Merge pull request #187 from yambo-code/develop

Develop

aiida_yambo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aiida-yambo
-Version: 1.1.1
+Version: 1.1.2
 Summary: YAMBO plugin and workflows for AiiDA
 Home-page: https://github.com/yambo-code/yambo-aiida
 Author: Miki Bonacci, Michael Atambo, Antimo Marrazzo, Prandini Gianluca

aiida_yambo/__init__.py

@@ -1 +1 @@
-__version__ = "1.1.0"
+__version__ = "1.1.2"

aiida_yambo/aiida_yambo.egg-info/PKG-INFO

@@ -1,2 +1,2 @@
 Name: aiida-yambo
-Version: 1.0.0
+Version: 1.1.2

aiida_yambo/calculations/yambo.py

@@ -134,8 +134,7 @@ def define(cls,spec):
 
     def prepare_for_submission(self, tempfolder):
 
-        _dbs_accepted = {'gw0': 'ndb.QP', 'HF_and_locXC': 'ndb.HF_and_locXC',
-                         'ns.db1': 'ns.db1',}
+        _dbs_accepted = {'gw0': 'ndb.QP', 'HF_and_locXC': 'ndb.HF_and_locXC',}
 
         local_copy_list = []
         remote_copy_list = []
@@ -353,8 +352,8 @@ def prepare_for_submission(self, tempfolder):
         extra_retrieved = []
 
         if initialise:
-            extra_retrieved.append('SAVE/'+_dbs_accepted['ns.db1'])
-
+        #    extra_retrieved.append('SAVE/'+_dbs_accepted['ns.db1'])
+            pass
         else:
             for dbs in _dbs_accepted.keys():
                 db = boolean_dict.pop(dbs,False)

aiida_yambo/parsers/ext_dep/yambofile.py

@@ -244,16 +244,19 @@ def parse_report(self):
                 else: #  data line B=x Eo = y ..
                     data_lines = [ i for i in spliter.split(line) if i.strip()]
                     for qp_data in data_lines:
-                        bindex, dft_energy, qp_energy, qp_correction, z_factor, \
-                        non_local_xc, local_xc, selfenergy_c = [float (i) for i in extract.match(qp_data).groups()]
-                        kp_results['bindex'].append(bindex)
-                        kp_results['dft_energy'].append(dft_energy)
-                        kp_results['qp_energy'].append(qp_energy)
-                        kp_results['qp_correction'].append(qp_correction)
-                        kp_results['z_factor'].append(z_factor)
-                        kp_results['non_local_xc'].append(non_local_xc)
-                        kp_results['local_xc'].append(local_xc)
-                        kp_results['selfenergy_c'].append(selfenergy_c)
+                        try:
+                            bindex, dft_energy, qp_energy, qp_correction, z_factor, \
+                            non_local_xc, local_xc, selfenergy_c = [float (i) for i in extract.match(qp_data).groups()]
+                            kp_results['bindex'].append(bindex)
+                            kp_results['dft_energy'].append(dft_energy)
+                            kp_results['qp_energy'].append(qp_energy)
+                            kp_results['qp_correction'].append(qp_correction)
+                            kp_results['z_factor'].append(z_factor)
+                            kp_results['non_local_xc'].append(non_local_xc)
+                            kp_results['local_xc'].append(local_xc)
+                            kp_results['selfenergy_c'].append(selfenergy_c)
+                        except:
+                            pass
             qp_results[kp_index] = kp_results
         self.data = qp_results
 

aiida_yambo/parsers/parsers.py

@@ -150,7 +150,7 @@ def parse(self, retrieved, **kwargs):
         'p2y_completed': False, 'last_time':0,\
         'requested_time':self._calc.attributes['max_wallclock_seconds'], 'time_units':'seconds',\
         'memstats':[], 'para_error':False, 'memory_error':False,'timing':[],'time_error': False, 'has_gpu': False,
-        'yambo_version':'4.5'}
+        'yambo_version':'4.5', 'Fermi(eV)':0}
         ndbqp = {}
         ndbhf = {}
 
