Sync temperature in hybridization and current steps

examples/coulomb_blockade/pentacene/curr.py

@@ -66,7 +66,7 @@ def compute_current(
     V_min=-2.5,
     V_max=2.5,
     dV=0.1,
-    temperature=9,
+    temperature=300.0,
     transmission_folder_path="transmission_folder",
 ) -> None:
     """docstring"""

examples/coulomb_blockade/pentacene/hybr.py

@@ -7,6 +7,7 @@
 from pathlib import Path
 
 import numpy as np
+from ase.units import kB
 from qtpyt.block_tridiag import greenfunction
 from qtpyt.continued_fraction import get_ao_charge
 from qtpyt.hybridization import Hybridization
@@ -21,13 +22,13 @@ def hybridize_orbitals(
     hs_list_ii,
     hs_list_ij,
     self_energies,
+    temperature=300.0,
     solver="dyson",
     eta=1e-4,
     E_min=-3.0,
     E_max=3.0,
     E_step=1e-2,
-    E_grid_size=3000,
-    beta=70.0,
+    matsubara_grid_scalar=1.0,
 ) -> None:
     """docstring"""
 
@@ -70,8 +71,10 @@ def hybridize_orbitals(
 
     # Matsubara
     gf.eta = 0.0
-    energies = 1.0j * (2 * np.arange(E_grid_size) + 1) * np.pi / beta
-    gd = GridDesc(energies, no, complex)
+    beta = 1 / (kB * temperature)
+    E_grid_size = len(energies) * matsubara_grid_scalar
+    matsubara_energies = 1.0j * (2 * np.arange(E_grid_size) + 1) * np.pi / beta
+    gd = GridDesc(matsubara_energies, no, complex)
     HB = gd.empty_aligned_orbs()
 
     for e, energy in enumerate(gd.energies):
@@ -81,7 +84,7 @@ def hybridize_orbitals(
 
     if comm.rank == 0:
         np.save(output_dir / "occupancies.npy", get_ao_charge(gfp))
-        np.save(output_dir / "matsubara_energies.npy", energies)
+        np.save(output_dir / "matsubara_energies.npy", matsubara_energies)
 
 
 if __name__ == "__main__":

examples/coulomb_blockade/tester.ipynb

@@ -262,16 +262,13 @@
     "    #         \"E_min\": -3.0,\n",
     "    #         \"E_max\": 3.0,\n",
     "    #         \"E_step\": 1e-2,\n",
+    "    #         \"matsubara_grid_scalar\": 1.0,\n",
     "    #     }\n",
     "    # ),\n",
     "    \"hybridization\": {\n",
     "        \"code\": orm.load_code(\"hybr-script\"),\n",
-    "        # \"parameters\": orm.Dict(\n",
-    "        #     {\n",
-    "        #         \"E_grid_size\": 3000,\n",
-    "        #         \"beta\": 70.0,\n",
-    "        #     }\n",
-    "        # ),\n",
+    "        \"temperature\": orm.Float(300.0),\n",
+    "        \"matsubara_grid_scalar\": orm.Float(1.0),\n",
     "        \"metadata\": metadata,\n",
     "    },\n",
     "    \"dmft\": {\n",
@@ -309,7 +306,6 @@
     "        #     \"V_min\": -2.5,\n",
     "        #     \"V_max\": 2.5,\n",
     "        #     \"dV\": 0.1,\n",
-    "        #     \"temperature\": 9,\n",
     "        # }),\n",
     "    },\n",
     "}"

src/aiida_quantum_transport/calculations/current.py

@@ -31,6 +31,13 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The current script",
         )
 
+        spec.input(
+            "temperature",
+            valid_type=orm.Float,
+            default=lambda: orm.Float(300.0),
+            help="The temperature in Kelvin",
+        )
+
         spec.input(
             "parameters",
             valid_type=orm.Dict,
@@ -83,8 +90,11 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
 
         parameters_filename = "parameters.pkl"
         with open(temp_input_dir / parameters_filename, "wb") as file:
-            parameters: orm.Dict = self.inputs.parameters
-            pickle.dump(parameters.get_dict(), file)
+            parameters = {
+                **self.inputs.parameters.get_dict(),
+                "temperature": self.inputs.temperature.value,
+            }
+            pickle.dump(parameters, file)
 
         precomputed_input_dir = input_dir / "precomputed"
         (temp_dir / precomputed_input_dir).mkdir()

src/aiida_quantum_transport/calculations/hybridize.py

@@ -43,6 +43,20 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             help="The results folder of the greens function parameters calculation",
         )
 
+        spec.input(
+            "temperature",
+            valid_type=orm.Float,
+            default=lambda: orm.Float(300.0),
+            help="The temperature in Kelvin",
+        )
+
+        spec.input(
+            "matsubara_grid_scalar",
+            valid_type=orm.Float,
+            default=lambda: orm.Float(1.0),
+            help="The scalar used to modify the matsubara energy grid",
+        )
+
         spec.input(
             "greens_function_parameters",
             valid_type=orm.Dict,
@@ -131,6 +145,8 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
                 **self.inputs.greens_function_parameters,
                 **self.inputs.energy_grid_parameters,
                 **self.inputs.parameters,
+                "temperature": self.inputs.temperature.value,
+                "matsubara_grid_scalar": self.inputs.matsubara_grid_scalar.value,
             }
             pickle.dump(parameters, file)
 

src/aiida_quantum_transport/workchains/coulomb_diamonds.py

@@ -96,7 +96,12 @@ def define(cls, spec: WorkChainSpec) -> None:
         spec.expose_inputs(
             HybridizationCalculation,
             namespace="hybridization",
-            include=["code", "parameters", "metadata"],
+            include=[
+                "code",
+                "temperature",
+                "matsubara_grid_scalar",
+                "metadata",
+            ],
         )
 
         spec.expose_inputs(
@@ -275,7 +280,6 @@ def compute_hybridization(self):
             },
             "greens_function_parameters": self.inputs.greens_function_parameters,
             "energy_grid_parameters": self.inputs.energy_grid_parameters,
-            "parameters": self.inputs.hybridization.parameters,
             **self.exposed_inputs(
                 HybridizationCalculation,
                 namespace="hybridization",
@@ -385,6 +389,7 @@ def compute_current(self):
             "transmission": {
                 "remote_results_folder": self.ctx.transmission.outputs.remote_results_folder,
             },
+            "temperature": self.inputs.hybridization.temperature,
             **self.exposed_inputs(
                 CurrentCalculation,
                 namespace="current",