Reworked CLI

aiida_fleur/cmdline/launch/__init__.py

@@ -15,7 +15,8 @@
 from .launch import launch_inpgen
 from .launch import launch_fleur
 from .launch import launch_scf
-from .launch import launch_banddos
+from .launch import launch_dos
+from .launch import launch_band
 from .launch import launch_relax
 from .launch import launch_eos
 from .launch import launch_corehole
@@ -36,7 +37,8 @@ def cmd_launch():
 cmd_launch.add_command(launch_inpgen)
 cmd_launch.add_command(launch_fleur)
 cmd_launch.add_command(launch_scf)
-cmd_launch.add_command(launch_banddos)
+cmd_launch.add_command(launch_dos)
+cmd_launch.add_command(launch_band)
 cmd_launch.add_command(launch_relax)
 cmd_launch.add_command(launch_eos)
 cmd_launch.add_command(launch_corehole)

aiida_fleur/cmdline/launch/launch.py

@@ -218,7 +218,7 @@ def launch_scf(structure, inpgen, calc_parameters, fleurinp, fleur, wf_parameter
                     f.write(wf.outputs.last_calc.retrieved.get_object_content(file,"rb"))
 
 @click.command('relax')
-@options.STRUCTURE_OR_FILE(default=defaults.get_si_bulk_structure, show_default=True)
+@options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
 @options.INPGEN()
 @options.CALC_PARAMETERS()
 @options.FLEUR()
@@ -234,9 +234,24 @@ def launch_relax(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_p
 
     # TODO final scf input
     """
-    workchain_class = WorkflowFactory('fleur.base_relax')
+    from aiida_fleur.workflows.relax import FleurRelaxWorkChain
+
+    if isinstance(structure, FleurinpData):
+        fleurinp=structure
+        structure=None
+        inpgen=None
+
+    # we need a scf_paramters dict to change the forcemix if required later
+    if scf_parameters==None:
+        scf_parameters=Dict(dict= {
+                'force_dict': {'forcemix': 'BFGS'},
+                'inpxml_changes': []
+                })
+
+    #workchain_class = WorkflowFactory('fleur.base_relax')
     inputs = {
         'scf': {
+            'fleurinp': fleurinp,
             'wf_parameters': scf_parameters,
             'structure': structure,
             'calc_parameters': calc_parameters,
@@ -246,11 +261,35 @@ def launch_relax(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_p
         },
         'wf_parameters': wf_parameters
     }
+
+
     inputs = clean_nones(inputs)
-    builder = workchain_class.get_builder()
+    builder = FleurRelaxWorkChain.get_builder()
     builder.update(inputs)
-    utils.launch_process(builder, daemon)
+    pk=utils.launch_process(builder, daemon)
+
+    #Now create output files
+    if fleurinp and not daemon:
+        from aiida.orm import load_node
+        wf=load_node(pk)
+        relax_output=wf.outputs.output_relax_wc_para.get_dict()
+        relax_output["Relax-uuid"]=wf.uuid
+        relax_output["retrieved-uuid"]=wf.outputs.last_scf.last_calc.retrieved.uuid
+
+
+        #json with dict
+        import json
+        with open("relax.json","w") as file:
+            json.dump(relax_output,file,indent=2)
+        #plot
+        from aiida_fleur.tools.plot.fleur import plot_fleur
+        plot_fleur([wf],save=True,show=False)
 
+        #store files
+        for file in ["relax.xml","out.xml","cdn1","cdn_last.hdf"]:
+            if file in wf.outputs.last_scf.last_calc.retrieved.list_object_names():
+                with open(file,"wb") as f:
+                    f.write(wf.outputs.last_scf.last_calc.retrieved.get_object_content(file,"rb"))
 
 @click.command('eos')
 @options.STRUCTURE_OR_FILE(default="inp.xml", show_default=True)
@@ -320,19 +359,47 @@ def launch_eos(structure, inpgen, calc_parameters, fleur, wf_parameters, scf_par
 
 
 
