1D Schrodinger equation in arbitrary potential

Published in �� 25th, 2014

The following application solves 1d Schrodinger equation in user defined potential. The app is written in Python and uses Numpy,SciPy for linear algebra and Matplotlib for visualization. The program can be used as a standalone application as well as python module implementing relevant calculations. Atomic units are used througout the interface. The precision of calculations […]

PyMol script for scanning potential energy surfaces

Published in �� 9th, 2013

Posted by Peter Mamonov in ��

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This PyMol script is capable of generating a set of a molecule’s conformations, which can be further used to calculate their potential energy or any other properties. The script enables one to vary several internal degrees of freedom (DOFs) synchronously as well as scanning over a multidimensional grid in a space of DOFs. To use […]

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Published in �� 16th, 2013

Posted by Peter Mamonov in ��

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Published in �� 12th, 2013

Posted by Peter Mamonov in ��

6 Comments

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Phase plane explorer

Published in �� 29th, 2012

Posted by Peter Mamonov in ��

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This small program named TRAX is capable of solving systems of ordinary differential equations and plotting the solution on a phase plane as well as function of time. The program is intended for educational purposes. See picture below for interface and capabilities overview as well as usage reference. The program runs on any Python-enabled platform, […]

plotting bifurcation diagram with pylab

Published in �� 21st, 2012

Posted by Peter Mamonov in ��

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Plotting bifurcation diagram of the following map using pylab

Potential energy surface scanner

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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This python script is capable of generating a set of GAMESS input files for potential energy surface scanning. It needs a reference GAMESS input and XML file specifying degrees of freedom to scan. PES scan can be done using linear translations, and rotations of atomic groups. Translation vectors can be specified using pair of atoms […]

Normal modes visualization for PyMol

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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This script allows one to visualize normal modes, calculated with GROMACS package, using PyMol. In particular the script loads Hessian matrix from an .mtx file produced by Gromacs, solves for it’s eigenvectors and eigenvalues and prints them out, and finally produce several frames corresponding to selected vibrational mode. See related media in the end of […]

Nanotubes generating script for PyMol

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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The script generates nanotubes of arbitrary structure. See related media in the end of the page. To use it, save script to some file, then load into PyMol with the command: PyMol> run /path/to/script.py then issue the command: PyMol> ntgen obj_name, n, m, l This will produce an object «obj_name», containing SWNT characterized by two […]

Visual approach to construction of &QMMM section of CP2K input file

Published in �� 16th, 2011

Posted by Peter Mamonov in ��

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The script is intended to be used from PyMol molecular visualization system and allows one to generate &QM_KIND, &LINK and &CELL parts of CP2K input easily. Given a molecular object name and QM part selection name (which can be defined using either approach available in PyMol) it generates output file with corresponding input groups. To […]

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