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Documentation #53

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merged 14 commits into from
Aug 28, 2020
Merged

Documentation #53

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405da18
beautify
BingqingCheng Aug 28, 2020
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fix conflict
BingqingCheng Aug 28, 2020
71f09a1
update docs
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update docstrings
BingqingCheng Aug 28, 2020
7723850
Merge remote-tracking branch 'origin' into documentation
BingqingCheng Aug 28, 2020
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update doc
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update doc
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update README
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update readme
BingqingCheng Aug 28, 2020
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added sample asap commands
BingqingCheng Aug 28, 2020
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small fix
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355 changes: 198 additions & 157 deletions asaplib/cli/cmd_asap.py
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89 changes: 54 additions & 35 deletions asaplib/cli/cmd_cli_options.py
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Original file line number Diff line number Diff line change
@@ -1,23 +1,27 @@
import click

from asaplib.io import ConvertStrToList


def state_input_options(f):
"""Create common options for I/O files"""
f = click.option('--in_file', '--in', '-i', type=click.Path('r'),
help='The state file that includes a dictionary-like specifications of descriptors to use.')(f)
return f


def file_input_options(f):
"""Create common options for I/O files"""
f = click.option('--fxyz', '-f',
type=str,
f = click.option('--fxyz', '-f',
type=str,
help='Input file that contains XYZ coordinates.\
See a list of possible input formats:\
https://wiki.fysik.dtu.dk/ase/ase/io/io.html\
If a wildcard * is used, all files matching the pattern is read.',
default=None)(f)
return f


def file_input_format_options(f):
"""Create common options for I/O files"""
f = click.option('--fxyz_format',
Expand All @@ -27,18 +31,21 @@ def file_input_format_options(f):
default=None)(f)
return f


def file_output_options(f):
"""Create common options for I/O files"""
f = click.option('--prefix', '-p',
help='Prefix to be used for the output file.',
default=None)(f)
return f


def dm_input_options(f):
"""common options for reading a design matrices, used for map, fit, kde, clustering, etc."""
f = click.option('--design_matrix', '-dm', cls=ConvertStrToList, default=[],
f = click.option('--design_matrix', '-dm', cls=ConvertStrToList, default='[*]',
help='Location of descriptor matrix file or name of the tags in ase xyz file\
the type is a list \'[dm1, dm2]\', as we can put together simutanously several design matrix.')(f)
the type is a list \'[dm1, dm2]\', as we can put together simutanously several design matrix.')(
f)
f = click.option('--use_atomic_descriptors', '--use_atomic', '-ua',
help='Use atomic descriptors instead of global ones.',
default=False, is_flag=True)(f)
Expand All @@ -48,12 +55,14 @@ def dm_input_options(f):
default=None)(f)
return f


def km_input_options(f):
"""common options for reading a kernel matrices, can be used for map, fit, kde, clustering, etc."""
f = click.option('--kernel_matrix', '-km', default='none',
help='Location of a kernel matrix file')(f)
return f


def output_setup_options(f):
"""Create common options for output results from clustering/KDE analysis"""
f = click.option('--savexyz/--no-savexyz',
Expand All @@ -64,57 +73,62 @@ def output_setup_options(f):
default=False)(f)
return f


def desc_options(f):
"""Create common options for computing descriptors"""
f = click.option('--tag',
help='Tag for the descriptors.',
default='cmd-desc')(f)
return f


def para_options(f):
"""Create common options for parallellization"""
f = click.option('--number_processes', '--nprocess', '-np', type=int,
help='Number of processes when compute the descriptors in parrallel.',
show_default=True, default=1)(f)
return f


def atomic_to_global_desc_options(f):
"""Create common options for global descriptors constructed based on atomic fingerprints """
f = click.option('--reducer_type', '-r',
help='type of operations to get global descriptors from the atomic soap vectors, e.g. \
[average], [sum], [moment_avg], [moment_sum].',
show_default=True, default='average', type=str)(f)
f = click.option('--zeta', '-z',
f = click.option('--zeta', '-z',
help='Moments to take when converting atomic descriptors to global ones.',
default=1, type=int)(f)
f = click.option('--element_wise', '-e',
f = click.option('--element_wise', '-e',
help='element-wise operation to get global descriptors from the atomic soap vectors',
show_default=True, default=False, is_flag=True)(f)
f = click.option('--peratom', '-pa',
help='Save the per-atom local descriptors.',
show_default=True, default=False, is_flag=True)(f)
return f


