Update docs from main

.gitattributes

@@ -0,0 +1,3 @@
+*.1relax linguist-detectable=false
+*.2relax linguist-detectable=false
+*.3static linguist-detectable=false

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Nigel Lee En Hew
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

examples/codespace/Fe3Pt.ipynb

@@ -19,6 +19,24 @@
     "4. You are now ready to run the cells below!"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "9ae53c39",
+   "metadata": {},
+   "source": [
+    "# Install pyzentropy in editable mode"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "124181fd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!cd ../../ && pip install -e ."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "8de285bd",
@@ -85,20 +103,7 @@
    "source": [
     "# PyZentropy Configuration Objects\n",
     "\n",
-    "This section constructs PyZentropy `Configuration` objects for each Fe₃Pt configuration. Properties at 0 K are excluded to avoid division by zero errors. For each configuration, internal energies and partition functions are calculated."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "eba55270",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Extract basic properties from the reference configuration\n",
-    "number_of_atoms = input[\"FM\"]['number_of_atoms']\n",
-    "volumes = input[\"FM\"]['volumes']\n",
-    "temperatures = input[\"FM\"]['temperatures'] "
+    "This section constructs PyZentropy `Configuration` objects for each Fe₃Pt configuration. For each configuration, the internal energies are calculated automatically."
    ]
   },
   {
@@ -118,38 +123,19 @@
     "    config_objects[config_name] = Configuration(\n",
     "        name=config_name,\n",
     "        multiplicity=config['multiplicity'],\n",
-    "        number_of_atoms=number_of_atoms,\n",
-    "        volumes=volumes,\n",
-    "        temperatures=temperatures,\n",
+    "        number_of_atoms=config['number_of_atoms'],\n",
+    "        volumes=config['volumes'],\n",
+    "        temperatures=config['temperatures'],\n",
     "        # Extract Helmholtz energies and their derivatives from DFTTK results\n",
-    "        helmholtz_energies=config['helmholtz_energy'],\n",
-    "        helmholtz_energies_dV=config['helmholtz_energy_dV'],\n",
-    "        helmholtz_energies_d2V2=config['helmholtz_energy_d2V2'],\n",
+    "        helmholtz_energies=config['helmholtz_energies'],\n",
+    "        helmholtz_energies_dV=config['helmholtz_energies_dV'],\n",
+    "        helmholtz_energies_d2V2=config['helmholtz_energies_d2V2'],\n",
     "        # Extract entropy and heat capacity data\n",
-    "        entropies=config['entropy'],\n",
-    "        heat_capacities=config['heat_capacity']\n",
+    "        entropies=config['entropies'],\n",
+    "        heat_capacities=config['heat_capacities']\n",
     "    )"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3e1b202a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Calculate internal energies for each configuration\n",
-    "for config in config_objects.values():\n",
-    "    config.calculate_internal_energies()\n",
-    "\n",
-    "# Use the ground state configuration as reference for partition function calculations\n",
-    "reference_helmholtz_energy = config_objects[\"FM\"].helmholtz_energies\n",
-    "\n",
-    "# Calculate partition functions for each configuration using the reference energy\n",
-    "for config in config_objects.values():\n",
-    "    config.calculate_partition_functions(reference_helmholtz_energy)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "2979bf50",
@@ -177,7 +163,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "config_objects[\"FM\"].plot(\"helmholtz_energy_vs_volume\")"
+    "config_objects[\"FM\"].plot_vt(\"helmholtz_energy_vs_volume\")"
    ]
   },
   {
@@ -190,7 +176,7 @@
     "# You can also plot for selected temperatures by passing an array of temperatures.\n",
     "# The code will automatically find and use the closest available temperatures.\n",
     "selected_temperatures = np.array([100, 300, 600, 900])\n",
-    "config_objects[\"FM\"].plot(\"helmholtz_energy_vs_volume\", selected_temperatures=selected_temperatures)"
+    "config_objects[\"FM\"].plot_vt(\"helmholtz_energy_vs_volume\", selected_temperatures=selected_temperatures)"
    ]
   },
   {
@@ -202,8 +188,8 @@
    "source": [
     "# You can also plot for selected volumes by passing an array of volumes.\n",
     "# The code will automatically find and use the closest available volumes.\n",
-    "selected_volumes = np.array([100, 120, 140, 160])\n",
-    "config_objects[\"FM\"].plot(\"helmholtz_energy_vs_temperature\", selected_volumes=selected_volumes)"
+    "selected_volumes = np.array([136, 140, 160])\n",
+    "config_objects[\"FM\"].plot_vt(\"helmholtz_energy_vs_temperature\", selected_volumes=selected_volumes)"
    ]
   },
   {
@@ -224,17 +210,7 @@
    "outputs": [],
    "source": [
     "# Create a System object from the configuration objects\n",
-    "system = System(config_objects)\n",
-    "\n",
-    "# Perform thermodynamic calculations for the system\n",
-    "system.calculate_partition_functions()\n",
-    "system.calculate_probabilities()\n",
-    "system.calculate_helmholtz_energies(reference_helmholtz_energy)\n",
-    "system.calculate_entropies()\n",
-    "system.calculate_helmholtz_energies_dV()\n",
-    "system.calculate_bulk_moduli()\n",
-    "system.calculate_helmholtz_energies_d2V2()\n",
-    "system.calculate_heat_capacities()"
+    "system = System(config_objects, ground_state=\"FM\")"
    ]
   },
   {
@@ -246,15 +222,15 @@
    "source": [
     "# Calculate phase diagrams with specified ground state configuration. \n",
     "# This also calculates all the properties at constant pressure.\n",
-    "system.calculate_phase_diagrams(ground_state=\"FM\")"
+    "system.calculate_phase_diagrams()"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "dc6c34ee",
    "metadata": {},
    "source": [
-    "The following are example plots vs. volume or temperature. For all of these plots, you can plot for `selected_temperatures` and `selected_volumes`. The available plots are:\n",
+    "The following are example plots vs. volume or temperature. For all of these plots (apart from vt_phase_diagram), you can plot for `selected_temperatures` and `selected_volumes`. The available plots are:\n",
     "\n",
     "**Helmholtz Energy**\n",
     "- \"helmholtz_energy_vs_volume\"\n",
@@ -292,36 +268,6 @@
     "system.plot_vt(\"helmholtz_energy_vs_volume\")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4f4b7ab4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "system.plot_vt(\"entropy_vs_temperature\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "987276f9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "system.plot_vt(\"heat_capacity_vs_temperature\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2f736a5a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "system.plot_vt(\"bulk_modulus_vs_temperature\")"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -337,7 +283,7 @@
    "id": "678a6f4f",
    "metadata": {},
    "source": [
-    "The following are example plots for properties at constant pressure. The available plots are:\n",
+    "The following are example plots for properties at constant pressure. You can plot for `selected_temperatures` for helmholtz_energy_pv_vs_volume. The available plots are:\n",
     "\n",
     "- \"probability_vs_temperature\"\n",
     "- \"helmholtz_energy_pv_vs_volume\"\n",
@@ -369,30 +315,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system.plot_pt(\"probability_vs_temperature\", ground_state=\"FM\", P=0)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2a171cbd",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "system.plot_pt(\"helmholtz_energy_pv_vs_volume\", P=0)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1ca0418c",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# You can also plot for selected temperatures by passing an array of temperatures.\n",
-    "# The code will automatically find and use the closest available temperatures.\n",
-    "selected_temperatures = np.array([100, 300, 600, 900])\n",
-    "system.plot_pt(\"helmholtz_energy_pv_vs_volume\", P=0, selected_temperatures=selected_temperatures)"
+    "system.plot_pt(\"probability_vs_temperature\", P=0)"
    ]
   },
   {
@@ -434,16 +357,6 @@
    "source": [
     "system.plot_pt(\"heat_capacity_vs_temperature\", P=0)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "bb30e4e6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "system.plot_pt(\"gibbs_energy_vs_temperature\", P=0)"
-   ]
   }
  ],
  "metadata": {

