How to create custom workflows with NOMAD entries¶
This how-to will walk you through how to use nomad-utility-workflows to generate the yaml file required to define a custom workflow.
Example Overview¶
To demonstrate, we will use the following 3 step molecular dynamics equilibration workflow:
-
geometry optimization (energy minimization)
-
equilibration MD simulation in NPT
-
production MD simulation in NVT
The final result will be the following workflow graph visualization in NOMAD:
Example Data¶
Each task in this workflow represents a supported entry in NOMAD, and all 3 simulations will be uploaded together with the workflow.archive.yaml file, within the following local filesystem:
upload.zip
├── workflow.archive.yaml
├── Emin
│ ├── mdrun_Emin.log # Geometry Optimization mainfile
│ └── ...other raw simulation files
├── Equil_NPT
│ ├── mdrun_Equil-NPT.log # NPT equilibration mainfile
│ └── ...other raw simulation files
└── Prod_NVT
├── mdrun_Prod-NVT.log # NVT production mainfile
└── ...other raw simulation files
You can obtain the simulation data in the GitHub repository of nomad-utility-workflows under tests/utils/workflow_yaml_examples/water_equilibration/ in the file simulation_data.zip
Imports¶
First, import the necessary imports (gravis is only used for graph visualization and is not strictly necessary):
import gravis as gv
import networkx as nx
from nomad_utility_workflows.utils.workflows import build_nomad_workflow, nodes_to_graph
Generate the input workflow graph¶
To generate the appropriate workflow yaml file to connect the entries in NOMAD, we need to create a graph representating
our workflow. For this workflow, we create a networkx.DiGraph(), named workflow_graph_input in this example, that looks like:
IMPORTANT
To ensure that all functionalities work correctly, the node keys must be unique integers that index the nodes. I.e., node_keys = [0, 1, 2, 3] for a graph with 4 nodes.
If you are using a workflow manager, you can probably extract a graph structure directly from the manager output, and then map this structure to an analogous structure with networkx, as described further below. If you do not have access to such a graph, you can Create an input graph manually or, alternatively, Create an input graph with nodes_to_graph().
Create an input graph manually¶
Use NetworkX Docs > DiGraph to contruct a networkx.DiGraph().
A series of NodeAttributes should be associated with each of the nodes in your graph. Here we print out the required node attributes in this example for the graph visualized above:
for node_key, node_attributes in workflow_graph_input.nodes(data=True):
print(node_key, node_attributes)
0 {'name': 'input system',
'type': 'input',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log',
'supersection_index': 0,
'section_index': 0,
'section_type': 'system'
},
}
1 {'name': 'Geometry Optimization',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log'
}
}
2 {'name': 'Equilibration NPT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'
},
}
3 {'name': 'Production NVT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
}
4 {'name': 'output system',
'type': 'output',
'path_info': {
'section_type': 'system',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
}
5 {'name': 'output properties',
'type': 'output',
'path_info': {
'section_type': 'calculation',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
}
Descriptions for each attribute are given in Explanation > Workflow > Node Attributes
The appropriate edges should be added to your graph:
for edge_1, edge_2, edge_attributes in workflow_graph_input.edges(data=True):
print(edge_1, edge_2, edge_attributes)
There are no necessary attributes to add to the edges. nomad-utility-workflows will automatically add edge attributes based on the node attribute inputs.
Create an input graph with nodes_to_graph()¶
If you are unfamiliar with networkx, nomad-utility-workflows can generate an input graph structure for you to use with build_workflow_yaml().
For this approach, simply create a dictionary of node keys and corresponding NodeAttributes:
node_attributes = {
0: {'name': 'input system',
'type': 'input',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log',
'supersection_index': 0,
'section_index': 0,
'section_type': 'system'
},
'out_edge_nodes': [1],
},
1: {'name': 'Geometry Optimization',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log'
}
},
2: {'name': 'Equilibration NPT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'
},
'in_edge_nodes': [1],
},
3: {'name': 'Production NVT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [2],
},
4: {'name': 'output system',
'type': 'output',
'path_info': {
'section_type': 'system',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [3],
},
5: {'name': 'output properties',
'type': 'output',
'path_info': {
'section_type': 'calculation',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [3],
}
}
Again, descriptions for each attribute are given in Explanation > Workflow > Node Attributes
Notice that this dictionary exactly corresponds to the printed attributes of the nodes displayed above, with the exception of the in_edge_nodes and out_edge_nodes attributes. These attributes are used to specify the graph edges.
