Cleaned up cand_opp and missing missing wrap() calls

e9f52417 · Malthe Kjær Bisbo · 531b2f5e · e9f52417 · e9f52417 · e9f52417
Commit e9f52417 authored Jan 27, 2020 by Malthe Kjær Bisbo
--- a/docs/_build/html/gofee.candidate_operations.html
+++ b/docs/_build/html/gofee.candidate_operations.html
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+  <title>gofee.candidate_operations package &mdash; GOFEE  documentation</title>
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+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
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+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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+            
+            
+              <!-- Local TOC -->
+              <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">gofee.candidate_operations package</a><ul>
+<li><a class="reference internal" href="#submodules">Submodules</a></li>
+<li><a class="reference internal" href="#gofee-candidate-operations-basic-mutations-module">gofee.candidate_operations.basic_mutations module</a></li>
+<li><a class="reference internal" href="#gofee-candidate-operations-candidate-generation-module">gofee.candidate_operations.candidate_generation module</a></li>
+<li><a class="reference internal" href="#module-contents">Module contents</a></li>
+</ul>
+</li>
+</ul>
+</div>
+            
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+<div role="navigation" aria-label="breadcrumbs navigation">
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+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="index.html">Docs</a> &raquo;</li>
+        
+      <li>gofee.candidate_operations package</li>
+    
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+      <li class="wy-breadcrumbs-aside">
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+            <a href="_sources/gofee.candidate_operations.rst.txt" rel="nofollow"> View page source</a>
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+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="gofee-candidate-operations-package">
+<h1>gofee.candidate_operations package<a class="headerlink" href="#gofee-candidate-operations-package" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="submodules">
+<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="gofee-candidate-operations-basic-mutations-module">
+<h2>gofee.candidate_operations.basic_mutations module<a class="headerlink" href="#gofee-candidate-operations-basic-mutations-module" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="gofee-candidate-operations-candidate-generation-module">
+<h2>gofee.candidate_operations.candidate_generation module<a class="headerlink" href="#gofee-candidate-operations-candidate-generation-module" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="module-contents">
+<h2>Module contents<a class="headerlink" href="#module-contents" title="Permalink to this headline">¶</a></h2>
+</div>
+</div>
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+           </div>
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+    <p>
+        &copy; Copyright 2020, Malthe Kjær Bisbo, Bjørk Hammer
+
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+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
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+</body>
+</html>
\ No newline at end of file
--- a/docs/_build/html/gofee.html
+++ b/docs/_build/html/gofee.html
--- a/docs/_build/html/gofee.surrogate.html
+++ b/docs/_build/html/gofee.surrogate.html
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
--- a/docs/_build/html/modules.html
+++ b/docs/_build/html/modules.html
--- a/docs/_build/html/objects.inv
+++ b/docs/_build/html/objects.inv
--- a/docs/_build/html/search.html
+++ b/docs/_build/html/search.html
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
