Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms

pymatgen/io/feff/inputs.py

@@ -482,11 +482,11 @@ def cluster_from_file(filename):
                 is the one at the origin.
         """
         atoms_string = Atoms.atoms_string_from_file(filename)
-        lines = [line.split() for line in atoms_string.splitlines()[3:]]
+        lines = [line.split() for line in atoms_string.splitlines()[1:]]
         coords = []
         symbols = []
         for line in lines:
-            if line:
+            if line and line[0].__contains__("*"):
                 coords.append([float(val) for val in line[:3]])
                 symbols.append(line[4])
         return Molecule(symbols, coords)

tests/files/ATOMS_test.inp

@@ -0,0 +1,64 @@
+TITLE COC_O3_cut_ori_100_l_5_19_site_0_n_4
+EDGE L3  
+S02 0.9
+
+COREHOLE FSR
+CONTROL 1 1 1 1 1 1
+
+FMS 7 0     
+EXCHANGE 0 1 0 2 
+SCF 7 0 100 0.1 1 
+DEBYE 80 230 0     
+
+
+XANES 20 0.05 0.1
+
+POTENTIALS
+0 78 Pt    
+1 78 Pt 
+
+
+POTENTIALS
+* ipot 	 Z 	 element 	 l_scmt 	 l_fms 	 stoichiometry
+0  78  Pt  -1  -1   0.001  0
+1  78  Pt  -1  -1  37      0
+
+ATOMS
+ 0       0      0     0  Pt   0         0
+-1.386  -1.386  1.96  1  Pt   2.77193  16
+ 1.386   1.386  1.96  1  Pt   2.77193  17
+ 1.386  -1.386  1.96  1  Pt   2.77193  21
+ 0      -2.772  0     1  Pt   2.772     1
+ 2.772   0      0     1  Pt   2.772     3
+ 2.772  -2.772  0     1  Pt   3.9202    4
+ 4.158   1.386  1.96  1  Pt   4.8012   23
+ 4.158  -1.386  1.96  1  Pt   4.8012   22
+ 1.386  -4.158  1.96  1  Pt   4.8012   20
+-1.386  -4.158  1.96  1  Pt   4.8012   19
+ 5.544   0      0     1  Pt   5.544     5
+ 0      -5.544  0     1  Pt   5.544     2
+ 4.158  -4.158  1.96  1  Pt   6.19835  28
+ 2.772  -5.544  0     1  Pt   6.19838   7
+ 5.544  -2.772  0     1  Pt   6.19838   9
+-1.386  -6.93   1.96  1  Pt   7.334    18
+ 6.93    1.386  1.96  1  Pt   7.334    24
+ 1.386  -6.93   1.96  1  Pt   7.334    26
+ 6.93   -1.386  1.96  1  Pt   7.334    30
+ 5.544  -5.544  0     1  Pt   7.8404   10
+ 4.158  -6.93   1.96  1  Pt   8.31598  27
+ 6.93   -4.158  1.96  1  Pt   8.31598  29
+ 0      -8.316  0     1  Pt   8.316     6
+ 8.316   0      0     1  Pt   8.316    11
+ 8.316  -2.772  0     1  Pt   8.76583  12
+ 2.772  -8.316  0     1  Pt   8.76583   8
+ 6.93   -6.93   1.96  1  Pt   9.99457  34
+ 9.702  -1.386  1.96  1  Pt   9.99457  31
+ 1.386  -9.702  1.96  1  Pt   9.99457  25
+ 8.316  -5.544  0     1  Pt   9.99459  14
+ 5.544  -8.316  0     1  Pt   9.99459  13
+ 4.158  -9.702  1.96  1  Pt  10.7359   32
+ 9.702  -4.158  1.96  1  Pt  10.7359   36
+ 8.316  -8.316  0     1  Pt  11.7606   15
+ 9.702  -6.93   1.96  1  Pt  12.0829   35
+ 6.93   -9.702  1.96  1  Pt  12.0829   33
+END

tests/io/feff/test_inputs.py

@@ -390,3 +390,9 @@ def test_paths_string(self):
         ]
         answer = "\n".join(lines)
         assert answer == str(self.paths)
+
+
+def test_atom_num(self):
+    atoms = Atoms.cluster_from_file("ATOMS_test.inp")
+    num_atom = 37
+    assert len(atoms) != num_atom