From b65b99dcffafd7b5738d23380120977c175e5b77 Mon Sep 17 00:00:00 2001 From: lbluque Date: Sun, 17 Sep 2023 22:56:58 -0700 Subject: [PATCH] update changes link --- _modules/index.html | 4 ++-- _modules/smol/capp/generate/enumerate.html | 4 ++-- .../smol/capp/generate/groundstate/upper_bound/solver.html | 4 ++-- _modules/smol/capp/generate/random.html | 4 ++-- _modules/smol/capp/generate/special/sqs.html | 4 ++-- _modules/smol/cofe/expansion.html | 4 ++-- _modules/smol/cofe/extern/ewald.html | 4 ++-- _modules/smol/cofe/space/basis.html | 4 ++-- _modules/smol/cofe/space/cluster.html | 4 ++-- _modules/smol/cofe/space/clusterspace.html | 4 ++-- _modules/smol/cofe/space/domain.html | 4 ++-- _modules/smol/cofe/space/orbit.html | 4 ++-- _modules/smol/cofe/wrangling/select.html | 4 ++-- _modules/smol/cofe/wrangling/tools.html | 4 ++-- _modules/smol/cofe/wrangling/wrangler.html | 4 ++-- _modules/smol/io.html | 4 ++-- _modules/smol/moca/ensemble.html | 4 ++-- _modules/smol/moca/kernel/bias.html | 4 ++-- _modules/smol/moca/kernel/mcusher.html | 4 ++-- _modules/smol/moca/kernel/metropolis.html | 4 ++-- _modules/smol/moca/kernel/random.html | 4 ++-- _modules/smol/moca/kernel/wanglandau.html | 4 ++-- _modules/smol/moca/processor/composite.html | 4 ++-- _modules/smol/moca/processor/ewald.html | 4 ++-- _modules/smol/moca/processor/expansion.html | 4 ++-- _modules/smol/moca/sampler/sampler.html | 4 ++-- _modules/smol/moca/sublattice.html | 4 ++-- api_reference/capp/generate.enumerate.html | 4 ++-- api_reference/capp/generate.groundstate.html | 4 ++-- api_reference/capp/generate.html | 4 ++-- api_reference/capp/generate.random.html | 4 ++-- api_reference/capp/generate.special.html | 4 ++-- api_reference/capp/index.html | 4 ++-- api_reference/cofe/clusterexpansion.html | 4 ++-- api_reference/cofe/clusterspace.html | 4 ++-- api_reference/cofe/extern.ewald.html | 4 ++-- api_reference/cofe/index.html | 4 ++-- api_reference/cofe/space.basis.html | 4 ++-- api_reference/cofe/space.cluster.html | 4 ++-- api_reference/cofe/space.domain.html | 4 ++-- api_reference/cofe/space.html | 4 ++-- api_reference/cofe/space.orbit.html | 4 ++-- api_reference/cofe/wrangling.html | 4 ++-- api_reference/cofe/wrangling.select.html | 4 ++-- api_reference/cofe/wrangling.sw.html | 4 ++-- api_reference/cofe/wrangling.tools.html | 4 ++-- api_reference/index.html | 4 ++-- api_reference/io.html | 4 ++-- api_reference/moca/ensemble.html | 4 ++-- api_reference/moca/index.html | 4 ++-- api_reference/moca/kernel.bias.html | 4 ++-- api_reference/moca/kernel.html | 4 ++-- api_reference/moca/kernel.kernels.html | 4 ++-- api_reference/moca/kernel.mcusher.html | 4 ++-- api_reference/moca/processors.composite.html | 4 ++-- api_reference/moca/processors.ewald.html | 4 ++-- api_reference/moca/processors.expansion.html | 4 ++-- api_reference/moca/processors.html | 4 ++-- api_reference/moca/sampler.container.html | 4 ++-- api_reference/moca/sampler.html | 4 ++-- api_reference/moca/sampler.sampler.html | 4 ++-- api_reference/moca/sublattice.html | 4 ++-- citing.html | 4 ++-- developer_guide/design.html | 4 ++-- developer_guide/guide.html | 4 ++-- developer_guide/index.html | 4 ++-- examples.html | 4 ++-- genindex.html | 4 ++-- getting_started.html | 4 ++-- index.html | 4 ++-- notebooks/adding-structures-in-parallel.html | 4 ++-- notebooks/ce-fit-w-centering.html | 4 ++-- notebooks/cluster-visualization.html | 4 ++-- notebooks/creating-a-ce-w-electrostatics.html | 4 ++-- notebooks/creating-a-ce.html | 4 ++-- notebooks/finding-groundstates.html | 4 ++-- notebooks/generating-sqs.html | 4 ++-- notebooks/index.html | 4 ++-- notebooks/lmo-drx-ce-mc.html | 4 ++-- notebooks/openmp-parallelism.html | 4 ++-- notebooks/running-canonical-mc.html | 4 ++-- notebooks/running-charge-balanced-gcmc.html | 4 ++-- notebooks/running-ewald-sim_anneal.html | 4 ++-- notebooks/running-semigrand-mc.html | 4 ++-- notebooks/setting-composition-constraints.html | 4 ++-- notebooks/training-data-preparation.html | 4 ++-- notebooks/wang-landau-ising.html | 4 ++-- notebooks/wip/basis-orthogonalization.html | 4 ++-- py-modindex.html | 4 ++-- search.html | 4 ++-- searchindex.js | 2 +- user_guide.html | 4 ++-- 92 files changed, 183 insertions(+), 183 deletions(-) diff --git a/_modules/index.html b/_modules/index.html index 241fd6873..a5f5d0c14 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -208,7 +208,7 @@
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"respect": 59, "concentr": 59, "measur": 59, "user": 60, "guid": 60, "diagram": 60, "main": 60, "class": 60, "samplecontain": 60, "stochasticsqsgener": 60, "periodicgroundstatesolv": 60}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "nbsphinx": 4, "sphinx": 60}, "alltitles": {"Generate": [[0, "generate"]], "Enumerate": [[1, "module-smol.capp.generate.enumerate"]], "Ground States": [[2, "ground-states"]], "Random": [[3, "module-smol.capp.generate.random"]], "Special Structures": [[4, "special-structures"]], "capp \u2014 Cluster Analysis and Applications": [[5, "capp-cluster-analysis-and-applications"]], "Expansion": [[6, "expansion"]], "ClusterExpansion": [[6, "clusterexpansion"]], "RegressionData": [[6, "regressiondata"]], "Cluster Spaces": [[7, "cluster-spaces"]], "ClusterSubspace": [[7, "clustersubspace"]], "PottsSubspace": [[7, "pottssubspace"]], "External Terms": [[8, "external-terms"]], "Ewald Term": [[8, "ewald-term"]], "cofe \u2014 Cluster-Orbit Function Expansion Module": [[9, "cofe-cluster-orbit-function-expansion-module"]], "Basis": [[11, "module-smol.cofe.space.basis"]], "Cluster": [[12, "module-smol.cofe.space.cluster"]], "Domain": [[13, "module-smol.cofe.space.domain"]], "Orbits": [[14, "module-smol.cofe.space.orbit"]], "Wrangling": [[15, "wrangling"]], "Filtering": [[16, "module-smol.cofe.wrangling.select"]], "Structure Wrangler": [[17, "structure-wrangler"]], "Analysis tools": [[18, "module-smol.cofe.wrangling.tools"]], "API Reference": [[19, "api-reference"]], "Autogenerated Indices": [[19, "autogenerated-indices"]], "io \u2014 Input and Output": [[20, "module-smol.io"]], "Ensembles": [[21, "ensembles"]], "moca \u2014 Monte Carlo Module": [[22, "moca-monte-carlo-module"]], "Kernels": [[23, "kernels"]], "Sampling Bias": [[24, "module-smol.moca.kernel.bias"]], "MCKernels": [[25, "mckernels"]], "MCUshers": [[26, "module-smol.moca.kernel.mcusher"]], "Processors": [[27, "processors"], [60, "processors"]], "Composite Processor": [[28, "module-smol.moca.processor.composite"]], "Ewald Processor": [[29, "module-smol.moca.processor.ewald"]], "Cluster Expansion & Decomposition Processors": [[30, "module-smol.moca.processor.expansion"]], "Sampling": [[31, "sampling"]], "Sampler": [[33, "sampler"], [60, "sampler"]], "Sublattice": [[34, "module-smol.moca.sublattice"]], "Citing": [[35, "citing"], [41, "citing"]], "Cluster expansion site basis sets": [[35, "cluster-expansion-site-basis-sets"]], "Cluster decomposition": [[35, "cluster-decomposition"]], "Cluster expansions with redundant function sets": [[35, "cluster-expansions-with-redundant-function-sets"]], "Special quasi-random structures (SQS)": [[35, "special-quasi-random-structures-sqs"]], "Coulomb electrostatic interactions": [[35, "coulomb-electrostatic-interactions"]], "Charge-neutral semigrand canonical sampling": [[35, "charge-neutral-semigrand-canonical-sampling"]], "Wang-Landau sampling": [[35, "wang-landau-sampling"]], "Orbit group-wise regularized fits": [[35, "orbit-group-wise-regularized-fits"]], "\\ell_0\\ell_2 MIQP fits with hierarchical constraints": [[35, "ell-0-ell-2-miqp-fits-with-hierarchical-constraints"]], "Ground state searches": [[35, "ground-state-searches"]], "Package Design": [[36, "package-design"]], "Overview & Mission": [[36, "overview-mission"]], "Module Design": [[36, "module-design"]], "smol.cofe": [[36, "smol-cofe"]], "smol.moca": [[36, "smol-moca"]], "Contributing & Developing Guidelines": [[37, "contributing-developing-guidelines"]], "Bugs, issues, input, questions, etc": [[37, "bugs-issues-input-questions-etc"]], "Developing": [[37, "developing"], [38, "developing"]], "Guidelines": [[37, "guidelines"]], "Installing a development version": [[37, "installing-a-development-version"]], "Adding code contributions": [[37, "adding-code-contributions"]], "Adding examples": [[37, "adding-examples"]], "Example Notebooks": [[39, "example-notebooks"]], "Basic Examples": [[39, "basic-examples"]], "Advanced Examples": [[39, "advanced-examples"]], "Getting Started": [[40, "getting-started"]], "Installation": [[40, "installation"]], "Basic Usage": [[40, "basic-usage"]], "Creating a cluster subspace": [[40, "creating-a-cluster-subspace"]], "Preparing training data": [[40, "preparing-training-data"]], "Fitting and creating a cluster expansion": [[40, "fitting-and-creating-a-cluster-expansion"]], "Creating an ensemble for Monte Carlo Sampling": [[40, "creating-an-ensemble-for-monte-carlo-sampling"]], "Running Monte Carlo sampling": [[40, "running-monte-carlo-sampling"]], "Saving the generated objects and data": [[40, "saving-the-generated-objects-and-data"]], "Statistical Mechanics on Lattices": [[41, "statistical-mechanics-on-lattices"]], "Functionality": [[41, "functionality"]], "License": [[41, "license"]], "Adding Structures in Parallel": [[42, "Adding-Structures-in-Parallel"]], "1) Preparing a StructureWrangler": [[42, "1)-Preparing-a-StructureWrangler"], [57, "1)-Preparing-a-StructureWrangler"]], "2) Add structures in parallel": [[42, "2)-Add-structures-in-parallel"]], "Fitting an ionic cluster expansion with energy centering": [[43, "Fitting-an-ionic-cluster-expansion-with-energy-centering"]], "Load the LMO DRX prim": [[43, "Load-the-LMO-DRX-prim"]], "1) Create the cluster subspace": [[43, "1)-Create-the-cluster-subspace"], [46, "1)-Create-the-cluster-subspace"]], "2) Load data into a Structure Wrangler": [[43, "2)-Load-data-into-a-Structure-Wrangler"]], "3) Perform a piecewise fit, with the first fit only using the Points and Ewald features.": [[43, "3)-Perform-a-piecewise-fit,-with-the-first-fit-only-using-the-Points-and-Ewald-features."]], "Perform initial fit with only Points and Ewald features, and determine the intercept.": [[43, "Perform-initial-fit-with-only-Points-and-Ewald-features,-and-determine-the-intercept."]], "Let\u2019s visualize the variance that these features can capture. To do so, we plot the \u201ccentered energies\u201d by subtracting the DFT energies by the contributions from the fitted Point and Ewald features.": [[43, "Let's-visualize-the-variance-that-these-features-can-capture.