potfit wiki

about

anonymous@undisclosed.example.com (Anonymous) — Sat, 14 Oct 2017 06:57:07 +0000

About potfit ---------- potfit was originally developed by Peter Brommer during his diploma thesis and doctoral thesis work at the Institute for Theoretical and Applied Physics in Stuttgart. This work was funded through the DFG, Collaborative Research Centre (SFB) 382 “Simulation physikalischer Prozesse auf Hochleistungsrechnern

analytic_potentials_punishments

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Mar 2013 08:57:38 +0000

Punishments for Analytic Potentials ---------- For analytic potentials it may sometimes be necessary to use additional punishments to keep the potential in a predefined parameter space. If the initial contraints, given in the parameter file can not achieve this, then there is a special function which is called before every force calculation. This function can be used to check for additional contraints on analytic potentials.$i<\text{ndim}$$i<\text{ndim}$

cell_scale

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Jan 2014 10:02:26 +0000

Global cell scaling ---------- With the cell_scale parameter the unit cells of all reference configurations can be scaled. This includes box vectors as well as atomic coordinates. Other properties like energy and stress remain unchanged. The default value is 1.0, which means no scaling.

contact

anonymous@undisclosed.example.com (Anonymous) — Mon, 06 Sep 2021 16:06:09 +0000

Contact ---------- The page provides an issue tracker which may also be used to submit general questions, help requests or bug reports. How to request help When asking for help please provide as much information as possible. This includes: *

contributors

anonymous@undisclosed.example.com (Anonymous) — Wed, 10 Jan 2018 17:20:28 +0000

Contributors ---------- Many different people have contributed to the potfit code. This list shows who was responsible for which parts of potfit: Name Contribution Peter Brommer Original idea and author of potfit Tabulated EAM potentials

debug

anonymous@undisclosed.example.com (Anonymous) — Fri, 01 Mar 2013 07:37:36 +0000

Debugging ---------- For debugging there are some very basic options already available in potfit: If you compile potfit with the debug target, the binary will give you some additional output. * For every configuration the box vectors, normals and heights are written to stdout. There the number of periodic images needed is also given.

dev

anonymous@undisclosed.example.com (Anonymous) — Fri, 01 Mar 2013 07:36:11 +0000

Dev's Corner ---------- Here we give some hints on how to extend potfit. In particular, we list some common pitfalls that are to be avoided. Indentation potfit source code is indented according to the default emacs indentation. The same effect can be achieved with the

download

anonymous@undisclosed.example.com (Anonymous) — Sun, 21 Apr 2024 18:21:00 +0000

Downloading potfit ---------- potfit is released under the GNU General Public Licence Version 2. By downloading the source code you agree to the conditions of that license. Latest version The latest version of potfit can be downloaded here: potfit-20211112.tar.gz Development versions

flagfile

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Mar 2013 06:50:36 +0000

Flagfile ---------- The flagfile can be used to interrupt a potfit run softly. Every few steps the presence of the flagfile is checked and if it is found, the current optimization algorithm is aborted. This means that if the simulated annealing algorithm is running and a flagfile is created, simulated annealing will be terminated and

fweight

anonymous@undisclosed.example.com (Anonymous) — Tue, 02 Jan 2018 15:49:12 +0000

fweight ---------- The target function for the optimization algorithms in potfit is defined as: $$Z_F(\boldsymbol\xi) = \sum_{k=1}^{3N}u_k(F_k(\boldsymbol\xi)-F_k^0)^2 + \sum_{l=1}^{M}w_E(E_l(\boldsymbol\xi)-E_l^0)^2+\ldots$$ where $F_k(\boldsymbol\xi)$ are the forces calculated from the potential and $F_k^0$ the reference value. The same notation is used for the energies $E$. The weights for the energies ($w_E$$u_k$$F_k$$$u_k=\frac{1}{(\boldsymbol F_k^0+\epsilon)^2},$$$\boldsymbol F_k^0$$k…

imd

anonymous@undisclosed.example.com (Anonymous) — Fri, 01 Mar 2013 08:52:01 +0000

IMD ---------- If imdpotsteps is given in the parameter file, potentials in IMD format will be written. The prefix of these files is determined with the imdpot parameter. The number of files depends on the potential model. After the optimization, potfit writes the names of all files it creates to stdout, e.g.:

license

anonymous@undisclosed.example.com (Anonymous) — Fri, 01 Mar 2013 08:09:46 +0000

GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

limitations

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Jan 2018 09:48:38 +0000

Limitations ---------- Limitations of the current implemetation: Spline Interpolation At the moment, potfit takes its tabulated potential functions through values at sampling points and spline interpolation in between. While this allows considerable flexibility, it also has some disadvantages. Especially for distance ranges with rapid changes in function values, the spline polynomials might produce overswings. Users need to keep an eye on the interpolated functions to check if they suffer fr…

