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

__init__.py

-from gofee import GOFEE
-
-__all__ = ['GOFEE']
\ No newline at end of file

build_code

 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 
-cd $DIR/surrogate/prior
+cd $DIR/gofee/surrogate/prior
+rm *.c *.o
 python3 setup.py clean
 python3 setup.py build_ext --inplace --force
 
-cd $DIR/surrogate/descriptor
+cd $DIR/gofee/surrogate/descriptor
+rm *.c *.o
 python3 setup.py clean
 python3 setup.py build_ext --inplace --force
\ No newline at end of file

docs/GOFEE/GOFEE.rst

@@ -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/GOFEE/GOFEE.html

@@ -168,7 +168,7 @@ defining the system, must always be set.
 In addition it is recomended to also set the <code class="docutils literal notranslate"><span class="pre">candidate_generatior</span></code>.</p>
 <dl class="class">
 <dt id="gofee.GOFEE">
-<em class="property">class </em><code class="sig-prename descclassname">gofee.</code><code class="sig-name descname">GOFEE</code><span class="sig-paren">(</span><em class="sig-param">structures=None</em>, <em class="sig-param">calc=None</em>, <em class="sig-param">gpr=None</em>, <em class="sig-param">startgenerator=None</em>, <em class="sig-param">candidate_generator=None</em>, <em class="sig-param">trajectory='structures.traj'</em>, <em class="sig-param">kappa=2</em>, <em class="sig-param">max_steps=200</em>, <em class="sig-param">Ninit=10</em>, <em class="sig-param">max_relax_dist=4</em>, <em class="sig-param">Ncandidates=30</em>, <em class="sig-param">population_size=10</em>, <em class="sig-param">dualpoint=True</em>, <em class="sig-param">min_certainty=0.7</em>, <em class="sig-param">restart='restart.pickl'</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.GOFEE" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="sig-prename descclassname">gofee.</code><code class="sig-name descname">GOFEE</code><span class="sig-paren">(</span><em class="sig-param">structures=None</em>, <em class="sig-param">calc=None</em>, <em class="sig-param">gpr=None</em>, <em class="sig-param">startgenerator=None</em>, <em class="sig-param">candidate_generator=None</em>, <em class="sig-param">kappa=2</em>, <em class="sig-param">max_steps=200</em>, <em class="sig-param">Ninit=10</em>, <em class="sig-param">max_relax_dist=4</em>, <em class="sig-param">Ncandidates=30</em>, <em class="sig-param">population_size=10</em>, <em class="sig-param">dualpoint=True</em>, <em class="sig-param">min_certainty=0.7</em>, <em class="sig-param">position_constraint=None</em>, <em class="sig-param">trajectory='structures.traj'</em>, <em class="sig-param">logfile='search.log'</em>, <em class="sig-param">restart='restart.pickl'</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.GOFEE" title="Permalink to this definition">¶</a></dt>
 <dd><p>GOFEE global structure search method.</p>
 <p>Parameters:</p>
 <dl class="simple">
@@ -195,6 +195,9 @@ structures. Must be supplied if structures if structues=None.
 <dt>trajectory: str</dt><dd><p>Name of trajectory to which all structures,
 evaluated during the search, is saved.</p>
 </dd>
+<dt>logfile: file object or str</dt><dd><p>If <em>logfile</em> is a string, a file with that name will be opened.
+Use ‘-‘ for stdout.</p>
+</dd>
 <dt>kappa: float</dt><dd><p>How much to weigh predicted uncertainty in the acquisition
 function.</p>
 </dd>
@@ -219,6 +222,10 @@ surrogate-relaxed in each search iteration.</p>
 considdered for evaluation. (in units of the maximum possible
 uncertainty.)</p>
 </dd>
+<dt>position_constraint: OperationConstraint object</dt><dd><p>Enforces constraints on the positions of the “free” atoms
+in the search. The constraint is enforces both during
+mutation/crossover operations and during surrogate-relaxation.</p>
+</dd>
 <dt>restart: str</dt><dd><p>Filename for restart file.</p>
 </dd>
 </dl>
@@ -237,8 +244,8 @@ the search. In addition it can be used to generate new candidates during
 the search, if it is included as an operation in the
 <code class="xref py py-class docutils literal notranslate"><span class="pre">CandidateGenerator</span></code>.</p>
 <dl class="class">
-<dt id="candidate_operations.candidate_generation.StartGenerator">
