Fea/xx/analyze on element very (#236)

* Add CLI for analyze element result in a bar figure

* Add eiger computers configure

* Analyse on-element

aiida_sssp_workflow/cli/inspect.py

@@ -228,7 +228,10 @@ def convergence_plot(
 @cmd_root.command("analyze")
 @click.argument("group")  # The group to inspect, name or pk of the group
 @click.option("--output", "-o", default="output", help="The output file name")
-def analyze(group, output):
+@click.option(
+    "--ylimit", "-y", default=0.5, help="The y limit for the plot", type=float
+)
+def analyze(group, output, ylimit):
     """Render the plot for the given pseudos and measure type."""
     from aiida_sssp_workflow.utils import ACWF_CONFIGURATIONS, parse_label
 
@@ -281,7 +284,7 @@ def analyze(group, output):
     ax.text(0 - d, 0.33 + d, "0.33 good agreement", color="black")
     ax.legend(loc="upper right", prop={"size": 10})
     ax.set_ylabel("ν -factor")
-    ax.set_ylim([0, 0.5])
+    ax.set_ylim([0, ylimit])
 
     xticks_shift = len(nodes_lst) * width / 2
     xticks = [i + xticks_shift for i in range(len(ACWF_CONFIGURATIONS))]
@@ -367,7 +370,10 @@ def inspect(node, output):
         # A4 canvas for plot
         # landscape mode, shoulder to shoulder for ecutwfc and ecutrho for each property
         # five rows for five properties
-        rows = len(wf_node.outputs.convergence)
+
+        # always plot 5 rows if the result is not accessable, add a text to indicate the property is not calculated
+        # rows = len(wf_node.outputs.convergence)
+        rows = 5
         fig, axs = plt.subplots(
             rows,
             2,
@@ -378,12 +384,19 @@ def inspect(node, output):
         subplot_index = 0
 
         for property in [
-            "bands",
-            "cohesive_energy",
             "pressure",
             "delta",
             "phonon_frequencies",
+            "cohesive_energy",
+            "bands",
         ]:
+            # plot to the ax
+            # ax1 on the left for ecutwfc
+            # ax2 on the right for ecutrho
+            # the ratio of the width is 3:1
+            ax1 = axs.flat[subplot_index]
+            ax2 = axs.flat[subplot_index + 1]
+
             # print summary of the convergence to a json file
             try:
                 convergence = wf_node.outputs.convergence[property]
@@ -392,6 +405,18 @@ def inspect(node, output):
                     f"Property {property} is not calculated for this workflow",
                     fg="red",
                 )
+                # add to ax1 and ax2 with a red text to indicate the property is not calculated
+                ax1.text(
+                    0.5,
+                    0.5,
+                    f"Convergence test of {property} is not run or failed.",
+                    color="red",
+                )
+                ax1.set_axis_off()
+                ax2.set_axis_off()
+                # jump to the next row
+                subplot_index += 2
+
                 continue
 
             cutoff_control_protocol = wf_node.inputs.convergence.cutoff_control.value
@@ -443,13 +468,6 @@ def inspect(node, output):
 
             convergence_summary[property] = property_summary
 
-            # plot to the ax
-            # ax1 on the left for ecutwfc
-            # ax2 on the right for ecutrho
-            # the ratio of the width is 3:1
-            ax1 = axs.flat[subplot_index]
-            ax2 = axs.flat[subplot_index + 1]
-
             # data preparation
             # Will only plot the measured properties e.g. for bands it is the eta_c
             _ConvergenceWorkChain = WorkflowFactory(

aiida_sssp_workflow/workflows/evaluate/_bands.py

@@ -66,7 +66,9 @@ class BandsWorkChain(_BaseEvaluateWorkChain):
 
     # maximum number of bands factor increase loop
     # to prevent the infinite loop in bands evaluation
-    _MAX_NUM_BANDS_FACTOR = 5
+    # If start from 1.5, and increase 2.0 every time, it will reach 11.5 at most.
+    _MAX_INCREMENT_BANDS_FACTOR = 10
+    _BANDS_FACTOR_INCREASE_STEP = 2.0
 
