parameters.yaml.bak

# //////////////////////////////////////////////////////////////////////////////
#
#                        SeisFlows YAML Parameter File
#
# //////////////////////////////////////////////////////////////////////////////
#
# Modules correspond to the structure of the source code, and determine
# SeisFlows' behavior at runtime. Each module requires its own sub-parameters.
#
# .. rubric::
#   - Determine available options for modules by running:
#       > seisflows print modules
#   - Auto-fill with docstrings and default values (recommended) by running:
#       > seisflows configure
#   - Swap out module parameters for a configured parameter file by running:
#       > seisflows swap {module} {name} (e.g., seisflows swap solver specfem3d)
#   - To set values as NoneType, use: null
#   - To set values as infinity, use: inf
#
#                                    MODULES
#                                    ///////
# workflow (str):    The types and order of functions for running SeisFlows
# system (str):      Computer architecture of the system being used
# solver (str):      External numerical solver to use for waveform simulations
# preprocess (str):  Preprocessing schema for waveform data
# optimize (str):    Optimization algorithm for the inverse problem
# ==============================================================================
workflow: inversion
system: workstation
solver: specfem2d
preprocess: pyaflowa
optimize: LBFGS
# =============================================================================
#
#    Forward Workflow
#    ----------------
#    Defines foundational structure for Workflow module. When used standalone 
#    is in charge of running forward solver in parallel and (optionally) 
#    calculating data-synthetic misfit and adjoint sources.
#
#    Parameters
#    ----------
#    :type modules: list of module
#    :param modules: instantiated SeisFlows modules which should have been
#        generated by the function `seisflows.config.import_seisflows` with a
#        parameter file generated by seisflows.configure
#    :type data_case: str
#    :param data_case: How to address 'data' in the workflow, available options:
#        'data': real data will be provided by the user in
#        `path_data/{source_name}` in the same format that the solver will
#        produce synthetics (controlled by `solver.format`) OR
#        synthetic': 'data' will be generated as synthetic seismograms using
#        a target model provided in `path_model_true`. If None, workflow will
#        not attempt to generate data.
#    :type stop_after: str
#    :param stop_after: optional name of task in task list (use
#        `seisflows print tasks` to get task list for given workflow) to stop
#        workflow after, allowing user to prematurely stop a workflow to explore
#        intermediate results or debug.
#    :type export_traces: bool
#    :param export_traces: export all waveforms that are generated by the
#        external solver to `path_output`. If False, solver traces stored in
#        scratch may be discarded at any time in the workflow
#    :type export_residuals: bool
#    :param export_residuals: export all residuals (data-synthetic misfit) that
#        are generated by the external solver to `path_output`. If False,
#        residuals stored in scratch may be discarded at any time in the 
#        workflow
#
#        
#    Migration Workflow
#    ------------------
#    Run forward and adjoint solver to produce event-dependent misfit kernels.
#    Sum and postprocess kernels to produce gradient. In seismic exploration
#    this is 'reverse time migration'.
#
#    Parameters
#    ----------
#    :type export_gradient: bool
#    :param export_gradient: export the gradient after it has been generated
#        in the scratch directory. If False, gradient can be discarded from
#        scratch at any time in the workflow
#    :type export_kernels: bool
#    :param export_kernels: export each sources event kernels after they have
#        been generated in the scratch directory. If False, gradient can be
#        discarded from scratch at any time in the workflow
#
#        
#    Inversion Workflow
#    ------------------
#    Peforms iterative nonlinear inversion using the machinery of the Forward
#    and Migration workflows, as well as a built-in optimization library.
#
#    Parameters
#    ----------
#    :type start: int
#    :param start: start inversion workflow at this iteration. 1 <= start <= inf
#    :type end: int
#    :param end: end inversion workflow at this iteration. start <= end <= inf
#    :type iteration: int
#    :param iteration: The current iteration of the workflow. If NoneType, takes
#        the value of `start` (i.e., first iteration of the workflow). User can
#        also set between `start` and `end` to resume a failed workflow.
#    :type thrifty: bool
#    :param thrifty: a thrifty inversion skips the costly intialization step
#        (i.e., forward simulations and misfit quantification) if the final
#        forward simulations from the previous iterations line search can be
#        used in the current one. Requires L-BFGS optimization.
#    :type export_model: bool
#    :param export_model: export best-fitting model from the line search to disk.
#        If False, new models can be discarded from scratch at any time.
#
#        
# =============================================================================
data_case: synthetic
