/bias/gaussian/rmsd.py
src/gdpx/bias/harmonic/__init__.py
src/gdpx/bias/harmonic/distance.py
src/gdpx/bias/harmonic/harmonic.py
src/gdpx/bias/harmonic/plane.py
src/gdpx/bias/utils/__init__.py
src/gdpx/bias/utils/bondpair.py
src/gdpx/builder/__init__.py
src/gdpx/builder/adsorb.py
src/gdpx/builder/builder.py
src/gdpx/builder/change_element.py
src/gdpx/builder/cleave_group.py
src/gdpx/builder/cleave_surface.py
src/gdpx/builder/composed.py
src/gdpx/builder/deform.py
src/gdpx/builder/dimer.py
src/gdpx/builder/direct.py
src/gdpx/builder/implant.py
src/gdpx/builder/packer.py
src/gdpx/builder/perturbator.py
src/gdpx/builder/random_bulk.py
src/gdpx/builder/random_structure.py
src/gdpx/builder/repeat.py
src/gdpx/builder/roulette.py
src/gdpx/builder/scale.py
src/gdpx/builder/species.py
src/gdpx/builder/trimer.py
src/gdpx/builder/utils.py
src/gdpx/builder/wulff.py
src/gdpx/builder/graph/__init__.py
src/gdpx/builder/graph/insert.py
src/gdpx/builder/graph/modifier.py
src/gdpx/builder/graph/remove.py
src/gdpx/builder/graph/swap.py
src/gdpx/builder/graph/utils.py
src/gdpx/builder/scan/angle.py
src/gdpx/builder/scan/hypercube.py
src/gdpx/builder/scan/intercoord.py
src/gdpx/cli/build.py
src/gdpx/cli/compute.py
src/gdpx/cli/convert.py
src/gdpx/cli/describe.py
src/gdpx/cli/explore.py
src/gdpx/cli/select.py
src/gdpx/cli/session.py
src/gdpx/cli/train.py
src/gdpx/cli/validate.py
src/gdpx/colvar/__init__.py
src/gdpx/colvar/distance.py
src/gdpx/colvar/fingerprint.py
src/gdpx/colvar/position.py
src/gdpx/colvar/rmsd.py
src/gdpx/comparator/__init__.py
src/gdpx/comparator/cartesian.py
src/gdpx/comparator/comparator.py
src/gdpx/comparator/coordination.py
src/gdpx/comparator/graph.py
src/gdpx/comparator/inertia_tensor.py
src/gdpx/comparator/reaction.py
src/gdpx/comparator/singlepoint.py
src/gdpx/computation/__init__.py
src/gdpx/computation/abacus.py
src/gdpx/computation/asedriver.py
src/gdpx/computation/cp2k.py
src/gdpx/computation/deepmd_jax.py
src/gdpx/computation/driver.py
src/gdpx/computation/espresso.py
src/gdpx/computation/jarex.py
src/gdpx/computation/lammps.py
src/gdpx/computation/lasp.py
src/gdpx/computation/observer.py
src/gdpx/computation/utils.py
src/gdpx/computation/vasp.py
src/gdpx/computation/mc/tfmc.py
src/gdpx/computation/md/md_utils.py
src/gdpx/computation/md/nosehoover.py
src/gdpx/core/__init__.py
src/gdpx/core/component.py
src/gdpx/core/register.py
src/gdpx/data/ClusterAndCUR.py
src/gdpx/data/__init__.py
src/gdpx/data/analyser.py
src/gdpx/data/array.py
src/gdpx/data/cleave_deviation.py
src/gdpx/data/convert.py
src/gdpx/data/correction.py
src/gdpx/data/database.py
src/gdpx/data/extatoms.py
src/gdpx/data/extract_evolution.py
src/gdpx/data/operators.py
src/gdpx/data/system.py
src/gdpx/dataloader/__init__.py
src/gdpx/dataloader/dataset.py
src/gdpx/dataloader/deepmd.py
src/gdpx/dataloader/mace.py
src/gdpx/dataloader/reann.py
src/gdpx/dataloader/singlexyz.py
src/gdpx/dataloader/utils.py
src/gdpx/describer/__init__.py
src/gdpx/describer/cluster.py
src/gdpx/describer/colvar.py
src/gdpx/describer/connectivity.py
src/gdpx/describer/coordinate.py
src/gdpx/describer/coordination.py
src/gdpx/describer/describer.py
src/gdpx/describer/dissociative.py
src/gdpx/describer/formation_energy.py
src/gdpx/describer/soap.py
src/gdpx/describer/spc.py
src/gdpx/expedition/__init__.py
src/gdpx/expedition/expedition.py
src/gdpx/expedition/accelerated_dynamics/prev_example.py
src/gdpx/expedition/artificial_force/afir.py
src/gdpx/expedition/genetic_algorithm/engine.py
src/gdpx/expedition/genetic_algorithm/operators.py
