MS-MCP
Allows interaction with BIOVIA Materials Studio, providing tools for modeling, simulation (Forcite, DMol3, CASTEP), GUI queue, and job monitoring via Dashboard.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@MS-MCPRun a Forcite geometry optimization on the current structure."
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
MS-MCP
面向 Windows 与 BIOVIA Materials Studio 的外部 Model Context Protocol(MCP)服务器。它让 Codex 或其他 MCP 客户端通过官方 MaterialsScript 运行时执行建模、Forcite、DMol3、CASTEP、GUI 队列和结果读取,并提供本地 Dashboard。
当前版本:
0.2.0。项目不是 BIOVIA/Dassault Systèmes 官方产品;使用前请确认 Materials Studio 许可证及 MaterialsScript 组件可用。
主要能力
检查 Materials Studio、
RunMatScript.bat、工作区和会话状态。创建/导入结构,维护当前 GUI 文档,并执行常用结构编辑。
执行 Forcite、DMol3、CASTEP 任务与预设工作流。
通过可选的 Materials Studio GUI 循环把脚本送入当前打开的项目。
从受限 HTTPS 白名单下载 CIF,并限制响应大小。
准备远程 CASTEP 任务,Dashboard 可通过 SSH 只读监控 Gateway 作业目录。
所有生成文件默认限制在独立工作区;任意 MaterialsScript 和外部输入默认关闭。
Related MCP server: Codex MCP Abaqus
系统要求
Windows 10/11(64 位)。
BIOVIA Materials Studio,且已安装 MaterialsScript;必须能找到:
MS_INSTALL_ROOT\etc\Scripting\bin\RunMatScript.bat。Node.js 20 或更高版本,包含
npm.cmd。Codex 或其他支持 stdio MCP 的客户端。
可选:Windows OpenSSH Client(只在远程 Dashboard 监控时使用)。
最快安装
下载 Release 压缩包或克隆仓库后,不要把项目放入随后会删除或改名的临时目录。推荐路径如 C:\Tools\MS-MCP。
双击
Configure-MS-MCP.bat,逐项确认 Node、Materials Studio、工作区等路径。双击
Install-MS-MCP.bat,以npm ci安装锁定依赖并检查发布文件。双击
Test-MS-MCP.bat,验证路径、安全默认值和 MCP stdio 通信。打开生成的
config\codex-ms-mcp.local.toml,把完整内容合并到%USERPROFILE%\.codex\config.toml。完全退出并重启 Codex,在 MCP 列表中确认
MS-MCP可用。
完整逐步说明、路径示例和安装后修改方法见 安装与配置指南。
配置 BAT 会生成什么
Configure-MS-MCP.bat 是唯一推荐的本机配置入口,内部调用 PowerShell 完成验证和安全写入:
config\ms-mcp.local.bat:供启动、测试、Dashboard、GUI 循环和 SSH 脚本统一读取。config\codex-ms-mcp.local.toml:供复制到 Codex 的 MCP 配置块。
这两个文件包含本机绝对路径,已由 .gitignore 排除,不能上传 GitHub。仓库只保留不含真实机器信息的 config\ms-mcp.example.bat、.mcp.example.json 和 codex-ms-mcp.toml.example。
必须根据机器修改的路径
变量/配置 | 含义 | 何时必须修改 |
|
| Node 安装位置变化或换电脑 |
| 与 Node 配套的 | Node 安装位置变化 |
| Materials Studio 安装根目录 | 版本、盘符或安装目录变化 |
| 可写的独立任务工作区 | 换电脑、迁移数据或调整存储盘 |
MCP | 本仓库 | 仓库移动、改名或重新解压 |
MCP | 本仓库根目录 | 仓库移动、改名或重新解压 |
| 已有 Materials Studio 模型目录 | 仅使用 Chapter 3 同步时设置 |
|
| 仅使用远程监控时设置 |
| SSH 私钥绝对路径 | 使用非默认密钥或用户目录变化 |
| Linux Gateway 作业根目录 | 远端版本、用户或 Gateway 根目录变化 |
仓库移动后不要逐个修改启动脚本;重新运行 Configure-MS-MCP.bat,再用新生成的 TOML 更新 Codex 即可。
启动方式
MCP 服务器
正常情况下由 Codex 按 TOML 自动启动。调试时可运行:
Run-MS-MCP.bat该进程使用 stdio 协议,命令窗口看似等待输入是正常现象;不要向 stdout 添加日志。
Dashboard
双击 Start-MS-MCP-Dashboard.bat,浏览器打开 http://127.0.0.1:4877/。端口可在重新配置时修改。MCP 也可在后台启动 Dashboard,但默认不会强制打开浏览器。
需要登录 Windows 后自动启动时,先完成配置与测试,再运行 Install-Dashboard-Autostart.bat。快捷方式使用相对仓库定位;若移动仓库,重新安装自启快捷方式。
Materials Studio GUI 循环
要把任务写入当前由用户打开的 Materials Studio 项目时:
先运行
Configure-MS-MCP.bat。在 Materials Studio 中打开目标项目。
从 Materials Studio 的脚本界面运行
materialscript\mcp_loop_gui.pl;或在正确的 Materials Studio 会话条件下使用materialscript\start_mcp_loop.bat。队列位于
%MS_MCP_WORK_ROOT%\.mcp-queue,停止标记为.mcp-queue\stop。
GUI 循环必须在 Materials Studio GUI 环境中运行,不能把普通 RunMatScript.bat 进程误当成已打开项目的 GUI 上下文。
远程 CASTEP Dashboard 监控(可选)
重新运行 Configure-MS-MCP.bat,填写 user@host 和远程 Gateway jobs 路径,然后运行 Setup-Dashboard-SSH.bat。脚本创建独立 Ed25519 密钥、把公钥加入远端 authorized_keys,并验证非交互登录。Dashboard 不保存服务器密码。
这只配置作业目录监控;Materials Studio Gateway、队列、许可证和计算核数仍需在 Materials Studio Job Control 中按实际服务器配置。
安全默认值
MS_MCP_ALLOW_ARBITRARY_SCRIPT=0:禁用任意 MaterialsScript。MS_MCP_ALLOW_GUI_QUEUE=1:允许结构化 GUI 队列工具。MS_MCP_ALLOW_EXTERNAL_INPUTS=0:禁止读取工作区外输入。CIF 仅允许配置的 HTTPS 主机,默认最大 10 MiB。
Dashboard 默认只监听
127.0.0.1;写操作默认关闭。启用写操作时必须配置至少 24 字符令牌。工作区路径经边界与 junction/symlink 检查,防止任务越界写入。
更详细的部署原则见 LOCAL-HARDENING.md,漏洞报告见 SECURITY.md。
开发与验证
在已经加载正确环境变量的终端中:
npm ci
npm run check
npm run smoke
npm run security-smoke
npm run mcp-smokeWindows 用户直接运行 Test-MS-MCP.bat 更简单,它会加载生成的本机配置。涉及真实 Forcite/DMol3/CASTEP 的计算仍应在授权的测试模型和服务器上单独验证。
仓库结构
MS-MCP/
├─ src/ MCP 服务器与 MaterialsScript 生成逻辑
├─ materialscript/ Materials Studio GUI 循环
├─ GUI-Dashboard/ 本地 Dashboard
├─ scripts/ 验证、解析、同步与远程准备脚本
├─ config/ 示例配置;本机生成配置不会上传
├─ docs/ 安装与配置文档
├─ examples/ 示例输入
├─ Configure-MS-MCP.bat 分步配置入口
├─ Install-MS-MCP.bat 锁定依赖安装
├─ Test-MS-MCP.bat 完整本机验证
