diff --git a/command_line.automatic_docs.html b/command_line.automatic_docs.html index 64c8a270..83a3059e 100644 --- a/command_line.automatic_docs.html +++ b/command_line.automatic_docs.html @@ -473,7 +473,7 @@

error
-cp, --config-properties <config_properties>#
-

Multiple Atoms.info calculated properties (to be prefixed by ref_property_prefix or calc_property_prefix) to compute error for. virial will be reconstructed from stress. Properties can end with /atom or /comp for different components being counted separately. Default of [“energy/atom”, “virial/atom/comp”]only used if neither config_properties nor atom_properties is present.

+

Multiple Atoms.info calculated properties (to be prefixed by ref_property_prefix or calc_property_prefix) to compute error for. virial will be reconstructed from stress. Properties can end with /atom or /comp for different components being counted separately. Default of [“energy/atom”, “virial/atom/comp”] only used if neither config_properties nor atom_properties is present.

diff --git a/genindex.html b/genindex.html index a2816833..0c1b3414 100644 --- a/genindex.html +++ b/genindex.html @@ -816,10 +816,10 @@

A

  • at_copy_save_results() (in module wfl.utils.at_copy_save_results)
    • - - + @@ -1475,8 +1487,12 @@

    R

    -
  • Module contents
    • +
  • Module contents +
    • @@ -449,7 +458,9 @@

    Submodules
    def autoparallelized_op(*args, **kwargs):
-    return autoparallelize(op, *args, default_autopara_info={"autoparallelize_keyword_param_1": val, "autoparallelize_keyword_param_2": val, ... }, **kwargs )
+    return autoparallelize(op, *args,
+        default_autopara_info={"autoparallelize_keyword_param_1": val, "autoparallelize_keyword_param_2": val, ... },
+        **kwargs )
 autoparallelized_op.doc = autopara_docstring(op.__doc__, "iterable_contents")
    @@ -465,7 +476,8 @@

    SubmodulesParameters

    • func (function) – function to wrap in _autoparallelize_ll()

      • -

    • *args (list) – positional arguments to func, plus optional first or first and second inputs (iterable) and outputs (OutputSpec) arguments to wrapped function

      • +

    • *args (list) – positional arguments to func, plus optional first or first and second inputs (iterable) and outputs (OutputSpec) arguments +to wrapped function

    • default_autopara_info (dict, default {}) – dict with default values for AutoparaInfo constructor keywords setting default autoparallelization info

    • **kwargs (dict) – keyword arguments to func, plus optional inputs (iterable), outputs (OutputSpec), and autopara_info (AutoparaInfo)

    @@ -571,7 +583,8 @@

    SubmodulesReturns -

    root_global_seed

    +

    root_global_seed – kwargs, or None if “autopara_rng_seed” is not in op’s signature

    Return type
    -

    int seed with value kwargs[“autopara_rng_seed”] or random int if value is None or not in kwargs, or None if “autopara_rng_seed” is not in op’s signature

    +

    int seed with value kwargs[“autopara_rng_seed”] or random int if value is None or not in

    @@ -677,6 +690,109 @@

    Submodules

    Module contents#

    +
    +
    +class wfl.autoparallelize.AutoparaInfo(**kwargs)#
    +

    Bases: object

    +

    Object containing information required to autoparallelize a function

    +
    +
    Parameters
    +
      +

    • num_inputs_per_python_subprocess (int, default 1) – number of inputs passed to each call of the low level operation.

      • +

    • iterable_arg (int / str, default 0) – index (int positional, str keyword) of input iterable argument in low level function

      • +

    • skip_failed (bool, default True) – skip output for failed low level function calls

      • +

    • initializer ((func, func_kwargs), default (None, [])) – initializer to be called when each python subprocess is started

      • +

    • num_python_subprocesses (int, default None) – number of python subprocesses

      • +

    • remote_info (RemoteInfo, default None) – information for running remotely

      • +

    • remote_label (str, default None) – string label to match to keys in remote_info dict

      • +
    +
    +
    +
    +
    +update_defaults(default_kwargs)#
    +

    Starting from object passed by user at runtime, update all unspecified fields to the defaults +specified when wrapping function, otherwise to class-wide defaults

    +
    + +
    + +
    +
    +class wfl.autoparallelize.RemoteInfo(sys_name, job_name, resources, num_inputs_per_queued_job=-100, pre_cmds=[], post_cmds=[], env_vars=[], input_files=[], output_files=[], header_extra=[], exact_fit=True, partial_node=False, timeout=3600, check_interval=30, ignore_failed_jobs=False, resubmit_killed_jobs=False, hash_ignore=[])#
    +