-<em class="property">class </em><code class="sig-prename descclassname">candidate_operations.candidate_generation.</code><code class="sig-name descname">StartGenerator</code><span class="sig-paren">(</span><em class="sig-param">slab</em>, <em class="sig-param">stoichiometry</em>, <em class="sig-param">box_to_place_in</em>, <em class="sig-param">cluster=False</em>, <em class="sig-param">description='StartGenerator'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.candidate_generation.StartGenerator" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.StartGenerator">
+<em class="property">class </em><code class="sig-prename descclassname">gofee.candidates.</code><code class="sig-name descname">StartGenerator</code><span class="sig-paren">(</span><em class="sig-param">slab</em>, <em class="sig-param">stoichiometry</em>, <em class="sig-param">box_to_place_in</em>, <em class="sig-param">cluster=False</em>, <em class="sig-param">description='StartGenerator'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.StartGenerator" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class used to generate random initial candidates.</p>
 <p>Generates new candidates by iteratively adding
 one atom at a time within a user-defined box.</p>
@@ -277,8 +284,8 @@ False the atoms in the slab are also included.</p>
 to generate new candidates based on a list on operations to use. Possible
 operation can be found below under the “Mutations” section.</p>
 <dl class="class">
-<dt id="candidate_operations.candidate_generation.CandidateGenerator">
-<em class="property">class </em><code class="sig-prename descclassname">candidate_operations.candidate_generation.</code><code class="sig-name descname">CandidateGenerator</code><span class="sig-paren">(</span><em class="sig-param">probabilities</em>, <em class="sig-param">operations</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.candidate_generation.CandidateGenerator" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.CandidateGenerator">
+<em class="property">class </em><code class="sig-prename descclassname">gofee.candidates.</code><code class="sig-name descname">CandidateGenerator</code><span class="sig-paren">(</span><em class="sig-param">probabilities</em>, <em class="sig-param">operations</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.CandidateGenerator" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to produce new candidates by applying one of the
 candidate generation operations which is supplied in the
 ‘operations’-list. The operations are drawn randomly according
@@ -295,8 +302,8 @@ in operations. Must have the same dimensions as operations.</p>
 </dd>
 </dl>
 <dl class="method">
-<dt id="candidate_operations.candidate_generation.CandidateGenerator.get_new_candidate">
-<code class="sig-name descname">get_new_candidate</code><span class="sig-paren">(</span><em class="sig-param">parents</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.candidate_generation.CandidateGenerator.get_new_candidate" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.CandidateGenerator.get_new_candidate">
+<code class="sig-name descname">get_new_candidate</code><span class="sig-paren">(</span><em class="sig-param">parents</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.CandidateGenerator.get_new_candidate" title="Permalink to this definition">¶</a></dt>
 <dd><p>Generate new candidate by applying a randomly drawn
 operation on the structures. This is done successively for
 each list of operations, if multiple are present.</p>
@@ -311,8 +318,8 @@ each list of operations, if multiple are present.</p>
 <div class="section" id="rattlemutation">
 <h3>RattleMutation<a class="headerlink" href="#rattlemutation" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
-<dt id="candidate_operations.basic_mutations.RattleMutation">
-<em class="property">class </em><code class="sig-prename descclassname">candidate_operations.basic_mutations.</code><code class="sig-name descname">RattleMutation</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Nrattle=3</em>, <em class="sig-param">rattle_range=3</em>, <em class="sig-param">description='RattleMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.basic_mutations.RattleMutation" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.RattleMutation">
