Python codes

Anaconda is a Python distribution, developed by Continuum Analytics, containing a number of common Python packages that are catered for scientific computing and data analysis. The Anaconda distribution also contains the Python interpreter, and hence there is no need to have Python installed on your computer prior to installing Anaconda. Jupyter is also bundled with the Anaconda distribution. An integrated development environment (IDE), called Spyder, is included for editing and executing Python code. 

Rate constants are calculated with our own Python code, which is interfaced to NWChem. Bimolecular rate constants are computed according to Eqs (7.19) and (7.20) except in our earlier work (Section 7.4.3.1) where we did not include tunneling corrections. (Simple tunneling corrections mostly cancel for the relative rate constants in Eq. (7.42).) Unimolecular rate constants are given by Eqs (7.20) and (7.21) and anharmonic effects are incorporated via Eq. (7.28) for low-frequency vibrations up to 110 cm This implies that on the order of 10 modes per transition state of hydrogen abstraction and about 5 modes per transition state of phenyl migration and reactants are anharmonically corrected. We employ the analytical kinetic model described in Section 13.23 to obtain a//3-selectivities in Section 7.4.3. 

Python Code for the numerical solution of the microkinetic model for CO oxidation and the generation of a two-dimensional volcano plot. 

Motmot Image acquisition, storage, and analysis GUI http //WWW. code. astraw. com /projects /motmot Python and C... 

CellProfiler is designed to analyze large amounts of images automatically (17, 18). Since the analysis of thousands of images is very computationally intensive, a version is available to run on a Linux cluster allowing the parallelization of the analysis. The software is written in the Python programming language and the source code can be downloaded and extended by the community. 

A Pipeline Pilot deployment includes a number of integration components that provide facilities to create a new component to capture a simple command line, or by coding up new functionality in Perl or Python scripts or in Java code, using a component API. To utilize network resources, the user can also configure telnet, ftp, or SOAP components. SOAP components can execute in a multithreaded fashion to parallelize the use of remote servers. 

FROWNS python modules are used to show a second way in which the core functions might be implemented. The following plpythonu code extends PostgreSQL with most of the core functions described in Chapter 7. The isosmiles and keksmiles functions are not included here because of limitations of FROWNS. 

Accessibility Python is free to use without restriction. It is freely available and easy to obtain on the Internet. Python is also well supported within the scientific and engineering community, which allows for easy troubleshooting of problematic code. 

Jupyter notebooks (previously known as IPython notebooks) are web applications that are best described as interactive documents containing code (i.e., written in a programming language such as Python), formatted explanatory text, interactive visualizations, and displayed mathematics, as shown in Figure C.l. 

There are several nodes that have specific tasks on the data. Predefined components can be chosen from the library, configured, redesigned or even created from scratch and documented. When a new component is made by collapsing a few components together, it is called subprotocol. Many custom script components are available in Pipeline Pilot that allows to include the code directly into the pipelines and maintain a library of components based on a preferred language, such as Perl, Java, VBScript,. NET, JavaScript, Python, Matlab etc. 

Analyzing the output of a simulation can be one of the most difficult aspects of molecular modeling research. At the end of an MD simulation you are left with a huge collection of energies, forces, atomic positions, and velocities. How do you extract from this the information you want One way is to write utility programs to do the analysis. There are many examples available to help with this, and standard textbooks provide good example codes. " If you do not want to do this, then some of the codes listed above have analysis utility tools that can help. LAMMPS, for example, has a collection of python-based pre- and postprocessing tools associated with it called Pizza.py. It can perform animations, extract thermodynamic data, read and... 

The group of Prof. McGehee in Stanford offers a free transfer matrix modelling code on their homepage. The code is available in Matlab and Python and contains a database with the complex refractive indices of common materials of relevance for photovoltaics. More information is available on http //www.stanford.edu/group/ mcgehee/transfermatrix/ (accessed 3/1/2013). 

RAVEN has been developed in a highly modular and pluggable way in order to enable easy integration of different programming languages (i.e., C-H-, Python) and, as already mentioned, coupling with any system code. 

Hence, RAVEN is coded in Python and is characterized by an object-oriented design. The core of the analysis performable through RAVEN is represented by a set of basic components (objects) the user can combine, in order to create a custom analysis flow. A list of these components and a summary of their most important functionaUties are reported as follows ... 

The External model allows the user to create, in a Python file (imported, at run-time, in the RAVEN framework), its own model (e.g. set of equations representing a physical model, connection to another code, control logic, etc.). This model will be interpreted/used by the framework and, at runtime, will become part of RAVEN itself... 

OPERATION STEEL BOX. In 1990, the U.S. Army successfully transferred more than 100,000 chemical weapons (CW) from West Germany to the Johnston AtoU in the Pacific Ocean. The transfer was given the code name Operation Steel Box but was known by some as Operation Golden Python. See also OPERATION RED HAT. 

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