Settings

App Layout

The interface supports four different layouts (Figure 100). The user can also toggle between dark mode and light mode and optionally hide the header bar depending on the selected layout.

Viewer Settings

You can configure default settings for both the Code Editor and the 3D viewer (Figure 101).

Code Editor Defaults:

• Enable or disable auto-complete.

• Define a code template that is inserted when selecting New from Template in the editor. By default, the template is collapsed; clicking the arrow expands it to a box where the user can edit the text.

3D Viewer Defaults:

• Start with axis displayed.

• Start with grid displayed.

• Start with cell outlines enabled.

• Choose whether to build the full lattice in the 3D CAD processor.

• Set the resolution of the CAD build.

• Adjust the parameterisation precision Cyclone uses when expanding parameters.

• Change the default background colour.

File Manager

The File Manager can be restricted to a specific folder, defined in this section. The user can also manage the list of recognised file extensions (Figure 102):

• MCNP file extensions – can be added, modified, or removed.

• Queue file extensions – can be added, modified, or removed (Enterprise Plan).

Executables Settings

The executable Settings section (Figure 103) defines the external programs that Cyclone calls during execution. These paths and commands determine how Cyclone launches MCNP and any other linked tools.

Server Executables (Enterprise Plan)

The server executable Settings section (Figure 104) defines the external programs that Cyclone calls during execution on the server, including the cyclone back end itself. These paths and commands determine how Cyclone launches MCNP and any other linked tools.

Server Settings

To communicate with a remote server, Cyclone requires connection details and path mappings (Figure 105).

• You can test the connection directly from this panel.

• Windows paths can be mapped to corresponding Unix paths so that files are correctly located on both systems.

• Authentication is handled through profiles, where the user define the username, hostname, port number, and private key location.

• The server-side location of Cyclone must also be specified.

• Finally, the location of queue scripts is set here, allowing Cyclone to interact with the remote Queue System.

Remote Server Queue Commands

For interfacing with a remote server, Cyclone must be provided with the location of the command files to be executed. The template used to generate the queue file for the remote server is also defined here (see Figure 106).

Clear Cache

Cyclone uses the temporary directory for its build processes. If a build fails, or if an input is built without being saved, the generated files are stored here. Over time, these files can accumulate. The user can either remove them manually or click the Clean Temporary Directory button to clear them automatically. See Figure 31.

Import/Export

Cyclone allows the user to save, export, and import their full environment configuration (viewer, file manager, executables, server connections, submission profiles), see Figure 99. All configurations are stored as a JSON document.

Supported Sections

Each JSON file may contain the following top-level sections:

• viewer-settings – Viewer and editor display preferences.

• file-manager-settings – File extension handling and restrictions.

• executables-settings – Local paths to MCNP/ADVANTG/MPI executables.

• server-executables-settings – Remote server paths to executables.

• submission-settings – Queue/profile settings for job submission.

Each section is optional. Only present fields will be applied during import.

Importing Settings

When importing:

1. JSON keys are normalized:

   • Case-insensitive.

   • Spaces/underscores → hyphens.

   • Multiple hyphens collapsed.

2. Each field is validated:

   • Booleans can be true/false or 1/0.

   • Strings must be strings.

   • Numbers must be valid numbers.

   • Lists must be arrays of the correct type.

3. Invalid fields are skipped, and errors are reported in the user interface.

Example – Minimal Import

JSON
Copy
1{
2  "viewer-settings": {
3    "axis": true,
4    "grid": "XY",
5    "resolution": 20,
6    "precision": 6,
7    "background-colour": [0.0, 0.0, 0.0, 1.0],
8    "template": "c cell 1", "1 0 -1"
9  },
10  "file-manager-settings": {
11    "mcnp-extensions": [".i", ".inp"],
12    "queue-extensions": [".q"],
13    "restricted-path": "C:\\restricted"
14  }
15}

This sets axis display on, uses an XY grid, sets resolution/precision, applies a black background colour (RGBA, normalised to 1), and loads a code template.

