Merge branch 'master' into asr_1d

Author: mesonepigreco

.github/workflows/python-testsuite.yml

@@ -13,11 +13,11 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-  
+
     strategy:
       matrix:
         python-version: [3.8]
-    
+
     services:
       rabbitmq:
           image: rabbitmq:latest
@@ -38,6 +38,7 @@ jobs:
         pip install flake8 pytest~=6.0 pgtest~=1.3 aiida-core~=2.3 aiida-quantumespresso~=4.3
         if [ ${{matrix.python-version}} -eq 2.7 ]; then pip install -r requirements2.txt;
         else pip install -r requirements.txt; fi
+        aiida-pseudo install
 
     - name: Lint with flake8
       run: |
@@ -54,7 +55,7 @@ jobs:
         cd CellConstructor
         python setup.py install --user
         cd ..
-        
+
         python setup.py install --user
 
         # Install julia requirements

CONTRIBUTING.md

@@ -0,0 +1,32 @@
+# Contributing Guidelines
+
+Welcome to python-sscha! We appreciate your interest in contributing. Below are the guidelines to contribute effectively to our codebase.
+
+## Forking and Pull Requests
+
+1. **Fork the Repository:** Start by forking the repository to your GitHub account. This creates a copy where you can make your changes.
+2. **Create a Branch:** Within your fork, create a new branch for your changes. This keeps the work organized and separate from the main codebase.
+3. **Open a Pull Request:** Once your changes are complete, open a pull request against the main repository. This is where your contributions will be reviewed before merging.
+
+## Making Atomic Changes
+
+- **Keep Changes Well-Localized:** Ensure that your changes are atomic. This means that each change should be self-contained and impact only a specific aspect of the code.
+- **Avoid Complete Rewrites:** Use existing code as a basis for your changes. Avoid rewriting everything or duplicating existing code unless absolutely necessary.
+- **Make use of CellConstructor** Most utility functions are implemented in CellConstructor, please, look into the code, specifically the Methods.py, Phonons.py and Structure.py to find helper and utility functions.
+- **Mind the final user** Do not expect the user to be an expert on what you are doing. Ideally, the final API for the user should be as much as black box as possible. Avoid making the user to do unit conversion from the standard SSCHA and CellConstructor units. 
+- **Ensure backward compatibility** Its very bad if an user updates the code and they cannot reuse all their scripts. Ideally, your change shoud not break any existing feature or require the user to change their scripts.
+
+## Adding Tests
+
+- **Write Complete Tests:** For every edit or addition, include a complete test. This ensures that your changes work as expected and do not break existing functionality.
+- **Tests inside the tests/ directory** Look for examples on other tests. Include files to reproduce your tests. The tests must be quick to run, maximum few seconds.
+- **Run the testsuit yourself** You can install pytest and run all the tests yourself to ensure everything is working before opening the pull request.
+
+## Documentation and Examples
+
+- **Document Your Changes:** Clearly document any changes or additions you make to the codebase. This helps others understand what you've done and why. Use docstrings for functions! (we use reStructuredText .rst format)
+- **Provide Usage Examples:** Include examples demonstrating how to use the new implementations or changes. Put an example inside the Examples/ directory.
+- **Write a tutorial** The best way to have your pull request quickly merged into the main code is to write a usefull tutorial for users on how to use your new functionality.
+
+By following these guidelines, you help maintain the quality and integrity of the SSCHA project. We look forward to your contributions!
+

Modules/AdvancedCalculations.py

@@ -11,7 +11,7 @@
 This module contains useful functions to do post-processing analysis of the SSCHA.
 
 For example, it implements custom cluster calculators to compute the electron-phonon effect on
-absorbption and the bandgap.
+absorption and the bandgap.
 
 '''
 
@@ -23,7 +23,7 @@ class OpticalQECluster(sscha.Cluster.Cluster):
     '''
 
     def __init__(self, new_k_grid = None, random_offset = True, epsilon_data = None,
-                epsilon_binary = 'epsilon.x -npool NPOOL -i PREFIX.pwi > PREFIX.pwo', 
+                epsilon_binary = 'epsilon.x -npool NPOOL -i PREFIX.pwi > PREFIX.pwo',
                 **kwargs):
         '''
         Initialize the cluster object.
@@ -40,7 +40,7 @@ def __init__(self, new_k_grid = None, random_offset = True, epsilon_data = None,
                 epsilon.x file
             epsilon_binary : string
                 The path to the epsilon.x binary inside the cluster.
-            **kwargs : 
+            **kwargs :
                 All other arguments to be passed to the cluster.
 