Now, simply run:
The resulting graph should be identical to the input graph visualized above, and can be therefore used in the same way to Generate the workflow yaml file.
Generate the workflow yaml¶
Now that we have generated the input workflow graph, we can use nomad-utility-workflows's build_nomad_workflow() function to create the workflow.archive.yaml file that will connect the individual example simulations within NOMAD:
workflow_metadata = {
'destination_filename': './workflow_minimal.archive.yaml',
'workflow_name': 'Equilibration Procedure',
}
workflow_graph_output = build_nomad_workflow(
workflow_metadata=workflow_metadata,
workflow_graph=nx.DiGraph(workflow_graph_input),
write_to_yaml=True,
)
Here we provide the full path and name of the output yaml in destination_filename and the overarching workflow name that will show up on top of the workflow graph visualization in workflow_name. The output workflow looks like:
gv.d3(
workflow_graph_output,
node_label_data_source='name',
edge_label_data_source='name',
zoom_factor=1.5,
node_hover_tooltip=True,
)
We see that our output graph looks signficantly different than the input. That's because nomad-utility-workflow is automatically adding some default input/outputs to ensure the proper node connections within the workflow visualizer. For nodes with entry_type = 'simulation', the automatically generated input defaults correspond to the System section from any incoming task node that exists. The automatically generated output defaults correspond to both the system and the Calculation section from the given node.
Let's examine the output workflow graph in more detail:
for node_key, node_attributes in workflow_graph_output_minimal.nodes(data=True):
print(node_key, node_attributes)
0 {'name': 'input system', 'type': 'input', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log', 'supersection_index': 0, 'section_index': 0, 'section_type': 'system'}}
1 {'name': 'Geometry Optimization', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log'}}
2 {'name': 'Equilibration NPT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
3 {'name': 'Production NVT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
4 {'name': 'output system', 'type': 'output', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
5 {'name': 'output properties', 'type': 'output', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
6 {'type': 'output', 'name': 'output system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
7 {'type': 'output', 'name': 'output calculation from Geometry Optimization', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
8 {'type': 'input', 'name': 'input system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
9 {'type': 'output', 'name': 'output system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
10 {'type': 'output', 'name': 'output calculation from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
11 {'type': 'input', 'name': 'input system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
12 {'type': 'output', 'name': 'output system from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
13 {'type': 'output', 'name': 'output calculation from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
and the edges:
for edge_1, edge_2, edge_attributes in workflow_graph_output_minimal.edges(data=True):
print(edge_1, edge_2, edge_attributes)
0 1 {'inputs': [], 'outputs': []}
1 2 {'inputs': [{'name': 'output system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}, {'name': 'output calculation from Geometry Optimization', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Emin/mdrun_Emin.log'}}], 'outputs': [{'name': 'input system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}]}
1 6 {}
1 7 {}
2 3 {'inputs': [{'name': 'output system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}, {'name': 'output calculation from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}], 'outputs': [{'name': 'input system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}]}
2 9 {}
2 10 {}
3 4 {'inputs': [{'name': 'output system from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}, {'name': 'output calculation from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}], 'outputs': []}
3 5 {'inputs': [], 'outputs': []}
3 12 {}
3 13 {}
8 2 {}
11 3 {}
Finally, the output workflow.archive.yaml:
'workflow2':
'name': 'Equilibration Procedure'
'inputs':
- 'name': 'input system'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/0'
'outputs':
- 'name': 'output system'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/system/-1'
- 'name': 'output properties'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/calculation/-1'
'tasks':
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Geometry Optimization'
'task': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/workflow2'
'inputs': []
'outputs':
- 'name': 'output system from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/-1'
- 'name': 'output calculation from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/calculation/-1'
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Equilibration NPT Molecular Dynamics'
'task': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/workflow2'
'inputs':
- 'name': 'input system from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/-1'
'outputs':
- 'name': 'output system from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/system/-1'
- 'name': 'output calculation from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/calculation/-1'
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Production NVT Molecular Dynamics'
'task': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/workflow2'
'inputs':
- 'name': 'input system from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/system/-1'
'outputs':
- 'name': 'output system from Production NVT Molecular Dynamics'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/system/-1'
- 'name': 'output calculation from Production NVT Molecular Dynamics'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/calculation/-1'
By uploading workflow.archive.yaml along with the Example Data, with the file structure as specified in Example Data, you should reproduce the workflow visualization graph seen in Example Overview within the workflow entry of your upload.
