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ChemCraft V1.8——化学软件

Chemcraft包含一组便于量子化计算的图形工具。它提供了方便的实用程序,有助于准备新的工作来计算和分析计算结果。其主要功能是对量子化学包生成的输出文件的可视化。主要支持的软件包是Gamess(美国版本和PCGamess)和Gaussian94-09。

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Chemcraft界面


Chemcraft对于Gamess用户
Chemcraft给Gamess-US输出文件提供了非常详细的可视化。文件中的下列数据可以以图形方式呈现:
原子坐标(对应于所有或对称唯一的原子,如果在文件中呈现对应的表);
如果文件中给出了键阶分析,文件中的结合物显示在图像上(否则通过距离算法计算结合物);
能量梯度可以以指针的形式显示(图2);
不同的原子属性可以以标签的形式显示:Mulliken种群和电荷、自旋密度、价态;
键序(以标签的形式显示在结合物上);
分子轨道可视为等值面或彩色平面;
振动模式可以动画或以指针的形式(位移矢量)显示;
偶极矩可视为指针;
MO能量可以以数字形式显示。


Chemcraft提供了输出文件以结构化的形式呈现。被读取的文件被分成单独的元素,例如单独的几何形状或振动模式。对于每个元素,从文件中提取所有可用数据:原子坐标、能量梯度等。所有元素都呈现在分层列表中(图1)。单击列表中的元素自动显示图像上的单独几何或模式,并允许显示不同的属性。该接口提供了计算数据的可靠可视化,包括非标准类型的计算、不完整的计算等。它还允许具有多个计算任务的复杂文件被可视化。对于能量扫描或IRC计算,通过扫描/IRC步骤将所有几何结构分成组。除了图形的数据表示之外,Chemcraft概述了输出文件的最基本部分,并为文件的每个元素显示了一个简短的“摘要”。

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能量梯度可视化实例


Chemcraft从Gamess-US输出文件中提取分子轨道系数和基组信息,以等密度面的形式呈现分子轨道或由密度值着色的表面(平面、球体)(参加图3)。Chemcraft提供用轨道执行操作的一些可能性(例如将一个轨道乘以另一个轨道)。创建轨道的公式取自GAMESS-US分发的PLTROB程序的源代码。用密度值计算立方体能被很好地优化。注意,如果文件中有多个分子轨道系数表,Chemcraft可以提取它们中的每一个并允许它们被渲染(例如,在MCSCF计算中,可以显示规范或自然轨道)。除了轨道的可视化,Chemcraft还提供了一个简单实用的工具,用于自动确定原子轨道形成每个分子轨道,这对分析轨道很有用。


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分子轨道可视化的例子


Chemcraft支持一个接口,用于快速创建具有非标准基组的GAMES-US输入文件的部分(图4)。从它们的描述中提取基集,可以在PNNL的网页上获得
(http://www.emsl.pnl.gov/forms/basisform.html)。她们还可以由用户指定gaussians来补充。


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基础集创建窗体


Chemcraft对于Gaussian用户
我们建议在Gaussian输入文件中输入#P GFINPUT POP(FULL, NBO),以通过Chemcraft实现Gaussian输入文件的可视化。#P选项支持扩展打印输出;GFINPUT选项允许打印基组信息(基组中的基元的描述),而POP(FULL)可打印所有分子轨道系数(POP(REGULAR)也可以使用)。后两个关键词允许Chemcraft可视化分子轨道。POP(NBO)实现了自然键轨道分析的打印输出,其中计算了分子中的键。所有这些关键词都是可取的,但不是必需的。至于GAMES文件,可以从文件中看到不同的数据:原子核上的能量(能量梯度)、原子电荷、自旋密度和其他原子属性、NBO键属性(使用量、能量)、正常模式、分子轨道(Cartesian(6d等)或internal(5d)函数都可以被可视化),MO能量。从文件中读取标准或输入/ Z矩阵方向上的坐标并显示在图像上(这是为了正确地可视原子核上的能量所必需的,因为它们通常以不同于其他属性的排列方向打印)。对于能量表面扫描和IRC作业,所有几何形状按扫描步骤分组。对于每一个几何或振动模式,最基本的数据概述并以“摘要”的形式显示(SCF能量,收敛标准等)。Chemcraft读取多步骤Gaussian作业,然后呈现为几个扩展节点的列表,每个节点表示文件中的单个作业。除了Gaussian输出文件外,Chemcraft还可以读取Formatted Checkpoint文件(.fch), 从文件中提取分子结构和轨道。对于分子轨道和其他性质的可视化,Gaussian立方体文件也可以读取。


Chemcraft从NMR计算(GIAO,CSGT)的Gaussian日志文件中读取各向同性屏蔽值。提供了一种简单的工具,用于将它们重新描述成化学位移和在指定原子组内的平均值。


Chemcraft对于ADF用户
Chemcraft读取ADF输出文件、ASCII TAPE21文件和ASCII TAPE41文件。目前,ADF输出文件的可视化不如GAMESS或Gaussian文件的可视化那样全面:提供了能量的提取、偶极矩的可视化和一些原子性质,但没有分子轨道可视化等。