└─ Run-MS-MCP.bat 手动 stdio 启动入口GitHub 上传清单与排除项见 RELEASE-FILES.md。
常见问题
找不到 RunMatScript.bat:MS_INSTALL_ROOT 填得太上层或太下层。应直接指向包含 etc\Scripting 的 Materials Studio 版本目录,然后重新配置。
移动仓库后 Codex 启动失败:重新运行配置 BAT,并替换 Codex TOML 中旧的 command、args、cwd 与环境路径。
Node 可用但 npm.cmd 不存在:安装完整的 Node.js Windows 发行版,而不是只复制 node.exe。
Dashboard 可打开但没有结构/作业:先检查工作区与当前 session;远程作业还需要 SSH target、key 和 jobs root 三项同时有效。
MCP 修改不到当前 GUI 项目:确认 GUI 循环是在目标 Materials Studio 会话中运行,而不是只启动了独立 MaterialsScript 进程。
贡献与许可
提交 Issue/PR 前请阅读 CONTRIBUTING.md,不要提交许可证文件、真实结构数据、服务器地址、私钥、本机配置或计算输出。项目采用 MIT License。
致谢与视频教程
本项目初始代码基于 shenghhe-svg/shengh_he,感谢原作者的工作与分享。
安装、配置及使用视频教程可在抖音搜索:抖音号
Au.Tom,昵称Dr.小叶。
独立的上游来源与教程声明见 NOTICE.md。
Available Tools
24 toolsms_castepB
Run a CASTEP task or preset calculation on an input document located under the MS-MCP work root. Presets include Energy, GeometryOptimization, Frequency/phonons, DOS, band structure, charge density, and density difference.
| Name | Required | Description | Default |
|---|---|---|---|
| task | No | CASTEP task name or high-level preset. Presets are mapped to the correct CASTEP task and property settings. | Energy |
| cores | No | ||
| project | No | ||
| settings | No | ||
| inputDocument | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description must disclose behavioral traits. It only says 'Run' with no details on execution mode, side effects, or requirements. Agents lack information on whether it blocks, modifies files, or requires licenses.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Description is a single sentence followed by a preset list. It is front-loaded and efficient, though the preset list could be integrated more seamlessly. No redundant phrases.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (5 params, nested objects, no output schema), the description omits return values, error handling, and detailed parameter usage. It is insufficient for agents to predict tool behavior fully.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is low (20%). Description adds meaning for 'inputDocument' (location under work root) and 'task' (lists presets), but fails to explain 'cores', 'project', and 'settings'. Agents need more parameter documentation.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states it runs a CASTEP task or preset calculation on an input document. It lists specific presets, making the purpose concrete and distinguishable from sibling tools like ms_forcite.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for CASTEP tasks under the MS-MCP work root but lacks explicit when-to-use or when-not-to-use guidance. It does not mention prerequisites or alternatives, so agents may misuse it.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_codex_configA
Return an MCP server config snippet that can be pasted into Codex settings.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Description implies a read-only, side-effect-free operation but does not confirm safety or disclose any behavioral traits; no annotations to compensate.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence with no wasted words, front-loaded purpose.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Sufficient for a simple tool with no parameters or output schema, but could hint at snippet format or usage context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
No parameters exist, so description adds no param info; baseline for 0 params is 4.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Description clearly states the tool returns an MCP server config snippet for Codex settings, distinct from sibling tools that focus on MS operations.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when or why to use this tool over alternatives; no context provided for integration with Codex settings.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_create_moleculeA
Create a standalone molecule/crystal document from explicit atoms and bonds using MaterialsScript. For the already-open GUI project, prefer ms_gui_create_current to avoid duplicate GUI documents.