Adding additional inputs/outputs¶
Now let's add some additional input/outputs to the nodes. We will use the nodes_to_graph() method to generate the input workflow graph:
node_attributes = {
0: {'name': 'input system',
'type': 'input',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log',
'supersection_index': 0,
'section_index': 0,
'section_type': 'system'
},
'out_edge_nodes': [1],
},
1: {'name': 'Geometry Optimization',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Emin/mdrun_Emin.log'
},
'outputs': [
{
'name': 'energies of the relaxed system',
'path_info': {
'section_type': 'energy',
'supersection_path': 'run/0/calculation', # this can be done, but at this point it's safer / easier to just use archive_path
'supersection_index': -1,
},
}
],
},
2: {'name': 'Equilibration NPT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'
},
'in_edge_nodes': [1],
'outputs': [
{
'name': 'MD workflow properties (structural and dynamical)',
'path_info': {
'section_type': 'results',
},
}
],
},
3: {'name': 'Production NVT Molecular Dynamics',
'type': 'workflow',
'entry_type': 'simulation',
'path_info': {
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [2],
'outputs': [
{
'name': 'MD workflow properties (structural and dynamical)',
'path_info': {
'section_type': 'results',
},
}
],
},
4: {'name': 'output system',
'type': 'output',
'path_info': {
'section_type': 'system',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [3],
},
5: {'name': 'output properties',
'type': 'output',
'path_info': {
'section_type': 'calculation',
'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'
},
'in_edge_nodes': [3],
}
}
workflow_graph_input = nodes_to_graph(node_attributes)
gv.d3(
workflow_graph_input,
node_label_data_source='name',
edge_label_data_source='name',
zoom_factor=1.5,
node_hover_tooltip=True,
)
for node_key, node_attributes in workflow_graph_input.nodes(data=True):
print(node_key, node_attributes)
0 {'name': 'input system', 'type': 'input', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log', 'supersection_index': 0, 'section_index': 0, 'section_type': 'system'}, 'out_edge_nodes': [1]}
1 {'name': 'Geometry Optimization', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log'}}
2 {'name': 'Equilibration NPT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}, 'in_edge_nodes': [1]}
3 {'name': 'Production NVT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [2]}
4 {'name': 'output system', 'type': 'output', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [3]}
5 {'name': 'output properties', 'type': 'output', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [3]}
6 {'type': 'output', 'name': 'energies of the relaxed system', 'path_info': {'section_type': 'energy', 'supersection_path': 'run/0/calculation', 'supersection_index': -1}}
7 {'type': 'output', 'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results'}}
8 {'type': 'output', 'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results'}}
for edge_1, edge_2, edge_attributes in workflow_graph_input.edges(data=True):
print(edge_1, edge_2, edge_attributes)
0 1 {}
1 6 {'inputs': [{'name': 'energies of the relaxed system', 'path_info': {'section_type': 'energy', 'supersection_path': 'run/0/calculation', 'supersection_index': -1}}]}
1 2 {}
2 7 {'inputs': [{'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results'}}]}
2 3 {}
3 8 {'inputs': [{'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results'}}]}
3 4 {}
3 5 {}
And again we generate the final workflow graph and yaml:
workflow_graph_output = build_nomad_workflow(
destination_filename='./workflow.archive.yaml',
workflow_name='Equilibration Procedure',
workflow_graph=nx.DiGraph(workflow_graph_input),
write_to_yaml=True,
)
gv.d3(
workflow_graph_output,
node_label_data_source='name',
edge_label_data_source='name',
zoom_factor=1.5,
node_hover_tooltip=True,
)
for node_key, node_attributes in workflow_graph_output.nodes(data=True):
print(node_key, node_attributes)
0 {'name': 'input system', 'type': 'input', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log', 'supersection_index': 0, 'section_index': 0, 'section_type': 'system'}, 'out_edge_nodes': [1]}
1 {'name': 'Geometry Optimization', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Emin/mdrun_Emin.log'}}
2 {'name': 'Equilibration NPT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}, 'in_edge_nodes': [1]}
3 {'name': 'Production NVT Molecular Dynamics', 'type': 'workflow', 'entry_type': 'simulation', 'path_info': {'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [2]}
4 {'name': 'output system', 'type': 'output', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [3]}
5 {'name': 'output properties', 'type': 'output', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}, 'in_edge_nodes': [3]}
6 {'type': 'output', 'name': 'energies of the relaxed system', 'path_info': {'section_type': 'energy', 'supersection_path': 'run/0/calculation', 'supersection_index': -1, 'mainfile_path': 'Emin/mdrun_Emin.log'}}
7 {'type': 'output', 'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
8 {'type': 'output', 'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