-To-do-so,-we-plot-the-%22centered-energies%22-by-subtracting-the-DFT-energies-by-the-contributions-from-the-fitted-Point-and-Ewald-features."]], "4) Perform cross validation on the rest of features to train the L1 hyperparameter.": [[43, "4)-Perform-cross-validation-on-the-rest-of-features-to-train-the-L1-hyperparameter."]], "5) Obtain the cluster expansion model that minimizes CV": [[43, "5)-Obtain-the-cluster-expansion-model-that-minimizes-CV"]], "6) Get an idea of the predictive capabilities of this cluster expansion": [[43, "6)-Get-an-idea-of-the-predictive-capabilities-of-this-cluster-expansion"]], "7) Plot the ECI": [[43, "7)-Plot-the-ECI"]], "Visualizing Clusters with Crystal-Toolkit": [[44, "Visualizing-Clusters-with-Crystal-Toolkit"]], "Load a cluster expansion": [[44, "Load-a-cluster-expansion"]], "Visualize the primitive structure": [[44, "Visualize-the-primitive-structure"]], "Visualize a pair cluster": [[44, "Visualize-a-pair-cluster"]], "Visualize a triplet cluster": [[44, "Visualize-a-triplet-cluster"]], "Using a plotting package to visualize clusters": [[44, "Using-a-plotting-package-to-visualize-clusters"]], "Creating a basic Cluster Expansion": [[45, "Creating-a-basic-Cluster-Expansion"]], "0) The prim structure": [[45, "0)-The-prim-structure"]], "1) The cluster subspace": [[45, "1)-The-cluster-subspace"]], "1.1) Computing a correlation vector.": [[45, "1.1)-Computing-a-correlation-vector."]], "2) The structure wrangler": [[45, "2)-The-structure-wrangler"]], "3.1) Check the quality of the fit": [[45, "3.1)-Check-the-quality-of-the-fit"]], "4) The cluster expansion": [[45, "4)-The-cluster-expansion"]], "5) Saving your work": [[45, "5)-Saving-your-work"]], "5.1) Loading previously saved work": [[45, "5.1)-Loading-previously-saved-work"]], "Creating a Cluster Expansion with an additional Ewald electrostatic term": [[46, "Creating-a-Cluster-Expansion-with-an-additional-Ewald-electrostatic-term"]], "2) Add the ewald term.": [[46, "2)-Add-the-ewald-term."]], "2.1) The Electrostatic term": [[46, "2.1)-The-Electrostatic-term"]], "3) Creating the cluster expansion": [[46, "3)-Creating-the-cluster-expansion"]], "3.1) Check the quality of the fit and the \u201cdielectric\u201d constant": [[46, "3.1)-Check-the-quality-of-the-fit-and-the-%22dielectric%22-constant"]], "4) Constraining the value of the \u201cdielectric\u201d constant": [[46, "4)-Constraining-the-value-of-the-%22dielectric%22-constant"]], "4.1) If you want to play with decorators you can also do the above in a cleaner looking way.": [[46, "4.1)-If-you-want-to-play-with-decorators-you-can-also-do-the-above-in-a-cleaner-looking-way."]], "5) Save work": [[46, "5)-Save-work"]], "Running periodic ground-state structure solver": [[47, "Running-periodic-ground-state-structure-solver"]], "0) Create a Cluster Subspace based on the disordered structure with an Ewald term": [[47, "0)-Create-a-Cluster-Subspace-based-on-the-disordered-structure-with-an-Ewald-term"]], "1) Create random ECIs and ClusterExpansion": [[47, "1)-Create-random-ECIs-and-ClusterExpansion"]], "2) Create a semi-grand canonical ensemble": [[47, "2)-Create-a-semi-grand-canonical-ensemble"]], "3) Create a solver instance from the ensemble": [[47, "3)-Create-a-solver-instance-from-the-ensemble"]], "4) Solve the problem in semi-grand canonical ensemble": [[47, "4)-Solve-the-problem-in-semi-grand-canonical-ensemble"]], "5) Create and solve a canonical ensemble problem": [[47, "5)-Create-and-solve-a-canonical-ensemble-problem"]], "Generating Special Quasirandom Structure (SQS)": [[48, "Generating-Special-Quasirandom-Structure-(SQS)"]], "1) Create a disordered prim structure": [[48, "1)-Create-a-disordered-prim-structure"]], "2) Create a SQS generator object": [[48, "2)-Create-a-SQS-generator-object"]], "3) Generate SQS by running simulated annealing": [[48, "3)-Generate-SQS-by-running-simulated-annealing"]], "4) Get the best SQSs candidates": [[48, "4)-Get-the-best-SQSs-candidates"]], "4.1) Compare the best SQS from both generation methods": [[48, "4.1)-Compare-the-best-SQS-from-both-generation-methods"]], "Compare with ATAT mcsqs": [[48, "Compare-with-ATAT-mcsqs"]], "# Statistical Mechanics on Lattices Examples": [[49, "#-Statistical-Mechanics-on-Lattices-Examples"]], "Notebook examples": [[49, "Notebook-examples"]], "Basic examples": [[49, "Basic-examples"]], "Advanced examples": [[49, "Advanced-examples"]], "LiMnO DRX Cluster Expansion": [[50, "LiMnO-DRX-Cluster-Expansion"]], "0) Load all data": [[50, "0)-Load-all-data"]], "1) Define a cluster expansion": [[50, "1)-Define-a-cluster-expansion"]], "Load and inspect the lattice primitive cell with multi-site disorder": [[50, "Load-and-inspect-the-lattice-primitive-cell-with-multi-site-disorder"]], "Specify cluster subspace information": [[50, "Specify-cluster-subspace-information"]], "2. Fit a cluster expansion": [[50, "2.-Fit-a-cluster-expansion"]], "Generate the Cluster Expansion object": [[50, "Generate-the-Cluster-Expansion-object"]], "3) Run Canonical Monte Carlo": [[50, "3)-Run-Canonical-Monte-Carlo"]], "First load the spinel structure": [[50, "First-load-the-spinel-structure"]], "Generate an ensemble for a given transformation of the starting spinel structure and convert the spinel structure into an initial occupancy": [[50, "Generate-an-ensemble-for-a-given-transformation-of-the-starting-spinel-structure-and-convert-the-spinel-structure-into-an-initial-occupancy"]], "Generate sampler for canonical MC disordering from T_0 = 300 K to T_f = 500 K in steps of 50 K as a mini simulation": [[50, "Generate-sampler-for-canonical-MC-disordering-from-T_0-=-300-K-to-T_f-=-500-K-in-steps-of-50-K-as-a-mini-simulation"]], "Now save the data": [[50, "Now-save-the-data"]], "Using OpenMP parallelism": [[51, "Using-OpenMP-parallelism"]], "0) Setup an ensemble and a sampler from a cluster expansion": [[51, "0)-Setup-an-ensemble-and-a-sampler-from-a-cluster-expansion"]], "1) Setting the number of threads to benchmark parallelism improvements": [[51, "1)-Setting-the-number-of-threads-to-benchmark-parallelism-improvements"]], "1.1) Benchmark performance improvement for full computations": [[51, "1.1)-Benchmark-performance-improvement-for-full-computations"]], "1.2) Benchmark performance improvement for computations of local changes": [[51, "1.2)-Benchmark-performance-improvement-for-computations-of-local-changes"]], "Running Canonical Monte Carlo Sampling": [[52, "Running-Canonical-Monte-Carlo-Sampling"]], "0) Load the previous LNO CE with electrostatics": [[52, "0)-Load-the-previous-LNO-CE-with-electrostatics"], [53, "0)-Load-the-previous-LNO-CE-with-electrostatics"], [55, "0)-Load-the-previous-LNO-CE-with-electrostatics"]], "1) Create a canonical ensemble": [[52, "1)-Create-a-canonical-ensemble"]], "3) Create an MC sampler": [[52, "3)-Create-an-MC-sampler"]], "3) Create an initial structure and get occupancies": [[52, "3)-Create-an-initial-structure-and-get-occupancies"], [55, "3)-Create-an-initial-structure-and-get-occupancies"]], "4) Run MC iterations": [[52, "4)-Run-MC-iterations"]], "4.1) Continuing or resetting the MC trajectory": [[52, "4.1)-Continuing-or-resetting-the-MC-trajectory"]], "5) Look at trajectory samples and averages": [[52, "5)-Look-at-trajectory-samples-and-averages"]], "Save your work": [[52, "Save-your-work"]], "Running Semigrand Canonical Monte Carlo Sampling with charge-balance": [[53, "Running-Semigrand-Canonical-Monte-Carlo-Sampling-with-charge-balance"]], "1) Create a semigrand ensemble": [[53, "1)-Create-a-semigrand-ensemble"], [55, "1)-Create-a-semigrand-ensemble"]], "2) Create an MC sampler": [[53, "2)-Create-an-MC-sampler"], [55, "2)-Create-an-MC-sampler"]], "Running Canonical Monte Carlo Simulated Annealing using an Ewald Hamiltonian": [[54, "Running-Canonical-Monte-Carlo-Simulated-Annealing-using-an-Ewald-Hamiltonian"]], "0) Create a Cluster Subspace based on the disordered structure with only the empty cluster and Ewald term": [[54, "0)-Create-a-Cluster-Subspace-based-on-the-disordered-structure-with-only-the-empty-cluster-and-Ewald-term"]], "1) Create an Ewald Processor": [[54, "1)-Create-an-Ewald-Processor"]], "2) Create a Canonical Ensemble": [[54, "2)-Create-a-Canonical-Ensemble"]], "3) Create the Sampler": [[54, "3)-Create-the-Sampler"]], "4) Generate an initial ordered structure to start the MC simulation.": [[54, "4)-Generate-an-initial-ordered-structure-to-start-the-MC-simulation."]], "5) Run MC simulated annealing": [[54, "5)-Run-MC-simulated-annealing"]], "6) Analyzing MC sampling at each temperature": [[54, "6)-Analyzing-MC-sampling-at-each-temperature"]], "Obtaining the ground state": [[54, "Obtaining-the-ground-state"]], "7) Plotting the results": [[54, "7)-Plotting-the-results"]], "Running Semigrand Canonical Monte Carlo Sampling": [[55, "Running-Semigrand-Canonical-Monte-Carlo-Sampling"]], "4) Sweeping chemical potentials": [[55, "4)-Sweeping-chemical-potentials"]], "Setting composition constraints for Monte Carlo sampling or ground state searches.": [[56, "Setting-composition-constraints-for-Monte-Carlo-sampling-or-ground-state-searches."]], "1) String