src/gdpx/expedition/genetic_algorithm/comparator/interatomic_distance.py
src/gdpx/expedition/genetic_algorithm/mutation/bounce.py
src/gdpx/expedition/genetic_algorithm/mutation/cluster.py
src/gdpx/expedition/genetic_algorithm/mutation/cluster_rotation.py
src/gdpx/expedition/genetic_algorithm/mutation/exchange.py
src/gdpx/expedition/genetic_algorithm/mutation/mirror.py
src/gdpx/expedition/genetic_algorithm/mutation/rattle.py
src/gdpx/expedition/genetic_algorithm/mutation/swap.py
src/gdpx/expedition/genetic_algorithm/population/manager.py
src/gdpx/expedition/genetic_algorithm/population/population.py
src/gdpx/expedition/monte_carlo/__init__.py
src/gdpx/expedition/monte_carlo/basin_hopping.py
src/gdpx/expedition/monte_carlo/concurrent_hopping.py
src/gdpx/expedition/monte_carlo/hybrid_monte_carlo.py
src/gdpx/expedition/monte_carlo/monte_carlo.py
src/gdpx/expedition/monte_carlo/utils.py
src/gdpx/expedition/monte_carlo/operators/__init__.py
src/gdpx/expedition/monte_carlo/operators/bounce.py
src/gdpx/expedition/monte_carlo/operators/move.py
src/gdpx/expedition/monte_carlo/operators/operator.py
src/gdpx/expedition/monte_carlo/operators/react.py
src/gdpx/expedition/monte_carlo/operators/statmech.py
src/gdpx/expedition/monte_carlo/operators/swap.py
src/gdpx/expedition/monte_carlo/operators/swap_type.py
src/gdpx/expedition/monte_carlo/operators/exchange/__init__.py
src/gdpx/expedition/monte_carlo/operators/exchange/adsorb.py
src/gdpx/expedition/monte_carlo/operators/exchange/basic.py
src/gdpx/expedition/monte_carlo/operators/exchange/cavity.py
src/gdpx/expedition/monte_carlo/operators/exchange/naive.py
src/gdpx/expedition/persist/database.py
src/gdpx/expedition/persist/thanos.py
src/gdpx/expedition/simulated_annealing/simulated_annealing.py
src/gdpx/factory/builder.py
src/gdpx/factory/computer.py
src/gdpx/factory/scheduler.py
src/gdpx/factory/validator.py
src/gdpx/geometry/__init__.py
src/gdpx/geometry/align.py
src/gdpx/geometry/bounce.py
src/gdpx/geometry/centre.py
src/gdpx/geometry/cleave.py
src/gdpx/geometry/composition.py
src/gdpx/geometry/exchange.py
src/gdpx/geometry/insert.py
src/gdpx/geometry/particle.py
src/gdpx/geometry/restraints.py
src/gdpx/geometry/spatial.py
src/gdpx/geometry/swap.py
src/gdpx/graph/__init__.py
src/gdpx/graph/adsorption.py
src/gdpx/graph/base.py
src/gdpx/graph/build.py
src/gdpx/graph/data.py
src/gdpx/graph/domain.py
src/gdpx/graph/expand.py
src/gdpx/graph/partial.py
src/gdpx/group/__init__.py
src/gdpx/group/constraint.py
src/gdpx/group/group.py
src/gdpx/group/molecule.py
src/gdpx/nodes/builder.py
src/gdpx/nodes/comparator.py
src/gdpx/nodes/computer.py
src/gdpx/nodes/data.py
src/gdpx/nodes/dataset.py
src/gdpx/nodes/describer.py
src/gdpx/nodes/driver.py
src/gdpx/nodes/expedition.py
src/gdpx/nodes/potential.py
src/gdpx/nodes/reactor.py
src/gdpx/nodes/region.py
src/gdpx/nodes/scheduler.py
src/gdpx/nodes/selector.py
src/gdpx/nodes/trainer.py
src/gdpx/nodes/validator.py
src/gdpx/potential/__init__.py
src/gdpx/potential/abacus.py
src/gdpx/potential/asepot.py
src/gdpx/potential/bias.py
src/gdpx/potential/classic.py
src/gdpx/potential/cp2k.py
src/gdpx/potential/dftd3.py
src/gdpx/potential/dftd4.py
src/gdpx/potential/eam.py
src/gdpx/potential/emt.py
src/gdpx/potential/espresso.py
src/gdpx/potential/fairchem.py
src/gdpx/potential/grid.py
src/gdpx/potential/lasp.py
src/gdpx/potential/mace.py
src/gdpx/potential/manager.py
src/gdpx/potential/mattersim.py
src/gdpx/potential/mixer.py
src/gdpx/potential/nequip.py
src/gdpx/potential/reax.py
src/gdpx/potential/tace.py
src/gdpx/potential/utils.py
src/gdpx/potential/vasp.py
src/gdpx/potential/xtb.py
