Base RaspaBaseWorkChain on BaseRestartWorkChain from aiida-core. (#56)

* Migrate all the examples to the new API
* Remove redundant files (old base restart and related things)
* Inject all process_handlers in the base restart work chain.

Dockerfile

@@ -17,8 +17,8 @@ RUN pip install coveralls
 # Install necessary codes to build RASPA2.
 RUN apt-get clean && rm -rf /var/lib/apt/lists/* && apt-get update && apt-get install -y --no-install-recommends  \
     automake \
-    libtool
-
+    libtool  \
+    mpich
 
 # Download, compile and install RASPA into ~/code folder.
 RUN git clone https://github.com/iRASPA/RASPA2.git RASPA2

aiida_raspa/utils/__init__.py

@@ -2,7 +2,4 @@
 """Raspa utils."""
 from .base_parser import parse_base_output
 from .base_input_generator import RaspaInput
-from .inspection_tools import check_widom_convergence, check_gcmc_convergence, check_gemc_convergence
-from .inspection_tools import check_gemc_box, add_write_binary_restart
-from .other_utilities import UnexpectedCalculationFailure, ErrorHandlerReport
-from .other_utilities import prepare_process_inputs, register_error_handler
+from .inspection_tools import add_write_binary_restart, modify_number_of_cycles, increase_box_lenght

aiida_raspa/utils/inspection_tools.py

@@ -2,9 +2,7 @@
 """RASPA inspection tools"""
 
 from aiida.engine import calcfunction
-from aiida.orm import Dict, Int, Str, Float
-
-from .other_utilities import ErrorHandlerReport
+from aiida.orm import Dict
 
 
 @calcfunction
@@ -14,7 +12,6 @@ def add_write_binary_restart(input_dict, write_every):
     return input_dict if input_dict.get_dict() == final_dict else Dict(dict=final_dict)
 
 
-@calcfunction
 def modify_number_of_cycles(input_dict, additional_init_cycle, additional_prod_cycle):
     """Modify number of cycles to improve the convergence."""
     final_dict = input_dict.get_dict()
@@ -52,145 +49,3 @@ def increase_box_lenght(input_dict, box_name, box_length_current):
     final_dict["System"][box_name.value]["BoxLengths"] = "{} {} {}".format(*box_one_length_new)
 