format": [[56, "1)-String-format"]], "2) Vector format": [[56, "2)-Vector-format"]], "One is also allowed to mix these two formats in the list passed into other_constraints.": [[56, "One-is-also-allowed-to-mix-these-two-formats-in-the-list-passed-into-other_constraints."]], "Training Data Preparation": [[57, "Training-Data-Preparation"]], "2) Modifying and adding new target properties": [[57, "2)-Modifying-and-adding-new-target-properties"]], "2.1) Another example of modifying target properties": [[57, "2.1)-Another-example-of-modifying-target-properties"]], "3) Obtaining and adding weights": [[57, "3)-Obtaining-and-adding-weights"]], "4) Structure Selection": [[57, "4)-Structure-Selection"]], "Wang-Landau sampling of an FCC anti-ferromagnetic Ising model": [[58, "Wang-Landau-sampling-of-an-FCC-anti-ferromagnetic-Ising-model"]], "1) Create an FCC Ising model": [[58, "1)-Create-an-FCC-Ising-model"]], "2) Create the ensemble and Wang-Landau sampler": [[58, "2)-Create-the-ensemble-and-Wang-Landau-sampler"]], "3) Carry out some sampling!": [[58, "3)-Carry-out-some-sampling!"]], "4) Look at modification factor for convergence": [[58, "4)-Look-at-modification-factor-for-convergence"]], "5) Look at the estimated density of states": [[58, "5)-Look-at-the-estimated-density-of-states"]], "Density of states": [[58, "Density-of-states"]], "5) Compute free energy, entropy and internal energy": [[58, "5)-Compute-free-energy,-entropy-and-internal-energy"]], "5) Finally compute heat capacity, magnetization and susceptibility": [[58, "5)-Finally-compute-heat-capacity,-magnetization-and-susceptibility"]], "Experimenting with orthogonality and different orthonormalizations (Under construction)": [[59, "Experimenting-with-orthogonality-and-different-orthonormalizations-(Under-construction)"]], "Orthogonal vs Non-orthogonal basis": [[59, "Orthogonal-vs-Non-orthogonal-basis"]], "Fit a CE with the two bases": [[59, "Fit-a-CE-with-the-two-bases"]], "Look at differences between a correlation vectors": [[59, "Look-at-differences-between-a-correlation-vectors"]], "Compare canonical Monte Carlo runs with the different bases": [[59, "Compare-canonical-Monte-Carlo-runs-with-the-different-bases"]], "Constructing a Cluster Subspace orthonormalized with respect to a concentration measure": [[59, "Constructing-a-Cluster-Subspace-orthonormalized-with-respect-to-a-concentration-measure"]], "User Guide": [[60, "user-guide"]], "Overview diagram": [[60, "overview-diagram"]], "Main classes": [[60, "main-classes"]], "Cluster Orbit Function Expansions package": [[60, "cluster-orbit-function-expansions-package"]], "Cluster subspace": [[60, "cluster-subspace"]], "Structure wrangler": [[60, "structure-wrangler"]], "Cluster expansion": [[60, "cluster-expansion"]], "Monte Carlo package": [[60, "monte-carlo-package"]], "Ensemble": [[60, "ensemble"]], "SampleContainer": [[60, "samplecontainer"]], "Cluster Analysis and Applications package": [[60, "cluster-analysis-and-applications-package"]], "StochasticSQSGenerator": [[60, "stochasticsqsgenerator"]], "PeriodicGroundStateSolver": [[60, "periodicgroundstatesolver"]], "Space": [[10, "space"]], "Sample Container": [[32, "sample-container"]]}, "indexentries": {"enumerate_supercell_matrices() (in module smol.capp.generate.enumerate)": [[1, "smol.capp.generate.enumerate.enumerate_supercell_matrices"]], "module": [[1, "module-smol.capp.generate.enumerate"], [2, "module-smol.capp.generate.groundstate.upper_bound.solver"], [3, "module-smol.capp.generate.random"], [4, "module-smol.capp.generate.special.sqs"], [8, "module-smol.cofe.extern.ewald"], [11, "module-smol.cofe.space.basis"], [12, "module-smol.cofe.space.cluster"], [13, "module-smol.cofe.space.domain"], [14, "module-smol.cofe.space.orbit"], [16, "module-smol.cofe.wrangling.select"], [17, "module-smol.cofe.wrangling.wrangler"], [18, "module-smol.cofe.wrangling.tools"], [20, "module-smol.io"], [21, "module-smol.moca.ensemble"], [24, "module-smol.moca.kernel.bias"], [25, "module-smol.moca.kernel.metropolis"], [25, "module-smol.moca.kernel.random"], [25, "module-smol.moca.kernel.wanglandau"], [26, "module-smol.moca.kernel.mcusher"], [28, "module-smol.moca.processor.composite"], [29, "module-smol.moca.processor.ewald"], [30, "module-smol.moca.processor.expansion"], [34, "module-smol.moca.sublattice"]], "smol.capp.generate.enumerate": [[1, "module-smol.capp.generate.enumerate"]], "periodicgroundstatesolver (class in smol.capp.generate.groundstate.upper_bound.solver)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver"]], "auxiliary_variables (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.auxiliary_variables"]], "canonicals (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.canonicals"]], "constraints (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.constraints"]], "ground_state_energy (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.ground_state_energy"]], "ground_state_occupancy (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.ground_state_occupancy"]], "ground_state_solution (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.ground_state_solution"]], "ground_state_structure (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.ground_state_structure"]], "indices_in_auxiliary_products (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.indices_in_auxiliary_products"]], "objective_function (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.objective_function"]], "problem (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.problem"]], "reset() (periodicgroundstatesolver method)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.reset"]], "smol.capp.generate.groundstate.upper_bound.solver": [[2, "module-smol.capp.generate.groundstate.upper_bound.solver"]], "solve() (periodicgroundstatesolver method)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.solve"]], "structure (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.structure"]], "sublattices (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.sublattices"]], "variable_indices (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.variable_indices"]], "variables (periodicgroundstatesolver property)": [[2, "smol.capp.generate.groundstate.upper_bound.solver.PeriodicGroundStateSolver.variables"]], "generate_random_ordered_occupancy() (in module smol.capp.generate.random)": [[3, "smol.capp.generate.random.generate_random_ordered_occupancy"]], "smol.capp.generate.random": [[3, "module-smol.capp.generate.random"]], "sqs (class in smol.capp.generate.special.sqs)": [[4, "smol.capp.generate.special.sqs.SQS"]], "stochasticsqsgenerator (class in smol.capp.generate.special.sqs)": [[4, "smol.capp.generate.special.sqs.StochasticSQSGenerator"]], "feature_distance (sqs attribute)": [[4, "smol.capp.generate.special.sqs.SQS.feature_distance"]], "generate() (stochasticsqsgenerator method)": [[4, "smol.capp.generate.special.sqs.StochasticSQSGenerator.generate"]], "sampler (stochasticsqsgenerator property)": [[4, "smol.capp.generate.special.sqs.StochasticSQSGenerator.sampler"]], "score (sqs attribute)": [[4, "smol.capp.generate.special.sqs.SQS.score"]], "smol.capp.generate.special.sqs": [[4, "module-smol.capp.generate.special.sqs"]], "structure (sqs attribute)": [[4, "smol.capp.generate.special.sqs.SQS.structure"]], "supercell_matrix (sqs attribute)": [[4, "smol.capp.generate.special.sqs.SQS.supercell_matrix"]], "clusterexpansion (class in smol.cofe.expansion)": [[6, "smol.cofe.expansion.ClusterExpansion"]], "regressiondata (class in smol.cofe.expansion)": [[6, "smol.cofe.expansion.RegressionData"]], "as_dict() (clusterexpansion method)": [[6, "smol.cofe.expansion.ClusterExpansion.as_dict"]], "cluster_interaction_tensors (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.cluster_interaction_tensors"]], "cluster_interactions_from_structure() (clusterexpansion method)": [[6, "smol.cofe.expansion.ClusterExpansion.cluster_interactions_from_structure"]], "cluster_subspace (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.cluster_subspace"]], "coefficients (clusterexpansion attribute)": [[6, "smol.cofe.expansion.ClusterExpansion.coefficients"]], "copy() (clusterexpansion method)": [[6, "smol.cofe.expansion.ClusterExpansion.copy"]], "eci (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.eci"]], "eci_orbit_ids (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.eci_orbit_ids"]], "effective_cluster_weights (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.effective_cluster_weights"]], "estimator_name (regressiondata attribute)": [[6, "smol.cofe.expansion.RegressionData.estimator_name"]], "expansion_structure (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.expansion_structure"]], "feature_matrix (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.feature_matrix"]], "feature_matrix (regressiondata attribute)": [[6, "smol.cofe.expansion.RegressionData.feature_matrix"]], "from_dict() (clusterexpansion class method)": [[6, "smol.cofe.expansion.ClusterExpansion.from_dict"]], "from_object() (regressiondata class method)": [[6, "smol.cofe.expansion.RegressionData.from_object"]], "from_sklearn() (regressiondata class method)": [[6, "smol.cofe.expansion.RegressionData.from_sklearn"]], "metadata (clusterexpansion attribute)": [[6, "smol.cofe.expansion.ClusterExpansion.metadata"]], "module (regressiondata attribute)": [[6, "smol.cofe.expansion.RegressionData.module"]], "parameters (regressiondata attribute)": [[6, "smol.cofe.expansion.RegressionData.parameters"]], "predict() (clusterexpansion method)": [[6, "smol.cofe.expansion.ClusterExpansion.predict"]], "property_vector (regressiondata attribute)": [[6, "smol.cofe.expansion.RegressionData.property_vector"]], "prune() (clusterexpansion method)": [[6, "smol.cofe.expansion.ClusterExpansion.prune"]], "structure (clusterexpansion