From 37323b8f164d7fd3699bc357d77aff626f173d9b Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Sat, 14 Sep 2019 13:52:06 -0600 Subject: [PATCH 1/5] Remove obsolete BMI metatdata These will be replaced by similar metadata in a new project in the pymt-lab org. See also the branch mdpiper/preserve-obsolete-metadata. --- .bmi.yaml | 10 -- .bmi/centered_parameter_study/api.yaml | 5 - .../centered_parameter_study/dakota.yaml.tmpl | 39 ----- .bmi/centered_parameter_study/info.yaml | 11 -- .bmi/centered_parameter_study/parameters.yaml | 79 --------- .bmi/multidim_parameter_study/api.yaml | 5 - .../multidim_parameter_study/dakota.yaml.tmpl | 38 ---- .bmi/multidim_parameter_study/info.yaml | 10 -- .bmi/multidim_parameter_study/parameters.yaml | 79 --------- .bmi/polynomial_chaos/api.yaml | 5 - .bmi/polynomial_chaos/dakota.yaml.tmpl | 52 ------ .bmi/polynomial_chaos/info.yaml | 10 -- .bmi/polynomial_chaos/parameters.yaml | 165 ------------------ .bmi/sampling/api.yaml | 5 - .bmi/sampling/dakota.yaml.tmpl | 45 ----- .bmi/sampling/info.yaml | 9 - .bmi/sampling/parameters.yaml | 150 ---------------- .bmi/stoch_collocation/api.yaml | 5 - .bmi/stoch_collocation/dakota.yaml.tmpl | 52 ------ .bmi/stoch_collocation/info.yaml | 17 -- .bmi/stoch_collocation/parameters.yaml | 165 ------------------ .bmi/vector_parameter_study/api.yaml | 5 - .bmi/vector_parameter_study/dakota.yaml.tmpl | 38 ---- .bmi/vector_parameter_study/info.yaml | 10 -- .bmi/vector_parameter_study/parameters.yaml | 82 --------- 25 files changed, 1091 deletions(-) delete mode 100644 .bmi.yaml delete mode 100644 .bmi/centered_parameter_study/api.yaml delete mode 100644 .bmi/centered_parameter_study/dakota.yaml.tmpl delete mode 100644 .bmi/centered_parameter_study/info.yaml delete mode 100644 .bmi/centered_parameter_study/parameters.yaml delete mode 100644 .bmi/multidim_parameter_study/api.yaml delete mode 100644 .bmi/multidim_parameter_study/dakota.yaml.tmpl delete mode 100644 .bmi/multidim_parameter_study/info.yaml delete mode 100644 .bmi/multidim_parameter_study/parameters.yaml delete mode 100644 .bmi/polynomial_chaos/api.yaml delete mode 100644 .bmi/polynomial_chaos/dakota.yaml.tmpl delete mode 100644 .bmi/polynomial_chaos/info.yaml delete mode 100644 .bmi/polynomial_chaos/parameters.yaml delete mode 100644 .bmi/sampling/api.yaml delete mode 100644 .bmi/sampling/dakota.yaml.tmpl delete mode 100644 .bmi/sampling/info.yaml delete mode 100644 .bmi/sampling/parameters.yaml delete mode 100644 .bmi/stoch_collocation/api.yaml delete mode 100644 .bmi/stoch_collocation/dakota.yaml.tmpl delete mode 100644 .bmi/stoch_collocation/info.yaml delete mode 100644 .bmi/stoch_collocation/parameters.yaml delete mode 100644 .bmi/vector_parameter_study/api.yaml delete mode 100644 .bmi/vector_parameter_study/dakota.yaml.tmpl delete mode 100644 .bmi/vector_parameter_study/info.yaml delete mode 100644 .bmi/vector_parameter_study/parameters.yaml diff --git a/.bmi.yaml b/.bmi.yaml deleted file mode 100644 index dabc121..0000000 --- a/.bmi.yaml +++ /dev/null @@ -1,10 +0,0 @@ -bmi_paths: - - .bmi/centered_parameter_study - - .bmi/multidim_parameter_study - - .bmi/vector_parameter_study - - .bmi/sampling - - .bmi/polynomial_chaos - - .bmi/stoch_collocation - -build: - - python setup.py install diff --git a/.bmi/centered_parameter_study/api.yaml b/.bmi/centered_parameter_study/api.yaml deleted file mode 100644 index c23c883..0000000 --- a/.bmi/centered_parameter_study/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: CenteredParameterStudy -language: python -package: dakotathon.bmi -class: CenteredParameterStudy -initialize_args: "dakota.yaml" diff --git a/.bmi/centered_parameter_study/dakota.yaml.tmpl b/.bmi/centered_parameter_study/dakota.yaml.tmpl deleted file mode 100644 index 4930ff2..0000000 --- a/.bmi/centered_parameter_study/dakota.yaml.tmpl +++ /dev/null @@ -1,39 +0,0 @@ -method: centered_parameter_study - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -evaluation_concurrency: 2 -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: {initial_point} -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: -max_iterations: -means: -output_file: dakota.out -plugin: {plugin} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -std_deviations: -steps_per_variable: {steps_per_variable} -step_vector: {step_vector} -template_file: "{template_file}" -upper_bounds: -variables: continuous_design - -# Notes: -# * The auxiliary_files, descriptors, initial_point, -# response_descriptors, response_statistics, step_per_variable, and -# step_vector parameters should be