stop_after: null
export_traces: False
export_residuals: False
export_gradient: True
export_kernels: False
start: 1
end: 30
export_model: True
thrifty: False
iteration: 1
# =============================================================================
#
#    Workstation System
#    ------------------
#    Defines foundational structure for System module. When used standalone,
#    runs solver tasks either in serial (if `nproc`==1; i.e., without MPI) or in
#    parallel (if `nproc`>1; i.e., with MPI). All other tasks are run in serial.
#
#    Parameters
#    ----------
#    :type ntask: int
#    :param ntask: number of individual tasks/events to run during workflow.
#        Must be <= the number of source files in `path_specfem_data`
#    :type nproc: int
#    :param nproc: number of processors to use for each simulation. Choose 1 for
#        serial simulations, and `nproc`>1 for parallel simulations.
#    :type mpiexec: str
#    :param mpiexec: MPI executable on system. Defaults to 'mpirun -n ${NPROC}'
#    :type log_level: str
#    :param log_level: logger level to pass to logging module.
#        Available: 'debug', 'info', 'warning', 'critical'
#    :type verbose: bool
#    :param verbose: if True, formats the log messages to include the file
#        name, line number and message type. Useful for debugging but
#        also very verbose.
#
#        
# =============================================================================
ntask: 10
nproc: 4
mpiexec: mpirun
log_level: DEBUG
verbose: False
# =============================================================================
#
#    Solver SPECFEM
#    --------------
#    Defines foundational structure for Specfem-based solver module. 
#    Generalized SPECFEM interface to manipulate SPECFEM2D/3D/3D_GLOBE w/ Python
#
#    Parameters
#    ----------
#    :type data_format: str
#    :param data_format: data format for reading traces into memory.
#        Available: ['SU': seismic unix format, 'ASCII': human-readable ascii]
#    :type materials: str
#    :param materials: Material parameters used to define model. Available:
#        ['ELASTIC': Vp, Vs, 'ACOUSTIC': Vp, 'ISOTROPIC', 'ANISOTROPIC']
#    :type density: bool
#    :param density: How to treat density during inversion. If True, updates
#        density during inversion. If False, keeps it constant.
#        TODO allow density scaling during an inversion
#    :type attenuation: bool
#    :param attenuation: How to treat attenuation during inversion.
#        if True, turns on attenuation during forward simulations only. If
#        False, attenuation is always set to False. Requires underlying
#        attenution (Q_mu, Q_kappa) model
#    :type smooth_h: float
#    :param smooth_h: Gaussian half-width for horizontal smoothing in units
#        of meters. If 0., no smoothing applied. Only applicable for workflows:
#        ['migration', 'inversion'], ignored for 'forward' workflow.
#    :type smooth_h: float
#    :param smooth_v: Gaussian half-width for vertical smoothing in units
#        of meters. Only applicable for workflows: ['migration', 'inversion'],
#        ignored for 'forward' workflow.
#    :type components: str
#    :param components: components to consider and tag data with. Should be
#        string of letters such as 'RTZ'
#    :type solver_io: str
#    :param solver_io: format of model/kernel/gradient files expected by the
#        numerical solver. Available: ['fortran_binary': default .bin files].
#        TODO: ['adios': ADIOS formatted files]
#    :type source_prefix: str
#    :param source_prefix: prefix of source/event/earthquake files. If None,
#        will attempt to guess based on the specific solver chosen.
#    :type mpiexec: str
#    :param mpiexec: MPI executable used to run parallel processes. Should also
#        be defined for the system module
#
#        
#    Solver SPECFEM2D
#    ----------------
#    SPECFEM2D-specific alterations to the base SPECFEM module
#
#    Parameters
#    ----------
#    :type source_prefix: str
#    :param source_prefix: Prefix of source files in path SPECFEM_DATA. Defaults
#        to 'SOURCE'
#    :type multiples: bool
#    :param multiples: set an absorbing top-boundary condition
#
#        
# =============================================================================
data_format: ascii
materials: elastic
density: False
attenuation: False
smooth_h: 5000.0
smooth_v: 5000.0
components: XZ
source_prefix: SOURCE
multiples: False
