Contact Nicole Perkins: nsperkin@umich.edu
The growing string method is a reaction path and transition state finding method developed in c++.
For more information, check out the wiki page: https://github.com/ZimmermanGroup/molecularGSM/wiki
Sample tutorial files can be found under the tutorial folder: https://github.com/ZimmermanGroup/molecularGSM/tree/master/tutorial
This code can be built using CMake. To do so:
- Load/install CMake
- Load Intel compilers (if not loaded)
- Clone this repository and checkout tribits branch
$ git clone https://github.com/ZimmermanGroup/molecularGSM.git
$ cd molecularGSM
$ git checkout tribits- Clone TriBITS repository
$ git clone https://github.com/TriBITSPub/TriBITS.git- Create a BUILD directory at the same level as GSM
$ mkdir BUILD
$ cd BUILD- Configure using CMake
$ cmake -D GSM_ENABLE_QCHEM=1 ../- other options:
- GSM_ENABLE_QCHEM_SF=1
- GSM_ENABLE_ORCA=1
- GSM_ENABLE_GAUSSIAN=1
- GSM_ENABLE_MOLPRO=1
- GSM_ENABLE_ASE=1
- If no option is specified, the code will use MOPAC as its energy calculator. Check mopac.cpp to make sure charge/multiplicity is correct, since that is hard-coded.
- After successful configuration. To compile:
$make -j8- An executable named "gsm.${CALCULATOR}.exe" will be created in BUILD/GSM directory, where ${CALCULATOR} is the name of the QM package.
To run gsm, copy the executable to the working directory (where the input files are) or reference it using the full path.
There are five test examples: alanine dipeptide isomerization, ammonia borane reactions, diels alder reaction, ethylene rotation, and methanol formaldehyde reaction. After building the executable you can use type $ ctest to run the tests. When each test is complete, the output will be compared with the standard output in each test directory. If the difference in coordinates of a each atom is more than 0.001, the test will fail.
The documentation is generated using Doxygen and hosted on github pages:
https://zimmermangroup.github.io/molecularGSM/
Maintaining this page is not very straightforward and it does not update every time one builds the documentation. Here are some links on how it works:
http://rickfoosusa.blogspot.com/2011/10/howto-use-doxygen-with-github.html
https://help.github.com/articles/configuring-a-publishing-source-for-github-pages/
https://help.github.com/articles/creating-project-pages-using-the-command-line/
This is apparently a better solution:
https://martinhh.github.io/2014/08/27/hosting-doxygen-as-github-page/
This how the main page can be accessed:
git clone git@github.com:TriBITSPub/TriBITS.git