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feat: 新增科研软件 benchmark 任务数据

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- 新增 avogadro/imagej/jade/origin/ovito/pymol/vesta 等科研软件任务 JSON
- 修改 vllm_eval.py，修改图片文件名称为第x步
- desktop_env.py 添加额外数据参数 config 和 metadata
This commit is contained in:
lizhanyuan
2026-02-25 15:19:36 +08:00
parent 613f55f0da
commit 9899d4a0c7
85 changed files with 4703 additions and 71 deletions
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57
evaluation_examples/examples/vesta/VESTA_Manual_task1.json Normal file
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{
"id": "VESTA_Manual_task1",
"snapshot": "vesta",
"instruction": "在 VESTA 中启动软件并加载结构文件 example_structure.cif。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/example_structure.cif",
"path": "C:\\Users\\user\\Desktop\\example_structure.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"example_structure.cif"
],
"steps": "1. 启动 VESTA 软件。\n2. 点击 File → Open。\n3. 在文件浏览窗口中选择 example_structure.cif 文件。\n4. 点击 Open 按钮加载文件。\n5. 确认结构已显示在视图窗口中。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task10.json Normal file
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{
"id": "VESTA_Manual_task10",
"snapshot": "vesta",
"instruction": "在 VESTA 中导入 Crystallographic Information File (CIF) 并查看其对称性。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/sample.cif",
"path": "C:\\Users\\user\\Desktop\\sample.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"sample.cif"
],
"steps": "1. 启动 VESTA 软件。\n2. 点击 File → Open，打开文件浏览器。\n3. 选择 sample.cif 文件并点击 Open。\n4. 加载文件后，点击 Edit → Data。\n5. 选择 Unit Cell 标签。\n6. 查看 Symmetry 选项卡中显示的对称性信息。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task11.json Normal file
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{
"id": "VESTA_Manual_task11",
"snapshot": "vesta",
"instruction": "在 VESTA 中生成 polyhedra 并调整其透明度。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/example_structure.cif",
"path": "C:\\Users\\user\\Desktop\\example_structure.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"example_structure.cif"
],
"steps": "1. 打开 VESTA 软件并加载 example_structure.vesta 文件。\n2. 点击 Edit → Properties。\n3. 在 Properties 对话框中选择 Polyhedra 标签。\n4. 勾选 Enable Polyhedra 绘图。\n5. 调整 Transparency 滑块到所需透明度值，例如 50%。\n6. 点击 OK 按钮保存设置。\n7. 验证主视图窗口中 Polyhedra 的更新显示。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task2.json Normal file
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{
"id": "VESTA_Manual_task2",
"snapshot": "vesta",
"instruction": "在 VESTA 中设置显示模式为 Ball-and-Stick，用于 example_structure.cif 文件。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/example_structure.cif",
"path": "C:\\Users\\user\\Desktop\\example_structure.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"example_structure.cif"
],
"steps": "1. 打开 VESTA 软件并加载文件 loaded_structure.vesta。\n2. 在顶部菜单中选择 View → Display Style。\n3. 在弹出的对话框中选择 Ball-and-Stick 模式。\n4. 点击 OK 按钮应用设置。\n5. 查看主视图窗口以确认显示模式已改变。"
}
}

44
evaluation_examples/examples/vesta/VESTA_Manual_task3.json Normal file
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{
"id": "VESTA_Manual_task3",
"snapshot": "vesta",
"instruction": "在 VESTA 中测量当前晶体中两个原子之间的距离。",
"source": "custom",
"config": [
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [],
"steps": "1. 在 VESTA 软件中打开任何结构文件。\n2. 点击垂直工具栏中的 Measure Distance 工具。\n3. 在主视图窗口中选择两个要测量距离的原子。\n4. 在 Measure Distance 工具下确认显示两个原子之间的距离。\n5. 验证输出的距离值是否正确显示。"
}
}

