Questions?

Contact Liz Doty: [email protected]

Overview

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

Running GSM with the XTB package (from the Grimme lab): https://github.com/grimme-lab/xtb_docs/blob/master/source/gsm.rst

Installation

Using Pixi (Recommended)

The easiest way to install GSM is with Pixi, which handles all dependencies automatically.

1. Install Pixi if you haven't already
2. Install GSM globally:

pixi global install \
    --git https://github.com/ZimmermanGroup/molecularGSM.git

This builds GSM with MOPAC support (default) and makes gsm available in your PATH.

Building with Different Backends

To build with a different energy calculator backend, set the appropriate environment variable:

Backend	Command
Q-Chem	GSM_ENABLE_QCHEM=1 pixi global install --git ...
Q-Chem SF	GSM_ENABLE_QCHEM_SF=1 pixi global install --git ...
ORCA	GSM_ENABLE_ORCA=1 pixi global install --git ...
Gaussian	GSM_ENABLE_GAUSSIAN=1 pixi global install --git ...
Molpro	GSM_ENABLE_MOLPRO=1 pixi global install --git ...
ASE	GSM_ENABLE_ASE=1 pixi global install --git ...
Turbomole	GSM_ENABLE_TURBOMOLE=1 pixi global install --git ...

For example, to install with Q-Chem:

GSM_ENABLE_QCHEM=1 pixi global install \
    --git https://github.com/ZimmermanGroup/molecularGSM.git

Development Setup

For development or to install from a local clone:

git clone https://github.com/ZimmermanGroup/molecularGSM.git
cd molecularGSM
pixi install

This makes the gsm executable available in the pixi environment:

pixi run gsm <input_number>
pixi run test  # run included test

You can also install globally from the local path:

pixi global install --path .

Using CMake (Manual Build)

Alternatively, this code can be built using CMake directly. To do so:

1. Load/install CMake
2. Load MKL (On Athena use intel/oneapi/mkl/2021.1.1 and GCC, e.g. gcc/12.1.0)
3. Clone this repository, use master branch

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

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

    $ mkdir BUILD
    $ cd BUILD

5. 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.

6. After successful configuration. To compile:

    $make -j8

7. An executable named gsm will be created in BUILD/GSM directory.

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.