Make StructureData optional, v0.3

aiidateam · Nov 6, 2017 · 05e85f8 · 05e85f8
1 parent b8aaf9e
commit 05e85f8
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Showing 3 changed files with 55 additions and 22 deletions.
diff --git a/aiida_cp2k/calculations/__init__.py b/aiida_cp2k/calculations/__init__.py
@@ -103,20 +103,19 @@ def _prepare_for_submission(self, tempfolder, inputdict):
 
         # write cp2k input file
         inp = Cp2kInput(params)
-        for i, a in enumerate('ABC'):
-            val = '{:<15} {:<15} {:<15}'.format(*structure.cell[i])
-            inp.add_keyword('FORCE_EVAL/SUBSYS/CELL/'+a, val)
-        inp.add_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_NAME", self._COORDS_FILE_NAME)
-        inp.add_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_FORMAT", "pdb")
+        if structure is not None:
+            struct_fn = tempfolder.get_abs_path(self._COORDS_FILE_NAME)
+            structure.get_ase().write(struct_fn, format="proteindatabank")
+            for i, a in enumerate('ABC'):
+                val = '{:<15} {:<15} {:<15}'.format(*structure.cell[i])
+                inp.add_keyword('FORCE_EVAL/SUBSYS/CELL/'+a, val)
+            inp.add_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_NAME", self._COORDS_FILE_NAME)
+            inp.add_keyword("FORCE_EVAL/SUBSYS/TOPOLOGY/COORD_FILE_FORMAT", "pdb")
         inp.add_keyword("GLOBAL/PROJECT", self._PROJECT_NAME)
         inp_fn = tempfolder.get_abs_path(self._INPUT_FILE_NAME)
         with open(inp_fn, "w") as f:
             f.write(inp.render())
 
-        # write structure file
-        struct_fn = tempfolder.get_abs_path(self._COORDS_FILE_NAME)
-        structure.get_ase().write(struct_fn, format="proteindatabank")
-
         # create code info
         codeinfo = CodeInfo()
         cmdline = settings.pop('cmdline', [])
@@ -162,12 +161,10 @@ def _verify_inlinks(self, inputdict):
         params = params_node.get_dict()
 
         # structure
-        try:
-            structure = inputdict.pop(self.get_linkname('structure'))
-        except KeyError:
-            raise InputValidationError("No structure specified for this calculation")
-        if not isinstance(structure, StructureData):
-            raise InputValidationError("structure is not of type StructureData")
+        structure = inputdict.pop(self.get_linkname('structure'), None)
+        if structure is not None:
+            if not isinstance(structure, StructureData):
+                raise InputValidationError("structure is not of type StructureData")
 
         # code
         try:

diff --git a/setup.json b/setup.json
@@ -1,5 +1,5 @@
 {
-    "version": "0.2.2",
+    "version": "0.3",
     "name": "aiida_cp2k",
     "url": "https://github.com/cp2k/aiida-cp2k",
     "license": "MIT License",

diff --git a/test/test.py b/test/test.py
@@ -36,6 +36,7 @@ def main():
 
     codename = sys.argv[1]
     code = test_and_get_code(codename, expected_code_type='cp2k')
+    test_no_structure_data(code)
     test_energy_mm(code)
     test_energy_dft(code)
     test_geo_opt_dft(code)
@@ -44,11 +45,10 @@ def main():
 
 #===============================================================================
 def test_energy_mm(code):
-    print("Testing CP2K ENERGY (MM) ...")
+    print("Testing CP2K ENERGY on H2O (MM) ...")
 
     # calc object
     calc = code.new_calc()
-    calc.label = "Test CP2K ENERGY on H2O (MM)"
 
     # parameters
     # based on cp2k/tests/Fist/regtest-1-1/water_1.inp
@@ -143,11 +143,10 @@ def test_energy_mm(code):
 
 #===============================================================================
 def test_energy_dft(code):
-    print("Testing CP2K ENERGY (DFT)...")
+    print("Testing CP2K ENERGY on H2O (DFT)...")
 
     # calc object
     calc = code.new_calc()
-    calc.label = "Test CP2K ENERGY on H2O (DFT)"
 
     # structure
     atoms = ase.build.molecule('H2O')
@@ -182,11 +181,10 @@ def test_energy_dft(code):
 
 #===============================================================================
 def test_geo_opt_dft(code):
-    print("Testing CP2K GEO_OPT (DFT)...")
+    print("Testing CP2K GEO_OPT on H2 (DFT)...")
 
     # calc object
     calc = code.new_calc()
-    calc.label = "Test CP2K GEO_OPT on H2 (DFT)"
 
     # structure
     atoms = ase.build.molecule('H2')
@@ -235,6 +233,44 @@ def test_geo_opt_dft(code):
         print "Actual dist value: {}".format(dist)
         sys.exit(3)
 
+#===============================================================================
+def test_no_structure_data(code):
+    print("Testing CP2K ENERGY on H2 (DFT) without StructureData...")
+
+    # calc object
+    calc = code.new_calc()
+
+    # structure directly included in parameters
+    force_eval = get_force_eval()
+    force_eval['SUBSYS']['CELL'] = {'ABC': '4.0   4.0   4.75'}
+    force_eval['SUBSYS']['COORD'] = {' ': ['H    2.0   2.0   2.737166',
+                                           'H    2.0   2.0   2.000000']}
+
+    # parameters
+    parameters = ParameterData(dict={'FORCE_EVAL':force_eval})
+    calc.use_parameters(parameters)
+
+    # resources
+    calc.set_max_wallclock_seconds(3*60) # 3 min
+    calc.set_resources({"num_machines": 1})
+
+    # store and submit
+    calc.store_all()
+    calc.submit()
+    print "submitted calculation: UUID=%s, pk=%s"%(calc.uuid,calc.dbnode.pk)
+
+    wait_for_calc(calc)
+
+    # check results
+    expected_energy = -1.14005678487
+    if abs(calc.res.energy - expected_energy) < 1e-10:
+        print "OK, energy has the expected value"
+    else:
+        print "ERROR!"
+        print "Expected energy value: {}".format(expected_energy)
+        print "Actual energy value: {}".format(calc.res.energy)
+        sys.exit(3)
+
 #===============================================================================
 def get_force_eval():
     return {