fix timestep bug

calphy/input.py

@@ -292,6 +292,7 @@ def _validate_pair_style(self) -> 'Input':
     def _validate_time(self) -> 'Input':
         if np.isscalar(self.n_switching_steps):
             self._n_sweep_steps = self.n_switching_steps
+            self._n_switching_steps = self.n_switching_steps
         else:
             self._n_sweep_steps = self.n_switching_steps[1]
             self._n_switching_steps = self.n_switching_steps[0]

calphy/routines.py

@@ -513,8 +513,12 @@ def routine_composition_scaling(job):
 
     flambda_arr, w_arr, q_arr, qerr_arr = job.thermodynamic_integration()
 
+    job.logger.info('performing mass rescaling')
+    job.logger.info(f'Ref. mass is {ref_mass}')
+    job.logger.info(f'Target masses are {target_masses}')
+
     #read the file
-    mcorrarr, mcorsum = job.mass_integration(flambda_arr, ref_mass, target_masses, target_counts)
+    mcorrarr, mcorsum = job.mass_integration(flambda_arr, target_masses, ref_mass, target_counts)
     netfe = w_arr - mcorrarr
 
     job.fe = job.fe - mcorsum

examples/example_10/analysis.ipynb

@@ -36,7 +36,7 @@
    "id": "0072d247-40eb-467b-9b26-4efe2be4e66b",
    "metadata": {},
    "source": [
-    "In the file [`ZrCu.dump`](ZrCu.dump), CuZr in B2 structure is provided. The file [`ZrCu_substitution.dump`](ZrCu_substitution.dump) contains the same structure, but a single atom of Zr is replaced with Cu. If the free energy of both structures are calculated, the difference between the two provides the free energy change when a substitutional Cu atom is introduced.\n",
+    "In the file [`ZrCu.data`](ZrCu.data), CuZr in B2 structure is provided. The file [`ZrCu_substitution.data`](ZrCu_substitution.data) contains the same structure, but a single atom of Zr is replaced with Cu. If the free energy of both structures are calculated, the difference between the two provides the free energy change when a substitutional Cu atom is introduced.\n",
     "\n",
     "The input files for the direct calculations are [`input-direct-1.yaml`](input-direct-1.yaml) and [`input-direct-2.yaml`](input-direct-2.yaml). The calculations can be run by `calphy -i inputfilename`. Once the calculations are over, we can read in the results and analyse them."
    ]
@@ -69,8 +69,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fe_ref_direct = read_report(\"fe-ZrCu.dump-800-0\")\n",
-    "fe_sub_direct = read_report(\"fe-ZrCu_substitution.dump-800-0\")"
+    "fe_ref_direct = read_report(\"fe-zrcu.data-solid-800-0\")\n",
+    "fe_sub_direct = read_report(\"fe-zrcu_substitution.data-solid-800-0\")"
    ]
   },
   {
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "id": "9255fe4d-a45d-46cb-b462-92dfe8586974",
    "metadata": {},
    "outputs": [],
@@ -102,17 +102,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "476a6026-b44c-4ce8-b055-97bb07a2c465",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "0.0036244140356958+/-0.0005247047613173691"
+       "0.003912274087720213+/-9.587447227178194e-05"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -131,9 +131,6 @@
     "\n",
     "```\n",
     "composition_scaling:\n",
-    "  input_chemical_composition:\n",
-    "     - Cu: 512\n",
-    "     - Zr: 512\n",
     "  output_chemical_composition:\n",
     "     - Cu: 513\n",
     "     - Zr: 511\n",
@@ -152,27 +149,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "id": "6633d120-1d07-4ae6-91bd-27c2ea16804a",
    "metadata": {},
    "outputs": [],
    "source": [
-    "fe_sub_comp = read_report(\"sub-composition_scaling-ZrCu.dump-800-0\")"
+    "fe_sub_comp = read_report(\"sub-composition_scaling-zrcu.data-solid-800-0\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 6,
    "id": "a138085b-a32f-408a-a0e6-c71006fd3a30",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "0.0037993834787761636+/-1.1368085265609911e-05"
+       "0.0037949501379965674+/-6.960984850256015e-06"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -182,6 +179,27 @@
     "fe_sub_comp"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "2b51f5a7-d635-4cdc-83ef-a926ecfd0568",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0038679727402182425"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "0.003831461439107405+3.6511301110837446e-05"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "91e5c163-9f5e-4644-8994-e2e814cc35aa",
@@ -356,7 +374,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,

examples/example_10/input-composition.yaml

@@ -1,15 +1,13 @@
 calculations:
 - composition_scaling:
-    input_chemical_composition:
-    - Cu: 512
-    - Zr: 512
     output_chemical_composition:
-    - Cu: 532
-    - Zr: 492
+      Cu: 532
+      Zr: 492
   element:
   - Zr
   - Cu
-  lattice: ZrCu.dump
+  lattice: ZrCu.data
+  equilibration_control: berendsen
   lattice_constant: 0.0
   mass:
   - 91.224

examples/example_10/input-direct-1.yaml

@@ -2,7 +2,8 @@ calculations:
 - element:
   - Zr
   - Cu
-  lattice: ZrCu.dump
+  lattice: ZrCu.data
+  equilibration_control: berendsen
   lattice_constant: 0.0
   mass:
   - 91.224

examples/example_10/input-direct-2.yaml

@@ -2,7 +2,8 @@ calculations:
 - element:
   - Zr
   - Cu
-  lattice: ZrCu_substitution.dump
+  lattice: ZrCu_substitution.data
+  equilibration_control: berendsen
   lattice_constant: 0.0
   mass:
   - 91.224

examples/example_10/input-substitution.yaml

@@ -1,23 +1,21 @@
 calculations:
 - composition_scaling:
-    input_chemical_composition:
-    - Cu: 512
-    - Zr: 512
     output_chemical_composition:
-    - Cu: 513
-    - Zr: 511
+      Cu: 513
+      Zr: 511
   element:
   - Zr
   - Cu
   folder_prefix: sub
-  lattice: ZrCu.dump
+  lattice: ZrCu.data
+  equilibration_control: berendsen
   lattice_constant: 0.0
   mass:
   - 91.224
   - 63.546
   mode: composition_scaling
   n_equilibration_steps: 5000
-  n_iterations: 3
+  n_iterations: 1
   n_switching_steps: 5000
   pair_coeff: '* * ../potentials/ZrCu.eam.fs Zr Cu'
   pair_style: eam/fs