Merge pull request #58 from pyiron/rename_calculator_to_workflow

Rename calculators to workflows

docs/source/materialproperties.md

@@ -17,7 +17,7 @@ from gpaw import GPAW, PW
 import numpy as np
 
 
-calculator = EnergyVolumeCurveWorkflow(
+workflow = EnergyVolumeCurveWorkflow(
     structure=bulk("Al", a=4.05, cubic=True),
     num_points=11,
     fit_type='polynomial',
@@ -26,7 +26,7 @@ calculator = EnergyVolumeCurveWorkflow(
     axes=['x', 'y', 'z'],
     strains=None,
 )
-task_dict = calculator.generate_structures()
+task_dict = workflow.generate_structures()
 result_dict = evaluate_with_ase(
     task_dict=task_dict,
     ase_calculator=GPAW(
@@ -35,7 +35,7 @@ result_dict = evaluate_with_ase(
         kpts=(3, 3, 3)
     )
 )
-fit_dict = calculator.analyse_structures(output_dict=result_dict)
+fit_dict = workflow.analyse_structures(output_dict=result_dict)
 print(fit_dict)
 ```
 
@@ -51,14 +51,14 @@ from gpaw import GPAW, PW
 import numpy as np
 
 
-calculator = ElasticMatrixWorkflow(
+workflow = ElasticMatrixWorkflow(
     structure=bulk("Al", a=4.0, cubic=True),
     num_of_point=5,
     eps_range=0.05,
     sqrt_eta=True,
     fit_order=2
 )
-task_dict = calculator.generate_structures()
+task_dict = workflow.generate_structures()
 result_dict = evaluate_with_ase(
     task_dict=task_dict,
     ase_calculator=GPAW(
@@ -67,7 +67,7 @@ result_dict = evaluate_with_ase(
         kpts=(3, 3, 3)
     )
 )
-elastic_dict = calculator.analyse_structures(output_dict=result_dict)
+elastic_dict = workflow.analyse_structures(output_dict=result_dict)
 print(elastic_dict)
 ```
 
@@ -135,7 +135,7 @@ pes.plot_contourf(show_min_erg_path=True)
 ```
 ### Quasi-Harmonic Approximation 
 ```
-calculator = QuasiHarmonicWorkflow(
+workflow = QuasiHarmonicWorkflow(
     structure=structure,
     num_points=11,
     vol_range=0.05,
@@ -146,13 +146,13 @@ calculator = QuasiHarmonicWorkflow(
     primitive_matrix=None,
     number_of_snapshots=None,
 )
-structure_dict = calculator.generate_structures()
+structure_dict = workflow.generate_structures()
 result_dict = evaluate_with_lammps(
     task_dict=structure_dict,
     potential_dataframe=potential_dataframe,
 )
-eng_internal_dict, mesh_collect_dict, dos_collect_dict = calculator.analyse_structures(output_dict=result_dict)
-tp_collect_dict = calculator.get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)  
+eng_internal_dict, mesh_collect_dict, dos_collect_dict = workflow.analyse_structures(output_dict=result_dict)
+tp_collect_dict = workflow.get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)  
 
 temperatures = tp_collect_dict[1.0]['temperatures']
 temperature_max = max(temperatures)

tests/test_elastic_emt.py

@@ -9,16 +9,16 @@
 
 class TestElastic(unittest.TestCase):
     def test_calc_elastic(self):
-        calculator = ElasticMatrixWorkflow(
+        workflow = ElasticMatrixWorkflow(
             structure=bulk("Al", a=4.0, cubic=True),
             num_of_point=5,
             eps_range=0.005,
             sqrt_eta=True,
             fit_order=2
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(task_dict=task_dict, ase_calculator=EMT())
-        elastic_dict = calculator.analyse_structures(output_dict=result_dict)
+        elastic_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(elastic_dict["C"][0, 0], 52.62435421))
         self.assertTrue(np.isclose(elastic_dict["C"][0, 1], 32.6743838))
         self.assertTrue(np.isclose(elastic_dict["C"][3, 3], 35.58677436))

tests/test_elastic_gpaw.py

@@ -18,14 +18,14 @@
 )
 class TestElastic(unittest.TestCase):
     def test_calc_elastic(self):
-        calculator = ElasticMatrixWorkflow(
+        workflow = ElasticMatrixWorkflow(
             structure=bulk("Al", a=4.0, cubic=True),
             num_of_point=5,
             eps_range=0.05,
             sqrt_eta=True,
             fit_order=2
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=GPAW(
@@ -34,8 +34,7 @@ def test_calc_elastic(self):
                 kpts=(3, 3, 3)
             )
         )
-        elastic_dict = calculator.analyse_structures(output_dict=result_dict)
-        print(elastic_dict)
+        elastic_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(elastic_dict["C"][0, 0], 125.66807354, atol=1e-04))
         self.assertTrue(np.isclose(elastic_dict["C"][0, 1], 68.41418321, atol=1e-04))
         self.assertTrue(np.isclose(elastic_dict["C"][3, 3], 99.29916329, atol=1e-04))

