From f84a60b349f98e7885cd676e4fee3d5d73dd77f4 Mon Sep 17 00:00:00 2001 From: Johannes Steinmetzer Date: Thu, 24 May 2018 13:16:47 +0200 Subject: [PATCH] expanded the documenatation --- README.md | 45 ------ docs/api/pysisyphus.calculators.rst | 174 ++++++++++++++++++++++ docs/api/pysisyphus.cos.rst | 54 +++++++ docs/api/pysisyphus.irc.rst | 78 ++++++++++ docs/api/pysisyphus.optimizers.rst | 94 ++++++++++++ docs/api/pysisyphus.plotters.rst | 30 ++++ docs/calculators.rst | 66 ++++++++ docs/conf.py | 30 +++- docs/examples.rst | 12 ++ docs/examples/test_g16_newargs.yaml | 13 ++ docs/index.rst | 19 ++- docs/installation.rst | 64 ++++++++ docs/optimizers.rst | 58 ++++++++ docs/pysisyphus.rst | 137 +++++++++++++++++ pysisyphus/calculators/Calculator.py | 26 ++++ pysisyphus/cos/NoSpringNeb.py | 2 +- pysisyphus/cos/OldTangentChainOfStates.py | 2 +- setup.py | 1 - 18 files changed, 847 insertions(+), 58 deletions(-) create mode 100644 docs/api/pysisyphus.calculators.rst create mode 100644 docs/api/pysisyphus.cos.rst create mode 100644 docs/api/pysisyphus.irc.rst create mode 100644 docs/api/pysisyphus.optimizers.rst create mode 100644 docs/api/pysisyphus.plotters.rst create mode 100644 docs/calculators.rst create mode 100644 docs/examples.rst create mode 100644 docs/examples/test_g16_newargs.yaml create mode 100644 docs/installation.rst create mode 100644 docs/optimizers.rst create mode 100644 docs/pysisyphus.rst diff --git a/README.md b/README.md index 1c2834f0aa..d5f487572e 100644 --- a/README.md +++ b/README.md @@ -3,51 +3,6 @@ pysisphus implements Chain Of States (COS) methods like Nudged Elastic Band (NEB **This software is still work in progress and shouldn't be used for production runs. Use at your own risk.** -## Dependencies - - python3.6+ - scipy - numpy - matplotlib - pytest - natsort - pyyaml - -Usage of pysisyphus within the **anaconda** distribution is recommended. - -## Installation -### Install the code -The **recommended way**, as the version on pypi may be outdated: - - cd [root dir where you want to keep pysisyphus] - git clone https://github.com/eljost/pysisyphus - cd pysisyphus - python setup.py develop - -or **(not recommended)**: - - pip install pysisyphus - -### Tell pysisyphus how to call your calculators -Create a file called `.pysisyphusrc` in your $HOME-directory containing the commands the call your installed calculators, e.g.: - - [orca] - cmd=/scratch/programme/orca-4.0.1.2/orca - - [xtb] - cmd=xtb - - [openmolcas] - cmd=pymolcas - - [gaussian09] - cmd=/usr/local/gaussian/g09/g09 - - [wfoverlap] - cmd=/scratch/wfoverlap_1.0/bin/wfoverlap.x - -When the specified path is not absolute but relative (as in the example config for xtb and openmolcas) the corresponding binaries have to be available on the $PATH! The **Turbomole** binaries are hardcoded and don't have to be specified here. - ## Usage pysisyphus provides three hooks that can be called from the shell (command line). The available commandas can be queried with the `-h` or `--help` arguments: diff --git a/docs/api/pysisyphus.calculators.rst b/docs/api/pysisyphus.calculators.rst new file mode 100644 index 0000000000..108e1f846b --- /dev/null +++ b/docs/api/pysisyphus.calculators.rst @@ -0,0 +1,174 @@ +pysisyphus.calculators package +============================== + +Submodules +---------- + +pysisyphus.calculators.AnaPot module +------------------------------------ + +.. automodule:: pysisyphus.calculators.AnaPot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPot2 module +------------------------------------- + +.. automodule:: pysisyphus.calculators.AnaPot2 + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPot2D module +-------------------------------------- + +.. automodule:: pysisyphus.calculators.AnaPot2D + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPot3 module +------------------------------------- + +.. automodule:: pysisyphus.calculators.AnaPot3 + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPot4 module +------------------------------------- + +.. automodule:: pysisyphus.calculators.AnaPot4 + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPotBase module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.AnaPotBase + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.AnaPotBase2D module +------------------------------------------ + +.. automodule:: pysisyphus.calculators.AnaPotBase2D + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.Calculator module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.Calculator + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.Gaussian09 module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.Gaussian09 + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.Gaussian16 module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.Gaussian16 + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.IDPP