modified moduse structure, added test of imports and changed documentation...

modified moduse structure, added test of imports and changed documentation accordingly as some import statements have changed as a result

docs/_build/html/_sources/GOFEE/GOFEE.rst.txt

@@ -19,7 +19,7 @@ the search. In addition it can be used to generate new candidates during
 the search, if it is included as an operation in the
 :class:`CandidateGenerator`.
 
-.. autoclass:: candidate_operations.candidate_generation.StartGenerator
+.. autoclass:: gofee.candidates.StartGenerator
     :exclude-members:
 
 CandidateGenerator
@@ -28,7 +28,7 @@ The :class:`CandidateGenerator` is used in each iteration in the GOFEE search
 to generate new candidates based on a list on operations to use. Possible
 operation can be found below under the "Mutations" section.
 
-.. autoclass:: candidate_operations.candidate_generation.CandidateGenerator
+.. autoclass:: gofee.candidates.CandidateGenerator
     :members: get_new_candidate
 
 
@@ -42,17 +42,17 @@ The mutations to chose from are listed below.
 RattleMutation
 --------------
 
-.. autoclass:: candidate_operations.basic_mutations.RattleMutation
+.. autoclass:: gofee.candidates.RattleMutation
     :exclude-members:
 
 RattleMutation2
 ---------------
 
-.. autoclass:: candidate_operations.basic_mutations.RattleMutation2
+.. autoclass:: gofee.candidates.RattleMutation2
     :exclude-members:
 
 PermutationMutation
 -------------------
 
-.. autoclass:: candidate_operations.basic_mutations.PermutationMutation
+.. autoclass:: gofee.candidates.PermutationMutation
     :exclude-members:
\ No newline at end of file

docs/_build/html/_sources/SLURM/SLURM.rst.txt

@@ -27,7 +27,7 @@ this (propperly modified for your setup)::
     source <GPAW stuff>
     source <DFTB stuff>  # if running DFTB
 
-    mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py > search.log
+    mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
     echo "========= Job finished at `date` =========="
 
 This job will be run locally in the submission folder on 10 cpu cores.

docs/_build/html/_sources/tutorial/au_on_cu/au_on_cu.rst.txt

+.. _au_on_cu_search:
+
+=======================
+Au7 in Cu(111) with EMT
+=======================
+
+In this tutorial we carry out a search for Au7-clusters on
+the Cu(111) surface.
+
+In this search we will utilize an :class:`OperationConstraint`
+to constraint the :class:`RattleMutation` to only rattle the
+atoms within a certain box in space that we define.
+

docs/_build/html/_sources/tutorial/modifying_surrogate_model/modifying_surrogate_model.rst.txt

@@ -23,8 +23,8 @@ One can for example apply a GPR model with another degree of regularization
 in the search. As the regularization is a parameter of the *kernel*, passed
 to the GPR model, the code will look like this::
 
-    from surrogate.gpr import GPR
-    from surrogate.kernel import double_gauss_kernel
+    from gofee.surrogate.gpr import GPR
+    from gofee.surrogate.kernel import double_gauss_kernel
 
     kernel = double_gauss_kernel(noise=1e-6)
     gpr = GPR(kernel=kernel)

docs/_build/html/_sources/tutorial/tio2_reconstruction/tio2_reconstruction.rst.txt

@@ -21,7 +21,7 @@ following code :download:`TiO2.py` is used to carry out the search:
 If ASE, GPAW and dftb are set up and sourced propperly, you can run
 the code as::
 
-    mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
+    mpiexec --mca mpi_warn_on_fork 0 gpaw-python TiO2.py
 
 Setting up the system - atoms in template
 =========================================

docs/_build/html/_sources/tutorial/tio_clusters/tio_clusters.rst.txt

@@ -18,7 +18,7 @@ explainted further below):
 If ASE, GPAW and dftb are set up and sourced propperly, you can run
 the code as::
 
-    mpiexec --mca mpi_warn_on_fork 0 gpaw-python run_search.py
+    mpiexec --mca mpi_warn_on_fork 0 gpaw-python Ti5O10.py
 