Example – Full Import

JSON
Copy
1{
2  "viewer-settings": {
3    "axis": true,
4    "auto-complete": true,
5    "outline-cells": false,
6    "cad-lattice": true,
7    "resolution": 25,
8    "precision": 8,
9    "background-colour": [1.0, 1.0, 1.0, 1.0],
10    "template": ["c example template", "10 0 -1"],
11    "grid": "OFF"
12  },
13  "file-manager-settings": {
14    "mcnp-extensions": [".i", ".inp"],
15    "queue-extensions": [".pbs", ".q"],
16    "restricted path": "C:\\restricted"
17  },
18  "executables-settings": {
19    "mcnp-executable": "mcnp6.exe",
20    "advantg-executable": "advantg.bat",
21    "mpi-executable": "mpiexec.exe",
22    "mcnp-mpi-executable": "mcnp6_mpi.exe",
23    "prepend-command": "module load mcnp",
24    "post-command": "echo Job finished"
25  },
26  "server-executables-settings": {
27    "mcnp-executable": "/opt/mcnp/mcnp6",
28    "advantg-executable": "/opt/advantg/advantg",
29    "mpi-executable": "/usr/bin/mpiexec",
30    "mcnp-mpi-executable": "/opt/mcnp/mcnp6_mpi",
31    "prepend-command": "module load mcnp",
32    "post-command": "echo Done",
33    "cyclone-executable": "/opt/cyclone/cyclone"
34  },
35  "submission-settings": {
36    "profiles": [
37      {
38        "username": "user1",
39        "hostname": "cluster1.example.com",
40        "port": 22,
41        "key": "C:\\keys\\id_rsa",
42        "location": "/home/user1/cyclone_jobs",
43        "template": ["#PBS -l nodes=1:ppn=4", "mcnp6 i=input"],
44        "submission-command": "qsub",
45        "queue-scripts": {
46          "get-queues": "qstat -q",
47          "get-jobs": "qstat -u $USER",
48          "get-jobs-full": "qstat -f",
49          "get-queue-machines": "pbsnodes -a",
50          "get-queue-info": "qstat -Qf",
51          "rerun-job": "qrerun",
52          "suspend-job": "qsuspend",
53          "resume-job": "qresume",
54          "hold-job": "qhold",
55          "release-job": "qrls",
56          "delete-job": "qdel",
57          "move-job": "qmove",
58          "hold-machine": "pbsnodes -o",
59          "clear-machine": "pbsnodes -c"
60        }
61      }
62    ],
63    "active-profile": 1,
64    "shared-drive-mappings": 
65      {
66        "windows": "Z:\\",
67        "unix": "/mnt/shared"
68      }
69    
70  }
71}

Exporting Settings

Export gathers the current application state into a JSON file.

• Arrays like template are split into multiple lines.

• Active profile is stored with a 1-based index.

• Shared drive mappings include both Windows and Unix paths.

Example – Exported File

JSON
Copy
1{
2  "viewer-settings": {
3    "axis": true,
4    "auto-complete": false,
5    "outline-cells": true,
6    "cad-lattice": false,
7    "resolution": 20,
8    "precision": 6,
9    "background-colour": [0.0, 0.0, 0.0, 1.0],
10    "template": ["c default template"],
11    "grid": "XY"
12  },
13  "file-manager-settings": {
14    "mcnp-extensions": [".i", ".inp"],
15    "queue-extensions": [".q"],
16    "restricted path": "C:\\restricted"
17  },
18  "executables-settings": {
19    "mcnp-executable": "mcnp6.exe",
20    "advantg-executable": "",
21    "mpi-executable": "",
22    "mcnp-mpi-executable": "",
23    "prepend-command": "",
24    "post-command": ""
25  },
26  "server-executables-settings": {
27    "mcnp-executable": "/opt/mcnp/mcnp6",
28    "advantg-executable": "",
29    "mpi-executable": "",
30    "mcnp-mpi-executable": "",
31    "prepend-command": "",
32    "post-command": "",
33    "cyclone-executable": "/opt/cyclone/cyclone"
34  },
35  "submission-settings": {
36    "profiles": [
37      {
38        "username": "user1",
39        "hostname": "cluster1.example.com",
40        "port": 22,
41        "key": "C:\\keys\\d_rsa",
42        "location": "/home/user1/cyclone_jobs",
43        "template": ["#PBS -l nodes=1:ppn=4", "mcnp6 i=input"],
44        "submission-command": "qsub",
45        "queue-scripts": {
46          "get-queues": "qstat -q",
47          "get-jobs": "qstat -u $USER",
48          "get-jobs-full": "qstat -f",
49          "get-queue-machines": "pbsnodes -a",
50          "get-queue-info": "qstat -Qf",
51          "rerun-job": "qrerun",
52          "suspend-job": "qsuspend",
53          "resume-job": "qresume",
54          "hold-job": "qhold",
55          "release-job": "qrls",
56          "delete-job": "qdel",
57          "move-job": "qmove",
58          "hold-machine": "pbsnodes -o",
59          "clear-machine": "pbsnodes -c"
60        }
61      }
62    ],
63    "active-profile": 1,
64    "shared-drive-mappings": 
65      {
66        "windows": "Z:\\",
67        "unix": "/mnt/shared"
68      }
69    
70  }
71}

Notes and Constraints

• Background Colour: must be a list of 4 numbers [R, G, B, A], each between 0 and 1.

• Grid: must be one of OFF, XY, YZ, XZ.

• Profiles: multiple profiles can be stored; active-profile selects which one is active.

• Drive mappings: always require both "windows" and "unix".

Figure 99: Settings – import/export

Figure 100: Settings – app layout

Figure 101: Settings – viewer settings

Figure 102: Settings – file manager settings

Figure 103: Settings – Executable settings

Figure 104: Settings – server executable settings

Figure 105: Settings – server settings

Figure 106: Settings – remote queue system files