FIX: ChemSage DAT: Case sensitivity of compound names in endmembers

pycalphad/io/cs_dat.py

@@ -33,8 +33,8 @@ def _parse_species_postfix_charge(formula) -> v.Species:
     else:
         charge = 0
     # assumes that the remaining formula is a pure element
-    constituents = dict(parse_chemical_formula(formula)[0])
-    return v.Species(name, constituents=constituents, charge=charge)
+    constituents = dict(parse_chemical_formula(formula.upper())[0])
+    return v.Species(name.upper(), constituents=constituents, charge=charge)
 
 class TokenParserError(Exception):
     """Exception raised when the TokenParser hits a parsing error."""
@@ -643,6 +643,7 @@ def insert(self, dbf: Database, phase_name: str, As: List[str], Xs: List[str], e
 
 def _species(el_chg):
     el, chg = el_chg
+    el = el.upper()
     name = rename_element_charge(el, chg)
     constituents = dict(parse_chemical_formula(el)[0])
     return v.Species(name, constituents=constituents, charge=chg)
@@ -794,7 +795,7 @@ def parse_header(toks: TokenParser) -> Header:
     num_soln_phases = toks.parse(int)
     list_soln_species_count = toks.parseN(num_soln_phases, int)
     num_stoich_phases = toks.parse(int)
-    pure_elements = toks.parseN(num_pure_elements, str)
+    pure_elements = [x.upper() for x in toks.parseN(num_pure_elements, str)]
     pure_elements_mass = toks.parseN(num_pure_elements, float)
     num_gibbs_coeffs = toks.parse(int)
     gibbs_coefficient_idxs = toks.parseN(num_gibbs_coeffs, int)
@@ -838,6 +839,20 @@ def parse_interval_heat_capacity(toks: TokenParser, num_gibbs_coeffs, H298, S298
 
 def parse_endmember(toks: TokenParser, num_pure_elements, num_gibbs_coeffs, is_stoichiometric=False):
     species_name = toks.parse(str)
+    # We are case-sensitive here, e.g., Co (cobalt) != CO (carbon monoxide)
+    # pycalphad's Species parser is not. We need to help that parser by leaving Co alone while converting CO to C1O1.
+    # We split the name on every capital letter. If the substring has no number at the end, add a '1'.
+    # Then we rejoin the string together and convert the species name to uppercase (the canonical form for Species).
+    possible_species = re.findall('.[^A-Z]*', species_name)
+    if len(possible_species) > 1:
+        rebuilt_species_name = []
+        for ps in possible_species:
+            if not (ps[-1].isdigit() or (ps[-1] in (')', ']'))):
+                rebuilt_species_name.append(ps+'1')
+            else:
+                rebuilt_species_name.append(ps)
+        species_name = ''.join(rebuilt_species_name)
+    species_name = species_name.upper()
     if toks[0] == '#':
         # special case for stoichiometric phases, this is a dummy species, skip it
         _ = toks.parse(str)
@@ -1116,7 +1131,7 @@ def parse_phase_aqueous(toks, phase_name, phase_type, num_pure_elements, num_gib
 
 def parse_phase(toks, num_pure_elements, num_gibbs_coeffs, num_excess_coeffs, num_const):
     """Dispatches to the correct parser depending on the phase type"""
-    phase_name = toks.parse(str)
+    phase_name = toks.parse(str).upper()
     phase_type = toks.parse(str)
     if phase_type in ('SUBQ', 'SUBG'):
         phase = parse_phase_subq(toks, phase_name, phase_type, num_pure_elements, num_gibbs_coeffs, num_excess_coeffs)
@@ -1170,7 +1185,7 @@ def read_cs_dat(dbf: Database, fd):
     fd : file-like
         File descriptor.
     """
-    header, solution_phases, stoichiometric_phases = parse_cs_dat(fd.read().upper())
+    header, solution_phases, stoichiometric_phases = parse_cs_dat(fd.read())
     # add elements and their reference states
     for el, mass in zip(header.pure_elements, header.pure_elements_mass):
         if 'E(' not in str(el):

pycalphad/tests/databases/issue425.dat

@@ -0,0 +1,36 @@
+ System Cu-Ni-Co-Fe-Mn-Sc-Ca-K-Cl-S-P-Si-Mg-O-N-C-B-H
+   18    1  2  0
+ Cu                       Ni                       Co
+ Fe                       Mn                       Sc
+ Ca                       K                        Cl
+ S                        P                        Si
+ Mg                       O                        N
+ C                        B                        H
+    63.54600000              58.69340000              58.93319500
+    55.84500000              54.93804500              44.95591200
+    40.07800000              39.09830000              35.45300000
+    32.06500000              30.97376200              28.08550000
+    24.30500000              15.99940000              14.00670000
+    12.01070000              10.81100000               1.00794000
+   6   1   2   3   4   5   6
+   6   1   2   3   4   5   6
+ gas_ideal
+ IDMX
+ CO
+   4  3    0.0    0.0    0.0    0.0    0.0    0.0    0.0    0.0    0.0    0.0
+    0.0    0.0    0.0    1.0    0.0    1.0    0.0    0.0
+  1700.0000     -203680.54      609.35468     -90.753584     0.31175713E-02
+ 0.00000000      770627.67
+ 2  32063.316      99.00 -10357.020       0.50
+  6000.0000     -224220.54      142.21490     -44.086320     0.00000000
+ 0.00000000      5816543.2
+ 2  20893.908      99.00 -2749.1074       0.50
+  6001.0000     -133600.03      72.371771     -38.372791     0.00000000
+ 0.00000000     0.00000000
+ 1 0.00000000       0.00
+ Co
+   4  1    0.0    0.0    1.0    0.0    0.0    0.0    0.0    0.0    0.0    0.0
+    0.0    0.0    0.0    0.0    0.0    0.0    0.0    0.0
+  6000.0000      421421.87     -3.5737662     -26.233680     0.00000000
+ 0.00000000     0.00000000
+ 1 0.00000000       0.00

pycalphad/tests/test_database.py

@@ -860,4 +860,8 @@ def test_database_symmetry_options_are_generated(load_database):
     # The parameters should be filtered out when when writing such that a
     # read/write is a no-op
     read_dbf = Database.from_string(dbf.to_string(fmt="tdb"), fmt="tdb")
-    assert len(read_dbf._parameters) == 375
+    assert len(read_dbf._parameters) == 375
+
+def test_dat_ambiguous_compound_names():
+    "Compound names in DAT files are case sensitive (gh-425)"
+    Database.from_file(files(pycalphad.tests.databases).joinpath("issue425.dat"), fmt='dat')