Resources

Software package

I have collected a bunch of stand-alone (linux) tools that I have made for analysis of numerical computations in the field of condensed matter physics/chemistry. Please see more on: urp.dk/tools.

RUVIS: Animate MD trajectory in a web-page

Molecular Dynamics Simulations in the browser to open a web applications that lets you perform simulations of molecules using the browser

The Interface Pinning method

A versatile method for computing solid-liquid Gibbs free energy differences and contructing phase diagrams.

Click here for details

Ph.D. thesis

Title:
Long-time simulations of viscous liquids - from strong correlations to crystallization

Thesis (no papers):
thesis_URPedersen_30jan09-NoPapers.pdf (3.3Mb).

Thesis (all):
thesis_URPedersen_30jan09.pdf (15Mb).

Click here for more details

Videos

I have made a few videos and made them available under the Creative Commons "by" license, so feel free to use them. Videos are up-loaded to YouTube, please pay a visit to http://www.youtube.com/user/urpedersen.

The Laves MgZn2 crystal of the Wahnstrom binary Lennard-Jones mixture

[YouTube] [mp4 (75Mb, 42 sek.)] [jpg.tar.gz (97Mb)]
The Laves MgZn2 crystal of the Wahnstrom binary Lennard-Jones mixture
by Ulf R. Pedersen is licensed under a Creative Commons Attribution 3.0 Unported License.

Wahnstrom binary Lennard-Jones mixture in glassy phase.

[YouTube] [mp4 (51Mb, 42 sek.)] [jpg.tar.gz (78Mb)]
Wahnstrom binary Lennard-Jones mixture in glassy phase
by Ulf R. Pedersen is licensed under a Creative Commons Attribution 3.0 Unported License.

Wahnstrom binary Lennard-Jones mixture in liquid phase.

[YouTube] [mp4 (82Mb, 42 sek.)] [jpg.tar.gz (81Mb)]
Wahnstrom binary Lennard-Jones mixture in liquid phase
by Ulf R. Pedersen is licensed under a Creative Commons Attribution 3.0 Unported License.

Wahnstrom binary Lennard-Jones mixture in gas phase.

[YouTube] [mp4 (34Mb, 42 sek.)] [jpg.tar.gz (44Mb)]
Wahnstrom binary Lennard-Jones mixture in gas phase
by Ulf R. Pedersen is licensed under a Creative Commons Attribution 3.0 Unported License.

MgZn2 crystal

MgZn2.gro

Lewis-Wahnstrom ortho-Terphenyl

lwotp_crystal.gro:
Crystal configuration (ascii file). See Figure 1 in [JCP 134, 114501 (2011)]. view (WebGL)

lwotp_topol.top, lwotp_grompp.mdp:
GROMACS input files. See [JCP 134, 114501 (2011)] and references within.

Scripts and Programs

xyz2gro: Bash/awk script for converting configurations from xyz format to gromacs format (*gro).

gro2xyz: Bash/awk script for converting configurations from gromacs format (*gro) to xyz format.

makeHexagonalGrid: Bash/awk script that prints a xyz formatted file with particles on a 2D hexagonal grid.

mc_lattice.tar.gz: mc_lattice - simulating a 2D lattice gas.

data2wav.tar.gz: data2wav - convert data stream into an audio file in the uncompressed PCM WAV format.