 What follows is a description of the python script above.
 

docs/_build/html/genindex.html

@@ -161,7 +161,7 @@
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.CandidateGenerator">CandidateGenerator (class in candidate_operations.candidate_generation)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.CandidateGenerator">CandidateGenerator (class in gofee.candidates)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -169,7 +169,7 @@
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.CandidateGenerator.get_new_candidate">get_new_candidate() (candidate_operations.candidate_generation.CandidateGenerator method)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.CandidateGenerator.get_new_candidate">get_new_candidate() (gofee.candidates.CandidateGenerator method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -181,7 +181,7 @@
 <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.PermutationMutation">PermutationMutation (class in candidate_operations.basic_mutations)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.PermutationMutation">PermutationMutation (class in gofee.candidates)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -189,11 +189,11 @@
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.RattleMutation">RattleMutation (class in candidate_operations.basic_mutations)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.RattleMutation">RattleMutation (class in gofee.candidates)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.basic_mutations.RattleMutation2">RattleMutation2 (class in candidate_operations.basic_mutations)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.RattleMutation2">RattleMutation2 (class in gofee.candidates)</a>
 </li>
       <li><a href="GOFEE/GOFEE.html#gofee.GOFEE.run">run() (gofee.GOFEE method)</a>
 </li>
@@ -203,7 +203,7 @@
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="GOFEE/GOFEE.html#candidate_operations.candidate_generation.StartGenerator">StartGenerator (class in candidate_operations.candidate_generation)</a>
+      <li><a href="GOFEE/GOFEE.html#gofee.candidates.StartGenerator">StartGenerator (class in gofee.candidates)</a>
 </li>
   </ul></td>
 </tr></table>