与其他格式一起工作
除了Gamess-US, Gaussian 和ADF文件,Chemcraft可以读取NWChem、Jaguar、Oraca、Dalton、GAMESE-UK、Turbomole、MMOPRO和QChem输出文件、HyperChem文件、MSI或PDB格式的文件(这些格式未被全面支持)和MolDraw and Priroda程序格式、NBO格式(.31-.40文件)、Molden文件、MFJ、SDF和Tinker、Crystal文件、VASP和Shellx文件、晶体学CIF文件和简单的文本文件与原子的Cartesian坐标。Chemcraft提供了一个通过剪贴板导入/导出文本格式的原子坐标的接口,这有助于使用任何类型的计算数据。将原子坐标导出到剪贴板中对于快速创建输入文件也是有用的。Chemcraft包含一个分数坐标转换的功能,用于晶体学测量和Cartesian,反之亦然,用于单元参数(a,b,c等)。


构建分子
Chencraft支持一组用于构造分子结构的工具,这些工具可用于准备计算或其他目的的初始猜测:
从标准分子片段(自由基等)中构建分子,提供了通过自定义剪贴板来补充该片段集并通过剪贴板复制/粘贴单个片段的可能性;
修改分子中的任何几何参数(距离、角度、二面角)。该修饰可以伴随着一个原子、两个原子或选定的原子群的位移;
用鼠标在分子图像上拖曳原子或碎片或旋转碎片的可能性(图5);
应用任意几何参数集合的迭代算法(图6);
一种易于使用的实用程序,用于将点群应用于分子(图8)。

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“拖曳”原子或沿键旋转碎片的例子


当“拖动”原子或执行其他结构修改时,任何几何参数都可以控制在图像上(见图5)。Chemcraft的界面允许人们轻松地改变任何原子的类型或插入/移除一个键。Chemcraft提供了快速获取Z矩阵的实用工具。Z矩阵是通过点击分子中的原子并指定一些附加信息来建立的(图7)。在使用这个工具之前,首先应该在Cartesian坐标中获得分子的结构。所有用于构建分子的上述工具都可用于此目的。

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应用一组指定的几何参数 Z矩阵的可视化构造


Chemcraft可以调节分子中的原子坐标以应用特定的对称性(图8)。这个工具在研究中非常有用,因为对称分子比非对称分子计算得更快。

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对称点群的应用


分子结构合并
Chemcraft支持一组用于构造分子结构的工具,这些工具可用于准备计算或其他目的的初始猜测。

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合并多个结构


在使用该实用程序之前,应该选择几个原子以最大程度地彼此靠近(图9这些原子标记为白色)。除了这个特性,Chemcraft还可以计算两个分子之间的均方根差值。


分子绘制的可能性


Chemcraft生成高质量的32位分子图像。它被设计成一个用于创建发布就绪图像的程序,不需要任何额外的修改。图片可以很容易地在原子/键和附加对象,如标签和线条。Chemcraft包含一个标准显示方案的集合。每个方案代表一组定义分子外观的参数:照明参数、单个原子和键的颜色和大小等。图10说明了四种集合方案。Chemcraft允许用户更改单个方案的参数,或者将自己的方案添加到集合中。Chemcraft的图形引擎不需要任何图形加速或额外的图形库。被很好的优化并提供,并提供高渲染速度,即使在过时的电脑。


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绘制具有不同显示方案和不同标签样式的分子的例子


创建动画效果
Chemcraft的Windows版本可以保存多个位图文件或动画GIF文件形式的分子动画图片。下面的动画类型提供:分子旋转的动画、振动频率和PES扫描的动画。


系统需求
Chemcraft适用于Windows和Linux系统。



Chemcraft basics
Chemcraft comprises a set of graphical tools for facilitating working with quantum chemistry computations. It provides convenient utilities, which help to prepare new jobs for calculation and analyze computed results. Among the main functions of the program is visualization of output files produced by quantum-chemical packages. The main supported packages are Gamess (US version and the PCGamess) and Gaussian94-03.

Chemcraft for Gamess users
Chemcraft provides very detailed visualization of Gamess-US output files. The following data from the files can be presented graphically:

- Atomic coordinates (corresponding to either all or symmetry unique atoms, if corresponding tables are presented in the file);
- If bond order analysis is presented in the file, bonds from the file are shown on the image (otherwise, bonds are calculated by distance algorithm);
- Energy gradient can be shown in the form of pointers (fig. 2);
- Different atomic properties can be shown as labels on atoms: Mulliken populations and charges, spin densities, valences;
- Bond orders (as labels on bonds);
- Molecular orbitals are visualized as isosurfaces or colored planes;
- Vibrational modes can be animated or shown in the form of pointers (displacement vectors);
- Dipole moment can be visualized as pointer.