| Name | Required | Description | Default |
|---|---|---|---|
| atoms | Yes | ||
| bonds | No | ||
| project | No | ||
| documentName | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided; description mentions 'using MaterialsScript' but does not disclose behavioral traits like side effects, permissions, or whether it modifies existing documents. Minimal behavioral context beyond the basic action.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two efficient sentences: first states purpose, second provides usage guidance. No fluff or redundancy.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given no output schema, no annotations, and 4 parameters, the description is too brief. It explains the tool's purpose and when to use alternatives, but lacks detail on return values, parameter behavior, and potential constraints.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema has 0% parameter description coverage; the description does not explain individual parameters. It implicitly mentions atoms and bonds but provides no details on formatting, constraints, or how they are used.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Clearly states the tool creates a standalone molecule/crystal document from explicit atoms and bonds using MaterialsScript. Distinguishes from sibling tool ms_gui_create_current by specifying it creates a standalone document, not in the GUI.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly advises to prefer ms_gui_create_current when working within an open GUI project to avoid duplicate documents, providing clear guidance on when to use this tool vs. alternatives.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_forciteC
Run a Forcite task on an input document located under the MS-MCP work root.
| Name | Required | Description | Default |
|---|---|---|---|
| task | No | Energy | |
| cores | No | ||
| project | No | ||
| settings | No | ||
| inputDocument | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are present, so the description carries full responsibility for behavioral disclosure. It only states that the tool runs a task, without mentioning side effects, whether it is synchronous, error handling, or required permissions. This is insufficient for an agent to anticipate the tool's behavior.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence and is concise, but it lacks critical information. While it has no filler, the brevity comes at the expense of completeness, failing to earn its place with substantive guidance.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (5 parameters, no output schema, no parameter descriptions, no annotations), the description is severely incomplete. It does not explain return values, how to structure input, or any constraints. An agent would have insufficient information to use the tool correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, meaning no parameter descriptions in the schema. The description does not add any meaning to parameters like 'inputDocument', 'task', 'cores', 'project', or 'settings'. For instance, 'inputDocument' is required but no format or location details are given. The tool's parameters remain completely undocumented.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states that the tool runs a Forcite task on an input document under the MS-MCP work root, using a specific verb and resource. However, it does not differentiate this tool from siblings like ms_castep or ms_run_materialscript, which also run computational tasks.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance is provided on when to use this tool versus alternatives (e.g., ms_castep). The description lacks context about prerequisites, typical use cases, or exclusions.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_add_vacuum_currentB
Add vacuum to the current GUI periodic document in place only when the user explicitly asks for vacuum. For an already-built 3D cell, extend_lattice increases the chosen lattice length while preserving Cartesian atom positions; for 2D surfaces, vacuum_slab uses CrystalBuilder VacuumSlab.
| Name | Required | Description | Default |
|---|---|---|---|
| axis | No | C | |
| mode | No | extend_lattice | |
| thickness | Yes | Vacuum thickness to add in Angstrom. | |
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | No | ||
| slabPosition | No | ||
| transferSymmetry | No | ||
| reorientAfterVacuumSlab | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description explains that the tool modifies the document in place and describes the behavior of the two modes. With no annotations provided, it adds some transparency but does not cover side effects, permissions, or prerequisites.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences with no redundant information. It front-loads the core purpose and follows with mode explanations, making it efficient and well-structured.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 9 parameters and no output schema, the description is insufficient. It covers the main action and two modes but omits parameter details, return behavior, and prerequisites, leaving the agent underinformed.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is only 11% (only thickness has a description). The description adds context for 'mode' and implies 'axis' by mentioning 'chosen lattice length', but does not explain other parameters like exportFile, ballAndStick, documentName, etc.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool adds vacuum to the current GUI periodic document 'in place' and only when explicitly requested. However, it does not differentiate from the sibling 'ms_gui_cleave_surface_vacuum_current', which also deals with vacuum.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly states the tool is used when the user asks for vacuum and explains when to use each mode (extend_lattice for 3D cells, vacuum_slab for 2D surfaces). However, it lacks guidance on when not to use this tool versus alternatives.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_apply_currentC
Queue a MaterialsScript body that modifies the current GUI document in place. Use this for 'on this molecule...' edits.
| Name | Required | Description | Default |
|---|---|---|---|
| body | Yes | MaterialsScript body. A variable named $doc is bound to the current target document. | |
| save | No | ||
| label | No | apply_current | |
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description bears full responsibility for behavioral disclosure. The description mentions 'queues' (implying asynchronous operation) and 'modifies in place', but does not elaborate on destructive potential, authentication requirements, rate limits, or what happens to the document state. This is insufficient for a tool that modifies the GUI.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description consists of two sentences and is front-loaded with the core purpose. It is concise with no redundant information. However, the brevity sacrifices completeness for a tool with six parameters.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (6 parameters, no output schema, no annotations), the description is far from complete. It does not explain return values, side effects, or parameter usage. The agent cannot fully understand how to invoke the tool correctly without additional context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is only 17%, meaning the description adds no value for most parameters. The tool description does not explain any parameter beyond what the schema already provides for 'body'. With 6 parameters (1 required) and no parameter descriptions in the description itself, the agent lacks essential semantic guidance.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the verb 'queue' and the resource 'MaterialsScript body that modifies the current GUI document'. It provides an example use case ('on this molecule...' edits), making the purpose clear. However, it does not explicitly differentiate from sibling tools like ms_gui_create_current or ms_gui_edit_current.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description includes guidance to 'Use this for 'on this molecule...' edits', implying a context for use. However, it does not specify when not to use this tool, nor does it mention alternatives among the many sibling GUI tools. The usage context is implied but not exhaustive.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_castep_currentC
Queue a CASTEP calculation on the current GUI document. Supports Energy, GeometryOptimization, phonon/frequency, DOS, band structure, charge density, and density difference presets.