     @classmethod
     def define(cls, spec):
@@ -108,7 +110,7 @@ def define(cls, spec):
         spec.exit_code(201, 'ERROR_SUB_PROCESS_FAILED_BANDS',
                     message='The `PwBandsWorkChain` sub process failed.')
         spec.exit_code(203, 'ERROR_REACH_MAX_BANDS_FACTOR_INCREASE_LOOP',
-                    message=f'The maximum number={cls._MAX_NUM_BANDS_FACTOR} of bands factor'
+                    message=f'The maximum number={cls._MAX_INCREMENT_BANDS_FACTOR} of bands factor'
                             'increase loop reached, but still cannot get enough bands.')
         spec.exit_code(204, 'ERROR_KPOINTS_DISTANCE_BAND_STRUCTURE_NOT_SET',
                     message=f'kpoints distance is not set in inputs.')
@@ -197,11 +199,11 @@ def increase_nbands(self):
         #
         # If the bands evaluation failed it will keeps on increasing the `nbands_factor`
         # which lead to the infinite loop to this work chain.
-        # Here I work around it by giving maximum nbands_factor loop to _MAX_NUM_BANDS_FACTOR=5.
+        # Here I work around it by giving maximum nbands_factor loop to _MAX_INCREMENT_BANDS_FACTOR=10.
         # And add a `break_increase_nbands` to break and get out from `should_run_bands` immediately.
         if (
             self.ctx.nbands_factor
-            > self.inputs.init_nbands_factor.value + self._MAX_NUM_BANDS_FACTOR
+            > self.inputs.init_nbands_factor.value + self._MAX_INCREMENT_BANDS_FACTOR
         ):
             return self.exit_codes.ERROR_REACH_MAX_BANDS_FACTOR_INCREASE_LOOP
 
@@ -210,9 +212,9 @@ def increase_nbands(self):
             # I should not increase it anyway because this ctx is used
             # for the input of band structure calculation.
             self.report(
-                f"increasing nbands_factor to from {self.ctx.nbands_factor} to {self.ctx.nbands_factor + 1.0}"
+                f"increasing nbands_factor to from {self.ctx.nbands_factor} to {self.ctx.nbands_factor + self._BANDS_FACTOR_INCREASE_STEP}"
             )
-            self.ctx.nbands_factor += 1.0
+            self.ctx.nbands_factor += self._BANDS_FACTOR_INCREASE_STEP
 
     def should_run_band_structure(self):
         """whether run band structure"""

aiida_sssp_workflow/workflows/evaluate/_eos.py

@@ -141,7 +141,7 @@ def inspect_eos(self):
         self.out("output_volume_energy", output_volume_energy)
 
         output_birch_murnaghan_fit, node = run_get_node(
-            birch_murnaghan_fit, output_volume_energy
+            birch_murnaghan_fit, volume_energy=output_volume_energy
         )
 
         if not node.is_finished_ok:

aiida_sssp_workflow/workflows/measure/__init__.py

@@ -15,7 +15,7 @@ class _BaseMeasureWorkChain(SelfCleanWorkChain):
 
     # ECUT for oxygen, remember to update this if the oxygen pseudo is changed
     # Currently the oxygen pseudo is `O.paw.z_6.ld1.psl.v0.1.upf`
-    _O_ECUTWFC = 75.0
+    _O_ECUTWFC = 70.0
     _O_ECUTRHO = 560.0
 
     # ECUT for nitrogen, remember to update this if the nitrogen pseudo is changed

setup.cfg

@@ -25,7 +25,7 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    aiida-core[atomic_tools]~=2.4.0
+    aiida-core[atomic_tools]~=2.4
     aiida-quantumespresso~=4.3.0
 python_requires = >=3.8
 include_package_data = True