@@ -242,7 +242,9 @@ def parse(self, retrieved, **kwargs):
 
         if success == False:
             if abs((float(output_params['last_time'])-float(output_params['requested_time'])) \
-                  / float(output_params['requested_time'])) < 0.25:
+                  / float(output_params['requested_time'])) < 0.25: 
+                return self.exit_codes.WALLTIME_ERROR
+            elif 'time_most_prob' in output_params['errors']:
                 return self.exit_codes.WALLTIME_ERROR
             elif output_params['para_error']:
                 return self.exit_codes.PARA_ERROR

aiida_yambo/parsers/utils.py

@@ -7,6 +7,18 @@
 import copy
 import glob, os, re
 
+def take_fermi_parser(file):  # calc_node_pk = node_conv_wfl.outputs.last_calculation
+
+    for line in file:
+        if '[X]Fermi Level' in line:
+            print('The Fermi level is {}'.format(line.split()[3]))
+            ef = float(line.split()[3])
+        if '[X] Fermi Level' in line:
+            print('The Fermi level is {}'.format(line.split()[4]))
+            ef = float(line.split()[4])
+
+    return ef
+
 def yambotiming_to_seconds(yt):
     t = 0
     th = 0
@@ -40,8 +52,9 @@ def parse_log(log, output_params):
     else:
         #Game over...
         game_over = re.compile('Game')
+        game_over_2 = re.compile('Clock:')
         for line in log.lines:
-            if game_over.findall(line):
+            if game_over.findall(line) or game_over_2.findall(line):
                 output_params['game_over'] = True
 
         #timing sections...
@@ -73,6 +86,7 @@ def parse_log(log, output_params):
         incomplete_para_error = re.compile('\[ERROR\]Incomplete')
         impossible_para_error = re.compile('\[ERROR\]Impossible')
         impossible_para_error2 = re.compile('\[ERROR\]USER parallel')
+        time_probably = re.compile('Alloc Xo%blc_d')
         X_par_mem = re.compile('\[ERROR\]Allocation of X_par%blc_d failed')
         reading_explosion_of_memory = re.compile('Reading')
         for line in log.lines:
@@ -85,30 +99,44 @@ def parse_log(log, output_params):
                 output_params['errors'].append('memory_general')
             elif  incomplete_para_error.findall(line) or impossible_para_error.findall(line) or impossible_para_error2.findall(line):
                 output_params['para_error'] = True
-        if  reading_explosion_of_memory.findall(log.lines[-1]):
-            output_params['memory_error'] = True
-            output_params['errors'].append('memory_general')
-        if  X_par_mem.findall(log.lines[-1]):
-            output_params['memory_error'] = True
-            output_params['errors'].append('X_par_allocation')
+            elif time_probably.findall(line):
+                output_params['errors'].append('time_most_prob')
+        try:
+            if  reading_explosion_of_memory.findall(log.lines[-1]):
+                output_params['memory_error'] = True
+                output_params['errors'].append('memory_general')
+        except:
+            pass
+        try:
+            if  X_par_mem.findall(log.lines[-1]):
+                output_params['memory_error'] = True
+                output_params['errors'].append('X_par_allocation')
+        except:
+            pass
         # if  alloc2_error.findall(log.lines[-1]):
         #    output_params['memory_error'] = True
         #    output_params['errors'].append('memory_general')
-
+        
 
     return output_params
 
 def parse_report(report, output_params):
+
+    try:
+        output_params['Fermi(eV)'] = take_fermi_parser(report.lines)
+    except:
+        pass
 
     if 'setup' in report.filename:
         pass
 
     else:
         #Game over...
         game_over = re.compile('Game')
+        game_over_2 = re.compile('Clock:')
         gpu_support = re.compile('CUDA')
         for line in report.lines:
-            if game_over.findall(line):
+            if game_over.findall(line) or game_over_2.findall(line):
                 output_params['game_over'] = True
 