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method"]},objtypes:{"0":"py:class","1":"py:method"},terms:{"1x4":[3,9],"20\u00e5x20\u00e5x20\u00e5":8,"30g":1,"3x3":8,"boolean":0,"case":[0,7,8],"class":[0,8],"default":[0,8],"export":[1,4],"final":[4,7],"float":0,"function":[0,4],"import":[6,7,8],"int":0,"new":[0,6,8],"super":0,"true":0,ASE:[0,2,4,7,8],For:[7,8],One:6,The:[0,3,4,7,8],Then:[4,7],These:8,Use:0,Used:0,With:8,abov:[7,8],accord:0,achiev:4,acquisit:0,activ:6,adding:0,addit:[0,2,8],after:4,all:[0,8],allow:0,alreadi:2,also:[0,2],altern:0,alwai:0,angstrom:0,anoth:6,appli:[0,6,8],arg:0,argument:6,arrai:[7,8],ase:[7,8],assum:4,atom:[0,2,5,8],atomist:[2,3],avali:4,averag:[0,8],avov:6,base:0,bash:1,basic:2,basic_mut:8,befor:[2,6,7],below:[0,8],best:8,between:0,bin:1,blmax:0,blmin:0,bool:0,both:[0,4],box:[0,5,7,8],box_to_place_in:0,build_cod:4,bulk:7,calc:[0,6,7,8],calcul:[0,1,7,8],call:4,can:[0,1,2,4,6,7,8],cancid:0,candid:[0,6,7,8],candidate_gener:[0,6,7,8],candidate_generatior:0,candidate_oper:[7,8],candidategener:[3,7],candomli:0,carri:[5,7,8],cell:[0,8],center:8,certain:5,chang:8,cheap:6,choos:7,chose:0,closest:0,cluster:[0,1,3,5,6,7,9],code:[1,4,6,7,8],compil:4,complet:[2,8],configur:8,consecut:0,considd:[0,8],constraint:[0,5,8],contain:[0,1,7,8],continu:2,coordin:0,core:1,corner:0,could:8,coval:0,cpu:1,creat:8,crossov:0,cymem:4,cython:4,d_cov:0,date:1,defin:[0,5,7,8],degre:6,depend:0,describ:[0,1,8],descript:[0,8],descriptor:4,desir:1,detail:7,dftb:[1,7,8],dict:0,differ:[7,8],dimens:0,directori:1,distanc:[0,8],done:[0,2,4,8],double_gauss_kernel:6,download:4,drawn:0,dualpoint:0,dure:[0,6,8],each:0,echo:1,either:[0,8],element:8,empti:[0,7,8],energi:[0,3,8],enforc:0,environ:2,especi:2,evalu:[0,4,8],exampl:[2,3,6,8],exclus:1,experi:2,explaint:8,explor:8,express:[0,3],extend:6,eye:8,fals:0,familiar:2,fermi:[7,8],file:[0,1,2,4,7],filenam:0,finish:1,first:[3,7],fix:[7,8],fixatom:8,folder:[1,4],follow:[6,7,8],form:[0,7],fors:8,found:0,free:0,from:[0,3,6,7,8],further:8,gaussian:[0,6],gener:[0,7,8],geometri:3,get:3,get_cel:7,get_new_candid:0,given:[7,8],global:[0,3],gofe:[1,2,4,6,7,9],gofee_test:1,goff:4,going:[2,8],gpaw:[1,4,7,8],gpr:[0,6],guid:2,hamiltonian_charg:[7,8],hamiltonian_fil:[7,8],hamiltonian_filling_empti:[7,8],hamiltonian_maxangularmomentum_:[7,8],hamiltonian_maxangularmomentum_o:[7,8],hamiltonian_maxangularmomentum_ti:[7,8],hamiltonian_scc:[7,8],handl:8,have:[0,2,4,8],heavili:2,height:7,how:[0,8],howev:[0,4,6],implement:[2,4],includ:[0,6],index:7,indic:0,indivitu:8,info:0,initi:[0,6,7],input:0,insid:4,instal:[2,3],interest:2,isol:[0,8],iter:[0,8],job:3,jobscript:1,kappa:0,kelvin:[7,8],kept:[0,8],kernel:6,kpt:[7,8],kwarg:0,label:[7,8],learn:6,len:[0,7,8],less:0,librari:2,like:[1,6],list:[0,7,8],local:1,log:0,logfil:0,look:[6,8],made:8,major:7,manag:1,mani:[0,8],master:[],matrix:[0,8],max:0,max_relax_dist:0,max_step:[0,6,7,8],maximum:[0,8],mca:[1,4,7,8],mean:4,mem:1,mention:[4,6],method:[0,2,3],min_certainti:0,minimum:0,model:[0,3,4,9],modifi:[1,3,9],more:7,most:[4,8],move:0,mpi4pi:4,mpi_warn_on_fork:[1,4,7,8],mpiexec:[1,4,7,8],much:0,multipl:0,must:[0,1],mutaion:8,mutat:[3,7,8],n_to_optim