-@click.command('banddos')
+@click.command('dos')
 @options.FLEURINP(default='inp.xml')
 @options.FLEUR()
 @options.WF_PARAMETERS()
 @options.REMOTE()
 @options.DAEMON()
 @options.SETTINGS()
 @options.OPTION_NODE()
-def launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node):
+def launch_dos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node):
     """
-    Launch a banddos workchain
+    Launch a banddos workchain (special command to set the dos as a default mode)
     """
+    if wf_parameters==None:
+        wf_parameters=Dict({"mode":"dos"})
+    else:
+        wf_dict=wf_parameters.get_dict()
+        wf_dict["mode"]="dos" 
+        wf_parameters=Dict(wf_dict)
+
+    launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node)
+
 
+@click.command('band')
+@options.FLEURINP(default='inp.xml')
+@options.FLEUR()
+@options.WF_PARAMETERS()
+@options.REMOTE()
+@options.DAEMON()
+@options.SETTINGS()
+@options.OPTION_NODE()
+def launch_band(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node):
+    """
+    Launch a banddos workchain in 'band' mode
+    """
+    #Band is default
+    launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node)
+
+def launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settings, option_node):
+    """
+    Launch a banddos workchain
+    """   
     workchain_class = WorkflowFactory('fleur.banddos')
     inputs = {
         'wf_parameters': wf_parameters,
@@ -354,6 +421,10 @@ def launch_banddos(fleurinp, fleur, wf_parameters, parent_folder, daemon, settin
     import json
     with open("banddos.json","w") as file:
         json.dump(banddos_output,file,indent=2)
+    #the banddos.hdf file    
+    with open(f"banddos.hdf","wb") as f:
+        f.write(wf.outputs.banddos_calc.retrieved.get_object_content("banddos.hdf",'rb'))
+
     #plot
     from aiida_fleur.tools.plot.fleur import plot_fleur
     plot_fleur(wf,save=True,show=False)

aiida_fleur/cmdline/util/types.py

@@ -26,15 +26,28 @@
                           '"energy_converged": 0.002,\n'
                           '"mode": "density",\n'
                           '"itmax_per_run": 30}',
-                    "banddos":'{"mode": "band",\n'
-                              '"kpath": "auto",\n'
-                              '"klistname": "path-3",\n'
-                              '"kpoints_number": None,\n'
-                              '"kpoints_distance": None,\n'
-                              '"kpoints_explicit": None,\n'  
-                              '"sigma": 0.005,\n'
-                              '"emin": -0.50,\n'
-                              '"emax": 0.90\n}'
+                    "band":'{\n'
+                              '// Select your k-points\n'
+                              '"kpath": "auto"// This can be "auto" (meaning you try to pick a good choice automatically from inp.xml) or "seek" to use seek-k-path\n'
+                              '//",klistname": "path-3"//You can specify directly a list in the inp.xml/kpts.xml\n'
+                              '//",kpoints_number": 200\n'
+                              '//",kpoints_distance": 0.1\n'
+                              '//",kpoints_explicit": None\n}',
+                    "dos":'{\n'
+                              '// Select your k-points\n'
+                              '//"klistname": "path-3",//You can specify directly a list in the inp.xml/kpts.xml\n'
+                              '//"kpoints_number": 200,\n'
+                              '//"kpoints_distance": 0.1,\n'
+                              '// These parameters are relevant for the DOS mode\n'
+                              '"sigma": 0.005\n'
+                              '",emin": -0.50\n'
+                              '",emax": 0.90\n}',
+                    "relax":'{\n'
+                              '"film_distance_relaxation": "False", // if True, sets relaxXYZ="FFT" for all atoms\n'
+                              '"force_criterion": 0.049,            // Sets the threshold of the largest force\n'
+                              '"relax_iter": 5                      // Maximum number of optimization iterations\n'
+                              '}'          
+
                     }
 
 
@@ -78,10 +91,11 @@ def convert(self,value,param,ctx):
             with open(value,"r") as f:
                 import json
                 dict_from_file=json.load(f)
-
-            scf_wf=load_node(dict_from_file["SCF-uuid"])
-            print(scf_wf)
-            return scf_wf.outputs.last_calc.remote_folder
+            if 'SCF-uuid' in dict_from_file:
+                scf_wf=load_node(dict_from_file["SCF-uuid"])
+                return scf_wf.outputs.last_calc.remote_folder
+            if 'retrieved-uuid' in dict_from_file:
+                return dict_from_file["retrieved-uuid"]
         except:
             return None
 