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evaluation_examples/examples/vesta/VESTA_Manual_task4.json Normal file
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{
"id": "VESTA_Manual_task4",
"snapshot": "vesta",
"instruction": "在 VESTA 中定义自定义绘图边界。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/MgB2.cif",
"path": "C:\\Users\\user\\Desktop\\MgB2.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"MgB2.cif"
],
"steps": "1. 打开 VESTA 软件并加载文件 MgB2.cif。\n2. 点击左侧侧边栏的 Objects → Boundary 按钮，打开 Boundary 对话框。\n3. 在对话框中调整范围 (x[min], x[max], y[min], y[max], z[min], z[max]) 为自定义值，例如 0 到 1。\n4. 点击 OK 或 Apply 按钮。\n5. 查看修改后的晶体绘图边界显示在主视图中。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task5.json Normal file
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{
"id": "VESTA_Manual_task5",
"snapshot": "vesta",
"instruction": "通过 VESTA 的 Properties 对话框调整晶体键的颜色和半径。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/xTiO2.cif",
"path": "C:\\Users\\user\\Desktop\\xTiO2.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"xTiO2.cif"
],
"steps": "1. 打开 VESTA 软件并加载 xTiO2.vesta 文件。\n2. 点击 Edit → Properties。\n3. 在对话框中导航到 Bonds 页面。\n4. 调整 Radius (cylinder) 输入框值，例如更改为 0.3。\n5. 修改颜色设置为 RGB 值 (100, 150, 200)。\n6. 点击 OK 按钮保存更改并关闭对话框。\n7. 确保更改在主视图中可见。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task6.json Normal file
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{
"id": "VESTA_Manual_task6",
"snapshot": "vesta",
"instruction": "在 VESTA 中切换晶体投影为 [110] 方向。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/Si.cif",
"path": "C:\\Users\\user\\Desktop\\Si.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"Si.cif"
],
"steps": "1. 打开 VESTA 软件并加载文件 Si.cif。\n2. 在顶部菜单中选择 View → Lattice Planes。\n3. 在对话框中选择 [110] 方向作为投影。\n4. 点击 OK 按钮应用更改。\n5. 确认主视图窗口中显示的是 [110] 方向的晶体投影。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task7.json Normal file
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{
"id": "VESTA_Manual_task7",
"snapshot": "vesta",
"instruction": "在 VESTA 中生成晶体的二维 (2D) 投影视图。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/rutile_TiO2.cif",
"path": "C:\\Users\\user\\Desktop\\rutile_TiO2.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"rutile_TiO2.cif"
],
"steps": "1. 打开 VESTA 软件并加载 rutile_TiO2.cif 文件。\n2. 在顶部菜单中选择 File → Export → 2D Image。\n3. 在弹出的对话框中设置输出格式为 PNG，并选择合适的分辨率 (例如 300 dpi)。\n4. 设置保存路径为桌面并命名文件为 projection.png。\n5. 点击 Save 以导出图像。\n6. 验证桌面的 PNG 文件是否正确生成。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task8.json Normal file
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{
"id": "VESTA_Manual_task8",
"snapshot": "vesta",
"instruction": "在 VESTA 中查看倒易晶格的详细几何参数。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/YBa2Cu3O7.cif",
"path": "C:\\Users\\user\\Desktop\\YBa2Cu3O7.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"YBa2Cu3O7.cif"
],
"steps": "1. 打开 VESTA 软件并加载文件 YBa2Cu3O7.vesta。\n2. 在顶部菜单中选择 Edit → Data → Reciprocal Lattice Parameters。\n3. 查看弹出的对话框中的倒易晶格详细数据。\n4. 点击 OK 关闭对话框。\n5. 验证数据是否已在 Text Area 中正确显示。"
}
}

57
evaluation_examples/examples/vesta/VESTA_Manual_task9.json Normal file
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{
"id": "VESTA_Manual_task9",
"snapshot": "vesta",
"instruction": "在 VESTA 中使用 Fourier Synthesis 生成电子密度图。",
"source": "custom",
"config": [
{
"type": "upload_file",
"parameters": {
"files": [
{
"local_path": "evaluation_examples/data/vesta/monazite.cif",
"path": "C:\\Users\\user\\Desktop\\monazite.cif"
}
]
}
},
{
"type": "launch",
"parameters": {
"command": [
"C:\\VESTA-win64\\VESTA.exe"
]
}
},
{
"type": "sleep",
"parameters": {
"seconds": 5
}
}
],
"trajectory": "trajectories/",
"related_apps": [
"vesta"
],
"evaluator": {
"postconfig": [
{
"type": "sleep",
"parameters": {
"seconds": 3
}
}
],
"func": "vllm_eval"
},
"proxy": false,
"fixed_ip": false,
"possibility_of_env_change": "low",
"metadata": {
"input_files": [
"monazite.cif"
],
"steps": "1. 打开 VESTA 软件并加载文件 monazite.vesta。\n2. 在顶部菜单中选择 Utilities → Fourier Synthesis。\n3. 在弹出的对话框中设置分辨率值为 0.05。\n4. 点击 Calculate 按钮开始生成电子密度图。\n5. 验证生成的图形是否出现在主视图中。"
}
}