tests/test_elastic_lammps.py

@@ -34,19 +34,19 @@ def test_calc_elastic(self):
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        calculator = ElasticMatrixWorkflow(
+        workflow = ElasticMatrixWorkflow(
             structure=result_dict["structure_with_optimized_positions_and_volume"],
             num_of_point=5,
             eps_range=0.005,
             sqrt_eta=True,
             fit_order=2
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_lammps(
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        elastic_dict = calculator.analyse_structures(output_dict=result_dict)
+        elastic_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(elastic_dict["C"][0, 0], 114.10393023))
         self.assertTrue(np.isclose(elastic_dict["C"][0, 1], 60.51098897))
         self.assertTrue(np.isclose(elastic_dict["C"][3, 3], 51.23853765))

tests/test_evcurve_abinit.py

@@ -34,7 +34,7 @@ def validate_fitdict(fit_dict):
 )
 class TestEvCurve(unittest.TestCase):
     def test_calc_evcurve(self):
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=bulk("Al", a=4.05, cubic=True),
             num_points=11,
             fit_type='polynomial',
@@ -43,7 +43,7 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=Abinit(
@@ -55,5 +55,5 @@ def test_calc_evcurve(self):
                 v8_legacy_format=False,
             )
         )
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(all(validate_fitdict(fit_dict=fit_dict)))

tests/test_evcurve_emt.py

@@ -9,7 +9,7 @@
 
 class TestEvCurve(unittest.TestCase):
     def test_calc_evcurve(self):
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=bulk("Al", a=4.0, cubic=True),
             num_points=11,
             fit_type='polynomial',
@@ -18,9 +18,9 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(task_dict=task_dict, ase_calculator=EMT())
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(fit_dict['volume_eq'], 63.72615218844302))
         self.assertTrue(np.isclose(fit_dict['bulkmodul_eq'], 39.544084907317895))
         self.assertTrue(np.isclose(fit_dict['b_prime_eq'], 2.2509394023322566))

tests/test_evcurve_gpaw.py

@@ -19,7 +19,7 @@
 )
 class TestEvCurve(unittest.TestCase):
     def test_calc_evcurve(self):
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=bulk("Al", a=4.05, cubic=True),
             num_points=11,
             fit_type='polynomial',
@@ -28,7 +28,7 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=GPAW(
@@ -37,8 +37,7 @@ def test_calc_evcurve(self):
                 kpts=(3, 3, 3)
             )
         )
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
-        print(fit_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(fit_dict['volume_eq'], 66.44252286131331, atol=1e-04))
         self.assertTrue(np.isclose(fit_dict['bulkmodul_eq'], 72.38919826652857, atol=1e-04))
         self.assertTrue(np.isclose(fit_dict['b_prime_eq'], 4.453836551712821, atol=1e-04))

tests/test_evcurve_lammps.py

@@ -35,7 +35,7 @@ def test_calc_evcurve(self):
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=result_dict["structure_with_optimized_positions_and_volume"],
             num_points=11,
             fit_type='polynomial',
@@ -44,12 +44,12 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_lammps(
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(np.isclose(fit_dict['volume_eq'], 66.43019853103964))
         self.assertTrue(np.isclose(fit_dict['bulkmodul_eq'], 77.7250135953191))
         self.assertTrue(np.isclose(fit_dict['b_prime_eq'], 1.2795467367276832))

tests/test_evcurve_qe.py

@@ -37,7 +37,7 @@ def validate_fitdict(fit_dict):
 class TestEvCurve(unittest.TestCase):
     def test_calc_evcurve(self):
         pseudopotentials = {"Al": "Al.pbe-n-kjpaw_psl.1.0.0.UPF"}
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=bulk("Al", a=4.15, cubic=True),
             num_points=11,
             fit_type='polynomial',
@@ -46,7 +46,7 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=Espresso(
@@ -56,5 +56,5 @@ def test_calc_evcurve(self):
                 kpts=(3, 3, 3),
             )
         )
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(all(validate_fitdict(fit_dict=fit_dict)))

tests/test_evcurve_siesta.py

@@ -38,7 +38,7 @@ def validate_fitdict(fit_dict):
 )
 class TestEvCurve(unittest.TestCase):
     def test_calc_evcurve(self):
-        calculator = EnergyVolumeCurveWorkflow(
+        workflow = EnergyVolumeCurveWorkflow(
             structure=bulk("Al", a=4.15, cubic=True),
             num_points=11,
             fit_type='polynomial',
@@ -47,7 +47,7 @@ def test_calc_evcurve(self):
             axes=['x', 'y', 'z'],
             strains=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=Siesta(
@@ -62,5 +62,5 @@ def test_calc_evcurve(self):
                 pseudo_qualifier="",
             )
         )
-        fit_dict = calculator.analyse_structures(output_dict=result_dict)
+        fit_dict = workflow.analyse_structures(output_dict=result_dict)
         self.assertTrue(all(validate_fitdict(fit_dict=fit_dict)))

