Overview

The growing string method (GSM) is a reaction path and transition state finding method developed in c++. GSM can be interfaced with packages ZStruct2 and Metal-Ligand Binding.

For more information, check out the wiki page: https://github.com/ZimmermanGroup/molecularGSM/wiki

Example calculations can be found in the src/GSM/TEST folder. Example calculations can be enabled by modifying the src/GSM/TEST/CMakeLists.txt file.

A discussion can be found: https://github.com/ZimmermanGroup/molecularGSM/tree/master/tutorial

Installation

This code can be built using CMake. To do so:

1. Load/install CMake
2. Load Intel compilers (if not loaded)
3. Clone this repository and checkout tribits branch

		$ git clone https://github.com/ZimmermanGroup/molecularGSM.git
        $ cd molecularGSM
		$ git checkout tribits

4. Clone TriBITS repository

	 $ git clone https://github.com/TriBITSPub/TriBITS.git

5. Create a BUILD directory at the same level as GSM

    $ mkdir BUILD
    $ cd BUILD

6. 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.

7. After successful configuration. To compile:

    $make -j8

8. 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. (THIS NEEDS FIXING).