Merge pull request #209 from ICAMS/ordering_bug

Ordering bug

Author: srmnitc

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.12
+current_version = 1.4.13
 commit = True
 tag = True
 

calphy/__init__.py

@@ -4,7 +4,7 @@
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.4.12"
+__version__ = "1.4.13"
 
 def addtest(a,b):
     return a+b

calphy/composition_transformation.py

@@ -532,10 +532,12 @@ def write_structure(self, outfilename):
             lines = f.readlines()
 
         # Find the Atoms section and replace type numbers
+        # Support different ASE formats: "Atoms # atomic", "Atoms # full", or just "Atoms"
         in_atoms_section = False
         atom_idx = 0
         for i, line in enumerate(lines):
-            if "Atoms" in line and "#" in line:
+            # More flexible detection of Atoms section header
+            if "Atoms" in line:
                 in_atoms_section = True
                 continue
 
@@ -550,6 +552,15 @@ def write_structure(self, outfilename):
                     if atom_idx >= len(self.pyscal_structure.atoms.types):
                         break
 
+        # Verify all atoms were updated
+        expected_atoms = len(self.pyscal_structure.atoms.types)
+        if atom_idx != expected_atoms:
+            raise RuntimeError(
+                f"Failed to update all atoms in {outfilename}. "
+                f"Expected {expected_atoms} atoms but only updated {atom_idx}. "
+                f"This may indicate a problem with ASE LAMMPS file formatting."
+            )
+
         # Update the number of atom types in the header
         required_ntypes = len(self.pair_list_old)
         for i, line in enumerate(lines):

calphy/input.py

@@ -49,7 +49,7 @@
 from ase.io import read, write
 import shutil
 
-__version__ = "1.4.12"
+__version__ = "1.4.13"
 
 
 def _check_equal(val):

setup.py

@@ -53,7 +53,7 @@
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.4.12',
+    version='1.4.13',
     zip_safe=False,
     entry_points={
         'console_scripts': [

tests/test_composition_transformation_bug.py

@@ -203,9 +203,14 @@ def test_composition_transformation_single_type_file(mg_structure_file):
     assert os.path.exists(output_structure)
 
     # Read and verify the written structure
+    import re
+
     with open(output_structure, "r") as f:
         content = f.read()
-        assert "2048 atoms" in content
+        # Check for "2048 atoms" with flexible whitespace (space or tab)
+        assert re.search(
+            r"2048\s+atoms", content
+        ), "Expected '2048 atoms' in output file"
 
     # Verify entropy contribution calculation
     entropy = comp.entropy_contribution