module +---------------------------------- + +.. automodule:: pysisyphus.calculators.IDPP + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.MullerBrownPot module +-------------------------------------------- + +.. automodule:: pysisyphus.calculators.MullerBrownPot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.MullerBrownSympyPot module +------------------------------------------------- + +.. automodule:: pysisyphus.calculators.MullerBrownSympyPot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.MullerBrownSympyPot2D module +--------------------------------------------------- + +.. automodule:: pysisyphus.calculators.MullerBrownSympyPot2D + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.ORCA module +---------------------------------- + +.. automodule:: pysisyphus.calculators.ORCA + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.OpenMolcas module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.OpenMolcas + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.Turbomole module +--------------------------------------- + +.. automodule:: pysisyphus.calculators.Turbomole + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.WFOWrapper module +---------------------------------------- + +.. automodule:: pysisyphus.calculators.WFOWrapper + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.XTB module +--------------------------------- + +.. automodule:: pysisyphus.calculators.XTB + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.calculators.parser module +------------------------------------ + +.. automodule:: pysisyphus.calculators.parser + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus.calculators + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/pysisyphus.cos.rst b/docs/api/pysisyphus.cos.rst new file mode 100644 index 0000000000..ddf893c7c3 --- /dev/null +++ b/docs/api/pysisyphus.cos.rst @@ -0,0 +1,54 @@ +pysisyphus.cos package +====================== + +Submodules +---------- + +pysisyphus.cos.ChainOfStates module +----------------------------------- + +.. automodule:: pysisyphus.cos.ChainOfStates + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.cos.NEB module +------------------------- + +.. automodule:: pysisyphus.cos.NEB + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.cos.NoSpringNeb module +--------------------------------- + +.. automodule:: pysisyphus.cos.NoSpringNeb + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.cos.OldTangentChainOfStates module +--------------------------------------------- + +.. automodule:: pysisyphus.cos.OldTangentChainOfStates + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.cos.SimpleZTS module +------------------------------- + +.. automodule:: pysisyphus.cos.SimpleZTS + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus.cos + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/pysisyphus.irc.rst b/docs/api/pysisyphus.irc.rst new file mode 100644 index 0000000000..605fdf7709 --- /dev/null +++ b/docs/api/pysisyphus.irc.rst @@ -0,0 +1,78 @@ +pysisyphus.irc package +====================== + +Submodules +---------- + +pysisyphus.irc.DampedVelocityVerlet module +------------------------------------------ + +.. automodule:: pysisyphus.irc.DampedVelocityVerlet + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.Euler module +--------------------------- + +.. automodule:: pysisyphus.irc.Euler + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.GonzalesSchlegel module +-------------------------------------- + +.. automodule:: pysisyphus.irc.GonzalesSchlegel + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.GonzalesSchlegelFail module +------------------------------------------ + +.. automodule:: pysisyphus.irc.GonzalesSchlegelFail + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.IMKMod module +---------------------------- + +.. automodule:: pysisyphus.irc.IMKMod + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.IRC module +------------------------- + +.. automodule:: pysisyphus.irc.IRC + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.ParamPlot module +------------------------------- + +.. automodule:: pysisyphus.irc.ParamPlot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.irc.PlotAnaPot module +-------------------------------- + +.. automodule:: pysisyphus.irc.PlotAnaPot + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus.irc + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/pysisyphus.optimizers.rst b/docs/api/pysisyphus.optimizers.rst new file mode 100644 index 0000000000..2eb21ce0a4 --- /dev/null +++ b/docs/api/pysisyphus.optimizers.rst @@ -0,0 +1,94 @@ +pysisyphus.optimizers package +============================= + +Submodules +---------- + +pysisyphus.optimizers.BFGS module +--------------------------------- + +.. automodule:: pysisyphus.optimizers.BFGS + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.BacktrackingOptimizer