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ChemCraft V1.8——化学软件

ChemCraft是与量子化学软件一起使用的图形用户界面程序,用于显示化学数据和准备计算任务。它主要作为Gamess(US)和Gaussian的图形用户界面而开发。

功能
1. 显示三维分子图。
2. Gamess(US)和Gaussian输出结果的可视化:从输出文件显示个别结构(优化的结构,每一步优化的结构,等),振动模式的动画,梯度的图形描述,显示分子轨道,等。
3. 显示Gaussian计算的NBO输出文件。
4. 构造分子和修改分子结构。
5. 根据定制的显示模式保存图像。
6. 用于准备输入文件的附加工具:显示Z-矩阵结构,用非标准基组自动产生输入文件。

Chemcraft V1.5新增功能:
1. 显示分子轨道,显示光谱等。
2. 读取ADF输出文件TAPE21和TAPE41,提取能量,显示偶极矩和一些原子特性。
3. 读取其它格式:NWChem输出文件,HyperChem文件,MSI文件或PDB格式,MolDraw程序格式,简单的原子笛卡尔坐标文本格式。但不提供对复杂功能的支持。
4. 晶体分数坐标和笛卡尔坐标坐标之间互相转化。

Chemcraft V1.6新增功能:
1. 支持Molpro格式(显示结构,笛卡尔坐标优化步骤,振动模式,能量,SCF迭代,Mulliken电荷,偶极矩)。
2. 支持Dalton格式(显示结构,坐标优化步骤,振动模式,力,能量,SCF迭代,偶极矩)。
3. 创建Gamess输入文件的非标准基组部分支持最新的EMSL格式。
4. 支持ORCA格式的输入输出文件和立方文件(显示结构,坐标优化步骤,振动模式,Mulliken电荷,偶极矩,SCF迭代,TDDFT电子谱,松弛PES扫描任务)。
5. 从PCGAMESS/Firefly输出显示mcqdpt2轨道和电子谱。
6. 对于GAMESS/Firefly和Gaussian的结构优化输出,显示最大RMS梯度对优化步数。
7. 对GAMESS/Firefly显示能量变化对优化步数。
8. 显示Molpro,NWChem,和Jaguar输入文件中的笛卡尔坐标。

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.