def map_setup_options(f):
"""Create common options for making 2D maps of the data set"""
f = click.option('--peratom',
f = click.option('--peratom',
help='Save the per-atom projection.',
default=False, is_flag=True)(f)
f = click.option('--adjusttext/--no-adjusttext',
f = click.option('--adjusttext/--no-adjusttext',
help='Adjust the annotation texts so they do not overlap.',
default=False)(f)
f = click.option('--annotate', '-a',
help='Location of tags to annotate the samples.',
default='none', type=str)(f)
f = click.option('--aspect_ratio', '-ar',
help='Aspect ratio of the plot',
show_default=True, default=2, type=float)(f)
help='Aspect ratio of the plot',
show_default=True, default=2, type=float)(f)
f = click.option('--style', '-s',
type=click.Choice(['default','journal'], case_sensitive=False),
help='Style of the plot.',
type=click.Choice(['default', 'journal'], case_sensitive=False),
help='Style of the plot.',
show_default=True, default='default')(f)
return f


def map_io_options(f):
"""Create common options for making 2D maps of the data set"""
f = click.option('--keepraw/--no-keepraw',
Expand All @@ -127,6 +141,7 @@ def map_io_options(f):
help='Additional properties to be read for each frmae in CSV format.')(f)
return f


def color_setup_options(f):
"""Create common options for handing color scales"""
f = click.option('--normalized_by_size', '-nbs',
Expand All @@ -150,30 +165,32 @@ def color_setup_options(f):
default='none', type=str)(f)
return f


def d_reduce_options(f):
"""Create common options for dimensionality reduction"""
f = click.option('--axes', nargs=2, type=click.Tuple([int, int]),
help='Plot the projection along which projection axes.',
default=[0,1])(f)
default=[0, 1])(f)
f = click.option('--dimension', '-d',
help='Number of the dimensions to keep in the output XYZ file.',
default=10)(f)
f = click.option('--scale/--no-scale',
f = click.option('--scale/--no-scale',
help='Standard scaling of the coordinates.',
default=True)(f)
return f


def fit_setup_options(f):
"""Create common options for making 2D maps of the data set"""
f = click.option('--lc_points', '-lcp', type=int,
help='the number of sub-samples to take when compute the learning curve',
show_default=True, default=8)(f)
f = click.option('--learning_curve', '-lc', type=int,
help='the number of points on the learning curve, <= 1 means no learning curve',
show_default=True, default=-1)(f)
f = click.option('--test_ratio', '--test', '-t', type=float,
help='Test ratio.',
show_default=True, default=0.05)(f)
f = click.option('--lc_points', '-lcp', type=int,
help='the number of sub-samples to take when compute the learning curve',
show_default=True, default=8)(f)
f = click.option('--learning_curve', '-lc', type=int,
help='the number of points on the learning curve, <= 1 means no learning curve',
show_default=True, default=-1)(f)
f = click.option('--test_ratio', '--test', '-t', type=float,
help='Test ratio.',
show_default=True, default=0.05)(f)
f = click.option('--normalized_by_size', '-nbs',
help='Normalize y by the number of atoms in each frame.',
show_default=True, default=False, is_flag=True)(f)
Expand All @@ -182,24 +199,26 @@ def fit_setup_options(f):
default='none', type=str)(f)
return f


def kernel_options(f):
"""Create common options for compute kernel functions"""
f = click.option('--kernel_parameter', '-kp', type=float,
help='Parameter used in the kernel function.',
default=None)(f)
f = click.option('--kernel_parameter', '-kp', type=float,
help='Parameter used in the kernel function.',
default=None)(f)
f = click.option('--kernel', '-k',
type=click.Choice(['linear', 'polynomial', 'cosine'], case_sensitive=False),
help='Kernel function for converting design matrix to kernel matrix.',
show_default=True, default='linear')(f)
type=click.Choice(['linear', 'polynomial', 'cosine'], case_sensitive=False),
help='Kernel function for converting design matrix to kernel matrix.',
show_default=True, default='linear')(f)
return f


def sparsification_options(f):
"""Create common options for sparsification"""
f = click.option('--n_sparse', '-n', type=int,
help='number of the representative samples, set negative if using no sparsification',
show_default=True, default=100)(f)
f = click.option('--n_sparse', '-n', type=int,
help='number of the representative samples, set negative if using no sparsification',
show_default=True, default=100)(f)
f = click.option('--sparse_mode', '-s',
type=click.Choice(['random', 'cur', 'fps', 'sequential'], case_sensitive=False),
help='Sparsification method to use.',
show_default=True, default='fps')(f)
type=click.Choice(['random', 'cur', 'fps', 'sequential'], case_sensitive=False),
help='Sparsification method to use.',
show_default=True, default='fps')(f)
return f
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