property)": [[6, "smol.cofe.expansion.ClusterExpansion.structure"]], "clustersubspace (class in smol.cofe.space.clusterspace)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace"]], "pottssubspace (class in smol.cofe.space.clusterspace)": [[7, "smol.cofe.space.clusterspace.PottsSubspace"]], "add_external_term() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.add_external_term"]], "as_dict() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.as_dict"]], "as_dict() (pottssubspace method)": [[7, "smol.cofe.space.clusterspace.PottsSubspace.as_dict"]], "basis_orthogonal (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.basis_orthogonal"]], "basis_orthonormal (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.basis_orthonormal"]], "basis_type (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.basis_type"]], "change_site_bases() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.change_site_bases"]], "copy() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.copy"]], "corr_from_structure() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.corr_from_structure"]], "cutoffs (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.cutoffs"]], "evaluator (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.evaluator"]], "expansion_structure (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.expansion_structure"]], "external_terms (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.external_terms"]], "from_cutoffs() (clustersubspace class method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.from_cutoffs"]], "from_cutoffs() (pottssubspace class method)": [[7, "smol.cofe.space.clusterspace.PottsSubspace.from_cutoffs"]], "from_dict() (clustersubspace class method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.from_dict"]], "from_dict() (pottssubspace class method)": [[7, "smol.cofe.space.clusterspace.PottsSubspace.from_dict"]], "function_hierarchy() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_hierarchy"]], "function_inds_by_size (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_inds_by_size"]], "function_inds_from_cutoffs() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_inds_from_cutoffs"]], "function_orbit_ids (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_orbit_ids"]], "function_ordering_multiplicities (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_ordering_multiplicities"]], "function_total_multiplicities (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.function_total_multiplicities"]], "gen_orbit_list() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.gen_orbit_list"]], "get_aliased_orbits() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.get_aliased_orbits"]], "get_function_decoration() (pottssubspace method)": [[7, "smol.cofe.space.clusterspace.PottsSubspace.get_function_decoration"]], "get_orbit_decorations() (pottssubspace method)": [[7, "smol.cofe.space.clusterspace.PottsSubspace.get_orbit_decorations"]], "get_orbit_indices() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.get_orbit_indices"]], "get_sub_function_ids() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.get_sub_function_ids"]], "get_sub_orbits() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.get_sub_orbits"]], "num_clusters (clustersubspace attribute)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_clusters"]], "num_corr_functions (clustersubspace attribute)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_corr_functions"]], "num_functions_per_orbit (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_functions_per_orbit"]], "num_orbits (clustersubspace attribute)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_orbits"]], "num_prims_from_matrix() (clustersubspace static method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_prims_from_matrix"]], "num_threads (clustersubspace attribute)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.num_threads"]], "occupancy_from_structure() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.occupancy_from_structure"]], "orbit_hierarchy() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbit_hierarchy"]], "orbit_multiplicities (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbit_multiplicities"]], "orbits (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbits"]], "orbits_by_cutoffs() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbits_by_cutoffs"]], "orbits_by_diameter (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbits_by_diameter"]], "orbits_by_size (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbits_by_size"]], "orbits_from_cutoffs() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.orbits_from_cutoffs"]], "refine_structure() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.refine_structure"]], "remove_corr_functions() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.remove_corr_functions"]], "remove_orbits() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.remove_orbits"]], "rotate_site_basis() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.rotate_site_basis"]], "scmatrix_from_structure() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.scmatrix_from_structure"]], "site_rotation_matrix (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.site_rotation_matrix"]], "structure (clustersubspace property)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.structure"]], "structure_site_mapping() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.structure_site_mapping"]], "supercell_orbit_mappings() (clustersubspace method)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.supercell_orbit_mappings"]], "symops (clustersubspace attribute)": [[7, "smol.cofe.space.clusterspace.ClusterSubspace.symops"]], "ewaldterm (class in smol.cofe.extern.ewald)": [[8, "smol.cofe.extern.ewald.EwaldTerm"]], "as_dict() (ewaldterm method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.as_dict"]], "ewald_term_options (ewaldterm attribute)": [[8, "smol.cofe.extern.ewald.EwaldTerm.ewald_term_options"]], "from_dict() (ewaldterm class method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.from_dict"]], "get_ewald_matrix() (ewaldterm method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.get_ewald_matrix"]], "get_ewald_occu() (ewaldterm static method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.get_ewald_occu"]], "get_ewald_structure() (ewaldterm static method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.get_ewald_structure"]], "smol.cofe.extern.ewald": [[8, "module-smol.cofe.extern.ewald"]], "value_from_occupancy() (ewaldterm method)": [[8, "smol.cofe.extern.ewald.EwaldTerm.value_from_occupancy"]], "basisiterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.BasisIterator"]], "chebysheviterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.ChebyshevIterator"]], "discretebasis (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.DiscreteBasis"]], "indicatorbasis (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.IndicatorBasis"]], "indicatoriterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.IndicatorIterator"]], "legendreiterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.LegendreIterator"]], "numpypolyiterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.NumpyPolyIterator"]], "polynomialiterator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.PolynomialIterator"]], "sinusoiditerator (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.SinusoidIterator"]], "standardbasis (class in smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.StandardBasis"]], "as_dict() (discretebasis method)": [[11, "smol.cofe.space.basis.DiscreteBasis.as_dict"]], "as_dict() (standardbasis method)": [[11, "smol.cofe.space.basis.StandardBasis.as_dict"]], "basis_factory() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.basis_factory"]], "cos_f() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.cos_f"]], "encode_domain() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.encode_domain"]], "flavor (basisiterator attribute)": [[11, "id0"], [11, "smol.cofe.space.basis.BasisIterator.flavor"]], "flavor (chebysheviterator attribute)": [[11, "smol.cofe.space.basis.ChebyshevIterator.flavor"]], "flavor (indicatoriterator attribute)": [[11, "smol.cofe.space.basis.IndicatorIterator.flavor"]], "flavor (legendreiterator attribute)": [[11, "smol.cofe.space.basis.LegendreIterator.flavor"]], "flavor (numpypolyiterator attribute)": [[11, "smol.cofe.space.basis.NumpyPolyIterator.flavor"]], "flavor (polynomialiterator attribute)": [[11, "smol.cofe.space.basis.PolynomialIterator.flavor"]], "flavor (sinusoiditerator attribute)": [[11, "smol.cofe.space.basis.SinusoidIterator.flavor"]], "from_dict() (discretebasis class method)": [[11, "smol.cofe.space.basis.DiscreteBasis.from_dict"]], "from_dict() (indicatorbasis class method)": [[11, "smol.cofe.space.basis.IndicatorBasis.from_dict"]], "from_dict() (standardbasis class method)": [[11, "smol.cofe.space.basis.StandardBasis.from_dict"]], "function_array (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.function_array"]], "function_array (standardbasis property)": [[11, "smol.cofe.space.basis.StandardBasis.function_array"]], "indicator() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.indicator"]], "is_orthogonal (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.is_orthogonal"]], "is_orthonormal (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.is_orthonormal"]], "measure_array (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.measure_array"]], "measure_vector (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.measure_vector"]], "orthonormalization_array (standardbasis property)": [[11, "smol.cofe.space.basis.StandardBasis.orthonormalization_array"]], "orthonormalize() (standardbasis method)": [[11, "smol.cofe.space.basis.StandardBasis.orthonormalize"]], "polyval (chebysheviterator