    Bases: object

    +

    Create a RemoteInfo object

    +
    +
    Parameters
    +
      +

    • sys_name (str) – name of system to run on

      • +

    • job_name (str) – name for job (unique within this project)

      • +

    • resources (dict or Resources) – expyre.resources.Resources or kwargs for its constructor

      • +

    • num_inputs_per_queued_job (int, default -100) – num_inputs_per_python_subprocess for each job. If negative will be multiplied by iterable_autopara_wrappable +num_inputs_per_python_subprocess

      • +

    • pre_cmds (list(str)) – commands to run before starting job

      • +

    • post_cmds (list(str)) – commands to run after finishing job

      • +

    • env_vars (list(str)) – environment variables to set before starting job

      • +

    • input_files (list(str)) – input_files to stage in starting job

      • +

    • output_files (list(str)) – output_files to stage out when job is done

      • +

    • header_extra (list(str), optional) – extra lines to add to queuing system header

      • +

    • exact_fit (bool, default True) – require exact fit to node size

      • +

    • partial_node (bool, default True) – allow jobs that take less than a whole node, overrides exact_fit

      • +

    • timeout (int) – time to wait in get_results before giving up

      • +

    • check_interval (int) – check_interval arg to pass to get_results

      • +

    • ignore_failed_jobs (bool, default False) – skip failures in remote jobs

      • +

    • resubmit_killed_jobs (bool, default False) – resubmit jobs that were killed without an exit status (out of walltime or crashed), +hoping that other parameters such as walltime or memory have been changed to make run complete this time

      • +

    • hash_ignore (list(str), default []) – list of arguments to ignore when doing hash of remote function arguments to determine if it’s already been done

      • +
    +
    +
    +
    + +
    +
    +wfl.autoparallelize.autoparallelize(func, *args, default_autopara_info={}, **kwargs)#
    +

    autoparallelize a function

    +

    Use by defining function “op” which takes an input iterable and returns list of configs, and _after_ do

    +
    def autoparallelized_op(*args, **kwargs):
+    return autoparallelize(op, *args,
+        default_autopara_info={"autoparallelize_keyword_param_1": val, "autoparallelize_keyword_param_2": val, ... },
+        **kwargs )
+autoparallelized_op.doc = autopara_docstring(op.__doc__, "iterable_contents")
+
    +
    +

    The autoparallelized function can then be called with

    +
    parallelized_op(inputs, outputs, [args of op], autopara_info=AutoparaInfo(arg1=val1, ...), [kwargs of op])
+
    +
    +

    If the op takes the argument autopara_per_item_info a list of dicts with info for each item will be +passed, currently including rng_seed and item_i.

    +

    If op takes the argument autopara_rng_seed it will be used as a global seed to generate the per-item seeds +from.

    +
    +
    Parameters
    +
      +

    • func (function) – function to wrap in _autoparallelize_ll()

      • +

    • *args (list) – positional arguments to func, plus optional first or first and second inputs (iterable) and outputs (OutputSpec) arguments +to wrapped function

      • +

    • default_autopara_info (dict, default {}) – dict with default values for AutoparaInfo constructor keywords setting default autoparallelization info

      • +

    • **kwargs (dict) – keyword arguments to func, plus optional inputs (iterable), outputs (OutputSpec), and autopara_info (AutoparaInfo)

      • +
    +
    +
    Returns
    +

    wrapped_func_out

    +
    +
    Return type
    +

    results of calling the function wrapped in autoparallelize via _autoparallelize_ll

    +
    +
    +
    + +
    +
    +wfl.autoparallelize.autoparallelize_docstring(wrapped_func, wrappable_func, input_iterable_type, input_arg=0)#
    +
    + @@ -761,7 +877,16 @@

    Submodulesset_autopara_per_item_info() -
  • Module contents
    • +
  • Module contents +
    • diff --git a/wfl.calculators.html b/wfl.calculators.html index 978e9839..888f3daf 100644 --- a/wfl.calculators.html +++ b/wfl.calculators.html @@ -767,7 +767,8 @@

    Parameter: class wfl.calculators.mopac.MOPAC(keep_files='default', rundir_prefix='run_MOPAC_', workdir=None, scratchdir=None, calculator_exec=None, **kwargs)#

    Bases: WFLFileIOCalculator, MOPAC

    -

    Extension of ASE’s MOPAC claculator so that it can be used by wfl.calculators.generic (mainly each calculation is run in a separate directory)