     return Dict(dict=final_dict)
-
-
-def check_widom_convergence(workchain, calc, conv_threshold=0.1, additional_cycle=0):
-    """
-    Checks whether a Widom particle insertion is converged.
-    Checking is based on the error bar on Henry coefficient.
-    """
-    output_widom = calc.outputs.output_parameters.get_dict()
-    structure_label = list(calc.get_incoming().nested()['framework'].keys())[0]
-    conv_stat = []
-
-    for comp in calc.inputs.parameters['Component']:
-        kh_average_comp = output_widom[structure_label]["components"][comp]["henry_coefficient_average"]
-        kh_dev_comp = output_widom[structure_label]["components"][comp]["henry_coefficient_dev"]
-
-        error = round((kh_dev_comp / kh_average_comp), 2)
-        if error <= conv_threshold:
-            conv_stat.append(True)
-        else:
-            conv_stat.append(False)
-
-    if not all(conv_stat):
-        workchain.report("Widom particle insertion calculation is NOT converged: repeating with more trials...")
-        workchain.ctx.inputs.retrieved_parent_folder = calc.outputs['retrieved']
-        workchain.ctx.inputs.parameters = modify_number_of_cycles(workchain.ctx.inputs.parameters,
-                                                                  additional_init_cycle=Int(0),
-                                                                  additional_prod_cycle=Int(additional_cycle))
-        return ErrorHandlerReport(True, False)
-
-    return None
-
-
-def check_gcmc_convergence(workchain, calc, conv_threshold=0.1, additional_init_cycle=0, additional_prod_cycle=0):
-    """
-    Checks whether a GCMC calc is converged.
-    Checking is based on the error bar on average loading.
-    """
-    output_gcmc = calc.outputs.output_parameters.get_dict()
-    structure_label = list(calc.get_incoming().nested()['framework'].keys())[0]
-    conv_stat = []
-
-    for comp in calc.inputs.parameters['Component']:
-
-        loading_average_comp = output_gcmc[structure_label]["components"][comp]["loading_absolute_average"]
-        loading_dev_comp = output_gcmc[structure_label]["components"][comp]["loading_absolute_dev"]
-
-        # It can happen for weekly adsorbed species.
-        # we need to think about a better way to handle it.
-        # Currently, if it happens for five iterations, workchain will not continue.
-        if loading_average_comp == 0:
-            conv_stat.append(False)
-        else:
-            error = round((loading_dev_comp / loading_average_comp), 2)
-            if error <= conv_threshold:
-                conv_stat.append(True)
-            else:
-                conv_stat.append(False)
-
-    if not all(conv_stat):
-        workchain.report("GCMC calculation is NOT converged: continuing from restart...")
-        workchain.ctx.inputs.retrieved_parent_folder = calc.outputs['retrieved']
-        workchain.ctx.inputs.parameters = modify_number_of_cycles(workchain.ctx.inputs.parameters,
-                                                                  additional_init_cycle=Int(additional_init_cycle),
-                                                                  additional_prod_cycle=Int(additional_prod_cycle))
-        return ErrorHandlerReport(True, False)
-
-    return None
-
-
-def check_gemc_convergence(workchain, calc, conv_threshold=0.1, additional_init_cycle=0, additional_prod_cycle=0):
-    """
-    Checks whether a GCMC calc is converged.
-    Checking is based on the error bar on average loading which is
-    average number of molecules in each simulation box.
-    """
-    output_gemc = calc.outputs.output_parameters.get_dict()
-    conv_stat = []
-
-    for comp in calc.inputs.parameters['Component']:
-        molec_per_box1_comp_average = output_gemc['box_one']["components"][comp]["loading_absolute_average"]
-        molec_per_box2_comp_average = output_gemc['box_two']["components"][comp]["loading_absolute_average"]
-        molec_per_box1_comp_dev = output_gemc['box_one']["components"][comp]["loading_absolute_dev"]
-        molec_per_box2_comp_dev = output_gemc['box_two']["components"][comp]["loading_absolute_dev"]
-
-        error_box1 = round((molec_per_box1_comp_dev / molec_per_box1_comp_average), 2)
-        error_box2 = round((molec_per_box2_comp_dev / molec_per_box2_comp_average), 2)
-
-        if (error_box1 <= conv_threshold) and (error_box2 <= conv_threshold):
-            conv_stat.append(True)
-        else:
-            conv_stat.append(False)
-
-    if not all(conv_stat):
-        workchain.report("GEMC calculation is NOT converged: continuing from restart...")
-        workchain.ctx.inputs.retrieved_parent_folder = calc.outputs['retrieved']
-        workchain.ctx.inputs.parameters = modify_number_of_cycles(workchain.ctx.inputs.parameters,
-                                                                  additional_init_cycle=Int(additional_init_cycle),
-                                                                  additional_prod_cycle=Int(additional_prod_cycle))
-        return ErrorHandlerReport(True, False)
-
-    return None
-
-
-def check_gemc_box(workchain, calc):
-    """
-    Checks whether each simulation box still satisfies minimum image convention.
-    """
-    output_gemc = calc.outputs.output_parameters.get_dict()
-    cutoff = calc.inputs.parameters['GeneralSettings']['CutOff']
-    box_one_stat = []
-    box_two_stat = []
-
-    box_one_length_current = []
-    box_two_length_current = []
-
-    for box_len_ave in ["box_ax_average", "box_by_average", "box_cz_average"]:
-        if output_gemc["box_one"]["general"][box_len_ave] > 2 * cutoff:
-            box_one_stat.append(True)
-        else:
-            box_one_stat.append(False)
-            box_one_length_current.append(output_gemc["box_one"]["general"][box_len_ave])
-
-        if output_gemc["box_two"]["general"][box_len_ave] > 2 * cutoff:
-            box_two_stat.append(True)
-        else:
-            box_two_stat.append(False)
-            box_two_length_current.append(output_gemc["box_two"]["general"][box_len_ave])
-
-    if not all(box_one_stat and box_two_stat):
-        workchain.report("GEMC box is NOT converged: repeating with increase box...")
-        # Fixing the issue.
-        if not all(box_one_stat):
-            workchain.ctx.inputs.parameters = increase_box_lenght(workchain.ctx.inputs.parameters, Str("box_one"),
-                                                                  Float(box_one_length_current[0]))
-
-        if not all(box_two_stat):
-            workchain.ctx.inputs.parameters = increase_box_lenght(workchain.ctx.inputs.parameters, Str("box_two"),
-                                                                  Float(box_two_length_current[0]))
-
-        return ErrorHandlerReport(True, False)
-
-    return None