| Name | Required | Description | Default |
|---|---|---|---|
| cores | No | ||
| quality | No | Medium | |
| exportFile | No | ||
| documentName | No | ||
| extraSettings | No | ||
| kPointQuality | No | Medium | |
| resultDocument | No | CASTEP.xsd | |
| calculationName | No | CASTEP_Calculation | |
| calculationType | No | High-level CASTEP calculation preset. | Energy |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are present, and the description fails to disclose behavioral traits such as blocking behavior, state changes, permissions required, or side effects of queuing. While it mentions 'queue a calculation,' it does not describe what happens after queuing, nor does it discuss error conditions or success indicators.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is brief with two sentences, no redundancy. However, the list of presets could be trimmed if the schema enum for calculationType is sufficiently descriptive. The structure is acceptable but could be improved with bullet points or clearer separation of presets from the main action.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (9 parameters, no annotations, no output schema), the description lacks essential context. It does not explain the meaning of 'current GUI document,' the output format, error handling, or any dependencies. The agent is left without enough information to use the tool confidently.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With only 11% schema description coverage, the description adds minimal value beyond listing the calculation presets that correspond to the calculationType parameter. It does not explain critical parameters like cores, quality, exportFile, or extraSettings, leaving the agent underinformed about their purpose and constraints.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool queues a CASTEP calculation on the current GUI document and lists supported presets. It specifies the action ('Queue') and resource ('CASTEP calculation'). However, it does not explicitly differentiate from sibling tools like ms_gui_prepare_remote_castep_batch or ms_castep, leaving room for ambiguity about local vs. remote execution.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance is provided on when to use this tool versus alternatives such as ms_gui_prepare_remote_castep_batch for remote submissions or ms_castep for general CASTEP tasks. The description lacks any usage context or prerequisites, making it harder for an agent to decide correctly.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_cleave_surface_vacuum_currentB
Cleave a surface from the current GUI crystal and build a vacuum slab through Materials Studio SurfaceBuilder + CrystalBuilder. Use only when the user explicitly asks to cleave/build a surface or create a vacuum slab by the manual surface workflow.
| Name | Required | Description | Default |
|---|---|---|---|
| h | No | ||
| k | No | ||
| l | No | ||
| capType | No | Hydrogen | |
| capBonds | No | ||
| cleaveRule | No | ||
| exportFile | No | ||
| vacuumAxis | No | C | |
| ballAndStick | No | ||
| documentName | No | ||
| slabThickness | Yes | Thickness of the cleaved slab in Angstrom. | |
| vacuumThickness | Yes | Vacuum thickness in Angstrom. | |
| transferSymmetry | No | ||
| reorientAfterVacuumSlab | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries full burden. It mentions using SurfaceBuilder + CrystalBuilder but fails to disclose whether the operation modifies the current crystal, creates a new document, or requires specific permissions. The agent is left unaware of side effects.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences with no redundant information. The key action is front-loaded, and the usage condition is stated directly. Every sentence adds value.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With 14 parameters, no output schema, and no explanation of common parameters, the description is insufficient. It does not cover what the tool returns or how parameters like h,k,l affect the result. The tool's complexity demands more context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is only 14% (2 out of 14 parameters have descriptions). The description adds no parameter information, failing to compensate for the low coverage. Most parameters like h,k,l, capType, cleaveRule, etc., remain unexplained.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool's action: 'Cleave a surface from the current GUI crystal and build a vacuum slab' using specific builders. It also distinguishes usage from siblings by specifying when to use it, referencing the manual surface workflow.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides explicit guidance: 'Use only when the user explicitly asks...' This sets a clear condition. However, it does not mention alternatives or when not to use, limiting differentiation from sibling tools like ms_gui_add_vacuum_current.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_create_crystal_currentA
Create or replace the current GUI document as a periodic crystal/unit cell from lattice parameters and atom coordinates. Before using this for a new crystal, first try ms_gui_find_cif_import_current against open CIF sources; use manual construction only when no reliable open CIF is found or the user provides credentials/API access for a restricted source. Do not add vacuum here unless the user explicitly requested vacuum in the initial cell parameters.
| Name | Required | Description | Default |
|---|---|---|---|
| a | Yes | Lattice length a in Angstrom. | |
| b | Yes | Lattice length b in Angstrom. | |
| c | Yes | Lattice length c in Angstrom. | |
| beta | No | ||
| alpha | No | ||
| atoms | Yes | Atoms in fractional or Cartesian coordinates depending on coordinateType. | |
| gamma | No | ||
| forceNew | No | ||
| exportFile | No | ||
| spaceGroup | No | P1 | |
| ballAndStick | No | ||
| documentName | Yes | ||
| calculateBonds | No | For periodic crystals this defaults to false to avoid incorrect cross-boundary bonding; use explicit bonding or a later targeted bond calculation when needed. | |
| coordinateType | No | fractional | |
| spaceGroupQualifier | No | ||
| useSpecialPositions | No | ||
| specialPositionTolerance | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description should disclose behavioral traits. It says 'create or replace' implying mutation of the current document, but doesn't elaborate on side effects (e.g., overwriting existing content), permissions, or undo capabilities. It mentions the vacuum constraint, but lacks depth on other behaviors like forceNew or coordination type handling.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is three sentences, each serving a distinct purpose: defining the action, providing usage priority, and setting a boundary. There is no redundancy or filler. It is front-loaded with the core purpose.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the complexity (17 parameters, no output schema, no annotations), the description is insufficient for complete agent understanding. It omits guidance on critical parameters like coordinate types, bond calculation, space group, and output handling. A more comprehensive description would cover these or reference documentation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is low (29%), so the description should add meaning for undocumented parameters. However, it only provides general context about vacuum and CIF alternatives, not explaining key params like a, b, c, atoms, coordinateType, spaceGroup, etc. This leaves agents guessing about parameter usage beyond what the schema provides.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Create or replace the current GUI document as a periodic crystal/unit cell from lattice parameters and atom coordinates.' It specifies the resource (GUI document) and action (create/replace), and distinguishes from siblings like ms_gui_find_cif_import_current by directing users to that tool first.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly advises to first try ms_gui_find_cif_import_current for new crystals, and to only use manual construction when no CIF is found or user provides credentials. It also warns against adding vacuum unless explicitly requested. This provides clear when-to-use and when-not-to-use guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_create_currentA
Create or replace the current GUI document from a MaterialsScript body. Before using this for a new structure, first try ms_gui_find_cif_import_current against open CIF sources; use manual construction only when no reliable open CIF is found or the user provides credentials/API access for a restricted source. By default it reuses the existing current/same-name document and rebuilds it in place to avoid duplicate .xsd files.