module +-------------------------------------------------- + +.. automodule:: pysisyphus.optimizers.BacktrackingOptimizer + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.ConjugateGradient module +---------------------------------------------- + +.. automodule:: pysisyphus.optimizers.ConjugateGradient + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.FIRE module +--------------------------------- + +.. automodule:: pysisyphus.optimizers.FIRE + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.NaiveSteepestDescent module +------------------------------------------------- + +.. automodule:: pysisyphus.optimizers.NaiveSteepestDescent + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.Optimizer module +-------------------------------------- + +.. automodule:: pysisyphus.optimizers.Optimizer + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.QuickMin module +------------------------------------- + +.. automodule:: pysisyphus.optimizers.QuickMin + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.RFOptimizer module +---------------------------------------- + +.. automodule:: pysisyphus.optimizers.RFOptimizer + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.SciPyOptimizer module +------------------------------------------- + +.. automodule:: pysisyphus.optimizers.SciPyOptimizer + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.optimizers.SteepestDescent module +-------------------------------------------- + +.. automodule:: pysisyphus.optimizers.SteepestDescent + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus.optimizers + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/pysisyphus.plotters.rst b/docs/api/pysisyphus.plotters.rst new file mode 100644 index 0000000000..076aaaccc4 --- /dev/null +++ b/docs/api/pysisyphus.plotters.rst @@ -0,0 +1,30 @@ +pysisyphus.plotters package +=========================== + +Submodules +---------- + +pysisyphus.plotters.AnimPlot module +----------------------------------- + +.. automodule:: pysisyphus.plotters.AnimPlot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.plotters.RFOPlotter module +------------------------------------- + +.. automodule:: pysisyphus.plotters.RFOPlotter + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus.plotters + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/calculators.rst b/docs/calculators.rst new file mode 100644 index 0000000000..4b07e22fba --- /dev/null +++ b/docs/calculators.rst @@ -0,0 +1,66 @@ +Calculators +============================== + +Gaussian16 +---------------------------------------- + +.. automodule:: pysisyphus.calculators.Gaussian16 + :members: + :undoc-members: + :show-inheritance: + +Gaussian09 +---------------------------------------- + +.. automodule:: pysisyphus.calculators.Gaussian09 + :members: + :undoc-members: + :show-inheritance: + +IDPP +---------------------------------- + +.. automodule:: pysisyphus.calculators.IDPP + :members: + :undoc-members: + :show-inheritance: + +ORCA 4 +---------------------------------- + +.. automodule:: pysisyphus.calculators.ORCA + :members: + :undoc-members: + :show-inheritance: + +OpenMolcas +---------------------------------------- + +.. automodule:: pysisyphus.calculators.OpenMolcas + :members: + :undoc-members: + :show-inheritance: + +Turbomole 7.1 +--------------------------------------- + +.. automodule:: pysisyphus.calculators.Turbomole + :members: + :undoc-members: + :show-inheritance: + +WFOWrapper +---------------------------------------- + +.. automodule:: pysisyphus.calculators.WFOWrapper + :members: + :undoc-members: + :show-inheritance: + +XTB 5.8 +--------------------------------- + +.. automodule:: pysisyphus.calculators.XTB + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/conf.py b/docs/conf.py index 283039f57e..62cb59709f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,9 +12,12 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) +import os +import sys +sys.path.insert(0, os.path.abspath('.')) + +import sphinx_rtd_theme +from pysisyphus._version import get_versions # -- Project information ----------------------------------------------------- @@ -24,9 +27,9 @@ author = 'Johannes Steinmetzer' # The short X.Y version -version = '' +version = f"{get_versions()['version']}" # The full version, including alpha/beta/rc tags -release = '' +release = version # -- General configuration --------------------------------------------------- @@ -41,6 +44,9 @@ extensions = [ 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', + 'sphinx.ext.napoleon', + 'sphinx.ext.autodoc', + 'sphinx.ext.autosummary', ] # Add any paths that contain templates here, relative to this directory. @@ -76,7 +82,7 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'alabaster' +html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the @@ -97,7 +103,9 @@ # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # -# html_sidebars = {} +html_sidebars = { '**': ['globaltoc.html', 'relations.html', + 'sourcelink.html', 'searchbox.html'] +} # -- Options for HTMLHelp output --------------------------------------------- @@ -157,4 +165,10 @@ ] -# -- Extension configuration ------------------------------------------------- \ No newline at end of file +# -- Extension configuration ------------------------------------------------- + +autosummary_generate = True +autodoc_default_flags = ['members', ] + +napoleon_google_docstring = False +napoleon_include_init_with_doc = True diff --git a/docs/examples.rst b/docs/examples.rst new file mode 100644 index 0000000000..dffcfee252 --- /dev/null +++ b/docs/examples.rst @@ -0,0 +1,12 @@ +Examples +======== + +Optimizations +------------- + +.. literalinclude:: examples/test_g16_newargs.yaml + :language: yaml + +Nudged elastic Band +------------------- + diff --git a/docs/examples/test_g16_newargs.yaml b/docs/examples/test_g16_newargs.yaml new file mode 100644 index 0000000000..4d519ee2e5 --- /dev/null +++ b/docs/examples/test_g16_newargs.yaml @@ -0,0 +1,13 @@ +opt: + type: cg + max_cycles: 2 + alpha: 0.5 + align: True +calc: + type: g16 + charge: 0 + mult: 1 + route: HF/STO-3G + gbs: "/home/ca82pez/gaussian/gbs/631GdMWB28.gbs" + pal: 4 +xyz: ch2s_bp86def2sv_opt.xyz diff --git a/docs/index.rst b/docs/index.rst index 1d2ef10354..23426a8c67 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -6,15 +6,30 @@ Welcome to pysisyphus's documentation! ====================================== +pysisphus implements Chain Of States (COS) methods like Nudged Elastic Band +(NEB) and Simple Zero Temperature String (SZTS) to converge minimum energy +paths and provide initial guesses for transition states (TS) optimizations. + +In addition pysisyphus provides serveral Intrinsic Reaction Coordinate +algorithms. The required gradients and/or hessians are calculated by +calling external quantum chemistry codes. By default everything is done +in cartesian coordinates but an internal coordinates implementation is +in progress. + .. toctree:: :maxdepth: 2 :caption: Contents: - + + installation.rst + calculators.rst + optimizers.rst + examples.rst + pysisyphus + Indices and tables ================== * :ref:`genindex` -* :ref:`modindex` * :ref:`search` diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000000..6c6676af86 --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,64 @@ +Installation +=========== + +Dependencies +------------ + +:: + + scipy + numpy + pytest + matplotlib + natsort + pyyaml + +Getting the code +------------------- + +The **recommended way**, as the version on pypi may be outdated: + +:: + + cd [root dir where you want to keep pysisyphus] + git clone https://github.com/eljost/pysisyphus + cd pysisyphus + python setup.py develop + +or **(not recommended)**: + +:: + + pip install pysisyphus + +Post-install configuration +-------------------------------------------- + +Create a file called ``.pysisyphusrc`` in your $HOME-directory +containing the commands to call your installed calculators, e.g.: + +:: + + [orca] + cmd=/scratch/programme/orca-4.0.1.2/orca + + [xtb] + cmd=xtb + + [openmolcas] + cmd=pymolcas + + [gaussian09] + cmd=/usr/local/gaussian/g09/g09 + + [gaussian16] + cmd=/usr/remote/gaussian/g16/g16 + + [wfoverlap] + cmd=/scratch/wfoverlap_1.0/bin/wfoverlap.x + +When the specified path is not absolute but relative (as above for xtb +and openmolcas) the corresponding binaries have to be +available on the $PATH! The **Turbomole** binaries (dscf, ridft, ...) are +hardcoded in the pysisyphus calculator and don't have to be specified here, +but they still have to be available on $PATH. diff --git a/docs/optimizers.rst b/docs/optimizers.rst new file mode 100644 index 0000000000..df2b16f897 --- /dev/null +++ b/docs/optimizers.rst @@ -0,0 +1,58 @@ +Optimizers +============================= + +BFGS +--------------------------------- + +.. automodule:: pysisyphus.optimizers.BFGS + :members: + :undoc-members: + :show-inheritance: + +Conjugate Gradient +---------------------------------------------- + +.. automodule:: pysisyphus.optimizers.ConjugateGradient + :members: + :undoc-members: + :show-inheritance: + +FIRE +--------------------------------- + +.. automodule:: pysisyphus.optimizers.FIRE + :members: + :undoc-members: + :show-inheritance: + +Quick-Min +------------------------------------- + +.. automodule:: pysisyphus.optimizers.QuickMin + :members: + :undoc-members: + :show-inheritance: + +RFOptimizer +---------------------------------------- + +.. automodule:: pysisyphus.optimizers.RFOptimizer + :members: + :undoc-members: + :show-inheritance: + +SciPyOptimizer +------------------------------------------- + +.. automodule:: pysisyphus.optimizers.SciPyOptimizer + :members: + :undoc-members: + :show-inheritance: + +SteepestDescent +-------------------------------------------- + +.. automodule:: pysisyphus.optimizers.SteepestDescent + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/pysisyphus.rst b/docs/pysisyphus.rst new file mode 100644 index 0000000000..f00f157ab3 --- /dev/null +++ b/docs/pysisyphus.rst @@ -0,0 +1,137 @@ +API +================== + +Subpackages +----------- + +.. toctree:: + + api/pysisyphus.calculators + api/pysisyphus.cos + api/pysisyphus.irc + api/pysisyphus.optimizers + api/pysisyphus.plotters + +Submodules +---------- + +pysisyphus.Geometry module +-------------------------- + +.. automodule:: pysisyphus.Geometry + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.InternalCoordinates module +------------------------------------- + +.. automodule:: pysisyphus.InternalCoordinates + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.ReferenceNEB module +------------------------------ + +.. automodule:: pysisyphus.ReferenceNEB + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.TableFormatter module +-------------------------------- + +.. automodule:: pysisyphus.TableFormatter + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.config module +------------------------ + +.. automodule:: pysisyphus.config + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.constants module +--------------------------- + +.. automodule:: pysisyphus.constants + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.elem\_data module +---------------------------- + +.. automodule:: pysisyphus.elem_data + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.helpers module +------------------------- + +.. automodule:: pysisyphus.helpers + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.init\_logging module +------------------------------- + +.. automodule:: pysisyphus.init_logging + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.peakdetect module +---------------------------- + +.. automodule:: pysisyphus.peakdetect + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.plot module +---------------------- + +.. automodule:: pysisyphus.plot + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.run module +--------------------- + +.. automodule:: pysisyphus.run + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.trj module +--------------------- + +.. automodule:: pysisyphus.trj + :members: + :undoc-members: + :show-inheritance: + +pysisyphus.xyzloader module +--------------------------- + +.. automodule:: pysisyphus.xyzloader + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: pysisyphus + :members: + :undoc-members: + :show-inheritance: diff --git a/pysisyphus/calculators/Calculator.py b/pysisyphus/calculators/Calculator.py index dd14ab4bde..408896750e 100644 --- a/pysisyphus/calculators/Calculator.py +++ b/pysisyphus/calculators/Calculator.py @@ -19,6 +19,32 @@ class Calculator: def __init__(self, calc_number=0, charge=0, mult=1, base_name="calculator", pal=1, last_calc_cycle=None, clean_after=True, out_dir="./"): + """Base-class of all calculators. + + Base-class of all calculators that is meant to be extended. + + Parameters + ---------- + calc_number : int + Identifier of the Calculator. Used in distinguishing it from + other Calculators, e.g. in ChainOfStates calculations. Also + used in the creation of filenames. + charge : int + Molecular charge. + mult : int + Molecular multiplicity (1 = singlet, 2 = doublet, ...) + base_name : str + Generated filenames will start with this string. + pal : int + Positive integer that gives the number of physical cores to + use on 1 node. + last_calc_cycle : int + Internal variable used in restarts. + clean_after : bool + Delete the temporary directory after calculations. + out_dir : str + Path that is prepended to generated filenames. + """ # Index of the image this calculator belongs too in # in a ChainOfStates calculation. self.calc_number = calc_number diff --git a/pysisyphus/cos/NoSpringNeb.py b/pysisyphus/cos/NoSpringNeb.py index b6d727cf67..0bf2f05bcb 100755 --- a/pysisyphus/cos/NoSpringNeb.py +++ b/pysisyphus/cos/NoSpringNeb.py @@ -2,7 +2,7 @@ import numpy as np -from cos.NEB import NEB +from pysisyphus.cos.NEB import NEB class NoSpringNEB(NEB): diff --git a/pysisyphus/cos/OldTangentChainOfStates.py b/pysisyphus/cos/OldTangentChainOfStates.py index ce2db79234..59c6495857 100755 --- a/pysisyphus/cos/OldTangentChainOfStates.py +++ b/pysisyphus/cos/OldTangentChainOfStates.py @@ -2,7 +2,7 @@ import numpy as np -from Geometry import Geometry +from pysisyphus.Geometry import Geometry from pysisyphus.xyzloader import make_trj_str class ChainOfStates: diff --git a/setup.py b/setup.py index 44d4bc1259..4b86404573 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,6 @@ install_requires=[ "scipy", "numpy", - "pytest", "matplotlib", "pytest", "natsort",