corrected cell vector association (with primitive not crystallograpic)

chrisjsewell · Aug 27, 2018 · 9781949 · 9781949
1 parent df5c4d0
commit 9781949
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Showing 11 changed files with 8,161 additions and 8,143 deletions.
diff --git a/ejplugins/__init__.py b/ejplugins/__init__.py
@@ -33,4 +33,4 @@ def load_all_encoders():
     return plugins.load_plugin_classes([Encode_Pymatgen, Encode_ASE])
 
 
-__version__ = "0.9.5"
+__version__ = "0.9.6"
diff --git a/ejplugins/crystal.py b/ejplugins/crystal.py
@@ -702,7 +702,7 @@ def get_geometry(dct, i, line, lines, startline=0):
                    "b": {"units": "angstrom", "magnitude": split_numbers(lines[i + 3])},
                    "c": {"units": "angstrom", "magnitude": split_numbers(lines[i + 4])}}
 
-        dct["crystallographic_cell"]["cell_vectors"] = vectors
+        dct["primitive_cell"]["cell_vectors"] = vectors
 
 
 def read_init(lines, startline):

diff --git a/ejplugins/pymatgen_decode.py b/ejplugins/pymatgen_decode.py
@@ -92,6 +92,7 @@ def from_json(self, obj):
             raise ValueError("the module {0} does not have the required class {1}".format(modname, classname))
 
     def to_str(self, obj):
-        return "SymOp({})".format(
-            str(obj).replace("\n", " ").replace("Rot: ", "R=").replace(" tau ", ", T=").replace("]  [", "],["))
+        outstr = str(obj).replace("\n", " ").replace("Rot: ", "R=").replace(" tau ", ", T=").replace("]  [", "],[")
+        outstr = outstr.replace("  ", " ").replace("[ ", "[")
+        return "SymOp({})".format(outstr)
 
diff --git a/ejplugins/schema/crystal_out.json b/ejplugins/schema/crystal_out.json
@@ -437,10 +437,7 @@
                 "c"
               ]
             }
-          },
-          "required": [
-            "cell_vectors"
-          ]
+          }
         },
         "scf": {
           "type": "array",
@@ -1367,10 +1364,7 @@
                 "c"
               ]
             }
-          },
-          "required": [
-            "cell_vectors"
-          ]
+          }
         },
         "energy": {
                   "type": "object",

diff --git a/ejplugins/test_files/crystal17_spin_opt.crystal.out.json b/ejplugins/test_files/crystal17_spin_opt.crystal.out.json
@@ -95,33 +95,6 @@
     true,
     true
    ],
-   "ccoords": {
-    "units": "angstrom",
-    "magnitude": [
-     [
-      0.0,
-      0.0,
-      0.0
-     ],
-     [
-      1.775572805,
-      1.775572805,
-      0.0
-     ],
-     [
-      -1.110223024625e-16,
-      1.775572805,
-      1.393426779074
-     ],
-     [
-      1.775572805,
-      7.885127240037e-16,
-      -1.393426779074
-     ]
-    ]
-   }
-  },
-  "crystallographic_cell": {
    "cell_vectors": {
     "a": {
      "units": "angstrom",
@@ -147,8 +120,34 @@
       5.35521437
      ]
     }
+   },
+   "ccoords": {
+    "units": "angstrom",
+    "magnitude": [
+     [
+      0.0,
+      0.0,
+      0.0
+     ],
+     [
+      1.775572805,
+      1.775572805,
+      0.0
+     ],
+     [
+      -1.110223024625e-16,
+      1.775572805,
+      1.393426779074
+     ],
+     [
+      1.775572805,
+      7.885127240037e-16,
+      -1.393426779074
+     ]
+    ]
    }
   },
+  "crystallographic_cell": {},
   "scf": [
    {
     "charge_normalization_factor": 1.0,
@@ -2516,33 +2515,6 @@
     true,
     true
    ],
-   "ccoords": {
-    "units": "angstrom",
-    "magnitude": [
-     [
-      0.0,
-      0.0,
-      0.0
-     ],
-     [
-      1.999303727667,
-      1.999303727667,
-      0.0
-     ],
-     [
-      -1.250116596416e-16,
-      1.999303727667,
-      1.214222603621
-     ],
-     [
-      1.999303727667,
-      8.878692126701e-16,
-      -1.214222603621
-     ]
-    ]
-   }
-  },
-  "crystallographic_cell": {
    "cell_vectors": {
     "a": {
      "units": "angstrom",
@@ -2568,8 +2540,34 @@
       4.62794929904
      ]
     }
+   },
+   "ccoords": {
+    "units": "angstrom",
+    "magnitude": [
+     [
+      0.0,
+      0.0,
+      0.0
+     ],
+     [
+      1.999303727667,
+      1.999303727667,
+      0.0
+     ],
+     [
+      -1.250116596416e-16,
+      1.999303727667,
+      1.214222603621
+     ],
+     [
+      1.999303727667,
+      8.878692126701e-16,
+      -1.214222603621
+     ]
+    ]
    }
   },
+  "crystallographic_cell": {},
   "band_gaps": {
    "alpha": {
     "magnitude": 2.4142,