         '''
@@ -67,7 +67,7 @@ def __init__(self, new_k_grid = None, random_offset = True, epsilon_data = None,
                 'wmax' : 40,
                 'nw' : 10000,
                 'temperature' : 300
-            }   
+            }
         }
         if epsilon_data is not None:
             self.epsilon_data = epsilon_data
@@ -79,10 +79,10 @@ def __setattr__(self, __name, __value):
         super().__setattr__(__name, __value)
 
         # Always regenerate the kpts
-        if __name == 'new_k_grid' and not __value is None: 
+        if __name == 'new_k_grid' and not __value is None:
             assert len(__value) == 3, 'Error, new_k_grid must be a tuple with 3 elements'
             self.generate_kpts()
-    
+
 
     def generate_kpts(self):
         '''
@@ -119,7 +119,7 @@ def get_execution_command(self, label):
 
         # Get the MPI command replacing NPROC
         new_mpicmd  = self.mpi_cmd.replace("NPROC", str(self.n_cpu))
-        
+
         # Replace the NPOOL variable and the PREFIX in the binary
         binary = self.binary.replace("NPOOL", str(self.n_pool)).replace("PREFIX", label)
         binary_nscf = self.binary.replace("NPOOL", str(self.n_pool)).replace("PREFIX", label + '_nscf')
@@ -147,6 +147,18 @@ def get_execution_command(self, label):
     def read_results(self, calc, label):
         '''
         Get the results
+
+        Parameters
+        ----------
+            calc : the ASE or CellConstructor calculator.
+                In this case, it works with quantum espresso
+            labels : List of strings
+                The unique name of this calculation
+        Returns
+        -------
+            results : array
+                An array containing the real part of epsilon, 
+                and the mean of the real and imaginary parst of epsilon.
         '''
 
         results = super().read_results(calc, label)
@@ -176,7 +188,31 @@ def read_results(self, calc, label):
     def prepare_input_file(self, structures, calc, labels):
         '''
         Prepare the input files for the cluster
-        '''    
+
+        This is specific for quantum espresso and must be inherit and replaced for
+        other calculators.
+
+        This crates the input files in the local working directory
+        self.local_workdir and it returns the list of all the files generated.
+
+
+        Parameters
+        ----------
+            structures : List of cellconstructor.Structure.Structure
+                The atomic structures.
+            calc : the ASE or CellConstructor calculator.
+                In this case, it works with quantum espresso
+            labels : List of strings
+                The unique name of this calculation
+
+        Returns
+        -------
+            List_of_input : list
+                List of strings containing all the input files
+            List_of_output : list
+                List of strings containing the output files expected
+                for the calculation
+        '''
 
 
         # Prepare the input file
@@ -185,7 +221,7 @@ def prepare_input_file(self, structures, calc, labels):
         for i, (label, structure) in enumerate(zip(labels, structures)):
             # Avoid thread conflict
             self.lock.acquire()
-            
+
             try:
                 calc.set_directory(self.local_workdir)
                 PREFIX = label
@@ -204,7 +240,7 @@ def prepare_input_file(self, structures, calc, labels):
                 input_file = '{}.pwi'.format(label)
                 output_file = '{}.pwo'.format(label)
 
-                list_of_inputs.append(input_file)     
+                list_of_inputs.append(input_file)
                 list_of_outputs.append(output_file)
 
                 # prepare the nscf calculation
@@ -218,7 +254,7 @@ def prepare_input_file(self, structures, calc, labels):
                 calc.write_input(structure)
                 input_file = '{}.pwi'.format(new_label)
                 output_file = '{}.pwo'.format(new_label)
-                list_of_inputs.append(input_file)     
+                list_of_inputs.append(input_file)
                 list_of_outputs.append(output_file)
 
 
@@ -239,8 +275,8 @@ def prepare_input_file(self, structures, calc, labels):
                     print('fname: {} prepared'.format(eps_in_filename))
 
 
-                
-                list_of_inputs.append(input_file)     
+
+                list_of_inputs.append(input_file)
                 list_of_outputs.append(output_file)
 
                 # Append also the imaginary and real part of epsilon and sigma
@@ -263,11 +299,11 @@ def prepare_input_file(self, structures, calc, labels):
                 print(e)
 
             # Release the lock on the threads
-            self.lock.release()            
+            self.lock.release()
 
         print('THREAD: {} inputs: {} outputs: {}'.format(threading.get_native_id(), list_of_inputs, list_of_outputs))
-            
-        
+
+
         return list_of_inputs, list_of_outputs
 
 
@@ -306,7 +342,7 @@ def get_optical_spectrum(ensemble, w_array = None):
 Error, the configuration {} has no 'epsilon' data.
 """.format(i)
             raise ValueError(ERR)
-        
+
         data = np.array(ensemble.all_properties[i]['epsilon'])
 
         if w_data is None:
@@ -330,13 +366,11 @@ def get_optical_spectrum(ensemble, w_array = None):
             kind = 'cubic', bounds_error = False, fill_value = 'extrapolate')
         eps_imag = f_imag(w_array)
         w_data = w_array
-    
+
     # Build the complex epsilon
     epsilon = eps_real + 1j * eps_imag
 
     # Build the refractive index
     n = np.sqrt(epsilon)
 
     return w_data, n
-
-