Get started

To get started, we provide show how to use different capabilities of MLatom on an example of geometry optimization.

Using input file

You can watch a short video demonstrating how to use the command-line options or input file to run some calculations on the XACS cloud.

MLatom can be run in the command line format using the command-line options or input file. To optimize geometry using the ANI-1ccx method, you can use the input file geomopt.inp which you can download or copy-paste from:

ANI-1ccx                # pre-trained model
geomopt                 # requests geometry optimization
xyzfile=init.xyz        # initial geometry guess
optxyz=opt.xyz          # file with optimized geometry

This input requires you to provide init.xyz file (which you need to upload as auxiliary file on XACS cloud)

Note

This self-contained input file without the need to provide auxiliary file also works:

ANI-1ccx                # pre-trained model
geomopt                 # requests geometry optimization
xyzfile='
8

C             0.0000000000000           0.0000000000000           0.7608350816719
H            -0.0000000000000           1.0182031026887           1.1438748775511
H             0.8817897531403          -0.5091015513443           1.1438748775511
H            -0.8817897531403          -0.5091015513443           1.1438748775511
C            -0.0000000000000          -0.0000000000000          -0.7608350816719
H            -0.8817897531403           0.5091015513443          -1.1438748775511
H             0.8817897531403           0.5091015513443          -1.1438748775511
H            -0.0000000000000          -1.0182031026887          -1.1438748775511
'

Then run MLatom simulations using this input file as:

mlatom geomopt.inp &> geomopt.out

The program will print out the relevant calculation information to the output file geomopt.out.

Using PyAPI

You can watch a short video demonstrating how to use PyAPI on the XACS cloud.

Below is an example of Python script using MLatom to optimize geometry at ANI-1ccx – the simulation task the same as in the above example with command-line execution:

import mlatom as ml                                                                         # import MLatom module.
ani = ml.models.methods(method='ANI-1ccx')                                                  # denfine an ANI-1cxx model.
init_mol = ml.data.molecule.from_xyz_file('init.xyz')                                       # load the molecular structure.
final_mol = ml.optimize_geometry(model=ani, initial_molecule=init_mol).optimized_molecule   # the optimized structure can be obtained by command.
final_mol.xyz_coordinates                                                                   # we can see the coordinates of the last molecule.
print(final_mol.get_xyz_string())                                                           # print the coordinates in ".xyz" format.
final_mol.write_file_with_xyz_coordinates(filename='opt.xyz')                              # save it in "final.xyz".