diff --git a/ejplugins/test_files/opt_merge_scflog.crystal.out.json b/ejplugins/test_files/opt_merge_scflog.crystal.out.json
@@ -69,6 +69,32 @@
     true,
     true
    ],
+   "cell_vectors": {
+    "a": {
+     "units": "angstrom",
+     "magnitude": [
+      -1.433,
+      1.433,
+      1.433
+     ]
+    },
+    "b": {
+     "units": "angstrom",
+     "magnitude": [
+      1.433,
+      -1.433,
+      1.433
+     ]
+    },
+    "c": {
+     "units": "angstrom",
+     "magnitude": [
+      1.433,
+      1.433,
+      -1.433
+     ]
+    }
+   },
    "ccoords": {
     "units": "angstrom",
     "magnitude": [
@@ -130,33 +156,7 @@
     true,
     true,
     true
-   ],
-   "cell_vectors": {
-    "a": {
-     "units": "angstrom",
-     "magnitude": [
-      -1.433,
-      1.433,
-      1.433
-     ]
-    },
-    "b": {
-     "units": "angstrom",
-     "magnitude": [
-      1.433,
-      -1.433,
-      1.433
-     ]
-    },
-    "c": {
-     "units": "angstrom",
-     "magnitude": [
-      1.433,
-      1.433,
-      -1.433
-     ]
-    }
-   }
+   ]
   },
   "scf": [
    {
@@ -10252,6 +10252,32 @@
     true,
     true
    ],
+   "cell_vectors": {
+    "a": {
+     "units": "angstrom",
+     "magnitude": [
+      -1.39664802344,
+      1.39664802344,
+      1.39664802344
+     ]
+    },
+    "b": {
+     "units": "angstrom",
+     "magnitude": [
+      1.39664802344,
+      -1.39664802344,
+      1.39664802344
+     ]
+    },
+    "c": {
+     "units": "angstrom",
+     "magnitude": [
+      1.39664802344,
+      1.39664802344,
+      -1.39664802344
+     ]
+    }
+   },
    "ccoords": {
     "units": "angstrom",
     "magnitude": [
@@ -10313,33 +10339,7 @@
     true,
     true,
     true
-   ],
-   "cell_vectors": {
-    "a": {
-     "units": "angstrom",
-     "magnitude": [
-      -1.39664802344,
-      1.39664802344,
-      1.39664802344
-     ]
-    },
-    "b": {
-     "units": "angstrom",
-     "magnitude": [
-      1.39664802344,
-      -1.39664802344,
-      1.39664802344
-     ]
-    },
-    "c": {
-     "units": "angstrom",
-     "magnitude": [
-      1.39664802344,
-      1.39664802344,
-      -1.39664802344
-     ]
-    }
-   }
+   ]
   },
   "energy": {
    "total_corrected": {
Original file line number	Diff line number	Diff line change
Expand Up		@@ -33,4 +33,4 @@ def load_all_encoders():
		return plugins.load_plugin_classes([Encode_Pymatgen, Encode_ASE])


		__version__ = "0.9.5"
		__version__ = "0.9.6"