+Search.setIndex({docnames:["gofee","gofee.candidate_operations","gofee.surrogate","index","modules","test"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,sphinx:56},filenames:["gofee.rst","gofee.candidate_operations.rst","gofee.surrogate.rst","index.rst","modules.rst","test.rst"],objects:{},objnames:{},objtypes:{},terms:{"import":5,"true":5,The:5,There:5,Using:5,all:5,argument:[],asdasda:[],asdasdasd:[],ase:5,ate:5,atom:5,basi:5,basic:3,basic_mut:[0,4],beta:5,bfgslinesearch_constrain:4,bfgslinesearch_zlim:4,blac:5,box:5,c6h6:5,calc:5,calcul:5,can:5,candidate_gener:[0,4],candidate_oper:[0,4],candidategener:3,cell:5,charg:[],collect:[],configur:5,contain:5,content:[3,4],creat:5,custom_calcul:[0,4],defin:5,determin:5,dzp:5,effici:5,energi:5,eps:5,explor:5,express:5,extra_paramet:5,fermidirac:5,first:[],fix:5,follow:5,form:5,from:5,gaussian:3,get_cel:5,global:[],gpaw:5,gpr:[0,3,4],gpr_calcul:[0,4],gpr_old:[0,4],gpt:5,h2gpt:5,here:[],how:[],idiv:5,index:3,inform:5,init:[],initi:5,initialis:5,introduct:5,just:5,kernel:[0,4],keyword:[],kpt:5,lcao:5,like:5,load:5,look:5,magmom:[],mass:[],max_step:5,maxit:5,method:5,mixer:5,mode:5,model:3,modul:[3,4],molecul:[],momenta:[],more:5,most:5,nband:5,nmaxold:5,non:5,number:[],numpi:5,object:5,occup:5,one:5,optim:5,other:[],packag:4,page:3,parallel_util:4,pbe:5,perform:[],piec:5,place:5,poissonsolv:5,popul:4,posit:5,possibl:[],potenti:5,process:3,random:5,randomli:5,read:[],regress:3,relax:5,reli:5,reshap:5,respect:5,run:5,sadasd:[],search:[3,5],set:3,simplest:[],slab:5,space:5,specifi:3,startgener:3,structs_init:[],structur:3,submodul:4,subpackag:4,suppli:3,surrog:[0,4],system:3,tag:[],test_descriptor:[0,4],test_gpr:[0,4],test_kernel:[0,4],thi:5,traj:5,trajectori:5,two:5,type:[],uniform:5,used:[],user:5,util:[4,5],wai:5,weight:5,what:5,when:5,which:5,within:5,write:[]},titles:["gofee package","gofee.candidate_operations package","gofee.surrogate package","Welcome to GOFEE\u2019s documentation!","gofee","GOFEE"],titleterms:{The:[],atom:[],basic:5,basic_mut:1,bfgslinesearch_constrain:0,bfgslinesearch_zlim:0,candidate_gener:1,candidate_oper:1,candidategener:5,content:[0,1,2],custom_calcul:2,document:3,gaussian:5,gofe:[0,1,2,3,4,5],gpr:[2,5],gpr_calcul:2,gpr_old:2,indic:3,kernel:2,model:5,modul:[0,1,2],object:[],packag:[0,1,2],parallel_util:0,popul:0,process:5,regress:5,set:5,specifi:5,startgener:5,structur:5,submodul:[0,1,2],subpackag:0,suppli:5,surrog:2,system:5,tabl:3,test_descriptor:2,test_gpr:2,test_kernel:2,util:0,welcom:3}})
\ No newline at end of file
--- a/docs/_build/html/test.html
+++ b/docs/_build/html/test.html
--- a/docs/conf.py
+++ b/docs/conf.py
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# 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('..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'GOFEE'
+copyright = '2020, Malthe Kjær Bisbo, Bjørk Hammer'
+author = 'Malthe Kjær Bisbo, Bjørk Hammer'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
\ No newline at end of file
--- a/docs/gofee.candidate_operations.rst
+++ b/docs/gofee.candidate_operations.rst
+gofee.candidate\_operations package
+===================================
+
+Submodules
+----------
+
+gofee.candidate\_operations.basic\_mutations module
+---------------------------------------------------
+
+.. automodule:: gofee.candidate_operations.basic_mutations
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gofee.candidate\_operations.candidate\_generation module
+--------------------------------------------------------
+
+.. automodule:: gofee.candidate_operations.candidate_generation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: gofee.candidate_operations
+   :members:
+   :undoc-members:
+   :show-inheritance:
--- a/docs/gofee.rst
+++ b/docs/gofee.rst
--- a/docs/gofee.surrogate.rst
+++ b/docs/gofee.surrogate.rst
--- a/docs/index.rst
+++ b/docs/index.rst
+.. GOFEE documentation master file, created by
+   sphinx-quickstart on Wed Jan 22 20:36:44 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to GOFEE's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   #modules
+   test
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
--- a/docs/make.bat
+++ b/docs/make.bat
--- a/docs/modules.rst
+++ b/docs/modules.rst
+gofee
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   gofee
--- a/docs/test.rst
+++ b/docs/test.rst
--- a/gofee.py
+++ b/gofee.py
--- a/parallel_utils.py
+++ b/parallel_utils.py
--- a/statistics_tools/survival_statistics/__pycache__/collect_events.cpython-36.pyc
+++ b/statistics_tools/survival_statistics/__pycache__/collect_events.cpython-36.pyc