Search Results for "ab initio"
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Showing 28 open source projects for "ab initio"
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atomes
Analysis, visualization, edition of 3D atomistic models
...atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K atomes is developed by Dr. Sébastien Le Roux, research engineer for the CNRS Dr. Sébastien Le Roux works at the Institut de Physique et Chimie des Matériaux de Strasbourg. -
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ALAMODE
Ab initio simulator for thermal transport and lattice anharmonicity
ALAMODE is designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the anharmonic force constants, you can also calculate lattice thermal conductivity from first principles. For more information about ALAMODE, please visit the following webpages: Documentation :... -
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DeepH-pack
Deep neural networks for density functional theory Hamiltonian
DeepH-pack is the official implementation of the DeepH (Deep Hamiltonian) method described in the paper Deep-learning density functional theory Hamiltonian for efficient ab initio electronic-structure calculation and in the Research Briefing. DeepH-pack supports DFT results made by ABACUS, OpenMX, FHI-aims or SIESTA and will support HONPAS. -
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Updated 2022-06-11 added option to allow use of atoms other than C-alpha Updated 2021-11-29 to enable compilation on stricter compilers. Ab Initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. Calibur is an efficient tool for finding the decoy with the most number of neighbors within a threshold distance. If you prefer to use GitHub, go to https://github.com/kalngyk/calibur
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RMGDFT
Real Space Multigrid based electronic structure code.
News: active RMG development has moved to github https://github.com/RMGDFT News: V4.1.0 released on 09/29/2020 News: V4.0.0 released on 09/01/2020 with major updates. News: V3.0.0 released on 06/09/2018 with major updates. News: V2.2.2 released on 10/14/2017 with minor bug fixes. News: V2.2 with performance enhancements, bug fixes and new features released on 06/26/2017. Sources are available with binaries to follow soon. News: V2.1 with many improvements released on... -
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GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
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PROPAB
PROPensity for Alpha and Beta
PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins Authors: Rifat Nawaz UL Islam1, Chittran Roy2, Parth Sarthi Sen Gupta3, Debanjan Mitra2, Sahini Banerjee4 and Amal Kumar Bandyopadhyay2* 1Department of Zoology, The University of Burdwan, West Bengal, 713104, India 2Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India 3Department of Chemistry, IISER, Berhampur, Odisha, 760010, India 4Department of... -
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The extensible PyPES library is based upon the PyPES library of high quality semi-global potential energy surfaces, http://pypes-lib.sourceforge.net Additionally, the extensible PyPES library provides the ability to construct force field expansions in curvilinear internal coordinates using ab initio data obtained from the GAMESS suite of quantum chemical software. These force fields may then be transformed into rectilinear normal mode coordinates for calculating anharmonic vibrational frequencies using the PyVCI program package, http://pyvci.sourceforge.net
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pyxaid
PYthon eXtension for Ab Initio Dynamics
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.
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ANT.1D
Quantum transport for tight-binding and ab initio Hamiltonians
ANT.1D is a stand-alone quantum transport code for essentially one-dimensional setups described by tight-binding or ab initio Kohn-Sham Hamiltonians obtained from other codes working with atomic basis sets (Gaussian, Crystal,SIESTA). Interfaces with Crystal and Gaussian codes are available. Electrodes are described either by nanowires of finite thickness or Bethe lattice electrodes. -
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potfit
potfit force-matching code
The potfit code uses the force-matching method to generate effective potentials from ab-initio reference data. -
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Gecko Hamaker
Calculates Hamaker coefficient,interaction free energy,force,torque.
...The machine-readable optical property database is available for download and as a web service and makes available the full spectral optical properties of over 150 materials from both ab initio calculations and experimental measurements. -
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IPred
Integrate ab initio and evidence based gene predictions
IPred (Integrate gene Predictions) is a program that combines the output of ab initio and evidence based (including comparative based) gene finders to improve on the overall prediction accuracy. IPred is written in Python and can be used from the command line as well as with the help of a GUI (java 7 based). It is available for linux, windows and mac. To install IPred, simply download the package and unpack it with >unzip IPred.zip. -
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The CCP1GUI
An extensible GUI for computational chemistry codes
The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes. -
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Tonto
Tonto - for Quantum Crystallography
...This site is now only for historical interest. ===== Tonto is a free library dedicated to quantum crystallography and quantum chemistry. It can refine crystal structures using ab initio wavefunctions. It can also fit electronic wavefunctions to X-ray diffraction data. === PLEASE READ BELOW === An updated release 3.1 (revision 3800) has been made in the Files part. Various linux executables have also been uploaded so you don't need to compile. For non-standard jobs, or for bug-fixes, get the latest version on branches/tonto-3.2 using subversion, like this: svn checkout svn://svn.code.sf.net/p/tonto-chem/code/branches/tonto-3.2 tonto-3.2 DO NOT check out the head, it is too unstable at the moment. -
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Project for develop force fields with using ab-initio calculations
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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psicode
An open-source quantum chemistry program package
PSI is an open-source program for computing molecular properties using high-accuracy, ab initio, quantum mechanical models. -
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This software allows to analyze the contigs generated by ab initio assembly and it produce the scaffold of genome after manual curation
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The aim of this project is to be a GUI front-end and visualization tools for the Vienna Ab-Initio Simulation Package, also know as VASP. VASP is density functional software which calculates a variety properties of solid state systems.
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The ab initio Spinor Project is a scientifc code project based on density functional theory (DFT) within the ab initio pseudopotential frame work. The code implements the fundamental Kohn-Sham functions in form of two-component spinors, hence allowing to
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DEXA is dedicated to providing post-experiment signal processing of DiffXAS signals. By combining ab initio theory with measured spectra, structural strain parameters may be extracted from the differential signals at an intrinsic, atomic scale.
