Merge branch 'master' into fourier_gradient

Author: mesonepigreco

.github/workflows/python-testsuite.yml

@@ -13,28 +13,39 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+  
     strategy:
       matrix:
         python-version: [3.8]
+    
+    services:
+      rabbitmq:
+          image: rabbitmq:latest
+          ports:
+          -   5672:5672
 
     steps:
     - uses: actions/checkout@v2
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        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
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Install
       run: |
         sudo apt-get update
@@ -49,8 +60,9 @@ jobs:
         # Install julia requirements
         python -c 'import julia; julia.install()'
     - name: Test with pytest
+      env:
+        OMP_NUM_THREADS: 1
       run: |
-        export OMP_NUM_THREADS=1
         cd tests
         rm -rf __pycache__
         # Test excluding very long running tests

.gitignore

@@ -0,0 +1,128 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Dev
+.vscode
+.history/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache
+input_tmp.in
+tmp_dyn*
+dyn_end_*
+dyn_start_*
+final_dyn*
+grad_*.dat
+u_population*.dat
+energies*.dat
+forces_*.dat
+prova
+scf_population*.dat
+frequencies*.*
+timer.json
+minim.dat
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+*~
+.DS_Store
+.idea
+submit_test/
+# Autogenerated API docs
+docs/*
+tox.ini

Modules/Cluster.py

@@ -1516,10 +1516,11 @@ def compute_single_jobarray(jobs_id, calc):
                     if error_struct > 1e-2:
                         print("ERROR IDENTIFYING STRUCTURE!")
                         MSG = """
-Error in thread {}.
-     Displacement between the expected structure {} and the one readed from the calculator
-     is of {} A.
-""".format(threading.get_native_id(), jobs_id[i], error_struct)
+                            Error in thread {}.
+                            Displacement between the expected structure {} 
+                            and the one readed from the calculator
+                            is of {} A.
+                        """.format(threading.get_native_id(), jobs_id[i], error_struct)
                         print(MSG)
                         ensemble.structures[jobs_id[i]].save_scf('t_{}_error_struct_generated_{}.scf'.format(threading.get_native_id(), jobs_id[i]))
                         structures[i].save_scf('t_{}_error_struct_cmp_local_{}.scf'.format(threading.get_native_id(), jobs_id[i]))

Modules/Ensemble.py

@@ -89,12 +89,22 @@
         from julia.api import Julia
         jl = Julia(compiled_modules=False)
         import julia.Main
-        julia.Main.include(os.path.join(os.path.dirname(__file__),
+        try:
+            julia.Main.include(os.path.join(os.path.dirname(__file__),
             "fourier_gradient.jl"))
-        __JULIA_EXT__ = True
-    except:
-        raise 
-    pass
+            __JULIA_EXT__ = True
+        except:
+            # Install the required modules
+            julia.install()
+            try:
+                julia.Main.include(os.path.join(os.path.dirname(__file__),
+                    "fourier_gradient.jl"))
+                __JULIA_EXT__ = True
+            except Exception as e:
+                warnings.warn("Julia extension not available.\nError: {}".format(e))
+    except Exception as e:
+        warnings.warn("Julia extension not available.\nError: {}".format(e))
+
 
 try:
     from ase.units import create_units

Modules/Relax.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from __future__ import print_function
+from __future__ import print_function, annotations
 
 """
 This module performs the relax over more
@@ -15,6 +15,7 @@
 import sscha.Utilities as Utilities
 import cellconstructor as CC
 import cellconstructor.symmetries
+from sscha.aiida_ensemble import AiiDAEnsemble
 
 import sys, os
 
@@ -49,8 +50,17 @@
 
 class SSCHA(object):
 
-    def __init__(self, minimizer = None, ase_calculator=None, N_configs=1, max_pop = 20,
-                 save_ensemble = False, cluster = None, **kwargs):
+    def __init__(
+        self,
+        minimizer = None,
+        ase_calculator=None, 
+        aiida_inputs: dict | None = None,
+        N_configs=1, 
+        max_pop = 20,
+        save_ensemble = False, 
+        cluster = None,
+        **kwargs
+    ):
         """
         This module initialize the relaxer. It may perform
         constant volume or pressure relaxation using fully anharmonic potentials.
@@ -63,6 +73,16 @@ def __init__(self, minimizer = None, ase_calculator=None, N_configs=1, max_pop =
             ase_calculator : ase.calculators...
                 An initialized ASE calculator. This will be used to compute energies and forces
                 for the relaxation of the SSCHA.
+            aiida_input: dict
+                Dictionary containing the input data for the 
+                :class:`~sscha.aiida_ensemble.AiiDAEnsemble.compute_ensmble`
+                method; namely:
+                    * pw_code: str,
+                    * protocol: str = 'moderate',
+                    * options: dict = None,
+                    * overrides: dict = None,
+                    * group_label: str = None,
+                    * kwargs
             N_configs : int
                 The number of configuration to be used for each population
             max_pop: int, optional
@@ -84,6 +104,7 @@ def __init__(self, minimizer = None, ase_calculator=None, N_configs=1, max_pop =
         self.N_configs = N_configs
         self.max_pop = max_pop
         self.cluster = cluster
+        self.aiida_inputs = aiida_inputs
         self.start_pop = 1
 
         # If the ensemble must be saved at each iteration.
@@ -351,8 +372,11 @@ def relax(self, restart_from_ens = False, get_stress = False,
                 self.minim.ensemble.generate(self.N_configs, sobol = sobol, sobol_scramble = sobol_scramble, sobol_scatter = sobol_scatter)
 
                 # Compute energies and forces
-                self.minim.ensemble.compute_ensemble(self.calc, get_stress,
-                                                 cluster = self.cluster)
+                if isinstance(self.minim.ensemble, AiiDAEnsemble):
+                    self.minim.ensemble.compute_ensemble(**self.aiida_inputs)
+                else:
+                    self.minim.ensemble.compute_ensemble(
+                        self.calc, get_stress, cluster = self.cluster)
                 #self.minim.ensemble.get_energy_forces(self.calc, get_stress)
 
                 if ensemble_loc is not None and self.save_ensemble:
@@ -573,8 +597,11 @@ def vc_relax(self, target_press = 0, static_bulk_modulus = 100,
                 #    self.minim.ensemble.save_bin(ensemble_loc, pop)
 
                 # Compute energies and forces
-                self.minim.ensemble.compute_ensemble(self.calc, True, stress_numerical,
-                                                 cluster = self.cluster)
+                if isinstance(self.minim.ensemble, AiiDAEnsemble):
+                    self.minim.ensemble.compute_ensemble(**self.aiida_inputs)
+                else:
+                    self.minim.ensemble.compute_ensemble(
+                        self.calc, True, stress_numerical, cluster = self.cluster)
                 #self.minim.ensemble.get_energy_forces(self.calc, True, stress_numerical = stress_numerical)
 
                 print("RELAX force length:", len(self.minim.ensemble.force_computed))