##Questions? Contact Cody Aldaz, email: [email protected]
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.
##CTest
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.
##Documentation
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 [email protected]:TriBITSPub/TriBITS.git