             if gpu_support.findall(line):
@@ -120,11 +148,12 @@ def parse_scheduler_stderr(stderr, output_params):
     m2 = re.compile('segmentation')
     m3 = re.compile('dumped')
     t1 = re.compile('walltime')
+    t2 = re.compile('time')
     for line in stderr.lines:
         if m1.findall(line) or m2.findall(line) or m3.findall(line):
             output_params['memory_error'] = True
             output_params['errors'].append('memory_general') 
-        elif t1.findall(line):
+        elif t1.findall(line) or t2.findall(line):
             output_params['time_error'] = True
 
 def yambo_wrote_dbs(output_params):

aiida_yambo/utils/parallel_namelists.py

@@ -26,7 +26,7 @@ def check_para_namelists(params, version):
 
     for key in params.keys():
         for level in namelists[version].keys():
-            if level in key and 'CPU' in key:
+            if level in key and '_CPU' in key:
                 if level+namelists[version][level]+'CPU' == key:
                     pass
                 else:

aiida_yambo/workflows/utils/helpers_aiida_yambo.py

@@ -171,4 +171,4 @@ def take_quantities(self, steps = 1, where = [], what = 'gap',backtrace=1):
         return quantities
 
     def start_from_converged(self, inputs, node):
-         inputs.yres.yambo.parameters = node.get_builder_restart().yres.yambo['parameters']
+         inputs.yres.yambo.parameters = node.called[0].get_builder_restart().yambo['parameters']

aiida_yambo/workflows/yamboconvergence.py

@@ -238,6 +238,9 @@ def do_p2y(self):
         self.report('Submitted YamboWorkflow up to p2y, pk = {}'.format(calc['p2y'].pk))
         self.ctx.p2y_inputs.yres.yambo.settings = update_dict(self.ctx.p2y_inputs.yres.yambo.settings, 'INITIALISE', False)
         self.ctx.p2y = calc['p2y']
+        self.report('setting label "p2y _on YC"')
+        load_node(calc['p2y'].pk).label = 'p2y _on YC'
+
         return ToContext(calc)
 
     def prepare_calculations(self):
@@ -266,6 +269,9 @@ def do_precalc(self):
         calc['PRE_CALC'] = self.submit(YamboWorkflow, **self.ctx.precalc_inputs) #################run
         self.report('Submitted preliminary YamboWorkflow, pk = {}'.format(calc['PRE_CALC'].pk))
         self.ctx.PRE = calc['PRE_CALC']
+        self.report('setting label "precalc _on YC"')
+        load_node(calc['PRE_CALC'].pk).label = 'precalc _on YC'
+
         return ToContext(calc)
 
     def post_processing(self):

aiida_yambo/workflows/yamborestart.py

@@ -149,6 +149,7 @@ def _handle_parallelism_error(self, calculation):
 
 
         if calculation.outputs.output_parameters.get_dict()['yambo_wrote_dbs'] :
+            self.ctx.inputs.parent_folder = calculation.outputs.remote_folder
             self.ctx.inputs.settings = update_dict(self.ctx.inputs.settings,'RESTART_YAMBO',True) # to link the dbs in aiida.out
             self.ctx.inputs.settings = update_dict(self.ctx.inputs.settings,'COPY_DBS', False)                   
 
@@ -169,6 +170,7 @@ def _handle_memory_error(self, calculation):
         new_para, new_resources  = fix_memory(self.ctx.inputs.metadata.options.resources, calculation, calculation.exit_status)
         self.ctx.inputs.metadata.options.resources = new_resources
         self.ctx.inputs.parameters = update_dict(self.ctx.inputs.parameters, list(new_para.keys()), list(new_para.values()))
+
 
         new_para = check_para_namelists(new_para, self.inputs.code_version.value)
         if new_para:
@@ -177,6 +179,7 @@ def _handle_memory_error(self, calculation):
 
 
         if calculation.outputs.output_parameters.get_dict()['yambo_wrote_dbs'] :
+            self.ctx.inputs.parent_folder = calculation.outputs.remote_folder
             self.ctx.inputs.settings = update_dict(self.ctx.inputs.settings,'RESTART_YAMBO',True) # to link the dbs in aiida.out
             self.ctx.inputs.settings = update_dict(self.ctx.inputs.settings,'COPY_DBS', False)                   
 

build/lib/aiida_yambo/calculations/yambo.py

@@ -134,8 +134,7 @@ def define(cls,spec):
 
     def prepare_for_submission(self, tempfolder):
 