9 {'type': 'output', 'name': 'output system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
10 {'type': 'output', 'name': 'output calculation from Geometry Optimization', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
11 {'type': 'input', 'name': 'input system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}
12 {'type': 'output', 'name': 'output system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
13 {'type': 'output', 'name': 'output calculation from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
14 {'type': 'input', 'name': 'input system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}
15 {'type': 'output', 'name': 'output system from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
16 {'type': 'output', 'name': 'output calculation from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}
for edge_1, edge_2, edge_attributes in workflow_graph_output.edges(data=True):
print(edge_1, edge_2, edge_attributes)
0 1 {'inputs': [], 'outputs': []}
1 6 {'inputs': [{'name': 'energies of the relaxed system', 'path_info': {'section_type': 'energy', 'supersection_path': 'run/0/calculation', 'supersection_index': -1, 'mainfile_path': 'Emin/mdrun_Emin.log'}}, {'name': 'output system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}, {'name': 'output calculation from Geometry Optimization', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Emin/mdrun_Emin.log'}}], 'outputs': []}
1 2 {'inputs': [], 'outputs': [{'name': 'input system from Geometry Optimization', 'path_info': {'section_type': 'system', 'mainfile_path': 'Emin/mdrun_Emin.log'}}]}
1 9 {}
1 10 {}
2 7 {'inputs': [{'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}, {'name': 'output system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}, {'name': 'output calculation from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}], 'outputs': []}
2 3 {'inputs': [], 'outputs': [{'name': 'input system from Equilibration NPT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Equil_NPT/mdrun_Equil-NPT.log'}}]}
2 12 {}
2 13 {}
3 8 {'inputs': [{'name': 'MD workflow properties (structural and dynamical)', 'path_info': {'section_type': 'results', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}, {'name': 'output system from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'system', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}, {'name': 'output calculation from Production NVT Molecular Dynamics', 'path_info': {'section_type': 'calculation', 'mainfile_path': 'Prod_NVT/mdrun_Prod-NVT.log'}}], 'outputs': []}
3 4 {'inputs': [], 'outputs': []}
3 5 {'inputs': [], 'outputs': []}
3 15 {}
3 16 {}
11 2 {}
14 3 {}
workflow_archive.yaml:
'workflow2':
'name': 'Equilibration Procedure'
'inputs':
- 'name': 'input system'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/0'
'outputs':
- 'name': 'MD workflow properties (structural and dynamical)'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/workflow2/results/-1'
- 'name': 'output system'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/system/-1'
- 'name': 'output properties'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/calculation/-1'
'tasks':
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Geometry Optimization'
'task': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/workflow2'
'inputs': []
'outputs':
- 'name': 'energies of the relaxed system'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/calculation/-1/energy/-1'
- 'name': 'output system from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/-1'
- 'name': 'output calculation from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/calculation/-1'
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Equilibration NPT Molecular Dynamics'
'task': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/workflow2'
'inputs':
- 'name': 'input system from Geometry Optimization'
'section': '../upload/archive/mainfile/Emin/mdrun_Emin.log#/run/0/system/-1'
'outputs':
- 'name': 'MD workflow properties (structural and dynamical)'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/workflow2/results/-1'
- 'name': 'output system from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/system/-1'
- 'name': 'output calculation from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/calculation/-1'
- 'm_def': 'nomad.datamodel.metainfo.workflow.TaskReference'
'name': 'Production NVT Molecular Dynamics'
'task': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/workflow2'
'inputs':
- 'name': 'input system from Equilibration NPT Molecular Dynamics'
'section': '../upload/archive/mainfile/Equil_NPT/mdrun_Equil-NPT.log#/run/0/system/-1'
'outputs':
- 'name': 'MD workflow properties (structural and dynamical)'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/workflow2/results/-1'
- 'name': 'output system from Production NVT Molecular Dynamics'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/system/-1'
- 'name': 'output calculation from Production NVT Molecular Dynamics'
'section': '../upload/archive/mainfile/Prod_NVT/mdrun_Prod-NVT.log#/run/0/calculation/-1'