property)": [[11, "smol.cofe.space.basis.ChebyshevIterator.polyval"]], "polyval (legendreiterator property)": [[11, "smol.cofe.space.basis.LegendreIterator.polyval"]], "polyval (numpypolyiterator property)": [[11, "smol.cofe.space.basis.NumpyPolyIterator.polyval"]], "polyval (polynomialiterator property)": [[11, "smol.cofe.space.basis.PolynomialIterator.polyval"]], "rotate() (standardbasis method)": [[11, "smol.cofe.space.basis.StandardBasis.rotate"]], "rotation_array (standardbasis property)": [[11, "smol.cofe.space.basis.StandardBasis.rotation_array"]], "sin_f() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.sin_f"]], "sinusoid_factory() (in module smol.cofe.space.basis)": [[11, "smol.cofe.space.basis.sinusoid_factory"]], "site_space (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.site_space"]], "smol.cofe.space.basis": [[11, "module-smol.cofe.space.basis"]], "species (discretebasis property)": [[11, "smol.cofe.space.basis.DiscreteBasis.species"]], "cluster (class in smol.cofe.space.cluster)": [[12, "smol.cofe.space.cluster.Cluster"]], "as_dict() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.as_dict"]], "assign_ids() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.assign_ids"]], "centroid (cluster attribute)": [[12, "smol.cofe.space.cluster.Cluster.centroid"]], "centroid (cluster property)": [[12, "id0"]], "copy() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.copy"]], "diameter (cluster property)": [[12, "smol.cofe.space.cluster.Cluster.diameter"]], "frac_coords (cluster attribute)": [[12, "smol.cofe.space.cluster.Cluster.frac_coords"]], "frac_coords (cluster property)": [[12, "id1"]], "from_dict() (cluster class method)": [[12, "smol.cofe.space.cluster.Cluster.from_dict"]], "from_file() (cluster class method)": [[12, "smol.cofe.space.cluster.Cluster.from_file"]], "from_sites() (cluster class method)": [[12, "smol.cofe.space.cluster.Cluster.from_sites"]], "from_str() (cluster class method)": [[12, "smol.cofe.space.cluster.Cluster.from_str"]], "get_cluster_scene() (in module smol.cofe.space.cluster)": [[12, "smol.cofe.space.cluster.get_cluster_scene"]], "get_distance() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.get_distance"]], "get_scene() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.get_scene"]], "id (cluster attribute)": [[12, "smol.cofe.space.cluster.Cluster.id"]], "lattice (cluster attribute)": [[12, "smol.cofe.space.cluster.Cluster.lattice"]], "lattice (cluster property)": [[12, "id2"]], "radius (cluster property)": [[12, "smol.cofe.space.cluster.Cluster.radius"]], "sites (cluster property)": [[12, "smol.cofe.space.cluster.Cluster.sites"]], "smol.cofe.space.cluster": [[12, "module-smol.cofe.space.cluster"]], "to() (cluster method)": [[12, "smol.cofe.space.cluster.Cluster.to"]], "sitespace (class in smol.cofe.space.domain)": [[13, "smol.cofe.space.domain.SiteSpace"]], "vacancy (class in smol.cofe.space.domain)": [[13, "smol.cofe.space.domain.Vacancy"]], "as_dict() (sitespace method)": [[13, "smol.cofe.space.domain.SiteSpace.as_dict"]], "codes (sitespace property)": [[13, "smol.cofe.space.domain.SiteSpace.codes"]], "composition (sitespace property)": [[13, "smol.cofe.space.domain.SiteSpace.composition"]], "from_dict() (sitespace class method)": [[13, "smol.cofe.space.domain.SiteSpace.from_dict"]], "get_allowed_species() (in module smol.cofe.space.domain)": [[13, "smol.cofe.space.domain.get_allowed_species"]], "get_site_spaces() (in module smol.cofe.space.domain)": [[13, "smol.cofe.space.domain.get_site_spaces"]], "get_species() (in module smol.cofe.space.domain)": [[13, "smol.cofe.space.domain.get_species"]], "smol.cofe.space.domain": [[13, "module-smol.cofe.space.domain"]], "orbit (class in smol.cofe.space.orbit)": [[14, "smol.cofe.space.orbit.Orbit"]], "as_dict() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.as_dict"]], "assign_ids() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.assign_ids"]], "basis_arrays (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.basis_arrays"]], "basis_orthogonal (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.basis_orthogonal"]], "basis_orthonormal (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.basis_orthonormal"]], "basis_type (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.basis_type"]], "bit_combo_multiplicities (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.bit_combo_multiplicities"]], "bit_combos (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.bit_combos"]], "bits (orbit attribute)": [[14, "smol.cofe.space.orbit.Orbit.bits"]], "cluster_permutations (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.cluster_permutations"]], "cluster_symops (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.cluster_symops"]], "clusters (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.clusters"]], "correlation_tensors (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.correlation_tensors"]], "flat_correlation_tensors (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.flat_correlation_tensors"]], "flat_tensor_indices (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.flat_tensor_indices"]], "from_dict() (orbit class method)": [[14, "smol.cofe.space.orbit.Orbit.from_dict"]], "is_sub_orbit() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.is_sub_orbit"]], "lattice (orbit attribute)": [[14, "smol.cofe.space.orbit.Orbit.lattice"]], "multiplicity (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.multiplicity"]], "remove_bit_combo() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.remove_bit_combo"]], "remove_bit_combos_by_inds() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.remove_bit_combos_by_inds"]], "reset_bases() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.reset_bases"]], "rotation_array (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.rotation_array"]], "site_bases (orbit attribute)": [[14, "smol.cofe.space.orbit.Orbit.site_bases"]], "site_spaces (orbit property)": [[14, "smol.cofe.space.orbit.Orbit.site_spaces"]], "smol.cofe.space.orbit": [[14, "module-smol.cofe.space.orbit"]], "structure_symops (orbit attribute)": [[14, "smol.cofe.space.orbit.Orbit.structure_symops"]], "sub_orbit_mappings() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.sub_orbit_mappings"]], "transform_site_bases() (orbit method)": [[14, "smol.cofe.space.orbit.Orbit.transform_site_bases"]], "composition_select() (in module smol.cofe.wrangling.select)": [[16, "smol.cofe.wrangling.select.composition_select"]], "full_row_rank_select() (in module smol.cofe.wrangling.select)": [[16, "smol.cofe.wrangling.select.full_row_rank_select"]], "gaussian_select() (in module smol.cofe.wrangling.select)": [[16, "smol.cofe.wrangling.select.gaussian_select"]], "smol.cofe.wrangling.select": [[16, "module-smol.cofe.wrangling.select"]], "structurewrangler (class in smol.cofe.wrangling.wrangler)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler"]], "add_data_indices() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.add_data_indices"]], "add_entry() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.add_entry"]], "add_properties() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.add_properties"]], "add_weights() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.add_weights"]], "append_entries() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.append_entries"]], "as_dict() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.as_dict"]], "available_indices (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.available_indices"]], "available_properties (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.available_properties"]], "available_weights (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.available_weights"]], "change_subspace() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.change_subspace"]], "cluster_subspace (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.cluster_subspace"]], "data_indices() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.data_indices"]], "entries (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.entries"]], "feature_matrix (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.feature_matrix"]], "from_dict() (structurewrangler class method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.from_dict"]], "get_condition_number() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_condition_number"]], "get_constant_features() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_constant_features"]], "get_duplicate_corr_indices() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_duplicate_corr_indices"]], "get_feature_matrix_orbit_rank() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_feature_matrix_orbit_rank"]], "get_feature_matrix_rank() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_feature_matrix_rank"]], "get_gram_matrix() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_gram_matrix"]], "get_matching_corr_duplicate_indices() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_matching_corr_duplicate_indices"]], "get_property_vector() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_property_vector"]], "get_similarity_matrix() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_similarity_matrix"]], "get_weights() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.get_weights"]], "metadata (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.metadata"]], "num_features (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.num_features"]], "num_structures (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.num_structures"]], "occupancy_strings (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.occupancy_strings"]], "process_entry() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.process_entry"]], "refined_structures (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.refined_structures"]], "remove_all_data() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.remove_all_data"]], "remove_entry() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.remove_entry"]], "remove_properties() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.remove_properties"]], "sizes (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.sizes"]], "smol.cofe.wrangling.wrangler": [[17, "module-smol.cofe.wrangling.wrangler"]], "structure_site_mappings (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.structure_site_mappings"]], "structures (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.structures"]], "supercell_matrices (structurewrangler property)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.supercell_matrices"]], "update_features() (structurewrangler method)": [[17, "smol.cofe.wrangling.wrangler.StructureWrangler.update_features"]], "max_ewald_energy_indices() (in module smol.cofe.wrangling.tools)": [[18, "smol.cofe.wrangling.tools.max_ewald_energy_indices"]], "smol.cofe.wrangling.tools": [[18, "module-smol.cofe.wrangling.tools"]], "unique_corr_vector_indices() (in module smol.cofe.wrangling.tools)": [[18, "smol.cofe.wrangling.tools.unique_corr_vector_indices"]], "weights_energy_above_composition() (in module smol.cofe.wrangling.tools)": [[18, "smol.cofe.wrangling.tools.weights_energy_above_composition"]], "weights_energy_above_hull() (in module smol.cofe.wrangling.tools)": [[18, "smol.cofe.wrangling.tools.weights_energy_above_hull"]], "load_work() (in module smol.io)": [[20, "smol.io.load_work"]], "save_work() (in module smol.io)": [[20, "smol.io.save_work"]], "smol.io": [[20, "module-smol.io"]], "ensemble (class in smol.moca.ensemble)": [[21, "smol.moca.ensemble.Ensemble"]], "active_sublattices (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.active_sublattices"]], "as_dict() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.as_dict"]], "chemical_potentials (ensemble attribute)": [[21, "smol.moca.ensemble.Ensemble.chemical_potentials"]], "compute_feature_vector() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.compute_feature_vector"]], "compute_feature_vector_change() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.compute_feature_vector_change"]], "from_cluster_expansion() (ensemble class method)": [[21, "smol.moca.ensemble.Ensemble.from_cluster_expansion"]], "from_dict() (ensemble class method)": [[21, "smol.moca.ensemble.Ensemble.from_dict"]], "natural_parameters (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.natural_parameters"]], "num_energy_coefs (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.num_energy_coefs"]], "num_sites (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.num_sites"]], "processor (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.processor"]], "reset_restricted_sites() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.reset_restricted_sites"]], "restrict_sites() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.restrict_sites"]], "restricted_sites (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.restricted_sites"]], "smol.moca.ensemble": [[21, "module-smol.moca.ensemble"]], "species (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.species"]], "split_sublattice_by_species() (ensemble method)": [[21, "smol.moca.ensemble.Ensemble.split_sublattice_by_species"]], "sublattices (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.sublattices"]], "system_size (ensemble property)": [[21, "smol.moca.ensemble.Ensemble.system_size"]], "thermo_boundaries (ensemble attribute)": [[21, "smol.moca.ensemble.Ensemble.thermo_boundaries"]], "fugacitybias (class in smol.moca.kernel.bias)": [[24, "smol.moca.kernel.bias.FugacityBias"]], "mcbias (class in smol.moca.kernel.bias)": [[24, "smol.moca.kernel.bias.MCBias"]], "squarechargebias (class in smol.moca.kernel.bias)": [[24, "smol.moca.kernel.bias.SquareChargeBias"]], "squarehyperplanebias (class in smol.moca.kernel.bias)": [[24, "smol.moca.kernel.bias.SquareHyperplaneBias"]], "compute_bias() (fugacitybias method)": [[24, "smol.moca.kernel.bias.FugacityBias.compute_bias"]], "compute_bias() (mcbias method)": [[24, "smol.moca.kernel.bias.MCBias.compute_bias"]], "compute_bias() (squarechargebias method)": [[24, "smol.moca.kernel.bias.SquareChargeBias.compute_bias"]], "compute_bias() (squarehyperplanebias method)": [[24, "smol.moca.kernel.bias.SquareHyperplaneBias.compute_bias"]], "compute_bias_change() (fugacitybias method)": [[24, "smol.moca.kernel.bias.FugacityBias.compute_bias_change"]], "compute_bias_change() (mcbias method)": [[24, "smol.moca.kernel.bias.MCBias.compute_bias_change"]], "fugacity_fractions (fugacitybias property)": [[24, "smol.moca.kernel.bias.FugacityBias.fugacity_fractions"]], "mcbias_factory() (in module smol.moca.kernel.bias)": [[24, "smol.moca.kernel.bias.mcbias_factory"]], "smol.moca.kernel.bias": [[24, "module-smol.moca.kernel.bias"]], "sublattices (mcbias attribute)": [[24, "smol.moca.kernel.bias.MCBias.sublattices"]], "metropolis (class in smol.moca.kernel.metropolis)": [[25, "smol.moca.kernel.metropolis.Metropolis"]], "multicellmetropolis (class in smol.moca.kernel.metropolis)": [[25, "smol.moca.kernel.metropolis.MulticellMetropolis"]], "uniformlyrandom (class in smol.moca.kernel.random)": [[25, "smol.moca.kernel.random.UniformlyRandom"]], "wanglandau (class in smol.moca.kernel.wanglandau)": [[25, "smol.moca.kernel.wanglandau.WangLandau"]], "bin_size (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.bin_size"]], "compute_initial_trace() (wanglandau method)": [[25, "smol.moca.kernel.wanglandau.WangLandau.compute_initial_trace"]], "dos (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.dos"]], "entropy (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.entropy"]], "histogram (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.histogram"]], "levels (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.levels"]], "mod_factor (wanglandau property)": [[25, "smol.moca.kernel.wanglandau.WangLandau.mod_factor"]], "set_aux_state() (wanglandau method)": [[25, "smol.moca.kernel.wanglandau.WangLandau.set_aux_state"]], "smol.moca.kernel.metropolis": [[25, "module-smol.moca.kernel.metropolis"]], "smol.moca.kernel.random": [[25, "module-smol.moca.kernel.random"]], "smol.moca.kernel.wanglandau": [[25, "module-smol.moca.kernel.wanglandau"]], "temperature (multicellmetropolis property)": [[25, "smol.moca.kernel.metropolis.MulticellMetropolis.temperature"]], "valid_bias (metropolis attribute)": [[25, "smol.moca.kernel.metropolis.Metropolis.valid_bias"]], "valid_bias (multicellmetropolis attribute)": [[25, "smol.moca.kernel.metropolis.MulticellMetropolis.valid_bias"]], "valid_bias (uniformlyrandom attribute)": [[25, "smol.moca.kernel.random.UniformlyRandom.valid_bias"]], "valid_bias (wanglandau attribute)": [[25, "smol.moca.kernel.wanglandau.WangLandau.valid_bias"]], "valid_mcushers (metropolis attribute)": [[25, "smol.moca.kernel.metropolis.Metropolis.valid_mcushers"]], "valid_mcushers (multicellmetropolis attribute)": [[25, "smol.moca.kernel.metropolis.MulticellMetropolis.valid_mcushers"]], "valid_mcushers (uniformlyrandom attribute)": [[25, "smol.moca.kernel.random.UniformlyRandom.valid_mcushers"]], "valid_mcushers (wanglandau attribute)": [[25, "smol.moca.kernel.wanglandau.WangLandau.valid_mcushers"]], "composite (class in smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.Composite"]], "flip (class in smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.Flip"]], "multistep (class in smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.MultiStep"]], "swap (class in smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.Swap"]], "tableflip (class in smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.TableFlip"]], "add_mcusher() (composite method)": [[26, "smol.moca.kernel.mcusher.Composite.add_mcusher"]], "compute_log_priori_factor() (tableflip method)": [[26, "smol.moca.kernel.mcusher.TableFlip.compute_log_priori_factor"]], "mcusher_factory() (in module smol.moca.kernel.mcusher)": [[26, "smol.moca.kernel.mcusher.mcusher_factory"]], "mcushers (composite property)": [[26, "smol.moca.kernel.mcusher.Composite.mcushers"]], "propose_step() (composite method)": [[26, "smol.moca.kernel.mcusher.Composite.propose_step"]], "propose_step() (flip method)": [[26, "smol.moca.kernel.mcusher.Flip.propose_step"]], "propose_step() (multistep method)": [[26, "smol.moca.kernel.mcusher.MultiStep.propose_step"]], "propose_step() (swap method)": [[26, "smol.moca.kernel.mcusher.Swap.propose_step"]], "propose_step() (tableflip method)": [[26, "smol.moca.kernel.mcusher.TableFlip.propose_step"]], "smol.moca.kernel.mcusher": [[26, "module-smol.moca.kernel.mcusher"]], "sublattice_probabilities (multistep property)": [[26, "smol.moca.kernel.mcusher.MultiStep.sublattice_probabilities"]], "weight (composite property)": [[26, "smol.moca.kernel.mcusher.Composite.weight"]], "compositeprocessor (class in smol.moca.processor.composite)": [[28, "smol.moca.processor.composite.CompositeProcessor"]], "add_processor() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.add_processor"]], "as_dict() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.as_dict"]], "compute_feature_vector() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.compute_feature_vector"]], "compute_feature_vector_change() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.compute_feature_vector_change"]], "compute_property() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.compute_property"]], "compute_property_change() (compositeprocessor method)": [[28, "smol.moca.processor.composite.CompositeProcessor.compute_property_change"]], "from_dict() (compositeprocessor class method)": [[28, "smol.moca.processor.composite.CompositeProcessor.from_dict"]], "processors (compositeprocessor