Difference between revisions of "Main Page"
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<big>'''Welcome to the Wales group software wiki!'''</big> |
<big>'''Welcome to the Wales group software wiki!'''</big> |
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| − | <span style="color:#ff0000">This wiki will contain the documentation for all the software we maintain in the group, along with worked examples and useful tips |
+ | <span style="color:#ff0000">This wiki will contain the documentation for all the software we maintain in the group, along with worked examples and useful tips.</span> |
--[[User:Csw34|Csw34]] 22:57, 20 July 2010 (UTC) |
--[[User:Csw34|Csw34]] 22:57, 20 July 2010 (UTC) |
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= Group Software = |
= Group Software = |
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| − | All of our software is freely available under the [http://www.gnu.org/licenses/gpl.html GPL]. However, there are cases when we interface to commercial codes such as [http://ambermd.org/ AMBER] and [http://www.charmm.org/ CHARMM]. These files are absent from the source tarball. If you do have a license, please contact Professor Wales for access to a full version. We work on three separate |
+ | All of our software is freely available under the [http://www.gnu.org/licenses/gpl.html GPL]. However, there are cases when we interface to commercial codes such as [http://ambermd.org/ AMBER] and [http://www.charmm.org/ CHARMM]. These files are absent from the source tarball. If you do have a license, please contact Professor Wales for access to a full version. We work on three separate programs: |
*[[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling. |
*[[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling. |
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*[[OPTIM]]: A program for optimizing geometries and calculating reaction pathways |
*[[OPTIM]]: A program for optimizing geometries and calculating reaction pathways |
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| − | The geometry optimization scheme in OPTIM is based on eigenvector-following and was originally built from the optimizer in the ACES package written |
+ | The geometry optimization scheme in OPTIM is based on eigenvector-following and was originally built from the optimizer in the ACES package written by Prof. John F. Stanton. OPTIM has analytic first and second derivatives coded for dozens of empirical potentials, and can also treat systems involving periodic boundary conditions and solve general optimization problems such as least squares fits. |
| − | *[[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis |
+ | *[[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. |
= Helpful Software = |
= Helpful Software = |
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We have developed many scripts within the group to use in conjunction with our software - all of which are provided here. We also use other programs which are linked below: |
We have developed many scripts within the group to use in conjunction with our software - all of which are provided here. We also use other programs which are linked below: |
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| − | Scripts etc here... |
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*[[DisconnectionDPS]] |
*[[DisconnectionDPS]] |
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Revision as of 15:15, 30 January 2014
Welcome to the Wales group software wiki!
This wiki will contain the documentation for all the software we maintain in the group, along with worked examples and useful tips. --Csw34 22:57, 20 July 2010 (UTC)
Group Software
All of our software is freely available under the GPL. However, there are cases when we interface to commercial codes such as AMBER and CHARMM. These files are absent from the source tarball. If you do have a license, please contact Professor Wales for access to a full version. We work on three separate programs:
- GMIN: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
GMIN employs the basin-hopping algorithm described by Wales and Doye (J. Phys. Chem. A, 101, 5111, 1997[1]) to locate global minima on a potential energy surface. Many potentials are included. The latest version also includes an implementation of basin-sampling as described in T.V. Bogdan, D.J. Wales and F. Calvo (J. Chem. Phys., 124, 044102, 2006[2]).
- OPTIM: A program for optimizing geometries and calculating reaction pathways
The geometry optimization scheme in OPTIM is based on eigenvector-following and was originally built from the optimizer in the ACES package written by Prof. John F. Stanton. OPTIM has analytic first and second derivatives coded for dozens of empirical potentials, and can also treat systems involving periodic boundary conditions and solve general optimization problems such as least squares fits.
- PATHSAMPLE: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
Helpful Software
We have developed many scripts within the group to use in conjunction with our software - all of which are provided here. We also use other programs which are linked below:
Contact details
If you have something to add to this wiki, or would like to contribute code, please get in touch with Professor Wales.