| Name | Required | Description | Default |
|---|---|---|---|
| body | Yes | MaterialsScript body. A variable named $doc is already created. | |
| forceNew | No | Create a new GUI document even if a current or same-name document exists. Use only when the user explicitly asks for a separate new document. | |
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries full burden. It discloses that by default the tool reuses existing documents to avoid duplicates, and that it can replace the current document. However, it does not explicitly mention side effects like overwriting without confirmation or error handling.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is three concise sentences: purpose, usage guidance, then default behavior. No redundant information, and critical guidance is front-loaded.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 5 parameters, no output schema, and no annotations, the description leaves gaps: it does not describe return values, validate the body input beyond mentioning it, or explain exportFile and ballAndStick behavior. More detail on outcomes and error cases would improve completeness.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is only 40%, but the description adds significant value: it explains that the body parameter should be a MaterialsScript with a pre-created $doc variable, and implies the forceNew parameter's effect by describing default reuse. However, exportFile and ballAndStick parameters are not elaborated.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool's verb ('Create or replace'), resource ('current GUI document'), and input ('MaterialsScript body'). It distinguishes from sibling tools like ms_gui_find_cif_import_current by recommending that for new structures.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicit guidance is provided: before using for a new structure, try ms_gui_find_cif_import_current first; use this tool only when no reliable open CIF or user credentials are available. This helps the agent decide when to invoke this tool versus alternatives.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_dmol3_optimize_currentC
Queue a DMol3 GeometryOptimization on the current GUI document and organize calculation outputs under a dedicated calculation name/folder.
| Name | Required | Description | Default |
|---|---|---|---|
| cores | No | ||
| charge | No | ||
| quality | No | Medium | |
| exportFile | No | ||
| theoryLevel | No | GGA | |
| documentName | No | ||
| extraSettings | No | ||
| resultDocument | No | dmol3_optimized.xsd | |
| calculationName | No | DMol3_GeometryOptimization |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Without annotations, the description carries full burden. It mentions queuing and output organization but does not disclose side effects, blocking behavior, error conditions, or any limitations. The agent lacks insight into what happens during execution.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence, efficient and front-loaded with the core action. However, it could be slightly expanded without becoming verbose to cover parameter or usage hints.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 9 parameters, no annotations, and sibling optimization tools, the description is incomplete. It does not address parameter roles, output behavior, or how the calculation name/folder is used. Lacks critical context for correct usage.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, and the description does not explain any of the 9 parameters. No parameter is described beyond their schema types. The description adds no semantic value for parameter usage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states it queues a DMol3 GeometryOptimization on the current GUI document and organizes outputs. The verb 'queue' and resource 'DMol3 GeometryOptimization' are specific, and it distinguishes from sibling tools like Forcite or CASTEP optimizations.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives (e.g., Forcite, CASTEP). No prerequisites (e.g., an open document) or conditions for use are mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_edit_currentB
Queue a basic molecule-building edit on the current GUI document, such as adding/deleting bonds, changing an atom element, adding/deleting atoms, recalculating bonds, Clean, or AdjustHydrogen.
| Name | Required | Description | Default |
|---|---|---|---|
| x | No | ||
| y | No | ||
| z | No | ||
| atom | No | Atom selector by atom Name or 1-based atom index. | |
| name | No | ||
| atom1 | No | First atom selector by atom Name or 1-based atom index. | |
| atom2 | No | Second atom selector by atom Name or 1-based atom index. | |
| element | No | ||
| bondType | No | Single | |
| operation | No | Clean | |
| cleanAfter | No | ||
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | No | ||
| cleanIterations | No | ||
| adjustHydrogenAfter | No | ||
| allowPeriodicBondGuess | No | Allow broad CalculateBonds on periodic documents. Keep false unless the user explicitly accepts periodic bond guessing. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are present, so the description carries the full burden. It mentions 'queue' but does not disclose asynchronous behavior, how to check completion, undo capabilities, or any side effects. The list of operations provides some insight but misses behavioral details.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence that is concise and front-loads the purpose. However, it could be slightly more structured by breaking into bullet points or sentences for clarity. No redundant information.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (17 parameters, no output schema, no annotations), the description is insufficient. It does not explain return values, the queueing mechanism, prerequisites, or the broader context of molecular modeling. The description leaves significant gaps.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is only 24% (4 out of 17 parameters have descriptions). The tool description adds context for the 'operation' parameter by listing examples but does not explain critical parameters like x, y, z, name, exportFile, or documentName. The parameter meanings remain unclear.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the verb 'Queue' and the resource 'current GUI document', and lists specific operations like adding/deleting bonds, changing element, etc. This distinguishes it from sibling tools like crystal creation or lattice settings.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for basic molecule-building edits on the current document but does not explicitly state when to use this tool versus alternatives like ms_gui_create_crystal_current or ms_gui_set_lattice_current. No 'when-not-to-use' guidance is provided.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_forcite_optimize_currentC
Queue a Forcite GeometryOptimization on the current GUI document using a manual-like calculation folder layout.
