# molecularGSM

**Repository Path**: wuping4321/molecularGSM

## Basic Information

- **Project Name**: molecularGSM
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-12-29
- **Last Updated**: 2025-12-29

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

## Questions?
Contact Liz Doty: lizdoty@umich.edu

## 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
This code can be built using CMake. 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

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

4. Create a BUILD directory at the same level as GSM
```bash
    $ mkdir BUILD
    $ cd BUILD
```

5. Configure using CMake
```bash
    $ 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:
```bash
    $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.