pyzentropy/configuration.py

@@ -99,7 +99,6 @@ def __init__(
         helmholtz_energies: np.ndarray,
         helmholtz_energies_dV: np.ndarray,
         helmholtz_energies_d2V2: np.ndarray,
-        reference_helmholtz_energies: np.ndarray,
         entropies: np.ndarray = None,
         heat_capacities: np.ndarray = None,
     ):
@@ -139,39 +138,12 @@ def __init__(
         if self.entropies is not None:
             self.calculate_internal_energies()
 
-        # Always calculate partition functions using the provided reference Helmholtz energies
-        self.calculate_partition_functions(reference_helmholtz_energies)
-
     def calculate_internal_energies(self) -> None:
         """
         Calculate internal energies using the formula: E = F + T*S.
         """
         self.internal_energies = self.helmholtz_energies + self.temperatures[:, np.newaxis] * self.entropies
 
-    def calculate_partition_functions(self, reference_helmholtz_energies: np.ndarray) -> None:
-        """
-        Calculate the partition function for each state, using a reference Helmholtz energy using the formula: Z = exp(-(F - F_ref) / (k_B * T)).
-
-        Args:
-            reference_helmholtz_energies (np.ndarray): Reference Helmholtz energies to shift by (shape: [n_temperatures, n_volumes])
-
-        Raises:
-            ValueError: If reference_helmholtz_energies does not match the expected shape.
-        """
-
-        if reference_helmholtz_energies.shape != (len(self.temperatures), len(self.volumes)):
-            raise ValueError(
-                f"reference_helmholtz_energies must have shape {(len(self.temperatures), len(self.volumes))} "
-                f"Received array with shape {reference_helmholtz_energies.shape}."
-            )
-
-        helmholtz_energy_shifted = self.helmholtz_energies - reference_helmholtz_energies
-        exponent = -helmholtz_energy_shifted / (BOLTZMANN_CONSTANT * self.temperatures[:, np.newaxis])
-        with np.errstate(over="ignore"):
-            partition_functions = np.exp(exponent)
-        partition_functions[np.isinf(partition_functions)] = np.nan
-        self.partition_functions = partition_functions
-
     def plot_vt(
         self,
         type: str,