| Name | Required | Description | Default |
|---|---|---|---|
| cores | No | ||
| quality | No | Medium | |
| exportFile | No | ||
| forcefield | No | Universal | |
| documentName | No | ||
| optimizeCell | No | ||
| extraSettings | No | ||
| maxIterations | No | ||
| resultDocument | No | Forcite.xsd | |
| calculationName | No | Forcite_GeometryOptimization | |
| chargeAssignment | No | Use current |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries full burden. It mentions 'Queue' implying asynchronous operation and 'manual-like calculation folder layout' but does not disclose side effects, required state, permission needs, or output behavior. Significant gaps remain.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence, so it is concise, but it lacks structure. It is appropriately sized for a simple tool but could be more informative without becoming verbose.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 11 parameters with zero schema descriptions, no annotations, and no output schema, the description is severely incomplete. It fails to explain parameter meanings, return values, prerequisites, or error conditions, leaving agents with insufficient information.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 0%, yet the description adds no explanation for any of the 11 parameters. It does not list or describe cores, quality, forcefield, etc. The description adds no value beyond the parameter names and defaults in the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states it queues a Forcite GeometryOptimization on the current GUI document, using a specific folder layout. It distinguishes from siblings like ms_gui_dmol3_optimize_current (different engine) and ms_gui_castep_current (different method), but does not explicitly differentiate from other Forcite-related tools.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
There is no guidance on when to use this tool versus alternatives. The description implies usage for Forcite optimization on the current document but lacks context on prerequisites, when not to use, or alternative tools for other tasks.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_make_supercell_currentC
Build a supercell from the current GUI periodic document in place, using Materials Studio BuildSuperCell.
| Name | Required | Description | Default |
|---|---|---|---|
| a | No | Multiplier along lattice A. | |
| b | No | Multiplier along lattice B. | |
| c | No | Multiplier along lattice C. Use 1 for 2D slabs/surfaces. | |
| surface2D | No | Use the two-parameter surface form BuildSuperCell(a,b). | |
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | No | ||
| calculateBonds | No | For periodic supercells this defaults to false to avoid incorrect cross-boundary bonding; use explicit bonding or a later targeted bond calculation when needed. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided, so description carries full burden. It mentions 'in place' implying modification but doesn't disclose whether the original is preserved, whether it's destructive, or any permissions needed. It references 'Materials Studio BuildSuperCell' but doesn't clarify side effects. Parameter calculateBonds has a good warning, but overall behavioral context is lacking.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence that directly states the purpose without unnecessary words. Efficient and front-loaded.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With 8 parameters, no output schema, and no annotations, the one-sentence description is insufficient. It omits context about return values, error conditions, overwriting behavior, or confirmation steps. More detail is needed for a tool that modifies the current document.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 63% (5 of 8 parameters described). The tool description does not add any meaning beyond the schema; it only names the underlying method. For a moderate coverage, the description should have compensated but didn't.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action ('Build a supercell') and the resource ('current GUI periodic document'), with specific verb and resource. It distinguishes from siblings like ms_gui_create_current or ms_gui_set_lattice_current by focusing on supercell construction. Minor vagueness in 'in place' prevents a 5.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives (e.g., ms_gui_create_current for new structures, ms_gui_set_lattice_current for lattice changes). No exclusions or prerequisites mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_prepare_remote_castep_batchB
Prepare independent native CASTEP geometry-optimization jobs or compatibility Script Job drivers. The default native_castep mode stages one XSD plus one CASTEP settings document per structure/spin task for separate submission from the CASTEP Calculation dialog, giving each calculation its own CASTEP Job Control entry and native convergence graphs.
| Name | Required | Description | Default |
|---|---|---|---|
| tasks | Yes | ||
| batchName | No | remote_castep_batch | |
| commonSettings | No | ||
| submissionMode | No | native_castep | |
| stopGuiLoopAfterPrepare | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries the burden. It explains the default native_castep mode and the staging process, but omits details about the submissionMode other modes, the effect of stopGuiLoopAfterPrepare, and potential side effects or prerequisites.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences and front-loaded with the core purpose. The second sentence adds relevant detail about the default mode but could be slightly tighter; still efficient overall.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (5 params, nested objects, no output schema), the description fails to cover parameters and return behavior. Important context like what happens after preparation or the output format is missing, making it incomplete for reliable invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%; the description does not explain any of the five parameters (tasks, batchName, commonSettings, submissionMode, stopGuiLoopAfterPrepare), leaving the agent without semantic guidance beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool prepares native CASTEP geometry-optimization jobs or script drivers, specifying two modes and how the default mode stages documents per task. It distinguishes itself from sibling tools like ms_castep and ms_gui_castep_current by focusing on batch preparation.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No explicit guidance on when to use this tool versus alternatives (e.g., ms_castep, ms_remote_castep_record_submission). The description mentions two modes but does not explain when to choose one over the other or provide context for decision-making.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_project_dirB
Ensure and return the current MS-MCP task/session output directory under the workspace.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The term 'Ensure' is ambiguous—it may imply creating the directory if it doesn't exist, which is a behavioral trait. Without annotations, the description does not clarify whether side effects (e.g., creation) occur, nor does it mention permissions, idempotency, or error conditions. This lack of transparency could lead to misuse.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence of 14 words, front-loading the key action ('ensure and return'). It is efficient, though the word 'ensure' could be clarified for better scannability.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the absence of annotations and output schema, the description carries the full burden of explaining the tool's behavior. It omits details about the return value format, whether the directory is created, and any required permissions. For a simple tool, this may be marginally adequate, but it lacks completeness for an AI agent to understand all nuances.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has zero parameters, so schema description coverage is 100%. According to guidelines, a baseline of 4 is appropriate. The description does not need to add parameter information, and it provides no misleading details.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly identifies the tool's purpose: to ensure and return the current MS-MCP session output directory. The verb 'ensure and return' combined with the resource 'directory' provides specific action and object, distinguishing it from sibling tools like ms_gui_state or ms_list_workspace which have different scopes.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage when the current session output directory is needed, but does not explicitly state when to use this tool versus alternatives like ms_list_workspace. No exclusions or prerequisites are provided, leaving the agent to infer context.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_set_lattice_currentC
Set lattice parameters on the current GUI crystal document in place.
