Reintroduce structure parser based on pdb format v0.5

aiida_cp2k/calculations/__init__.py

@@ -35,6 +35,8 @@ def _init_internal_params(self):
         self._OUTPUT_FILE_NAME = 'aiida.out'
         self._DEFAULT_INPUT_FILE  = self._INPUT_FILE_NAME
         self._DEFAULT_OUTPUT_FILE = self._OUTPUT_FILE_NAME
+        self._PROJECT_NAME = 'aiida'
+        self._TRAJ_FILE_NAME = self._PROJECT_NAME + '-pos-1.pdb'
         self._COORDS_FILE_NAME = 'aiida.coords.pdb'
         self._default_parser = 'cp2k'
 
@@ -101,6 +103,8 @@ def _prepare_for_submission(self, tempfolder, inputdict):
 
         # write cp2k input file
         inp = Cp2kInput(params)
+        inp.add_keyword("GLOBAL/PROJECT", self._PROJECT_NAME)
+        inp.add_keyword("MOTION/PRINT/TRAJECTORY/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")
@@ -135,7 +139,7 @@ def _prepare_for_submission(self, tempfolder, inputdict):
         calcinfo.remote_symlink_list = []
         calcinfo.local_copy_list = local_copy_list
         calcinfo.remote_copy_list = []
-        calcinfo.retrieve_list = [self._OUTPUT_FILE_NAME]
+        calcinfo.retrieve_list = [self._OUTPUT_FILE_NAME, self._TRAJ_FILE_NAME]
         calcinfo.retrieve_list += settings.pop('additional_retrieve_list', [])
 
         # check for left over settings

aiida_cp2k/parsers/__init__.py

@@ -8,10 +8,13 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 
+import re
 import ase.io
+from StringIO import StringIO
 
 from aiida.parsers.parser import Parser
 from aiida.orm.data.parameter import ParameterData
+from aiida.orm.data.structure import StructureData
 from aiida.parsers.exceptions import OutputParsingError
 from aiida_cp2k.calculations import Cp2kCalculation
 
@@ -41,6 +44,7 @@ def parse_with_retrieved(self, retrieved):
 
         new_nodes_list = []
         self._parse_stdout(out_folder, new_nodes_list)
+        self._parse_trajectory(out_folder, new_nodes_list)
 
         return True, new_nodes_list
 
@@ -57,8 +61,31 @@ def _parse_stdout(self, out_folder, new_nodes_list):
                 if line.startswith(' ENERGY| '):
                     result_dict['energy'] = float(line.split()[8])
                     result_dict['energy_units'] = "a.u."
+                if line.startswith(' The number of warnings for this run is :'):
+                    result_dict['nwarnings'] = int(line.split()[-1])
 
         pair = (self.get_linkname_outparams(), ParameterData(dict=result_dict))
         new_nodes_list.append(pair)
 
+    #---------------------------------------------------------------------------
+    def _parse_trajectory(self, out_folder, new_nodes_list):
+        fn = self._calc._TRAJ_FILE_NAME
+        if fn not in out_folder.get_folder_list():
+            return  # not every run type produces a trajectory
+
+        abs_fn = out_folder.get_abs_path(fn)
+        content = open(abs_fn).read()
+        frames = re.findall(r"\n(REMARK.*?\nEND)", content, re.DOTALL)
+        atoms = ase.io.read(StringIO(frames[-1]), format='proteindatabank')
+        pair = (self.get_linkname_outstructure(), StructureData(ase=atoms))
+        new_nodes_list.append(pair)
+
+    #---------------------------------------------------------------------------
+    def get_linkname_outstructure(self):
+        """
+        Returns the name of the link to the output_structure
+        """
+        return 'output_structure'
+
+
 #EOF

setup.json

@@ -1,5 +1,5 @@
 {
-    "version": "0.4",
+    "version": "0.5",
     "name": "aiida_cp2k",
     "url": "https://github.com/cp2k/aiida-cp2k",
     "license": "MIT License",

test/test.py

@@ -36,10 +36,10 @@ 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)
+    test_no_structure_data(code)
     print("All tests passed :-)")
     sys.exit(0)
 
@@ -122,6 +122,9 @@ def test_energy_mm(code):
 
     wait_for_calc(calc)
 
+    # check warnings
+    assert calc.res.nwarnings == 0
+
     # check energy
     expected_energy = 0.146927412614e-3
     if abs(calc.res.energy - expected_energy) < 1e-10:
@@ -201,10 +204,6 @@ def test_geo_opt_dft(code):
     })
     calc.use_parameters(parameters)
 
-    # settings
-    settings = ParameterData(dict={'additional_retrieve_list':['*.xyz']})
-    calc.use_settings(settings)
-
     # resources
     calc.set_max_wallclock_seconds(3*60) # 3 min
     calc.set_resources({"num_machines": 1})
@@ -227,9 +226,8 @@ def test_geo_opt_dft(code):
         sys.exit(3)
 
     # check geometry
-    expected_dist = 0.736125211
-    traj_fn = calc.out.retrieved.get_abs_path('PROJECT-pos-1.xyz')
-    dist = ase.io.read(traj_fn, index='-1').get_distance(0, 1)
+    expected_dist = 0.737 # pdb format has only three digits
+    dist = calc.out.output_structure.get_ase().get_distance(0, 1)
     if abs(dist - expected_dist) < 1e-7:
         print "OK, H-H distance has the expected value"
     else:
@@ -329,14 +327,20 @@ def wait_for_calc(calc, timeout_secs=5*60.0):
         except subprocess.CalledProcessError as e:
             print "Note: the command failed, message: {}".format(e.message)
         if calc.has_finished():
-            print "Calculation terminated its execution"
+            print "Calculation terminated its execution."
             exited_with_timeout = False
             break
 
-    # check exit status
+    # check for timeout
     if exited_with_timeout:
-        print "Timeout!! Calculation did not complete after {} seconds".format(
-            timeout_secs)
+        print "Timeout!! Calculation did not complete after %i seconds" % timeout_secs
+        os.system("cat ~/.aiida/daemon/log/aiida_daemon.log")
+        sys.exit(2)
+
+    # check calculation status
+    if calc.has_failed():
+        print "Calculation failed with state: " + calc.get_state()
+        os.system("cat ~/.aiida/daemon/log/aiida_daemon.log")
         sys.exit(2)
 
 #===============================================================================