:[7,8],n_top:0,name:[0,1],natom:8,natur:8,ncandid:0,neccisari:2,need:[4,7,8],newer:4,ninit:0,node:1,nois:6,none:0,note:1,now:7,npermut:[0,7],nrattl:[0,7,8],ntask:1,number:[0,6,7,8],numpi:[7,8],nymber:8,object:[0,2,8],one:[0,6,7,8],ones:0,onli:[4,5],open:0,oper:[0,8],operationconstraint:[0,5],operationselector:0,optim:[0,3,6,7,8],origin:0,other:[0,6,8],otherwis:2,out:[5,7,8],overview:0,oxid:8,oxygen:8,pair:0,paramet:[0,6,7,8],parent:0,part:[4,8],particular:[2,4],partit:1,pass:6,path:[1,4],pbc:8,per:1,perform:0,permut:[0,7,8],permutaionmut:8,permutationmut:7,pickl:0,place:[0,7,8],point:8,popul:[0,8],population_s:[0,6,7,8],posit:[0,7],position_constraint:0,possibl:0,potenti:0,predict:0,prerequisit:[2,8],present:[0,6,7],previou:[6,7],principl:3,prior:[2,4],probabl:[0,8],process:[0,6],produc:0,program:2,propperli:[1,7,8],purpos:8,python:[1,2,4,7,8],pythonpath:[1,4],r_cov_i:0,r_cov_j:0,radiu:0,random:[0,8],randomli:[0,7,8],rattl:[0,5,7,8],rattle_rang:[0,7,8],rattlemut:[5,7,8],read:7,readi:8,recomend:[0,6,7],recommend:0,reconstruct:[3,9],regress:[0,6],regular:6,relax:[0,8],reli:[2,8],remain:0,repres:7,requir:[0,3],respect:0,restart:0,result:8,run:[0,1,4,7],run_search:1,safe:0,same:0,save:0,sbatch:1,script:[4,8],script_calling_gofe:4,search:[0,2,3,5,6,9],section:0,see:8,select:0,sesarch:0,set:[0,2],setup:[1,4],shift:8,shold:8,should:0,shown:0,similar:7,simul:2,sinc:8,singl:0,size:8,slab:[0,7,8],slap:7,slightli:7,slurm:3,slurm_submit_dir:1,some:[2,8],sourc:[1,3,7,8],space:[5,8],span:[0,8],specif:0,specifi:[0,8],sphere:0,squar:8,start:[0,1,3,7,8],startgener:[3,6,7,8],stdout:0,step:0,stoichiometri:[0,7,8],str:0,string:0,structu:0,structur:[0,7,9],stuff:1,submiss:1,submit:1,success:0,suppli:[0,8],surfac:[0,5],surrog:[0,3,4,8,9],swap:0,system:[0,2,3],take:[6,8],taken:8,tar:4,task:1,temperatur:[7,8],templat:8,test:4,than:0,thei:8,therefor:[2,6],thi:[0,1,4,5,6,7,8,9],thing:7,three:[0,8],through:2,ti5o10:8,time:[0,1,4],timecrit:4,tio2:[3,9],tio2_slab:7,tio2_surfac:[7,8],tio:[3,6,7,9],tiorg:[7,8],titanium:8,top:[0,7],traj:[0,7,8],trajectori:[0,2],turori:9,tutori:[1,2,3,5,6,7,8],type:8,uncertainti:0,under:0,understand:2,uniformli:0,unit:0,unlik:0,unpack:4,use:[0,1,2,7,8],used:[0,2,3,4,6,7,8],user:0,uses:8,using:[0,1,4,8],util:5,vector:[0,8],veri:7,visin:0,visit:8,vspan:0,wai:0,want:7,weigh:0,well:[0,2],wether:0,what:8,when:4,where:[0,1],whether:0,which:[0,1,6,7,8],witch:0,within:[0,5,7],work:4,written:4,you:[1,2,4,6,7,8],your:[1,4],yourfil:[],zxvf:4},titles:["GOFEE","SLURM job examples","Getting started","Welcome to the documentation for GOFEE!","Installation","Au7 in Cu(111) with EMT","Modifying surrogate model","Searching for the TiO2(001)-(1x4) reconstruction","Searching for TiO clusters","Tutorial"],titleterms:{"1x4":7,atom:7,au7:5,candidategener:[0,8],cluster:8,document:3,emt:5,exampl:1,from:4,get:2,gofe:[0,3,8],initi:8,instal:4,job:1,make:8,model:6,modifi:6,mutat:0,permutationmut:0,rattlemut:0,rattlemutation2:0,reconstruct:7,requir:4,run:8,search:[7,8],set:[7,8],slurm:1,sourc:4,start:2,startgener:0,startgenerat:8,structur:8,surrog:6,system:[7,8],templat:7,tio2:7,tio:8,tutori:9,welcom:3}})
\ No newline at end of file

