System Flow

flowchart LR
    A((<a href='https://google.com'>Begin\nSimulation</a>)) --> subB
    subgraph subB [Initialize Parameters]
        direction TB
        top1[Read in from\ninput files] --> bottom1[Calculate\nparameters]
    end
    subB --> C((Diagnostics\nn=1))
    C --> D((Pre-push\nn=1));
    D --> subsubE
    subgraph subE [Timesteps]
        direction TB
        subsubE --> E1
        subgraph subsubE ["Calculate E_(n+1)"]
            direction TB
            top3[Gather particles\nfrom nodes] --> bottom3[Solve Poisson's\nequation]
        end
        E1([Final Push\nn]) --> E2([Wall Losses])
        E2 --> E3([Collisions]);
        E3 --> E4([Diagnostics\nn+1]);
        E4 --> E5([Pre-push\nn+1]);
        E5 --> |if t < T\nn=n+1| subsubE;
    end
    E5 --> J((End\nSimulation));
    linkStyle 11 stroke-dasharray: 5, 5;

    %% Set labels for nodes
    classDef startNode fill:#9EEBCF,stroke:#333,stroke-width:2px;
    classDef stepNode fill:#FFD97D,stroke:#333,stroke-width:2px;
    classDef endNode fill:#FFA8A8,stroke:#333,stroke-width:2px;
    class A, startNode;
    class C,D stepNode;
    class J endNode;

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