tests/test_phonons_emt.py

@@ -9,7 +9,7 @@
 
 class TestPhonons(unittest.TestCase):
     def test_calc_phonons(self):
-        calculator = PhonopyWorkflow(
+        workflow = PhonopyWorkflow(
             structure=bulk("Al", a=4.0, cubic=True),
             interaction_range=10,
             factor=VaspToTHz,
@@ -18,10 +18,10 @@ def test_calc_phonons(self):
             primitive_matrix=None,
             number_of_snapshots=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(task_dict=task_dict, ase_calculator=EMT())
-        mesh_dict, dos_dict = calculator.analyse_structures(output_dict=result_dict)
-        self.assertEqual((324, 324), calculator.get_hesse_matrix().shape)
+        mesh_dict, dos_dict = workflow.analyse_structures(output_dict=result_dict)
+        self.assertEqual((324, 324), workflow.get_hesse_matrix().shape)
         self.assertTrue('qpoints' in mesh_dict.keys())
         self.assertTrue('weights' in mesh_dict.keys())
         self.assertTrue('frequencies' in mesh_dict.keys())

tests/test_phonons_gpaw.py

@@ -18,7 +18,7 @@
 )
 class TestPhonons(unittest.TestCase):
     def test_calc_phonons(self):
-        calculator = PhonopyWorkflow(
+        workflow = PhonopyWorkflow(
             structure=bulk("Al", a=4.05, cubic=True),
             interaction_range=10,
             factor=VaspToTHz,
@@ -27,7 +27,7 @@ def test_calc_phonons(self):
             primitive_matrix=None,
             number_of_snapshots=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=GPAW(
@@ -36,8 +36,8 @@ def test_calc_phonons(self):
                 kpts=(3, 3, 3)
             )
         )
-        mesh_dict, dos_dict = calculator.analyse_structures(output_dict=result_dict)
-        self.assertEqual((324, 324), calculator.get_hesse_matrix().shape)
+        mesh_dict, dos_dict = workflow.analyse_structures(output_dict=result_dict)
+        self.assertEqual((324, 324), workflow.get_hesse_matrix().shape)
         self.assertTrue('qpoints' in mesh_dict.keys())
         self.assertTrue('weights' in mesh_dict.keys())
         self.assertTrue('frequencies' in mesh_dict.keys())

tests/test_phonons_lammps.py

@@ -34,7 +34,7 @@ def test_calc_phonons(self):
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        calculator = PhonopyWorkflow(
+        workflow = PhonopyWorkflow(
             structure=result_dict["structure_with_optimized_positions_and_volume"],
             interaction_range=10,
             factor=VaspToTHz,
@@ -43,13 +43,13 @@ def test_calc_phonons(self):
             primitive_matrix=None,
             number_of_snapshots=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_lammps(
             task_dict=task_dict,
             potential_dataframe=df_pot_selected,
         )
-        mesh_dict, dos_dict = calculator.analyse_structures(output_dict=result_dict)
-        self.assertEqual((324, 324), calculator.get_hesse_matrix().shape)
+        mesh_dict, dos_dict = workflow.analyse_structures(output_dict=result_dict)
+        self.assertEqual((324, 324), workflow.get_hesse_matrix().shape)
         self.assertTrue('qpoints' in mesh_dict.keys())
         self.assertTrue('weights' in mesh_dict.keys())
         self.assertTrue('frequencies' in mesh_dict.keys())

tests/test_quasiharmonic_emt.py

@@ -9,7 +9,7 @@
 
 class TestPhonons(unittest.TestCase):
     def test_calc_phonons(self):
-        calculator = QuasiHarmonicWorkflow(
+        workflow = QuasiHarmonicWorkflow(
             structure=bulk("Al", a=4.0, cubic=True),
             num_points=11,
             vol_range=0.05,
@@ -20,12 +20,12 @@ def test_calc_phonons(self):
             primitive_matrix=None,
             number_of_snapshots=None,
         )
-        task_dict = calculator.generate_structures()
+        task_dict = workflow.generate_structures()
         result_dict = evaluate_with_ase(
             task_dict=task_dict,
             ase_calculator=EMT()
         )
-        eng_internal_dict, mesh_collect_dict, dos_collect_dict = calculator.analyse_structures(output_dict=result_dict)
-        tp_collect_dict = calculator.get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)
+        eng_internal_dict, mesh_collect_dict, dos_collect_dict = workflow.analyse_structures(output_dict=result_dict)
+        tp_collect_dict = workflow.get_thermal_properties(t_min=1, t_max=1500, t_step=50, temperatures=None)
         self.assertEqual(len(eng_internal_dict.keys()), 11)
         self.assertEqual(len(tp_collect_dict.keys()), 11)