| Name | Required | Description | Default |
|---|---|---|---|
| a | No | ||
| b | No | ||
| c | No | ||
| beta | No | ||
| alpha | No | ||
| gamma | No | ||
| exportFile | No | ||
| ballAndStick | No | ||
| documentName | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided. The description says 'in place' implying mutation, but does not disclose side effects, required document state, or any destructive behavior. Minimal transparency.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence, concise but under-specified. It earns a middle score due to brevity, but lacks necessary details.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With 9 parameters, no output schema, and no annotations, the description is severely incomplete. It fails to explain parameter usage, units, or behavior, making it inadequate for correct agent invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, and the description does not mention any parameters. The 9 parameters (a, b, c, alpha, beta, gamma, exportFile, ballAndStick, documentName) are completely undocumented in the description, providing no semantic guidance beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action (set) and resource (lattice parameters on current GUI crystal document, in place). It is specific enough to distinguish from other GUI tools like create or make supercell, though not explicitly differentiated from siblings.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance provided on when to use this tool vs alternatives (e.g., creating a new crystal or modifying via other tools). No prerequisites or conditions mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_gui_stateA
Get the stateful GUI session target: current document, current exported file, last job, and history.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the burden. It states the tool retrieves information (a read operation) but does not disclose any behavioral traits such as side effects, performance implications, or prerequisites. The description is accurate but minimal.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single, front-loaded sentence that efficiently conveys the core purpose. It is concise but could be slightly expanded to clarify what 'history' entails. Still, it earns its place without waste.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description lists what the tool returns but does not provide details on the return format or structure, and there is no output schema. For a tool that aggregates multiple state pieces, more completeness would be beneficial. Among sibling tools, it is a query tool, but the description leaves some ambiguity.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has no parameters (empty properties), and schema description coverage is 100% (trivially). With no parameters, the description does not need to add meaning beyond what the schema provides. Baseline score of 4 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly identifies the tool's purpose: retrieving the stateful GUI session target, listing specific elements (current document, exported file, last job, history). It distinguishes itself from sibling tools that perform actions on the GUI state.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies using the tool to query GUI state, but provides no explicit guidance on when to use it versus alternatives like ms_gui_apply_current or ms_gui_edit_current. There are no usage conditions or exclusions mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_list_workspaceC
List files under the MS-MCP work root.
| Name | Required | Description | Default |
|---|---|---|---|
| subdir | No | . | |
| maxFiles | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must disclose behavioral traits. It only states 'list files' without indicating if the operation is read-only, has side effects, or requires authentication. The lack of transparency is significant for a tool with no annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single short sentence, which is concise, but it sacrifices necessary detail. It is under-specified for an effective tool description, though no redundant information is present.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool complexity (2 parameters, no output schema, no annotations), the description is incomplete. It does not explain parameter usage, return format, or filtering behavior, leaving the agent without crucial information for correct invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, meaning parameters have no descriptions. The tool description does not mention parameters at all, providing no additional meaning for 'subdir' or 'maxFiles'. The agent cannot infer their semantics from the description.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool lists files under the MS-MCP work root, providing a specific verb and resource. It is not a tautology and distinguishes from siblings like ms_status or ms_gui_project_dir. However, it lacks detail on whether directories are included or recursion behavior.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives. The description does not mention context, prerequisites, or exclusions, leaving the agent to infer usage from the name alone.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_queue_statusB
Inspect the optional MS-MCP GUI queue folders.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided. Description does not disclose whether the operation is read-only, requires authentication, or what happens if queues are empty or folders missing.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single concise sentence with no redundancy. Could be more structured, but adequately conveys purpose with minimal words.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
No output schema and no description of return values. Lacks information on what the user can expect after invoking the tool (e.g., list of queue folders or status messages).
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Tool has no parameters, so schema coverage is complete. Description adds context by naming the specific resource being inspected, which is meaningful beyond the empty schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description specifies a clear verb 'Inspect' and resource 'optional MS-MCP GUI queue folders', distinguishing it from siblings like 'ms_status'.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives such as 'ms_status' or 'ms_remote_castep_batch_status'.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_remote_castep_batch_statusB
Read the local preparation markers, submission receipt, and downloaded result summary available for a remote CASTEP batch.
| Name | Required | Description | Default |
|---|---|---|---|
| batchName | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must disclose behavioral traits. It states what is read but fails to mention safety, authentication needs, side effects, or error behavior, leaving significant gaps.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence with no extraneous words, making it efficient. However, it could be more specific without adding length.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a tool with one parameter and no output schema, the description omits critical context such as return format, error conditions, prerequisites (e.g., batch must be submitted), and any side effects.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 0% schema description coverage, the description should add meaning for the single parameter 'batchName'. It only references 'remote CASTEP batch' without clarifying the parameter's format, semantics, or how it relates to the batch.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action ('Read') and the specific resources ('local preparation markers, submission receipt, and downloaded result summary') for a remote CASTEP batch, effectively distinguishing it from sibling tools like ms_remote_castep_record_submission.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage after a remote CASTEP batch is prepared and submitted, but lacks explicit guidance on when to use versus alternatives or any prerequisites or exclusions.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_remote_castep_record_submissionB
Record one Materials Studio Job Control receipt. For native_castep preparation, call this once per calculationName after submitting its XSD from the CASTEP Calculation dialog.