@@ -104,14 +118,17 @@ def convert(self,value,param,ctx):
             try:
                 with open(value,"r") as f:
                     import json
-                    wf_param=json.load(f)
-            except:
+                    from json_minify import json_minify
+
+                    wf_param=json.loads(json_minify(f.read()))
+            except RuntimeError as error:
+                print(error)
                 print(f"{value} could not be converted into a dict")
                 os.abort()
             aiida_dict=DataFactory("dict")
             wf_dict=aiida_dict(wf_param)
 
-            return wf_dict.store()
+            return wf_dict
 
         #Now load from aiida
         wf_dict = types.DataParamType(sub_classes=('aiida.data:core.dict',)).convert(value, param, ctx)

aiida_fleur/parsers/fleur.py

@@ -280,7 +280,7 @@ def parse(self, **kwargs):
             except NotExistent:
                 old_relax_text = ''
             else:
-                if relax_name in fleurinp.list_object_names():
+                if relax_name in fleurinp.base.repository.list_object_names():
                     with fleurinp.open(relax_name, 'r') as rlx:
                         old_relax_text = rlx.read()
                 else:

aiida_fleur/tools/plot/fleur.py

@@ -62,11 +62,12 @@ def plot_fleur(*args, save=False, show_dict=False, show=True, backend=None, **kw
     for arg in args:
         if isinstance(arg, list):
             # try plot together
+            print("mn:",arg)
             p1 = plot_fleur_mn(arg, save=save, show=show, backend=backend, **kwargs)
             if len(p1) == 1:
                 p1 = p1[0]
         else:
-            #print(arg)
+            print("sn:",arg)
             # plot alone
             p1 = plot_fleur_sn(arg, show_dict=show_dict, show=show, save=save, backend=backend, **kwargs)
         all_plots.append(p1)
@@ -90,7 +91,7 @@ def plot_fleur_sn(node, show_dict=False, **kwargs):
     except KeyError as exc:
         raise ValueError('Sorry, I do not know how to visualize'
                          f' this node in plot_fleur: {workflow_name} {node}') from exc
-
+    print(plot_nodes)
     plot_result = plotf(*plot_nodes, **kwargs)
 
     return plot_result
@@ -432,16 +433,44 @@ def plot_fleur_banddos_wc(param_node,
     return plot_res
 
 
-def plot_fleur_relax_wc(node, labels=None, save=False, show=True, **kwargs):
+def plot_fleur_relax_wc(node, labels=None, save=False, show=True, backend='bokeh', **kwargs):
     """
     This methods takes an AiiDA output parameter node from a relaxation
     workchain and plots some information about atom movements and forces
     """
+    from masci_tools.vis.common import convergence_plot
+
     if labels is None:
-        labels = []
+        labels = [n.pk for n in node]
+
+    if isinstance(node, list):
+        if len(node) > 2:
+            return  # TODO
+        else:
+            node = node[0]
+
+    output_d = node.get_dict()
+    forces = output_d.get('force')
+    total_energies=output_d.get('energy')
+    iteration=range(len(forces))
+
+    add_args = {}
+    if backend == 'bokeh':
+        add_args['legend_label'] = labels
+    else:
+        add_args['plot_label'] = labels
 
-    raise NotImplementedError
 
+    plot_res = convergence_plot(iteration,
+                                forces,
+                                total_energies,
+                                show=show,
+                                save_plots=save,
+                                backend=backend,
+                                saveas_distance="force_convergence",
+                                ylabel_distance="Largest force [Htr/bohr]",
+                                **kwargs)
+    return plot_res
 
 def plot_fleur_corehole_wc(nodes, labels=None, save=False, show=True, **kwargs):
     """
@@ -618,6 +647,7 @@ def plot_fleur_cfcoeff_wc(param_node,
     'FleurBandWorkChain': plot_fleur_band_wc,
     'FleurBandDosWorkChain': plot_fleur_banddos_wc,
     'FleurCFCoeffWorkChain': plot_fleur_cfcoeff_wc,
+    'FleurRelaxWorkChain': plot_fleur_relax_wc,
     #'fleur_corehole_wc' : plot_fleur_corehole_wc,  #support of < 1.5 release
     #'fleur_initial_cls_wc' : plot_fleur_initial_cls_wc,  #support of < 1.5 release
     #'FleurInitialCLSWorkChain' : plot_fleur_initial_cls_wc,