property)": [[28, "smol.moca.processor.composite.CompositeProcessor.processors"]], "smol.moca.processor.composite": [[28, "module-smol.moca.processor.composite"]], "ewaldprocessor (class in smol.moca.processor.ewald)": [[29, "smol.moca.processor.ewald.EwaldProcessor"]], "as_dict() (ewaldprocessor method)": [[29, "smol.moca.processor.ewald.EwaldProcessor.as_dict"]], "compute_feature_vector() (ewaldprocessor method)": [[29, "smol.moca.processor.ewald.EwaldProcessor.compute_feature_vector"]], "compute_feature_vector_change() (ewaldprocessor method)": [[29, "smol.moca.processor.ewald.EwaldProcessor.compute_feature_vector_change"]], "compute_property() (ewaldprocessor method)": [[29, "smol.moca.processor.ewald.EwaldProcessor.compute_property"]], 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"pleas": [2, 26, 35, 37, 41, 47, 58], "see": [2, 4, 6, 7, 8, 11, 17, 24, 25, 41, 43, 44, 45, 46, 47, 48, 50, 52, 53, 54, 55, 59], "94": [2, 35, 43, 47, 50, 54], "134424": [2, 35, 47], "The": [2, 6, 7, 8, 11, 12, 13, 14, 17, 18, 19, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60], "number": [2, 4, 7, 8, 11, 13, 14, 16, 17, 21, 25, 26, 27, 30, 33, 36, 39, 43, 45, 47, 48, 49, 50, 54, 56, 58, 60], "term": [2, 4, 6, 7, 9, 17, 18, 19, 21, 24, 26, 27, 28, 29, 30, 35, 36, 40, 41, 42, 43, 45, 49, 50, 52, 58, 60], "constraint": [2, 24, 26, 47, 53], "underli": [2, 7, 11, 12, 13, 14, 17, 21, 28, 33, 41, 52, 57, 60], "mix": [2, 21, 26, 28, 34, 35, 47, 57, 60], "integ": [2, 3, 13, 25, 26, 34, 35, 47, 56, 60], "grow": [2, 47, 58], "veri": [2, 6, 16, 25, 26, 37, 42, 44, 47, 50, 54, 57, 58, 60], "rapidli": [2, 47], "allow": [2, 6, 7, 11, 13, 17, 21, 22, 25, 26, 30, 33, 34, 36, 45, 47, 51, 52, 55, 58, 60], "speci": 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42, 43, 45, 46, 48, 50, 51, 52, 54, 55, 57, 58, 60], "been": [2, 6, 7, 17, 36, 60], "arrai": [2, 3, 6, 7, 8, 11, 14, 16, 17, 18, 21, 24, 28, 29, 30, 33, 34, 43, 47, 50, 51, 52, 53, 54, 55, 58, 59], "count": [2, 17, 24, 43, 58], "format": [2, 12, 24, 26, 37, 40, 50], "compositionspac": [2, 24, 26, 34, 56], "moca": [2, 19, 38, 40, 47, 50, 51, 52, 53, 54, 55, 56, 58, 59, 60], "unit": [2, 4, 7, 14, 16, 17, 25, 36, 37, 43, 44, 45, 46, 47, 50, 58, 60], "per": [2, 4, 7, 14, 17, 18, 20, 24, 30, 36, 48, 51, 55, 57, 58, 60], "chemic": [2, 7, 21, 24, 33, 47, 52, 53, 56, 58, 60], "potenti": [2, 7, 21, 22, 24, 33, 36, 47, 49, 52, 53, 58, 60], "need": [2, 6, 7, 12, 13, 14, 16, 17, 23, 24, 25, 27, 30, 33, 36, 37, 40, 42, 45, 46, 47, 48, 50, 52, 53, 55, 57, 58, 60], "constrain": [2, 35, 56, 58], "while": [2, 6, 37, 43, 60], "Will": [2, 17, 33, 46], "ignor": [2, 3, 4, 7, 17, 50], "semi": 2, "grand": 2, "respons": [2, 6, 7, 11, 17, 25], "ensur": [2, 6, 13, 14, 17, 25, 26, 37, 58, 60], "thei": [2, 6, 7, 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26, 27, 28, 30, 36, 45, 48, 52, 57, 58, 60], "less": [2, 4, 26, 48, 56, 57, 58], "includ": [2, 6, 7, 8, 11, 12, 13, 14, 16, 17, 21, 22, 24, 26, 29, 30, 32, 34, 35, 36, 37, 40, 41, 45, 47, 50, 56, 57, 60], "optim": [2, 26, 29, 30, 35, 43, 47, 49, 50, 51, 60], "everi": [2, 11, 17, 33, 52, 54, 56, 59], "str": [2, 4, 6, 7, 8, 11, 12, 13, 14, 17, 18, 20, 21, 24, 25, 26, 33], "specifi": [2, 3, 7, 11, 12, 13, 17, 23, 24, 25, 26, 33, 41, 45, 47, 48, 52, 53, 54, 55, 56, 60], "becaus": [2, 13, 25, 26, 45, 50, 58, 60], "doe": [2, 6, 7, 11, 13, 14, 17, 26, 37, 45, 46, 50, 52, 59], "requir": [2, 7, 8, 14, 21, 25, 36, 37, 40, 41, 46, 47, 48, 51, 60], "linear": [2, 6, 7, 17, 40, 56, 57, 60], "pseudo": [2, 47], "cvxpy": [2, 47], "pysciopt": 2, "document": [2, 4, 7, 8, 19, 24, 37, 41, 47, 49, 53, 58, 60], "how": [2, 4, 7, 11, 17, 38, 40, 44, 45, 47, 49, 50, 51, 54, 58, 59], "correctli": [2, 17, 28, 36, 45], "previou": [2, 4, 40, 48], "current": [2, 7, 11, 25, 26, 33, 36, 41, 45, 52, 57, 59], "dict": 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8, 13, 35, 43, 50], "present": [3, 36], "otherwis": [3, 6, 7, 12, 13, 17, 24, 26, 33, 41], "array_lik": 3, "seedsequ": [3, 16], "bitgener": 3, "seed": [3, 16, 25, 33, 52, 53, 54, 55], "defauly_rng": 3, "score": [4, 6, 43, 48], "feature_dist": 4, "supercell_matrix": [4, 17, 21, 28, 29, 30, 40, 48, 54], "creat": [4, 6, 7, 8, 11, 12, 13, 14, 17, 23, 25, 26, 28, 29, 30, 32, 33, 34, 36, 37, 39, 42, 44, 49, 50, 51, 57, 59, 60], "new": [4, 6, 7, 14, 17, 21, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 45, 49, 52, 54, 60], "instanc": [4, 7, 8, 21, 23, 24, 25, 26, 29, 33, 36, 40, 44, 45, 48, 51, 60], "alia": 4, "field": [4, 7, 17, 58], "2": [4, 7, 11, 12, 14, 17, 24, 26, 40, 41, 44, 52, 59], "3": [4, 7, 14, 26, 37, 40, 41, 42, 44, 51, 53, 56, 59], "cluster_subspac": [4, 6, 17, 28, 29, 30, 40, 43, 44, 48, 50, 51, 53, 54, 57, 59], "supercell_s": [4, 7, 42, 43, 45, 46, 48, 50, 54, 57, 59], "feature_typ": [4, 48], "correl": [4, 6, 7, 11, 14, 17, 18, 21, 27, 28, 29, 30, 36, 37, 40, 41, 42, 43, 46, 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"basic-examples"]], "Advanced Examples": [[39, "advanced-examples"]], "Getting Started": [[40, "getting-started"]], "Installation": [[40, "installation"]], "Basic Usage": [[40, "basic-usage"]], "Creating a cluster subspace": [[40, "creating-a-cluster-subspace"]], "Preparing training data": [[40, "preparing-training-data"]], "Fitting and creating a cluster expansion": [[40, "fitting-and-creating-a-cluster-expansion"]], "Creating an ensemble for Monte Carlo Sampling": [[40, "creating-an-ensemble-for-monte-carlo-sampling"]], "Running Monte Carlo sampling": [[40, "running-monte-carlo-sampling"]], "Saving the generated objects and data": [[40, "saving-the-generated-objects-and-data"]], "Statistical Mechanics on Lattices": [[41, "statistical-mechanics-on-lattices"]], "Functionality": [[41, "functionality"]], "License": [[41, "license"]], "Adding Structures in Parallel": [[42, "Adding-Structures-in-Parallel"]], "1) Preparing a StructureWrangler": [[42, "1)-Preparing-a-StructureWrangler"], [57, "1)-Preparing-a-StructureWrangler"]], "2) Add structures in parallel": [[42, "2)-Add-structures-in-parallel"]], "Fitting an ionic cluster expansion with energy centering": [[43, "Fitting-an-ionic-cluster-expansion-with-energy-centering"]], "Load the LMO DRX prim": [[43, "Load-the-LMO-DRX-prim"]], "1) Create the cluster subspace": [[43, "1)-Create-the-cluster-subspace"], [46, "1)-Create-the-cluster-subspace"]], "2) Load data into a Structure Wrangler": [[43, "2)-Load-data-into-a-Structure-Wrangler"]], "3) Perform a piecewise fit, with the first fit only using the Points and Ewald features.": [[43, "3)-Perform-a-piecewise-fit,-with-the-first-fit-only-using-the-Points-and-Ewald-features."]], "Perform initial fit with only Points and Ewald features, and determine the intercept.": [[43, "Perform-initial-fit-with-only-Points-and-Ewald-features,-and-determine-the-intercept."]], "Let\u2019s visualize the variance that these features can capture. To do so, we plot the \u201ccentered energies\u201d by subtracting the DFT energies by the contributions from the fitted Point and Ewald features.": [[43, "Let's-visualize-the-variance-that-these-features-can-capture.-To-do-so,-we-plot-the-%22centered-energies%22-by-subtracting-the-DFT-energies-by-the-contributions-from-the-fitted-Point-and-Ewald-features."]], "4) Perform cross validation on the rest of features to train the L1 hyperparameter.": [[43, "4)-Perform-cross-validation-on-the-rest-of-features-to-train-the-L1-hyperparameter."]], "5) Obtain the cluster expansion model that minimizes CV": [[43, "5)-Obtain-the-cluster-expansion-model-that-minimizes-CV"]], "6) Get an idea of the predictive capabilities of this cluster expansion": [[43, "6)-Get-an-idea-of-the-predictive-capabilities-of-this-cluster-expansion"]], "7) Plot the ECI": [[43, "7)-Plot-the-ECI"]], "Visualizing Clusters with Crystal-Toolkit": [[44, "Visualizing-Clusters-with-Crystal-Toolkit"]], "Load a cluster expansion": [[44, "Load-a-cluster-expansion"]], "Visualize the primitive structure": [[44, "Visualize-the-primitive-structure"]], "Visualize a pair cluster": [[44, "Visualize-a-pair-cluster"]], "Visualize a triplet cluster": [[44, "Visualize-a-triplet-cluster"]], "Using a plotting package to visualize clusters": [[44, "Using-a-plotting-package-to-visualize-clusters"]], "Creating a basic Cluster Expansion": [[45, "Creating-a-basic-Cluster-Expansion"]], "0) The prim structure": [[45, "0)-The-prim-structure"]], "1) The cluster subspace": [[45, "1)-The-cluster-subspace"]], "1.1) Computing a correlation vector.": [[45, "1.1)-Computing-a-correlation-vector."]], "2) The structure wrangler": [[45, "2)-The-structure-wrangler"]], "3.1) Check the quality of the fit": [[45, "3.1)-Check-the-quality-of-the-fit"]], "4) The cluster expansion": [[45, "4)-The-cluster-expansion"]], "5) Saving your work": [[45, "5)-Saving-your-work"]], "5.1) Loading previously saved work": [[45, "5.1)-Loading-previously-saved-work"]], "Creating a Cluster Expansion with an additional Ewald electrostatic term": [[46, "Creating-a-Cluster-Expansion-with-an-additional-Ewald-electrostatic-term"]], "2) Add the ewald term.": [[46, "2)-Add-the-ewald-term."]], "2.1) The Electrostatic term": [[46, "2.1)-The-Electrostatic-term"]], "3) Creating the cluster expansion": [[46, "3)-Creating-the-cluster-expansion"]], "3.1) Check the quality of the fit and the \u201cdielectric\u201d constant": [[46, "3.1)-Check-the-quality-of-the-fit-and-the-%22dielectric%22-constant"]], "4) Constraining the value of the \u201cdielectric\u201d constant": [[46, "4)-Constraining-the-value-of-the-%22dielectric%22-constant"]], "4.1) If you want to play with decorators you can also do the above in a cleaner looking way.": [[46, "4.1)-If-you-want-to-play-with-decorators-you-can-also-do-the-above-in-a-cleaner-looking-way."]], "5) Save work": [[46, "5)-Save-work"]], "Running periodic ground-state structure