version 0.1.0 of APTrajectories

Author: skatnagallu

.DS_Store

@@ -1,4 +1,11 @@
-$Robin-Rolland^{[1]}$ type simulations for APT trajectories.
+# Installation
+
+Install by using
+'''pip install APTrajectories'''
+
+For usage, see the [example Notebook](example.ipynb) notebook
+
+# $Robin-Rolland^{[1]}$ type simulations for APT trajectories.
 
 ![conductor surface](conductor_surface.PNG)
 

Example/fin_evapos.h5

@@ -1,77 +1,70 @@
+"""Module for pyiron job based on the RRmodel module"""
 from pyiron_base.utils.error import ImportAlarm
 from pyiron_base.jobs.job.template import TemplateJob
-import h5py
-import numpy as np
 from pyiron_base.jobs.job.jobtype import JobType
+import h5io
 try:
     from RobinRollandModel.main import RRModel
     from RobinRollandModel.datautils import TipGenerator
 except ImportError:
     import_alarm = ImportAlarm("Unable to import RobinRollandmodel")
 
+
 class RRModelAPTjob(TemplateJob):
+    """pyiron job class for RRModelAPT simulation"""
+
     def __init__(self, project, job_name):
         super().__init__(project, job_name)
-        self.input['e_field'] = 4
-        self.input['tip_height'] = 80
-        self.input['tip_radius'] = 20
-        self.input['z_height'] = 50
-        self.input['tip_shank_angle'] = None
-        self.input['basic_structure'] = None
-        self.input['num_atoms'] = 5 #number of atoms to evaporate
+        self.input["e_field"] = 4
+        self.input["tip_height"] = 80
+        self.input["tip_radius"] = 20
+        self.input["z_height"] = 50
+        self.input["tip_shank_angle"] = None
+        self.input["basic_structure"] = None
+        self.input["num_atoms"] = 5  # number of atoms to evaporate
 
     def create_input_structure(self):
-        tip_generator = TipGenerator(structure=self.input.basic_structure,
-                                                   h=self.input.tip_height,
-                                                   ah=self.input.tip_radius,
-                                                   alpha=self.input.tip_shank_angle,
-                                                   zheight=self.input.z_height)
-        self.input['structure'] = tip_generator.create_tip_pyiron(self.project) # structure of the tip
+        """Creates the tip structure"""
+        tip_generator = TipGenerator(
+            structure=self.input.basic_structure,
+            h=self.input.tip_height,
+            ah=self.input.tip_radius,
+            alpha=self.input.tip_shank_angle,
+            zheight=self.input.z_height,
+        )
+        self.input["structure"] = tip_generator.create_tip_pyiron(
+            self.project
+        )  # structure of the tip
         return tip_generator
 
-    def run_static(self,**kwargs):
+    def run_static(self, **kwargs):
         tip_generator = self.create_input_structure()
-        #self.input['structure']= tip_generator.create_tip_pyiron(self.project)
-        job = RRModel(tip_generator=tip_generator,
-                      structure=self.input.structure,
-                      e_field=self.input.e_field)
-        job.run_evaporation(num_atoms=self.input.num_atoms,path=self.working_directory,**kwargs)
+        # self.input['structure']= tip_generator.create_tip_pyiron(self.project)
+        job = RRModel(
+            tip_generator=tip_generator,
+            structure=self.input.structure,
+            e_field=self.input.e_field,
+        )
+        job.run_evaporation(
+            num_atoms=self.input.num_atoms, path=self.working_directory, **kwargs
+        )
         self.collect_output()
-        
-        self.status.finished = True
 
+        self.status.finished = True
 
     def collect_output(self, path=None):
         if path is None:
             path = self.working_directory
-        
-        fin_evapos = {}
-        with h5py.File(f'{path}/fin_evapos.h5','r') as output:
-            for varname in output.keys ():
-                atom = float(str(varname).replace('step=',''))
-                fin_evapos[atom] = np.asarray(output[varname])
-        self.output['evaporation_trajectories'] = fin_evapos
-        
-        tip_pos = {}
-        with h5py.File(f'{path}/tip_pos.h5','r') as output:
-            for varname in output.keys ():
-                atom = float(str(varname).replace('step=',''))
-                tip_pos[atom] = np.asarray(output[varname])
-        self.output['tip_structures'] = tip_pos
-        
-        tip_pos_charge = {}
-        with h5py.File(f'{path}/tip_pos_charge.h5','r') as output:
-            for varname in output.keys ():
-                atom = float(str(varname).replace('step=',''))
-                tip_pos_charge[atom] = np.asarray(output[varname])
-        self.output['equilibrium_charges'] = tip_pos_charge
-        
-        tip_surf_ind = {}
-        with h5py.File(f'{path}/tip_surf_ind.h5','r') as output:
-            for varname in output.keys ():
-                atom = float(str(varname).replace('step=',''))
-                tip_surf_ind[atom] = np.asarray(output[varname])
-        self.output['surface_indices'] = tip_surf_ind
-        #self.to_hdf() #is a duplication of output to job hdf5 file
 
-JobType.register(RRModelAPTjob)
+        fin_evapos = h5io.read_hdf5(f'{path}/fin_evapos.h5')
+        tip_pos = h5io.read_hdf5(f'{path}/tip_pos.h5')
+        tip_pos_charge = h5io.read_hdf5(f'{path}/tip_pos_charge.h5')
+        tip_surf_ind = h5io.read_hdf5(f'{path}/tip_surf_ind.h5')
+        self.output["evaporation_trajectories"] = fin_evapos
+        self.output["tip_structures"] = tip_pos
+        self.output["equilibrium_charges"] = tip_pos_charge
+        self.output["surface_indices"] = tip_surf_ind
+        self.to_hdf() #is a duplication of output to job hdf5 file
+
+
+JobType.register(RRModelAPTjob)