| Name | Required | Description | Default |
|---|---|---|---|
| jobId | Yes | ||
| status | No | unknown | |
| gateway | Yes | ||
| batchName | Yes | ||
| serverType | No | ||
| submittedAt | No | ||
| driverDocument | No | ||
| submissionMode | No | native_castep | |
| calculationName | No | ||
| structureDocument | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the full burden. It says 'Record one Materials Studio Job Control receipt', implying a write operation, but does not disclose whether the operation is idempotent, what happens on duplicates, or any side effects. It gives basic context but lacks depth on behavior.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences, front-loading the purpose and then the usage guideline. Every sentence is concise and to the point, with no verbose or redundant content.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 10 parameters, no output schema, and no annotations, the description is incomplete. It covers purpose and a specific use case but lacks parameter details, return value information, and full behavioral context. An agent would need additional information to use it correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, and the description only provides meaning for calculationName (via the usage instruction). Other parameters like jobId, gateway, status, etc., are not explained. The description adds minimal value beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool records a Materials Studio Job Control receipt and specifies the context: for native_castep preparation, call after submitting XSD. It gives a specific verb and resource, but doesn't explicitly differentiate from sibling tools like ms_remote_castep_batch_status, though the purpose is distinct.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides explicit usage guidance: call once per calculationName after submitting XSD. It clearly indicates when to use the tool but does not mention exclusions or alternatives. This is still effective for an agent.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_run_materialscriptB
Run a MaterialsScript Perl script through RunMatScript. Disabled by default unless MS_MCP_ALLOW_ARBITRARY_SCRIPT=1.
| Name | Required | Description | Default |
|---|---|---|---|
| args | No | ||
| name | No | custom_job | |
| cores | No | ||
| script | Yes | ||
| project | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description bears full responsibility. It mentions the disabling mechanism but does not disclose side effects, authentication needs, error handling, or resource consumption. For a tool that runs arbitrary scripts, this is insufficiently transparent.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence plus a two-part condition. Every word serves a purpose with no redundancy, starting directly with the action verb 'Run'.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (5 parameters, no output schema, no annotations) and its potential danger (arbitrary script execution), the description is severely incomplete. It lacks details on script format, return values, error behavior, and prerequisite setup beyond the env var.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The parameter schema has 0% description coverage, and the description adds no semantic meaning to any of the five parameters. The script, args, name, cores, and project parameters are not explained beyond their types and defaults in the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Run a MaterialsScript Perl script', specifying the verb and resource. It also mentions the disabling mechanism, distinguishing it from sibling tools like ms_castep or ms_forcite that handle specific computations.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly notes it is disabled by default unless the environment variable MS_MCP_ALLOW_ARBITRARY_SCRIPT is set to 1. This provides clear when-to-use and when-not-to-use guidance, though it lacks references to alternative tools for non-arbitrary script execution.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
ms_statusA
Check Materials Studio paths, RunMatScript availability, and MS-MCP workspace.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description implies a read-only check but does not explicitly state whether it modifies state, requires authentication, or has side effects. With no annotations provided, the description carries the full burden, and it partially fulfills it by indicating 'check' but lacks detail.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single, clear sentence front-loading the action and scope. No unnecessary words; every part earns its place.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a simple status check with no parameters and no output schema, the description adequately covers the tool's function. It could detail return format or behavior, but contextually it is sufficient.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has zero parameters, so baseline is 4. The description adds meaning beyond the schema by specifying what the tool checks (paths, availability, workspace), which is sufficient for a parameterless tool.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description explicitly states the tool checks three specific aspects: Materials Studio paths, RunMatScript availability, and MS-MCP workspace. This clearly distinguishes it from sibling tools that perform actions like running scripts, queue management, or GUI operations.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No explicit guidance on when to use this tool versus alternatives. However, the purpose implies it serves as a pre-check before other MS operations, so usage context is somewhat implied but not stated.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.
24 tool updates
v0.2.0- First observed
ms_castep - First observed
ms_codex_config - First observed
ms_create_molecule - First observed
ms_forcite - First observed
ms_gui_add_vacuum_current - First observed
ms_gui_apply_current - First observed
ms_gui_castep_current - First observed
ms_gui_cleave_surface_vacuum_current - First observed
ms_gui_create_crystal_current - First observed
ms_gui_create_current - First observed
ms_gui_dmol3_optimize_current - First observed
ms_gui_edit_current - First observed
ms_gui_forcite_optimize_current - First observed
ms_gui_make_supercell_current - First observed
ms_gui_prepare_remote_castep_batch - First observed
ms_gui_project_dir - First observed
ms_gui_set_lattice_current - First observed
ms_gui_state - First observed
ms_list_workspace - First observed
ms_queue_status - First observed
ms_remote_castep_batch_status - First observed
ms_remote_castep_record_submission - First observed
ms_run_materialscript - First observed
ms_status
TDQS
Most tools have distinct purposes, but some overlap exists, e.g., ms_gui_create_crystal_current vs. ms_gui_create_current, and multiple CASTEP-related tools could confuse. Descriptions are detailed enough to resolve ambiguity in most cases.
The naming follows a general ms_<area>_<action>_<object> pattern, but inconsistencies exist: ms_list_workspace lacks an area prefix, ms_status and ms_codex_config deviate. The frequent use of 'current' suffix is not universal.
24 tools is on the higher side for an MCP server, but the domain (Materials Studio) is complex. However, many tools are specialized (e.g., 5 CASTEP tools), making the set feel slightly bloated.
The tool set covers core workflows (GUI manipulation, calculations, status checks) but has notable gaps: no delete/removal tools, no general job management, and limited non-CASTEP module support. Some operations require multiple tools where a single one might suffice.
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