solver": [[47, "Running-periodic-ground-state-structure-solver"]], "0) Create a Cluster Subspace based on the disordered structure with an Ewald term": [[47, "0)-Create-a-Cluster-Subspace-based-on-the-disordered-structure-with-an-Ewald-term"]], "1) Create random ECIs and ClusterExpansion": [[47, "1)-Create-random-ECIs-and-ClusterExpansion"]], "2) Create a semi-grand canonical ensemble": [[47, "2)-Create-a-semi-grand-canonical-ensemble"]], "3) Create a solver instance from the ensemble": [[47, "3)-Create-a-solver-instance-from-the-ensemble"]], "4) Solve the problem in semi-grand canonical ensemble": [[47, "4)-Solve-the-problem-in-semi-grand-canonical-ensemble"]], "5) Create and solve a canonical ensemble problem": [[47, "5)-Create-and-solve-a-canonical-ensemble-problem"]], "Generating Special Quasirandom Structure (SQS)": [[48, "Generating-Special-Quasirandom-Structure-(SQS)"]], "1) Create a disordered prim structure": [[48, "1)-Create-a-disordered-prim-structure"]], "2) Create a SQS generator object": [[48, "2)-Create-a-SQS-generator-object"]], "3) Generate SQS by running simulated annealing": [[48, "3)-Generate-SQS-by-running-simulated-annealing"]], "4) Get the best SQSs candidates": [[48, "4)-Get-the-best-SQSs-candidates"]], "4.1) Compare the best SQS from both generation methods": [[48, "4.1)-Compare-the-best-SQS-from-both-generation-methods"]], "Compare with ATAT mcsqs": [[48, "Compare-with-ATAT-mcsqs"]], "# Statistical Mechanics on Lattices Examples": [[49, "#-Statistical-Mechanics-on-Lattices-Examples"]], "Notebook examples": [[49, "Notebook-examples"]], "Basic examples": [[49, "Basic-examples"]], "Advanced examples": [[49, "Advanced-examples"]], "LiMnO DRX Cluster Expansion": [[50, "LiMnO-DRX-Cluster-Expansion"]], "0) Load all data": [[50, "0)-Load-all-data"]], "1) Define a cluster expansion": [[50, "1)-Define-a-cluster-expansion"]], "Load and inspect the lattice primitive cell with multi-site disorder": [[50, "Load-and-inspect-the-lattice-primitive-cell-with-multi-site-disorder"]], "Specify cluster subspace information": [[50, "Specify-cluster-subspace-information"]], "2. Fit a cluster expansion": [[50, "2.-Fit-a-cluster-expansion"]], "Generate the Cluster Expansion object": [[50, "Generate-the-Cluster-Expansion-object"]], "3) Run Canonical Monte Carlo": [[50, "3)-Run-Canonical-Monte-Carlo"]], "First load the spinel structure": [[50, "First-load-the-spinel-structure"]], "Generate an ensemble for a given transformation of the starting spinel structure and convert the spinel structure into an initial occupancy": [[50, "Generate-an-ensemble-for-a-given-transformation-of-the-starting-spinel-structure-and-convert-the-spinel-structure-into-an-initial-occupancy"]], "Generate sampler for canonical MC disordering from T_0 = 300 K to T_f = 500 K in steps of 50 K as a mini simulation": [[50, "Generate-sampler-for-canonical-MC-disordering-from-T_0-=-300-K-to-T_f-=-500-K-in-steps-of-50-K-as-a-mini-simulation"]], "Now save the data": [[50, "Now-save-the-data"]], "Using OpenMP parallelism": [[51, "Using-OpenMP-parallelism"]], "0) Setup an ensemble and a sampler from a cluster expansion": [[51, "0)-Setup-an-ensemble-and-a-sampler-from-a-cluster-expansion"]], "1) Setting the number of threads to benchmark parallelism improvements": [[51, "1)-Setting-the-number-of-threads-to-benchmark-parallelism-improvements"]], "1.1) Benchmark performance improvement for full computations": [[51, "1.1)-Benchmark-performance-improvement-for-full-computations"]], "1.2) Benchmark performance improvement for computations of local changes": [[51, "1.2)-Benchmark-performance-improvement-for-computations-of-local-changes"]], "Running Canonical Monte Carlo Sampling": [[52, "Running-Canonical-Monte-Carlo-Sampling"]], "0) Load the previous LNO CE with electrostatics": [[52, "0)-Load-the-previous-LNO-CE-with-electrostatics"], [53, "0)-Load-the-previous-LNO-CE-with-electrostatics"], [55, "0)-Load-the-previous-LNO-CE-with-electrostatics"]], "1) Create a canonical ensemble": [[52, "1)-Create-a-canonical-ensemble"]], "3) Create an MC sampler": [[52, "3)-Create-an-MC-sampler"]], "3) Create an initial structure and get occupancies": [[52, "3)-Create-an-initial-structure-and-get-occupancies"], [55, "3)-Create-an-initial-structure-and-get-occupancies"]], "4) Run MC iterations": [[52, "4)-Run-MC-iterations"]], "4.1) Continuing or resetting the MC trajectory": [[52, "4.1)-Continuing-or-resetting-the-MC-trajectory"]], "5) Look at trajectory samples and averages": [[52, "5)-Look-at-trajectory-samples-and-averages"]], "Save your work": [[52, "Save-your-work"]], "Running Semigrand Canonical Monte Carlo Sampling with charge-balance": [[53, "Running-Semigrand-Canonical-Monte-Carlo-Sampling-with-charge-balance"]], "1) Create a semigrand ensemble": [[53, "1)-Create-a-semigrand-ensemble"], [55, "1)-Create-a-semigrand-ensemble"]], "2) Create an MC sampler": [[53, "2)-Create-an-MC-sampler"], [55, "2)-Create-an-MC-sampler"]], "Running Canonical Monte Carlo Simulated Annealing using an Ewald Hamiltonian": [[54, "Running-Canonical-Monte-Carlo-Simulated-Annealing-using-an-Ewald-Hamiltonian"]], "0) Create a Cluster Subspace based on the disordered structure with only the empty cluster and Ewald term": [[54, "0)-Create-a-Cluster-Subspace-based-on-the-disordered-structure-with-only-the-empty-cluster-and-Ewald-term"]], "1) Create an Ewald Processor": [[54, "1)-Create-an-Ewald-Processor"]], "2) Create a Canonical Ensemble": [[54, "2)-Create-a-Canonical-Ensemble"]], "3) Create the Sampler": [[54, "3)-Create-the-Sampler"]], "4) Generate an initial ordered structure to start the MC simulation.": [[54, "4)-Generate-an-initial-ordered-structure-to-start-the-MC-simulation."]], "5) Run MC simulated annealing": [[54, "5)-Run-MC-simulated-annealing"]], "6) Analyzing MC sampling at each temperature": [[54, "6)-Analyzing-MC-sampling-at-each-temperature"]], "Obtaining the ground state": [[54, "Obtaining-the-ground-state"]], "7) Plotting the results": [[54, "7)-Plotting-the-results"]], "Running Semigrand Canonical Monte Carlo Sampling": [[55, "Running-Semigrand-Canonical-Monte-Carlo-Sampling"]], "4) Sweeping chemical potentials": [[55, "4)-Sweeping-chemical-potentials"]], "Setting composition constraints for Monte Carlo sampling or ground state searches.": [[56, "Setting-composition-constraints-for-Monte-Carlo-sampling-or-ground-state-searches."]], "1) String format": [[56, "1)-String-format"]], "2) Vector format": [[56, "2)-Vector-format"]], "One is also allowed to mix these two formats in the list passed into other_constraints.": [[56, "One-is-also-allowed-to-mix-these-two-formats-in-the-list-passed-into-other_constraints."]], "Training Data Preparation": [[57, "Training-Data-Preparation"]], "2) Modifying and adding new target properties": [[57, "2)-Modifying-and-adding-new-target-properties"]], "2.1) Another example of modifying target properties": [[57, "2.1)-Another-example-of-modifying-target-properties"]], "3) Obtaining and adding weights": [[57, "3)-Obtaining-and-adding-weights"]], "4) Structure Selection": [[57, "4)-Structure-Selection"]], "Wang-Landau sampling of an FCC anti-ferromagnetic Ising model": [[58, "Wang-Landau-sampling-of-an-FCC-anti-ferromagnetic-Ising-model"]], "1) Create an FCC Ising model": [[58, "1)-Create-an-FCC-Ising-model"]], "2) Create the ensemble and Wang-Landau sampler": [[58, "2)-Create-the-ensemble-and-Wang-Landau-sampler"]], "3) Carry out some sampling!": [[58, "3)-Carry-out-some-sampling!"]], "4) Look at modification factor for convergence": [[58, "4)-Look-at-modification-factor-for-convergence"]], "5) Look at the estimated density of states": [[58, "5)-Look-at-the-estimated-density-of-states"]], "Density of states": [[58, "Density-of-states"]], "5) Compute free energy, entropy and internal energy": [[58, "5)-Compute-free-energy,-entropy-and-internal-energy"]], "5) Finally compute heat capacity, magnetization and susceptibility": [[58, "5)-Finally-compute-heat-capacity,-magnetization-and-susceptibility"]], "Experimenting with orthogonality and different orthonormalizations (Under construction)": [[59, "Experimenting-with-orthogonality-and-different-orthonormalizations-(Under-construction)"]], "Orthogonal vs Non-orthogonal basis": [[59, "Orthogonal-vs-Non-orthogonal-basis"]], "Fit a CE with the two bases": [[59, "Fit-a-CE-with-the-two-bases"]], "Look at differences between a correlation vectors": [[59, "Look-at-differences-between-a-correlation-vectors"]], "Compare canonical Monte Carlo runs with the different bases": [[59, "Compare-canonical-Monte-Carlo-runs-with-the-different-bases"]], "Constructing a Cluster Subspace orthonormalized with respect to a concentration measure": [[59, "Constructing-a-Cluster-Subspace-orthonormalized-with-respect-to-a-concentration-measure"]], "User Guide": [[60, "user-guide"]], "Overview diagram": [[60, "overview-diagram"]], "Main classes": [[60, "main-classes"]], "Cluster Orbit Function Expansions package": [[60, "cluster-orbit-function-expansions-package"]], "Cluster subspace": [[60, "cluster-subspace"]], "Structure wrangler": [[60, "structure-wrangler"]], "Cluster expansion": [[60, "cluster-expansion"]], "Monte Carlo package": [[60, "monte-carlo-package"]], "Ensemble": [[60, "ensemble"]], "SampleContainer": [[60, "samplecontainer"]], "Cluster Analysis and Applications package": [[60, "cluster-analysis-and-applications-package"]], "StochasticSQSGenerator": [[60, "stochasticsqsgenerator"]], "PeriodicGroundStateSolver": [[60, "periodicgroundstatesolver"]], "Space": [[10, "space"]], "Sample Container": [[32, "sample-container"]]}, "indexentries": {}}) \ No newline at end of file diff --git a/user_guide.html b/user_guide.html index 6f2fddb1e..20fb513cf 100644 --- a/user_guide.html +++ b/user_guide.html @@ -211,7 +211,7 @@
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