mailinglist

anonymous@undisclosed.example.com (Anonymous) — Thu, 28 Feb 2013 15:15:56 +0000

potfit Mailing list ---------- You can subscribe to the list easily via the web interface. Your e-mail address is not visible to other list members. potfit-users This mailing list is for general discussion on potfit. Here you can post your questions, discuss with other users, request new features, submit bug reports,

maxchfile

anonymous@undisclosed.example.com (Anonymous) — Wed, 10 Jan 2018 17:26:00 +0000

Maxch file ---------- This file can be used to limit the changes in the tabulated version of the Powell algorithm. If a change greater than this value is about to be done, this change is dismissed and the inner loop of the algorithm is restarted. For other algorithms and analytic potentials this file is ignored.$a_i$$a_k$$k^{\text{th}}$

nopunish

anonymous@undisclosed.example.com (Anonymous) — Tue, 05 Mar 2013 06:48:56 +0000

nopunish ---------- During the force-matching potfit uses numerical punishments to fix several gauge degrees of freedom. If you enable the nopunish option, these gauge degrees will not be fixed. This will make it a lot harder for the optimization algorithm to find an optimal potential for your system. It however might be desirable in some special cases.

parameters

anonymous@undisclosed.example.com (Anonymous) — Sun, 11 Aug 2019 10:11:41 +0000

Parameters ---------- Following is a complete list of all potfit parameters, together with a short description of their meaning, and indications when they are needed. Floating point numbers should be given in decimal notation. Vectors are given as a list of components, separated by spaces or tabs (all on one line).

publications

anonymous@undisclosed.example.com (Anonymous) — Wed, 01 Sep 2021 22:15:44 +0000

Publications ---------- References introducing potfit Please cite these references when referring to potfit in your publications. potfit in general P. Brommer, A. Kiselev, D. Schopf, P. Beck, J. Roth, and H.-R. Trebin Classical interaction potentials for diverse materials from ab initio data: a review of

references

anonymous@undisclosed.example.com (Anonymous) — Wed, 10 Jan 2018 17:14:52 +0000

References ---------- This page provides a list of references to algorithms used in potfit: Force-matching Ercolessi, F. and Adams, J. B.: Interatomic Potentials from First-Principles Calculations: the Force-Matching Method. Europhys. Lett., 26

resc

anonymous@undisclosed.example.com (Anonymous) — Thu, 23 Jan 2014 09:39:21 +0000

Rescaling option ---------- Up to potfit 0.6.0 the rescaling option was automatically enabled for all tabulated potentials which supported it (EAM, ADP and MEAM). It could be disabled with the noresc compilation flag. With the release of potfit 0.7.0 it has been disabled by default and can be enabled with the

sidebar

anonymous@undisclosed.example.com (Anonymous) — Sat, 23 Feb 2019 08:45:38 +0000

Main page ---------- Download Publications Contact About potfit User Guide * Compiling potfit * Options * Running potfit * Parameters * Configuration files * Potential models * Potential files * Interactions * Algorithms * Output * Units * Utilities * Limitations Examples * Configurations * Potentials * Parameter files * Advanced Examples * Tutorials Potential Databases * potfit potentials * EAM potentials (Sheng) * NIST repository More * …

start

anonymous@undisclosed.example.com (Anonymous) — Wed, 06 Mar 2019 17:49:24 +0000

Welcome to the potfit wiki ---------- potfit is a free implementation of the force-matching algorithm to generate effective potentials from ab-initio reference data. Features * Fit empirical potentials for molecular dynamics with the force-matching algorithm

stress

anonymous@undisclosed.example.com (Anonymous) — Wed, 19 Sep 2018 15:48:15 +0000

Stress ---------- To enable the calculation of the stress tensor you have to add stress to the compilation options of potfit. The stress tensor has to be given in the configuration file with the prefix #S. If no #S line is found for a configuration, then the calculation of stresses is disabled for this configuration.$$\boldsymbol\sigma^{\text{virial}} = \frac{1}{2\Omega}\sum_i\sum_{j\neq i}\boldsymbol r_{ij}\otimes\boldsymbol f_{ij}$$$\Omega$$i$$j$$\boldsymbol r_{ij}=\boldsymbol r_j-\boldsymb…

units

anonymous@undisclosed.example.com (Anonymous) — Fri, 05 Jan 2018 09:07:22 +0000

Units ---------- potfit does not need a particular system of units. It can work with any system. The units used by potfit are implicitly defined in the configuration and potential files, and possibly by certain parameters specifying the potential. $$1~\unicode{x212B} = 1\cdot 10^{-10}~\mathrm{m},$$$$1~\mathrm{eV} = 1.602\cdot 10^{-19}~\mathrm{J}$$$11594~\mathrm{K}$$$160.2~\mathrm{GPa} = 1602~\mathrm{kbar},$$$$1~\frac{\mathrm{eV}}{\unicode{x212B}} = 1.602\cdot 10^{-9}~\mathrm{N}.$$