-        _dbs_accepted = {'gw0': 'ndb.QP', 'HF_and_locXC': 'ndb.HF_and_locXC',
-                         'ns.db1': 'ns.db1',}
+        _dbs_accepted = {'gw0': 'ndb.QP', 'HF_and_locXC': 'ndb.HF_and_locXC',}
 
         local_copy_list = []
         remote_copy_list = []
@@ -353,8 +352,8 @@ def prepare_for_submission(self, tempfolder):
         extra_retrieved = []
 
         if initialise:
-            extra_retrieved.append('SAVE/'+_dbs_accepted['ns.db1'])
-
+        #    extra_retrieved.append('SAVE/'+_dbs_accepted['ns.db1'])
+            pass
         else:
             for dbs in _dbs_accepted.keys():
                 db = boolean_dict.pop(dbs,False)

build/lib/aiida_yambo/parsers/ext_dep/yambofile.py

@@ -244,16 +244,19 @@ def parse_report(self):
                 else: #  data line B=x Eo = y ..
                     data_lines = [ i for i in spliter.split(line) if i.strip()]
                     for qp_data in data_lines:
-                        bindex, dft_energy, qp_energy, qp_correction, z_factor, \
-                        non_local_xc, local_xc, selfenergy_c = [float (i) for i in extract.match(qp_data).groups()]
-                        kp_results['bindex'].append(bindex)
-                        kp_results['dft_energy'].append(dft_energy)
-                        kp_results['qp_energy'].append(qp_energy)
-                        kp_results['qp_correction'].append(qp_correction)
-                        kp_results['z_factor'].append(z_factor)
-                        kp_results['non_local_xc'].append(non_local_xc)
-                        kp_results['local_xc'].append(local_xc)
-                        kp_results['selfenergy_c'].append(selfenergy_c)
+                        try:
+                            bindex, dft_energy, qp_energy, qp_correction, z_factor, \
+                            non_local_xc, local_xc, selfenergy_c = [float (i) for i in extract.match(qp_data).groups()]
+                            kp_results['bindex'].append(bindex)
+                            kp_results['dft_energy'].append(dft_energy)
+                            kp_results['qp_energy'].append(qp_energy)
+                            kp_results['qp_correction'].append(qp_correction)
+                            kp_results['z_factor'].append(z_factor)
+                            kp_results['non_local_xc'].append(non_local_xc)
+                            kp_results['local_xc'].append(local_xc)
+                            kp_results['selfenergy_c'].append(selfenergy_c)
+                        except:
+                            pass
             qp_results[kp_index] = kp_results
         self.data = qp_results
 

build/lib/aiida_yambo/parsers/parsers.py

@@ -150,7 +150,7 @@ def parse(self, retrieved, **kwargs):
         'p2y_completed': False, 'last_time':0,\
         'requested_time':self._calc.attributes['max_wallclock_seconds'], 'time_units':'seconds',\
         'memstats':[], 'para_error':False, 'memory_error':False,'timing':[],'time_error': False, 'has_gpu': False,
-        'yambo_version':'4.5'}
+        'yambo_version':'4.5', 'Fermi(eV)':0}
         ndbqp = {}
         ndbhf = {}
 
@@ -242,7 +242,9 @@ def parse(self, retrieved, **kwargs):
 
         if success == False:
             if abs((float(output_params['last_time'])-float(output_params['requested_time'])) \
-                  / float(output_params['requested_time'])) < 0.25:
+                  / float(output_params['requested_time'])) < 0.25: 
+                return self.exit_codes.WALLTIME_ERROR
+            elif 'time_most_prob' in output_params['errors']:
                 return self.exit_codes.WALLTIME_ERROR
             elif output_params['para_error']:
                 return self.exit_codes.PARA_ERROR