docs/_build/html/tutorial/au_on_cu/au_on_cu.html

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+            
+  <div class="section" id="au7-in-cu-111-with-emt">
+<span id="au-on-cu-search"></span><h1>Au7 in Cu(111) with EMT<a class="headerlink" href="#au7-in-cu-111-with-emt" title="Permalink to this headline">¶</a></h1>
+<p>In this tutorial we carry out a search for Au7-clusters on
+the Cu(111) surface.</p>
+<p>In this search we will utilize an <code class="xref py py-class docutils literal notranslate"><span class="pre">OperationConstraint</span></code>
+to constraint the <code class="xref py py-class docutils literal notranslate"><span class="pre">RattleMutation</span></code> to only rattle the
+atoms within a certain box in space that we define.</p>
+</div>
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docs/_build/html/tutorial/modifying_surrogate_model/modifying_surrogate_model.html

@@ -177,8 +177,8 @@ during the search and used for cheap optimization of new candidates.</p>
 <p>One can for example apply a GPR model with another degree of regularization
 in the search. As the regularization is a parameter of the <em>kernel</em>, passed
 to the GPR model, the code will look like this:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">surrogate.gpr</span> <span class="k">import</span> <span class="n">GPR</span>
-<span class="kn">from</span> <span class="nn">surrogate.kernel</span> <span class="k">import</span> <span class="n">double_gauss_kernel</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">gofee.surrogate.gpr</span> <span class="k">import</span> <span class="n">GPR</span>
+<span class="kn">from</span> <span class="nn">gofee.surrogate.kernel</span> <span class="k">import</span> <span class="n">double_gauss_kernel</span>
 
 <span class="n">kernel</span> <span class="o">=</span> <span class="n">double_gauss_kernel</span><span class="p">(</span><span class="n">noise</span><span class="o">=</span><span class="mf">1e-6</span><span class="p">)</span>
 <span class="n">gpr</span> <span class="o">=</span> <span class="n">GPR</span><span class="p">(</span><span class="n">kernel</span><span class="o">=</span><span class="n">kernel</span><span class="p">)</span>

docs/_build/html/tutorial/tio2_reconstruction/tio2_reconstruction.html

@@ -177,8 +177,8 @@ following code <a class="reference download internal" download="" href="../../_d
 <span class="kn">from</span> <span class="nn">ase.calculators.dftb</span> <span class="k">import</span> <span class="n">Dftb</span>
 <span class="kn">from</span> <span class="nn">ase.io</span> <span class="k">import</span> <span class="n">read</span>
 
-<span class="kn">from</span> <span class="nn">candidate_operations.candidate_generation</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
-<span class="kn">from</span> <span class="nn">candidate_operations.basic_mutations</span> <span class="k">import</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
+<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
+<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
 <span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
 
 <span class="c1">### Define calculator ###</span>
@@ -227,7 +227,7 @@ following code <a class="reference download internal" download="" href="../../_d
 </div>
 <p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
 the code as:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">run_search</span><span class="o">.</span><span class="n">py</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">TiO2</span><span class="o">.</span><span class="n">py</span>
 </pre></div>
 </div>
 <div class="section" id="setting-up-the-system-atoms-in-template">

docs/_build/html/tutorial/tio_clusters/tio_clusters.html

@@ -177,8 +177,7 @@ explainted further below):</p>
 <span class="kn">from</span> <span class="nn">ase</span> <span class="k">import</span> <span class="n">Atoms</span>
 <span class="kn">from</span> <span class="nn">ase.calculators.dftb</span> <span class="k">import</span> <span class="n">Dftb</span>
 
-<span class="kn">from</span> <span class="nn">candidate_operations.candidate_generation</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span>
-<span class="kn">from</span> <span class="nn">candidate_operations.basic_mutations</span> <span class="k">import</span> <span class="n">RattleMutation</span>
+<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span><span class="p">,</span> <span class="n">RattleMutation</span>
 <span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
 
 <span class="c1">### Define calculator ###</span>
@@ -228,7 +227,7 @@ explainted further below):</p>
 </div>
 <p>If ASE, GPAW and dftb are set up and sourced propperly, you can run
 the code as:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">run_search</span><span class="o">.</span><span class="n">py</span>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">Ti5O10</span><span class="o">.</span><span class="n">py</span>
 </pre></div>
 </div>
 <p>What follows is a description of the python script above.</p>