The program provides structured presentation of output files. The file being read is divided into separate elements, such as individual geometries or vibrational modes. For each element all available data is extracted from the file: atomic coordinates, energy gradient, etc. All elements are presented in hierarchical list (see fig. 1). Clicking on the elements of the list automatically displays individual geometries or modes on the image and allows different properties to be visualized. This interface provides reliable visualization of computational data, including non-standard types of calculation, incomplete calculations, etc. It also allows complicated files with multiple calculation jobs to be visualized. For energy scan or IRC calculations, all geometries are divided into groups by scan/IRC steps. Besides graphical presentation of data, Chemcraft outlines the most essential parts of output file and shows a brief "abstract" for each element of the file.

Chemcraft for Gaussian users
We recommend to type #P GFINPUT POP(FULL, NBO) in Gaussian input files for visualization of Gaussian outputs via Chemcraft. #P option enables extended printout; GFINPUT option enables printout of basis set information (description of primitives in basis set), while POP(FULL) enables printout of all molecular orbitals coefficients (POP(REGULAR) can be also used). The latter two keywords allow Chemcraft to visualize molecular orbitals. POP(NBO) enables printout of Natural Bond Orbitals analysis, in which the bonds in the molecule are computed. All these keywords are advisable but not necessary. As for GAMESS files, different data from the file can be visualized: forces on the nuclei (energy gradient), atomic charges, spin densities and other atomic properties, NBO bond properties (occupations, energies), normal modes, molecular orbitals (either Cartesian (6d, etc) or internal (5d) functions can be visualized).
Coordinates in either standard or input/Z-matrix orientation are read from the file and shown on the image (this is necessary for correct visualization of forces on the nuclei, because they are usually printed in different orientation than other properties). For energy surface scan and IRC jobs, all geometries are grouped by scan steps. For each individual geometry or vibrational mode, the most essential data is outlined and shown as an "abstract" (SCF energy, convergence criteria, etc). Chemcraft reads multi-step Gaussian jobs and presents then as the list of several expanding nodes, each node representing individual job in the file.

In addition to Gaussian output files, Chemcraft can read Formatted Checkpoint files (.fch), extracting molecular structure and orbitals from the file. For visualization of molecular orbitals and other properties, Gaussian Cube files can be also read.

Chemcraft reads isotropic shielding values from Gaussian log files with NMR calculations (GIAO, CSGT). A simple utility for recounting them into chemical shifts and averaging within specified groups of atoms is provided.

Chemcraft for ADF users
Chemcraft reads ADF output files, ASCII TAPE21 files and ASCII TAPE41 files. At the moment the visualization of ADF output files is not as comprehensive as the visualization of GAMESS or Gaussian files: extraction of energies, visualization of dipole moment and some atomic properties is provided, but no molecular orbitals visualization, etc.

Working with other formats
Besides Gamess, Gaussian and ADF files, Chemcraft can read NWChem, Jaguar and Orca output files, HyperChem files, files of MSI or PDB formats (these formats are not comprehensively supported) and of MolDraw and Priroda programs format, NBO format (.31-.40 files) and simple text files with Cartesian coordinates of atoms. Chemcraft provides an interface to import/export coordinates of atoms in text format through clipboard, which helps to use the data from any type of calculations. Exporting atomic coordinates into the clipboard can be also useful for quickly creating input files.
Chemcraft comprises a utility for the conversion of fractional coordinates, used in crystallographic measurements, into Cartesian, and conversely, using unit cell parameters (a, b, c, etc).

Constructing molecules
Chemcraft supports a set of tools for constructing molecular structures, which can be used for preparing an initial guess for calculations or other purposes:
- Constructing molecule from standard molecular fragments (radicals, etc). The possibility to supplement the set of fragments with custom ones and to copy/paste individual fragments via clipboard is provided;
- Modifying any geometrical parameter in the molecule (distance, angle, dihedral). The modification can be accompanied with displacement of one atom, two atoms or selected group of atoms;
- The possibility to "drag" an atom or a fragment on the molecule’s image or rotate a fragment using the mouse (fig. 5);
- Iterative algorithm for applying an arbitrary set of geometrical parameters (fig. 6);
- An easy to use utility for applying a point group to the molecule (fig. 8).

Molecule rendering possibilities
Chemcraft produces high-quality 32-bit pictures of molecules. It is designed as a program for creating publication-ready images, which do not require any additional modification. The pictures can be easily supplemented with captions on atoms/bonds and additional objects, such as labels and lines. Chemcraft comprises a collection of standard display schemes. Each scheme represents a set of parameters defining the appearance of the molecule: lighting parameters, colors and sizes of individual atoms and bonds, etc. Fig. 9 illustrates four schemes of the collection. Chemcraft allows the user to change the parameters of individual schemes or add his own schemes to the collection.
The graphical engine of Chemcraft does not require either any graphical acceleration or additional graphical libraries. It is well-optimized and provides high rendering speed even on outdated computers.

Creating animations
The Windows version of Chemcraft can save animated pictures of molecules in the form of multiple bitmap files or animated gif files. The following standard types of animations are provided: animation of molecule rotation, vibrational frequencies, and animation of PES scans.