# =============================================================================
#
#    Pyaflowa Preprocess
#    -------------------
#    Preprocessing and misfit quantification using Python's Adjoint Tomography
#    Operations Assistance (Pyatoa)
#
#    Parameters
#    ----------
#    :type min_period: float
#    :param min_period: Minimum filter corner in unit seconds. Bandpass
#    filter if set with `max_period`, highpass filter if set without
#    `max_period`, no filtering if not set and `max_period also not set
#    :type max_period: float
#    :param max_period: Maximum filter corner in unit seconds. Bandpass
#        filter if set with `min_period`, lowpass filter if set without
#        `min_period`, no filtering if not set and `min_period also not set
#   :type filter_corners: int
#    :param filter_corners: number of filter corners applied to filtering
#    :type client: str
#    :param client: Client name for ObsPy FDSN data gathering. Pyatoa will
#        attempt to collect waveform and metadata based on network and
#        station codes provided in the SPECFEM STATIONS file. If set None,
#        no FDSN gathering will be attempted
#    :type rotate: bool
#    :param rotate: Attempt to rotate waveform components from NEZ -> RTZ
#    :type pyflex_preset: str
#    :param pyflex_preset: Parameter map for misfit window configuration
#        defined by Pyflex. IF None, misfit and adjoint sources will be
#        calculated on whole traces. For available choices, see Pyatoa docs
#        page (pyatoa.rtfd.io)
#    :type fix_windows: bool or str
#    :param fix_windows: How to address misfit window evaluation at each
#        evaluation. Options to re-use misfit windows collected during an
#        inversion, available options:
#        [True, False, 'ITER', 'ONCE']
#        True: Re-use windows after first evaluation (i01s00);
#        False: Calculate new windows each evaluation;
#        'ITER': Calculate new windows at first evaluation of
#        each iteration (e.g., i01s00... i02s00...
#        'ONCE': Calculate new windows at first evaluation of
#        the workflow, i.e., at self.par.BEGIN
#    :type adj_src_type: str
#    :param adj_src_type: Adjoint source type to evaluate misfit, defined by
#        Pyadjoint. Currently available options: ['cc': cross-correlation,
#        'mt': multitaper, 'wav': waveform']
#    :type plot: bool
#    :param plot: plot waveform figures and source receiver maps during
#        the preprocessing stage
#    :type pyatoa_log_level: str
#    :param pyatoa_log_level: Log level to set Pyatoa, Pyflex, Pyadjoint.
#        Available: ['null': no logging, 'warning': warnings only,
#        'info': task tracking, 'debug': log all small details (recommended)]
#    :type unit_output: str
#    :param unit_output: Data units. Must match the synthetic output of
#        external solver. Available: ['DISP': displacement, 'VEL': velocity,
#        'ACC': acceleration]
#    :type export_datasets: bool
#    :param export_datasets: periodically save the output ASDFDataSets which
#        contain data, metadata and results collected during the
#        preprocessing procedure
#    :type export_figures: bool
#    :param export_figures: periodically save the output basemaps and
#        data-synthetic waveform comparison figures
#    :type export_log_files: bool
#    :param export_log_files: periodically save log files created by Pyatoa
#
#        
# =============================================================================
min_period: 10.0
max_period: 200.0
filter_corners: 4
client: null
rotate: False
pyflex_preset: null
fix_windows: False
adj_src_type: cc
plot: True
pyatoa_log_level: DEBUG
unit_output: DISP
max_workers: null
export_datasets: True
export_figures: True
export_log_files: True
# =============================================================================
#
#    Gradient Optimization
#    ---------------------
#    Defines foundational structure for Optimization module. Applies a 
#    gradient/steepest descent optimization algorithm.
#
#    Parameters
#    ----------
#    :type line_search_method: str
#    :param line_search_method: chosen line_search algorithm. Currently available
#        are 'bracket' and 'backtrack'. See seisflows.plugins.line_search
#        for all available options
#    :type preconditioner: str
#    :param preconditioner: algorithm for preconditioning gradients. Currently
#        available: 'diagonal'. Requires `path_preconditioner` to point to a
#        set of files that define the preconditioner, formatted the same as the
#        input model
#    :type step_count_max: int
#    :param step_count_max: maximum number of trial steps to perform during
#        the line search before a change in line search behavior is
#        considered, or a line search is considered to have failed.
#    :type step_len_init: float
#    :param step_len_init: initial line search step length guess, provided
#        as a fraction of current model parameters.
#    :type step_len_max: float
#    :param step_len_max: maximum allowable step length during the line
#        search. Set as a fraction of the current model parameters
#
#        
#    L-BFGS Optimization
#    -------------------
#    Limited memory BFGS nonlienar optimization algorithm
#
#    Parameters
#    ----------
#    :type lbfgs_mem: int
#    :param lbfgs_mem: L-BFGS memory. Max number of previous gradients to
#        retain in local memory for approximating the objective function.
#    :type lbfgs_max: L-BFGS periodic restart interval. Must be
#        1 <= lbfgs_max <= infinity.
#    :type lbfgs_thresh: L-BFGS angle restart threshold. If the angle between
#        the current and previous search direction exceeds this value,
#        optimization algorithm will be restarted.
#
#        
# =============================================================================
preconditioner: null