+<em class="property">class </em><code class="sig-prename descclassname">gofee.candidates.</code><code class="sig-name descname">RattleMutation</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Nrattle=3</em>, <em class="sig-param">rattle_range=3</em>, <em class="sig-param">description='RattleMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.RattleMutation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to perform rattle mutations on structures.</p>
 <p>Rattles a number of randomly selected atoms within a sphere
 of radius ‘rattle_range’ of their original positions.</p>
@@ -344,8 +351,8 @@ info-dict of structures, on which the operation is applied.</p>
 <div class="section" id="rattlemutation2">
 <h3>RattleMutation2<a class="headerlink" href="#rattlemutation2" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
-<dt id="candidate_operations.basic_mutations.RattleMutation2">
-<em class="property">class </em><code class="sig-prename descclassname">candidate_operations.basic_mutations.</code><code class="sig-name descname">RattleMutation2</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Nrattle=3</em>, <em class="sig-param">description='RattleMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.basic_mutations.RattleMutation2" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.RattleMutation2">
+<em class="property">class </em><code class="sig-prename descclassname">gofee.candidates.</code><code class="sig-name descname">RattleMutation2</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Nrattle=3</em>, <em class="sig-param">description='RattleMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.RattleMutation2" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to perform rattle mutations on structures.</p>
 <p>Rattles a number of randomly selected atom to the visinity
 of other candomly selected atoms random atom.</p>
@@ -373,8 +380,8 @@ info-dict of structures, on which the operation is applied.</p>
 <div class="section" id="permutationmutation">
 <h3>PermutationMutation<a class="headerlink" href="#permutationmutation" title="Permalink to this headline">¶</a></h3>
 <dl class="class">
-<dt id="candidate_operations.basic_mutations.PermutationMutation">
-<em class="property">class </em><code class="sig-prename descclassname">candidate_operations.basic_mutations.</code><code class="sig-name descname">PermutationMutation</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Npermute=3</em>, <em class="sig-param">description='PermutationMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#candidate_operations.basic_mutations.PermutationMutation" title="Permalink to this definition">¶</a></dt>
+<dt id="gofee.candidates.PermutationMutation">
+<em class="property">class </em><code class="sig-prename descclassname">gofee.candidates.</code><code class="sig-name descname">PermutationMutation</code><span class="sig-paren">(</span><em class="sig-param">n_top</em>, <em class="sig-param">Npermute=3</em>, <em class="sig-param">description='PermutationMutation'</em>, <em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#gofee.candidates.PermutationMutation" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class to perform permutation mutations on structures.</p>
 <p>Swaps the positions of a number of pairs of unlike atoms.</p>
 <p>Parameters:</p>

docs/_build/html/SLURM/SLURM.html

@@ -174,7 +174,7 @@ source <python stuff>
 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` =========="
 </pre></div>
 </div>

docs/_build/html/_downloads/19ab4ff0523b6603bbb89aab36f4db1b/TiO2.py

@@ -3,8 +3,8 @@ import numpy as np
 from ase.calculators.dftb import Dftb
 from ase.io import read
 
-from candidate_operations.candidate_generation import CandidateGenerator, StartGenerator
-from candidate_operations.basic_mutations import RattleMutation, PermutationMutation
+from gofee.candidates import CandidateGenerator, StartGenerator
+from gofee.candidates import RattleMutation, PermutationMutation
 from gofee import GOFEE
 
 ### Define calculator ###

docs/_build/html/_downloads/8108152e19011a5e65bb02f10ec97d04/Ti5O10.py

@@ -4,8 +4,7 @@ import numpy as np
 from ase import Atoms
 from ase.calculators.dftb import Dftb
 
-from candidate_operations.candidate_generation import CandidateGenerator, StartGenerator
-from candidate_operations.basic_mutations import RattleMutation
+from gofee.candidates import CandidateGenerator, StartGenerator, RattleMutation
 from gofee import GOFEE
 
 ### Define calculator ###