scalars or lists. diff --git a/.bmi/centered_parameter_study/info.yaml b/.bmi/centered_parameter_study/info.yaml deleted file mode 100644 index b0c3481..0000000 --- a/.bmi/centered_parameter_study/info.yaml +++ /dev/null @@ -1,11 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-centered_parameter_study.html -author: Sandia National Laboratories -version: 6.1 -summary: "Dakota's centered parameter study computes response data - sets along multiple coordinate-based vectors, one per parameter, - centered about the initial values from the variables' - specification. This is useful for investigation of function contours - with respect to each parameter individually in the vicinity of a - specific point (e.g., post-optimality analysis for verification of a - minimum), thereby avoiding the cost associated with a - multidimensional grid." diff --git a/.bmi/centered_parameter_study/parameters.yaml b/.bmi/centered_parameter_study/parameters.yaml deleted file mode 100644 index 31d487c..0000000 --- a/.bmi/centered_parameter_study/parameters.yaml +++ /dev/null @@ -1,79 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: Input variable name - value: - type: list - default: [] -initial_point: - description: Start point (center value) for study variable - value: - type: list - default: [0.0] -steps_per_variable: - description: Number of steps to take in each direction - value: - type: list - default: [1] -step_vector: - description: Step size in each direction - value: - type: list - default: [1.0] -response_descriptors: - description: Response variable name - value: - type: list - default: [] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] -response_statistics: - description: Statistic computed on response - value: - type: list - default: ['mean'] diff --git a/.bmi/multidim_parameter_study/api.yaml b/.bmi/multidim_parameter_study/api.yaml deleted file mode 100644 index d5004f7..0000000 --- a/.bmi/multidim_parameter_study/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: MultidimParameterStudy -language: python -package: dakotathon.bmi -class: MultidimParameterStudy -initialize_args: "dakota.yaml" diff --git a/.bmi/multidim_parameter_study/dakota.yaml.tmpl b/.bmi/multidim_parameter_study/dakota.yaml.tmpl deleted file mode 100644 index a9cc151..0000000 --- a/.bmi/multidim_parameter_study/dakota.yaml.tmpl +++ /dev/null @@ -1,38 +0,0 @@ -method: multidim_parameter_study - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -evaluation_concurrency: 2 -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: {lower_bounds} -max_iterations: -means: -output_file: dakota.out -partitions: {partitions} -plugin: {plugin} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -std_deviations: -template_file: "{template_file}" -upper_bounds: {upper_bounds} -variables: continuous_design - -# Notes: -# * The auxiliary_files, descriptors, initial_point, lower_bounds, -# partitions, response_descriptors, response_statistics, and -# upper_bounds parameters should be scalars or lists. diff --git a/.bmi/multidim_parameter_study/info.yaml b/.bmi/multidim_parameter_study/info.yaml deleted file mode 100644 index e4c04b5..0000000 --- a/.bmi/multidim_parameter_study/info.yaml +++ /dev/null @@ -1,10 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-multidim_parameter_study.html -author: Sandia National Laboratories -version: 6.1 -summary: "Dakota's multidimensional parameter study computes response - data sets for an n-dimensional grid of points. Each continuous and - discrete range variable is partitioned into equally spaced intervals - between its upper and lower bounds, each discrete set variable is - partitioned into equally spaced index intervals. The partition - boundaries in n-dimensional space define a grid of points, and every - point is evaluated." diff --git a/.bmi/multidim_parameter_study/parameters.yaml b/.bmi/multidim_parameter_study/parameters.yaml deleted file mode 100644 index 7dfaad4..0000000 --- a/.bmi/multidim_parameter_study/parameters.yaml +++ /dev/null @@ -1,79 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: Input variable name - value: - type: list - default: [] -lower_bounds: - description: Lower bound on values of study variable - value: - type: float - default: [0.0] -upper_bounds: - description: Upper bound on values of study variable - value: - type: list - default: [1.0] -partitions: - description: Number of partitions between lower and upper bounds - value: - type: list - default: [2] -response_descriptors: - description: Response variable name - value: - type: list - default: [] -response_statistics: - description: Statistic computed on response - value: - type: list - default: ['mean'] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] diff --git a/.bmi/polynomial_chaos/api.yaml b/.bmi/polynomial_chaos/api.yaml deleted file mode 100644 index 10b1175..0000000 --- a/.bmi/polynomial_chaos/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: PolynomialChaos -language: python -package: dakotathon.bmi -class: PolynomialChaos -initialize_args: "dakota.yaml" diff --git a/.bmi/polynomial_chaos/dakota.yaml.tmpl b/.bmi/polynomial_chaos/dakota.yaml.tmpl deleted file mode 100644 index bb7357b..0000000 --- a/.bmi/polynomial_chaos/dakota.yaml.tmpl +++ /dev/null @@ -1,52 +0,0 @@ -method: polynomial_chaos - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -basis_polynomial_family: extended -coefficient_estimation_approach: quadrature_order_sequence -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -dimension_preference: [] -evaluation_concurrency: 2 -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: {lower_bounds} -max_iterations: -means: {means} -nested: false -output_file: dakota.out -plugin: {plugin} -probability_levels: {probability_levels} -quadrature_order: {quadrature_order} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_levels: {response_levels} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -sample_type: {sample_type} -samples: {samples} -seed: {seed} -std_deviations: {std_deviations} -template_file: "{template_file}" -upper_bounds: {upper_bounds} -variables: {variable_type} -variance_based_decomp: {variance_based_decomp} - -# Notes: -# * For uniform_uncertain variables, ignore means and std_deviations. -# * The descriptors, lower_bounds, upper_bounds, means, std_deviations, -# probability_levels, response_levels, response_descriptors, -# and response_statistics parameters should be scalars or lists. -# * coefficient_estimation_approach must be set, but the only option -# currently is quadrature_order_sequence. -# * dimension_preference isn't implemented, but has a list placeholder. diff --git a/.bmi/polynomial_chaos/info.yaml b/.bmi/polynomial_chaos/info.yaml deleted file mode 100644 index 0ed6e64..0000000 --- a/.bmi/polynomial_chaos/info.yaml +++ /dev/null @@ -1,10 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-polynomial_chaos.html -author: Sandia National Laboratories -version: 6.1 -summary: "The polynomial chaos expansion (PCE) is a general framework - for the approximate representation of random response functions in - terms of finite-dimensional series expansions in standardized random - variables. An important distinguishing feature of the methodology is - that the functional relationship between random inputs and outputs - is captured, not merely the output statistics as in the case of many - nondeterministic methodologies." diff --git a/.bmi/polynomial_chaos/parameters.yaml b/.bmi/polynomial_chaos/parameters.yaml deleted file mode 100644 index 5f17886..0000000 --- a/.bmi/polynomial_chaos/parameters.yaml +++ /dev/null @@ -1,165 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: - Input variable name - value: - type: list - default: -lower_bounds: - description: - Lower bound on values of study variable - value: - type: list - default: [0.0] -upper_bounds: - description: - Upper bound on values of study variable - value: - type: list - default: [1.0] -means: - description: - Mean of the study variable distribution - value: - type: list - default: [0.0] -std_deviations: - description: - Standard deviation of the study variable distribution - value: - type: list - default: [1.0] - -response_descriptors: - description: - Response variable name - value: - type: list - default: [] -response_statistics: - description: - Statistic computed on response - value: - type: list - default: ['mean'] -probability_levels: - description: - Probabilities at which to estimate response values - value: - type: list - default: [0.1, 0.5, 0.9] -response_levels: - description: - Levels at which to estimate response PDF and CDF - value: - type: list - default: [] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] - -quadrature_order: - description: - The highest order polynomial used by the method - value: - type: choice - default: 2 - choices: - - 1 - - 2 - - 3 - - 4 - - 5 - - 6 - - 7 - - 8 -sample_type: - description: - Technique for choosing samples - value: - type: choice - default: random - choices: - - random - - lhs -samples: - description: - Number of samples in experiment - value: - type: int - default: 10 - range: - min: 1 - max: 1e6 -seed: - description: - Seed for random number generator (0 = randomly selected) - value: - type: int - default: 0 - range: - min: 0 - max: 1e6 -variance_based_decomp: - description: - Activate global sensitivity analysis based on decomposition of response variance - value: - type: choice - default: False - choices: - - False - - True -variable_type: - description: - Variable type used in the experiment - value: - type: choice - default: uniform_uncertain - choices: - - uniform_uncertain - - normal_uncertain diff --git a/.bmi/sampling/api.yaml b/.bmi/sampling/api.yaml deleted file mode 100644 index ec49a62..0000000 --- a/.bmi/sampling/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: Sampling -language: python -package: dakotathon.bmi -class: Sampling -initialize_args: "dakota.yaml" diff --git a/.bmi/sampling/dakota.yaml.tmpl b/.bmi/sampling/dakota.yaml.tmpl deleted file mode 100644 index 81c9882..0000000 --- a/.bmi/sampling/dakota.yaml.tmpl +++ /dev/null @@ -1,45 +0,0 @@ -method: sampling - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -basis_polynomial_family: extended -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -evaluation_concurrency: 2 -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: {lower_bounds} -max_iterations: -means: {means} -output_file: dakota.out -plugin: {plugin} -probability_levels: {probability_levels} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_levels: {response_levels} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -sample_type: {sample_type} -samples: {samples} -seed: {seed} -std_deviations: {std_deviations} -template_file: "{template_file}" -upper_bounds: {upper_bounds} -variables: {variable_type} -variance_based_decomp: {variance_based_decomp} - -# Notes: -# * For uniform_uncertain variables, ignore means and std_deviations. -# * The descriptors, lower_bounds, upper_bounds, means, std_deviations, -# probability_levels, response_levels, response_descriptors, -# and response_statistics parameters should be scalars or lists. diff --git a/.bmi/sampling/info.yaml b/.bmi/sampling/info.yaml deleted file mode 100644 index 61a4202..0000000 --- a/.bmi/sampling/info.yaml +++ /dev/null @@ -1,9 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-sampling.html -author: Sandia National Laboratories -version: 6.1 -summary: "Dakota's sampling method generates parameter values by - drawing samples from the specified uncertain variable probability - distributions. The computational model is executed over all - generated parameter values to compute the responses for which - statistics are computed. The statistics support sensitivity analysis - and uncertainty quantification." diff --git a/.bmi/sampling/parameters.yaml b/.bmi/sampling/parameters.yaml deleted file mode 100644 index 450533e..0000000 --- a/.bmi/sampling/parameters.yaml +++ /dev/null @@ -1,150 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: - Input variable name - value: - type: list - default: -lower_bounds: - description: - Lower bound on values of study variable - value: - type: list - default: [0.0] -upper_bounds: - description: - Upper bound on values of study variable - value: - type: list - default: [1.0] -means: - description: - Mean of the study variable distribution - value: - type: list - default: [0.0] -std_deviations: - description: - Standard deviation of the study variable distribution - value: - type: list - default: [1.0] - -response_descriptors: - description: - Response variable name - value: - type: list - default: [] -response_statistics: - description: - Statistic computed on response - value: - type: list - default: ['mean'] -probability_levels: - description: - Probabilities at which to estimate response values - value: - type: list - default: [0.1, 0.5, 0.9] -response_levels: - description: - Levels at which to estimate response PDF and CDF - value: - type: list - default: [] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] - -sample_type: - description: - Technique for choosing samples - value: - type: choice - default: random - choices: - - random - - lhs -samples: - description: - Number of samples in experiment - value: - type: int - default: 10 - range: - min: 1 - max: 1e6 -seed: - description: - Seed for random number generator (0 = randomly selected) - value: - type: int - default: 0 - range: - min: 0 - max: 1e6 -variance_based_decomp: - description: - Activate global sensitivity analysis based on decomposition of response variance - value: - type: choice - default: False - choices: - - False - - True -variable_type: - description: - Variable type used