step_count_max: 5
step_len_init: 0.05
step_len_max: 0.5
line_search_method: Backtrack
LBFGS_mem: 3
LBFGS_max: inf
LBFGS_thresh: 0.0
# =============================================================================
#
#	 Paths
#	 -----
#    :type workdir: str
#    :param workdir: working directory in which to perform a SeisFlows workflow.
#        SeisFlows internal directory structure will be created here. Default cwd
#    :type path_output: str
#    :param path_output: path to directory used for permanent storage on disk.
#        Results and exported scratch files are saved here.
#    :type path_data: str
#    :param path_data: path to any externally stored data required by the solver
#    :type path_state_file: str
#    :param path_state_file: path to a text file used to track the current
#        status of a workflow (i.e., what functions have already been completed),
#        used for checkpointing and resuming workflows
#    :type path_model_init: str
#    :param path_model_init: path to the starting model used to calculate the
#        initial misfit. Must match the expected `solver_io` format.
#    :type path_model_true: str
#    :param path_model_true: path to a target model if `case`=='synthetic' and
#        a set of synthetic 'observations' are required for workflow.
#    :type path_eval_grad: str
#    :param path_eval_grad: scratch path to store files for gradient evaluation,
#        including models, kernels, gradient and residuals.
#        :type path_mask: str
#    :param path_mask: optional path to a masking function which is used to
#        mask out or scale parts of the gradient. The user-defined mask must
#        match the file format of the input model (e.g., .bin files).
#        :type path_eval_func: str
#    :param path_eval_func: scratch path to store files for line search objective
#        function evaluations, including models, misfit and residuals
#        
#    :type path_output_log: str
#    :param path_output_log: path to a text file used to store the outputs of
#        the package wide logger, which are also written to stdout
#    :type path_par_file: str
#    :param path_par_file: path to parameter file which is used to instantiate
#        the package
#    :type path_log_files: str
#    :param path_log_files: path to a directory where individual log files are
#        saved whenever a number of parallel tasks are run on the system.
#        
#    :type path_data: str
#    :param path_data: path to any externally stored data required by the solver
#    :type path_specfem_bin: str
#    :param path_specfem_bin: path to SPECFEM bin/ directory which
#        contains binary executables for running SPECFEM
#    :type path_specfem_data: str
#    :param path_specfem_data: path to SPECFEM DATA/ directory which must
#        contain the CMTSOLUTION, STATIONS and Par_file files used for
#        running SPECFEM
#            
#    :type path_preprocess: str
#    :param path_preprocess: scratch path for preprocessing related steps
#        
#    :type path_preconditioner: str
#    :param path_preconditioner: optional path to a set of preconditioner files
#        formatted the same as the input model (or output model of solver).
#        Required to exist and contain files if `preconditioner`==True
#            
# =============================================================================
path_workdir: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3
path_scratch: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/scratch
path_eval_grad: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/scratch/eval_grad
path_output: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/output
path_model_init: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/specfem2d_workdir/OUTPUT_FILES_INIT
path_model_true: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/specfem2d_workdir/OUTPUT_FILES_TRUE
path_state_file: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/sfstate.txt
path_data: null
path_mask: null
path_eval_func: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/scratch/eval_func
path_par_file: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/parameters.yaml
path_log_files: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/logs
path_output_log: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/sflog.txt
path_specfem_bin: /home/zhangzhiyu/MyProjects/Seisflows/specfem2d/bin
path_specfem_data: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/specfem2d_workdir/DATA
path_solver: /home/zhangzhiyu/MyProjects/Seisflows/work/day_3/3/scratch/solver
path_preconditioner: null