Latest revision as of 11:58, 1 July 2021

Welcome to the Wales group software wiki

For info on compiling our code from the source tarball, see the cmake page.

Members

The writable (Raven login required with admitto password) version is located here. If you modify the writable version, the changes will appear on the read only version.

Contact details

If you have something to add to this wiki, or would like to contribute code, please get in touch with Professor Wales.

Comprehensive Contents Page

Please click here for a comprehensive, organised list of all of the pages comprising this wiki + some other useful links.

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:

DisconnectionDPS

DISCOTRESS

Group Members Only

Please click here for group members-only pages.

@@ Line 1: / Line 1: @@
-<big>'''Welcome to the Wales group software wiki!'''</big>
+<big>'''Welcome to the Wales group software wiki'''</big>
+For info on compiling our code from the source tarball, see the [[Compiling Wales Group code using CMake | cmake]] page.
-<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. We're currently in the process of migrating from an old website so please bear with us while we hammer out the problems and set things up.</span>
---[[User:Csw34|Csw34]] 22:57, 20 July 2010 (UTC)
+== Members ==
+The writable (Raven login required with admitto password) version is located [http://wikis.ch.cam.ac.uk/walesdocs/wiki/ here]. If you modify the writable version, the changes will appear on the read only version.
+= Contact details =
+If you have something to add to this wiki, or would like to contribute code, please get in touch with Professor Wales.
+= Comprehensive Contents Page =
+Please click [[Comprehensive Contents Page | here]] for a comprehensive, organised list of all of the pages comprising this wiki + some other useful links.
 = Group Software =
-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.
@@ Line 12: / Line 20: @@
 *[[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.
+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 =
 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:
+*[[DisconnectionDPS]]
-Scripts etc here...
+*[[DISCOTRESS]]
-= Contact details =
+= Group Members Only =
-If you have something to add to this wiki, or would like to contribute code, please get in touch with Professor Wales.
+Please click [[wales:Group-Only Contents Page | here]] for group members-only pages.

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