src/gdpx/potential/deepmd/__init__.py
src/gdpx/potential/deepmd/calculator.py
src/gdpx/potential/deepmd/calculator_v3.py
src/gdpx/potential/deepmd/deepmd.py
src/gdpx/potential/deepmd/deepmd_jax.py
src/gdpx/potential/deepmd/deepmd_jax_x.py
src/gdpx/potential/deepmd/dpjax.py
src/gdpx/potential/gp/__init__.py
src/gdpx/potential/gp/bench.py
src/gdpx/potential/gp/fgp.py
src/gdpx/potential/gp/gptools.py
src/gdpx/potential/gp/representation.py
src/gdpx/potential/gp/sgp.py
src/gdpx/potential/plumed/plumed.py
src/gdpx/potential/plumed/calculators/plumed.py
src/gdpx/potential/plumed/calculators/plumed2.py
src/gdpx/potential/reann/beann.py
src/gdpx/potential/reann/reann.py
src/gdpx/potential/reann/calculators/reann.py
src/gdpx/reactor/__init__.py
src/gdpx/reactor/energy_profile.py
src/gdpx/reactor/reactor.py
src/gdpx/reactor/utils.py
src/gdpx/reactor/string/__init__.py
src/gdpx/reactor/string/cp2k.py
src/gdpx/reactor/string/grid.py
src/gdpx/reactor/string/pathway.py
src/gdpx/reactor/string/string.py
src/gdpx/reactor/string/vasp.py
src/gdpx/region/__init__.py
src/gdpx/region/region.py
src/gdpx/scheduler/__init__.py
src/gdpx/scheduler/local.py
src/gdpx/scheduler/lsf.py
src/gdpx/scheduler/pbs.py
src/gdpx/scheduler/remote.py
src/gdpx/scheduler/scheduler.py
src/gdpx/scheduler/slurm.py
src/gdpx/selector/__init__.py
src/gdpx/selector/basin.py
src/gdpx/selector/clustering.py
src/gdpx/selector/compare.py
src/gdpx/selector/composition.py
src/gdpx/selector/descriptor.py
src/gdpx/selector/graph.py
src/gdpx/selector/interval.py
src/gdpx/selector/invariant.py
src/gdpx/selector/locate.py
src/gdpx/selector/property.py
src/gdpx/selector/random.py
src/gdpx/selector/scf.py
src/gdpx/selector/selector.py
src/gdpx/selector/sinfo.py
src/gdpx/selector/sparsification.py
src/gdpx/selector/utils.py
src/gdpx/session/__init__.py
src/gdpx/session/active.py
src/gdpx/session/interface.py
src/gdpx/session/operation.py
src/gdpx/session/placeholder.py
src/gdpx/session/sequential.py
src/gdpx/session/session.py
src/gdpx/session/utils.py
src/gdpx/session/variable.py
src/gdpx/trainer/__init__.py
src/gdpx/trainer/mace.py
src/gdpx/trainer/nequip.py
src/gdpx/trainer/trainer.py
src/gdpx/trainer/deepmd/convert.py
src/gdpx/trainer/deepmd/deepmd.py
src/gdpx/trainer/deepmd/deepmd_jax.py
src/gdpx/trainer/deepmd/utils.py
src/gdpx/trainer/reann/beann.py
src/gdpx/trainer/reann/reann.py
src/gdpx/utils/__init__.py
src/gdpx/utils/atomUtils.py
src/gdpx/utils/atoms_tags.py
src/gdpx/utils/cleave_cluster.py
src/gdpx/utils/cmdrun.py
src/gdpx/utils/cmp_refdat.py
src/gdpx/utils/comparision.py
src/gdpx/utils/parser.py
src/gdpx/utils/profiler.py
src/gdpx/utils/reduce_dataset.py
src/gdpx/utils/second_reduce.py
src/gdpx/utils/strconv.py
src/gdpx/utils/strucopy.py
src/gdpx/validator/__init__.py
src/gdpx/validator/correlation.py
src/gdpx/validator/dimer.py
src/gdpx/validator/equation_of_state.py
src/gdpx/validator/mass_distribution.py
src/gdpx/validator/mean_squared_displacement.py
src/gdpx/validator/melting_point.py
src/gdpx/validator/minima.py
src/gdpx/validator/radial_distribution.py
src/gdpx/validator/rank.py
src/gdpx/validator/rxn.py
src/gdpx/validator/spc.py
src/gdpx/validator/surface_energy.py
src/gdpx/validator/trimer.py
src/gdpx/validator/uncertainty.py
src/gdpx/validator/utils.py
src/gdpx/validator/validator.py
src/gdpx/worker/__init__.py
src/gdpx/worker/drive.py
src/gdpx/worker/explore.py
src/gdpx/worker/grid.py
src/gdpx/worker/react.py
src/gdpx/worker/single.py
src/gdpx/worker/train.py
src/gdpx/worker/utils.py
src/gdpx/worker/worker.py
tests/test_restraints.py