    +

    Extension of ASE’s MOPAC claculator so that it can be used by wfl.calculators.generic (mainly each +calculation is run in a separate directory)

    calculate(atoms=None, properties=['energy', 'forces'], system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])#
    diff --git a/wfl.fit.html b/wfl.fit.html index 9c9230f6..918ee489 100644 --- a/wfl.fit.html +++ b/wfl.fit.html @@ -488,7 +488,7 @@

    Submoduleswfl.autoparallelize.RemoteInfo, or ‘_IGNORE’ or None) – If present and not None and not ‘_IGNORE’, RemoteInfo or dict with kwargs for RemoteInfo +

  • remote_info (dict or wfl.autoparallelize.RemoteInfo, or ‘_IGNORE’ or None) – If present and not None and not ‘_IGNORE’, RemoteInfo or dict with kwargs for RemoteInfo constructor which triggers running job in separately queued job on remote machine. If None, will try to use env var WFL_EXPYRE_INFO used (see above). ‘_IGNORE’ is for internal use, to ensure that remotely running job does not itself attempt to spawn another @@ -573,7 +573,7 @@

    Submoduleswfl.autoparallelize.RemoteInfo, or ‘_IGNORE’ or None) – If present and not None and not ‘_IGNORE’, RemoteInfo or dict with kwargs for RemoteInfo +

  • remote_info (dict or wfl.autoparallelize.RemoteInfo, or ‘_IGNORE’ or None) – If present and not None and not ‘_IGNORE’, RemoteInfo or dict with kwargs for RemoteInfo constructor which triggers running job in separately queued job on remote machine. If None, will try to use env var WFL_EXPYRE_INFO used (see below). ‘_IGNORE’ is for internal use, to ensure that remotely running job does not itself attempt to spawn another @@ -742,15 +742,15 @@

    Submodules
    Parameters
      -

    • fitting_configs (ConfigSet) – set of configurations to fit

      • +

    • fitting_configs (ConfigSet) – set of configurations to fit (mace param “train_file”)

    • mace_name (str) – name of MACE label

    • mace_fit_params (dict) – parameters for fitting a MACE model.

    • mace_fit_cmd (str, default None.) – command for excecuting the MACE fitting. (For example, “python ~/path_to_mace_cripts/run_train.py”) Alternatively set by WFL_MACE_FIT_COMMAND env var.

      • -

    • ref_property_prefix (str, default "REF_") – string prefix added to atoms.info/arrays keys (energy, forces, virial, stress)

      • +

    • ref_property_prefix (str, default “REF_”) – string prefix added to atoms.info/arrays keys (energy, forces, virial, stress)

    • prev_checkpoint_file (str, default None) – Previous checkpoint file to restart from.

      • -

    • valid_configs (ConfigSet, default None) – set of configurations to validate (“valid_file”)

      • -

    • test_configs (ConfigSet, default None) – set of configurtions to test (“test_file”)

      • +

    • valid_configs (ConfigSet, default None) – set of configurations to validate (mace param “valid_file”)

      • +

    • test_configs (ConfigSet, default None) – set of configurtions to test (mace param “test_file”)

    • skip_if_present (bool, default True) – skip if final MACE file exists in expected place

    • run_dir (str, default '.') – directory to run fitting in

    • verbose (bool default True) – verbose output

      • diff --git a/wfl.generate.html b/wfl.generate.html index 29f94a02..5c109a7b 100644 --- a/wfl.generate.html +++ b/wfl.generate.html @@ -957,7 +957,8 @@

      SubmodulesOutputSpec or None) – where to write output atomic configs, or None for no output (i.e. only side-effects)

    • calculator (Calculator / (initializer, args, kwargs)) – ASE calculator or routine to call to create calculator

      • -

    • dt (float) –

      time step (fs) -integrator: str, default “NVTBerendsen”

      -
      -

      Select integrator. Default is Berendsen but also langevin can be used

      -
      -

      • +

    • dt (float) – time step (fs)

      • +

    • integrator (str, default "NVTBerendsen") – Select integrator. Default is Berendsen but also langevin can be used

    • steps (int) – number of steps

    • temperature (float or (float, float, [int]]), or list of dicts default None) – temperature control (Kelvin) - float: constant T diff --git a/wfl.html b/wfl.html index 08e89bf8..6cd2ad2f 100644 --- a/wfl.html +++ b/wfl.html @@ -442,7 +442,16 @@

      Subpackagesset_autopara_per_item_info()

    • -
  • Module contents
    • +
  • Module contents +

  • wfl.calculators package