fix: clean miscellaneous errors.

docs/examples/sequential_fit_example.py

@@ -16,20 +16,20 @@ def main():
         output_result_dir=str(output_folder),
         filename_order_pattern=r"(\d+)K\.gr",
         refinable_variable_names=[
-            "a_1",
+            "a_phase_1",
             "s0",
-            "Uiso_0_1",
-            "delta2_1",
+            "Uiso_phase_1_atom_1",
+            "delta2_phase_1",
             "qdamp",
             "qbroad",
         ],
         initial_variable_values={
             "s0": 0.4,
             "qdamp": 0.04,
             "qbroad": 0.02,
-            "a_1": 3.52,
-            "Uiso_0_1": 0.005,
-            "delta2_1": 2,
+            "a_phase_1": 3.52,
+            "Uiso_phase_1_atom_1": 0.005,
+            "delta2_phase_1": 2,
         },
         xmin=1.5,
         xmax=25.0,

news/fix-miscellaneous.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: fix miscellaneous errors.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/pdfbl/sequential/pdfadapter.py

@@ -252,6 +252,14 @@ def initialize_recipe(
                 - constrain variables of the scatters
                 - change symmetry constraints
         """
+
+        def modify_xyz_adp_name(parname, nth_phase):
+            parname, nth_atom = parname.split("_")
+            return f"{parname}_phase_{nth_phase+1}_atom_{int(nth_atom)+1}"
+
+        def modify_lat_delta_name(parname, nth_phase):
+            return f"{parname}_phase_{nth_phase+1}"
+
         recipe = FitRecipe()
         recipe.addContribution(self.contribution)
         qdamp = recipe.newVar("qdamp", fixed=False, value=0.04)
@@ -264,7 +272,9 @@ def initialize_recipe(
                 "delta2",
             ]:
                 par = getattr(pdfgenerator, pname)
-                recipe.addVar(par, name=pname + f"_{i+1}", fixed=False)
+                recipe.addVar(
+                    par, name=modify_lat_delta_name(pname, i), fixed=False
+                )
             if len(self.pdfgenerators) > 1:
                 recipe.addVar(
                     getattr(self.contribution, f"s{i+1}"),
@@ -277,11 +287,17 @@ def initialize_recipe(
             stru_parset = pdfgenerator.phase
             spacegroupparams = constrainAsSpaceGroup(stru_parset, spacegroup)
             for par in spacegroupparams.xyzpars:
-                recipe.addVar(par, name=par.name + f"_{i+1}", fixed=False)
+                recipe.addVar(
+                    par, name=modify_xyz_adp_name(par.name, i), fixed=False
+                )
             for par in spacegroupparams.latpars:
-                recipe.addVar(par, name=par.name + f"_{i+1}", fixed=False)
+                recipe.addVar(
+                    par, name=modify_lat_delta_name(par.name, i), fixed=False
+                )
             for par in spacegroupparams.adppars:
-                recipe.addVar(par, name=par.name + f"_{i+1}", fixed=False)
+                recipe.addVar(
+                    par, name=modify_xyz_adp_name(par.name, i), fixed=False
+                )
         recipe.addVar(self.contribution.s0, name="s0", fixed=False)
         recipe.fix("all")
         recipe.fithooks[0].verbose = 0
@@ -313,12 +329,18 @@ def residual(self, p=[]):
             The residual array.
         """
         residual = self.recipe.residual(p)
-        if self.intermediate_results is not None:
-            fitresults = FitResults(self.recipe)
-            for (key, step), values in self.intermediate_results.items():
-                if (self.iter_count % step) == 0:
-                    value = getattr(fitresults, key)
-                    values.put(value)
+        fitresults_dict = None
+        for (key, step), values in self.intermediate_results.items():
+            if (self.iter_count % step) == 0:
+                if fitresults_dict is None:
+                    fitresults_dict = self.save_results(mode="dict")
+                value = fitresults_dict.get(key, None)
+                if value is None:
+                    raise KeyError(
+                        f"{key} is not found in the fit results. "
+                        f"Available keys are: {list(fitresults_dict.keys())}"
+                    )
+                values.put(value)
         self.iter_count += 1
         return residual
 

src/pdfbl/sequential/sequential_cmi_runner.py

@@ -9,7 +9,6 @@
 from typing import Literal
 
 from bg_mpl_stylesheets.styles import all_styles
-from diffpy.srfit.fitbase import FitResults
 from matplotlib import pyplot as plt
 from prompt_toolkit import PromptSession
 from prompt_toolkit.patch_stdout import patch_stdout
@@ -476,8 +475,8 @@ def _run_one_cycle(self, stop_event=SimpleNamespace(is_set=lambda: False)):
                     new_value
                 )
             for entry_name in self.visualization_data.get("results", {}):
-                fit_results = FitResults(self.adapter.recipe)
-                entry_value = getattr(fit_results, entry_name)
+                fitresults_dict = self.adapter.save_results(mode="dict")
+                entry_value = fitresults_dict.get(entry_name, None)
                 self.visualization_data["results"][entry_name]["ydata"].put(
                     entry_value
                 )