in the experiment - value: - type: choice - default: uniform_uncertain - choices: - - uniform_uncertain - - normal_uncertain diff --git a/.bmi/stoch_collocation/api.yaml b/.bmi/stoch_collocation/api.yaml deleted file mode 100644 index fee7da5..0000000 --- a/.bmi/stoch_collocation/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: StochasticCollocation -language: python -package: dakotathon.bmi -class: StochasticCollocation -initialize_args: "dakota.yaml" diff --git a/.bmi/stoch_collocation/dakota.yaml.tmpl b/.bmi/stoch_collocation/dakota.yaml.tmpl deleted file mode 100644 index d783402..0000000 --- a/.bmi/stoch_collocation/dakota.yaml.tmpl +++ /dev/null @@ -1,52 +0,0 @@ -method: stoch_collocation - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -basis_polynomial_family: extended -coefficient_estimation_approach: quadrature_order_sequence -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -dimension_preference: [] -evaluation_concurrency: 2 -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: {lower_bounds} -max_iterations: -means: {means} -nested: false -output_file: dakota.out -plugin: {plugin} -probability_levels: {probability_levels} -quadrature_order: {quadrature_order} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_levels: {response_levels} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -sample_type: {sample_type} -samples: {samples} -seed: {seed} -std_deviations: {std_deviations} -template_file: "{template_file}" -upper_bounds: {upper_bounds} -variables: {variable_type} -variance_based_decomp: {variance_based_decomp} - -# Notes: -# * For uniform_uncertain variables, ignore means and std_deviations. -# * The descriptors, lower_bounds, upper_bounds, means, std_deviations, -# probability_levels, response_levels, response_descriptors, -# and response_statistics parameters should be scalars or lists. -# * coefficient_estimation_approach must be set, but the only option -# currently is quadrature_order_sequence. -# * dimension_preference isn't implemented, but has a list placeholder. diff --git a/.bmi/stoch_collocation/info.yaml b/.bmi/stoch_collocation/info.yaml deleted file mode 100644 index a31422a..0000000 --- a/.bmi/stoch_collocation/info.yaml +++ /dev/null @@ -1,17 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-stoch_collocation.html -author: Sandia National Laboratories -version: 6.1 -summary: "Stochastic collocation is a general framework for - approximate representation of random response functions in terms of - finite-dimensional interpolation bases. The stochastic collocation - (SC) method is very similar to polynomial chaos (PCE), with the key - difference that the orthogonal polynomial basis functions are - replaced with interpolation polynomial bases. The interpolation - polynomials may be either local or global and either value-based or - gradient-enhanced. In the local case, valued-based are piecewise - linear splines and gradient-enhanced are piecewise cubic splines, - and in the global case, valued-based are Lagrange interpolants and - gradient-enhanced are Hermite interpolants. Thus, in PCE, one forms - coefficients for known orthogonal polynomial basis functions, - whereas SC forms multidimensional interpolation functions for known - coefficients." diff --git a/.bmi/stoch_collocation/parameters.yaml b/.bmi/stoch_collocation/parameters.yaml deleted file mode 100644 index 5f17886..0000000 --- a/.bmi/stoch_collocation/parameters.yaml +++ /dev/null @@ -1,165 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: - Input variable name - value: - type: list - default: -lower_bounds: - description: - Lower bound on values of study variable - value: - type: list - default: [0.0] -upper_bounds: - description: - Upper bound on values of study variable - value: - type: list - default: [1.0] -means: - description: - Mean of the study variable distribution - value: - type: list - default: [0.0] -std_deviations: - description: - Standard deviation of the study variable distribution - value: - type: list - default: [1.0] - -response_descriptors: - description: - Response variable name - value: - type: list - default: [] -response_statistics: - description: - Statistic computed on response - value: - type: list - default: ['mean'] -probability_levels: - description: - Probabilities at which to estimate response values - value: - type: list - default: [0.1, 0.5, 0.9] -response_levels: - description: - Levels at which to estimate response PDF and CDF - value: - type: list - default: [] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] - -quadrature_order: - description: - The highest order polynomial used by the method - value: - type: choice - default: 2 - choices: - - 1 - - 2 - - 3 - - 4 - - 5 - - 6 - - 7 - - 8 -sample_type: - description: - Technique for choosing samples - value: - type: choice - default: random - choices: - - random - - lhs -samples: - description: - Number of samples in experiment - value: - type: int - default: 10 - range: - min: 1 - max: 1e6 -seed: - description: - Seed for random number generator (0 = randomly selected) - value: - type: int - default: 0 - range: - min: 0 - max: 1e6 -variance_based_decomp: - description: - Activate global sensitivity analysis based on decomposition of response variance - value: - type: choice - default: False - choices: - - False - - True -variable_type: - description: - Variable type used in the experiment - value: - type: choice - default: uniform_uncertain - choices: - - uniform_uncertain - - normal_uncertain diff --git a/.bmi/vector_parameter_study/api.yaml b/.bmi/vector_parameter_study/api.yaml deleted file mode 100644 index 4012cd8..0000000 --- a/.bmi/vector_parameter_study/api.yaml +++ /dev/null @@ -1,5 +0,0 @@ -name: VectorParameterStudy -language: python -package: dakotathon.bmi -class: VectorParameterStudy -initialize_args: "dakota.yaml" diff --git a/.bmi/vector_parameter_study/dakota.yaml.tmpl b/.bmi/vector_parameter_study/dakota.yaml.tmpl deleted file mode 100644 index 0a860b9..0000000 --- a/.bmi/vector_parameter_study/dakota.yaml.tmpl +++ /dev/null @@ -1,38 +0,0 @@ -method: vector_parameter_study - -analysis_driver: {analysis_driver} -asynchronous: false -auxiliary_files: {auxiliary_files} -component: {component} -configuration_file: dakota.yaml -convergence_tolerance: -data_file: dakota.dat -descriptors: {descriptors} -evaluation_concurrency: 2 -final_point: {final_point} -gradients: no_gradients -hessians: no_hessians -id_interface: {id_interface} -initial_point: {initial_point} -initialize_args: {initialize_args} -input_file: dakota.in -interface: fork -lower_bounds: -max_iterations: -means: -n_steps: {n_steps} -output_file: dakota.out -plugin: {plugin} -response_descriptors: {response_descriptors} -response_files: {response_files} -response_statistics: {response_statistics} -responses: response_functions -run_directory: {run_directory} -std_deviations: -template_file: "{template_file}" -upper_bounds: -variables: continuous_design - -# Notes: -# * The descriptors, final_point, initial_point, response_descriptors, -# and response_statistics parameters should be scalars or lists. diff --git a/.bmi/vector_parameter_study/info.yaml b/.bmi/vector_parameter_study/info.yaml deleted file mode 100644 index 25dfafd..0000000 --- a/.bmi/vector_parameter_study/info.yaml +++ /dev/null @@ -1,10 +0,0 @@ -url: https://dakota.sandia.gov/sites/default/files/docs/6.1/html-ref/method-vector_parameter_study.html -author: Sandia National Laboratories -version: 6.1 -summary: "Dakota's vector parameter study computes response data sets - at selected intervals along a vector in parameter space. It is often - used for single-coordinate parameter studies (to study the effect of - a single variable on a response set), but it can be used more - generally for multiple coordinate vector studies (to investigate the - response variations along some n-dimensional vector such as an - optimizer search direction)." diff --git a/.bmi/vector_parameter_study/parameters.yaml b/.bmi/vector_parameter_study/parameters.yaml deleted file mode 100644 index da792f1..0000000 --- a/.bmi/vector_parameter_study/parameters.yaml +++ /dev/null @@ -1,82 +0,0 @@ -component: - description: Name of CSDMS component - value: - type: string - default: -plugin: - description: Name of model plugin - value: - type: string - default: -run_directory: - description: Directory in which Dakota experiment is run - value: - type: string - default: '.' -template_file: - description: Dakota template of model configuration file - value: - type: string - default: 'dakota.yaml.dtmpl' -auxiliary_files: - description: Additional model input files - value: - type: list - default: [] -analysis_driver: - description: Dakota analysis driver program - value: - type: choice - default: dakota_run_plugin - choices: - - dakota_run_plugin - - dakota_run_component -id_interface: - description: Name of the interface block - value: - type: string - default: CSDMS -initialize_args: - description: Arguments passed to component initialize method - value: - type: string - default: '' - -descriptors: - description: Input variable name - value: - type: list - default: [] -initial_point: - description: Start point for study variable - value: - type: list - default: [0.0] -final_point: - description: End point for study variable - value: - type: list - default: [1.0] -n_steps: - description: Number of steps to take along vector - value: - type: int - default: 5 - range: - min: 1 - max: 1e3 -response_descriptors: - description: Response variable name - value: - type: list - default: [] -response_statistics: - description: Statistic computed on response - value: - type: list - default: ['mean'] -response_files: - description: Model output files used for calculating response - value: - type: list - default: [] From 5a6f3926ae5dace76f0c2f15853ab4cfaf895157 Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Sat, 14 Sep 2019 14:02:14 -0600 Subject: [PATCH 2/5] Only install Dakota for testing on Linux The Dakota binary from the csdms-stack channel was built against a now-obsolete version of openmpi. So it's busted. Temporarily disable its use in testing here until I can fix it. --- .travis.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 81f4319..cc05ad5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,11 +37,11 @@ install: before_script: - | - if [[ $TRAVIS_OS_NAME == "osx" ]]; then - conda install openmpi=1.6 + if [[ $TRAVIS_OS_NAME != "osx" ]]; then + conda install -c conda-forge -c csdms-stack dakota + dakota --version fi - - conda install -c conda-forge -c csdms-stack dakota hydrotrend coveralls - - dakota --version + - conda install -c conda-forge coveralls hydrotrend script: - nosetests --with-doctest --with-coverage --cover-package=dakotathon From 7d5d1266ae631db5db0d3057729420bfaf8860ba Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Sat, 14 Sep 2019 14:07:46 -0600 Subject: [PATCH 3/5] Test coverage only on Linux Several tests are disabled on macOS because of the broken Dakota binary from the csdms-stack chennel. --- .travis.yml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index cc05ad5..82cbace 100644 --- a/.travis.yml +++ b/.travis.yml @@ -44,7 +44,15 @@ before_script: - conda install -c conda-forge coveralls hydrotrend script: - - nosetests --with-doctest --with-coverage --cover-package=dakotathon + - | + if [[ $TRAVIS_OS_NAME != "osx" ]]; then + nosetests --with-doctest --with-coverage --cover-package=dakotathon + else + nosetests --with-doctest + fi after_success: - - coveralls + - | + if [[ $TRAVIS_OS_NAME != "osx" ]]; then + coveralls + fi From 7f0be5eaf2acc5d3913e1135d2fc373453f8f19c Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Sat, 14 Sep 2019 14:39:21 -0600 Subject: [PATCH 4/5] Disable test_changing_parameter_names test if Dakota not installed --- dakotathon/tests/test_dakota.py | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/dakotathon/tests/test_dakota.py b/dakotathon/tests/test_dakota.py index f0dc8cf..c80459f 100644 --- a/dakotathon/tests/test_dakota.py +++ b/dakotathon/tests/test_dakota.py @@ -218,23 +218,24 @@ def test_changing_parameter_names(): configuration_file = "an_excellent_yaml.yaml" run_log = "run_output_here.log" error_log = "no_errors_here.log" - k = Dakota( - method="vector_parameter_study", - run_directory=run_directory, - configuration_file=configuration_file, - run_log=run_log, - error_log=error_log, - ) - k.write_input_file() - k.serialize() - k.run() + if is_dakota_installed(): + k = Dakota( + method="vector_parameter_study", + run_directory=run_directory, + configuration_file=configuration_file, + run_log=run_log, + error_log=error_log, + ) + k.write_input_file() + k.serialize() + k.run() - os.remove(configuration_file) - os.remove(run_log) - os.remove(error_log) - teardown_module() - os.chdir("..") - os.rmdir(run_directory) + os.remove(configuration_file) + os.remove(run_log) + os.remove(error_log) + teardown_module() + os.chdir("..") + os.rmdir(run_directory) @nottest From 81d11820b71083087dcf97d8f6b6fa9fa98cc4da Mon Sep 17 00:00:00 2001 From: Mark Piper Date: Sat, 14 Sep 2019 14:53:44 -0600 Subject: [PATCH 5/5] Run coverage on macos but don't submit to coveralls This partially reverts 7d5d1266ae631db5db0d3057729420bfaf8860ba. --- .travis.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 82cbace..4bcb0a6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -44,12 +44,7 @@ before_script: - conda install -c conda-forge coveralls hydrotrend script: - - | - if [[ $TRAVIS_OS_NAME != "osx" ]]; then - nosetests --with-doctest --with-coverage --cover-package=dakotathon - else - nosetests --with-doctest - fi + - nosetests --with-doctest --with-coverage --cover-package=dakotathon after_success: - |