dralgroup / mlatom Goto Github PK

i am just learning mlatom, and i found that the input files are missing for the example of KREG at http://mlatom.com/kreg/

the tutorial says to go to XACS to use the example, but in XACS, the folder /home/mlatom/tutorial is also missing

so, where can i get the input files for GREG example? thanks.

by the way, this example looks like being written in "command line" type, can this be written in python type?

I am a beginner for mlatom. And now I have some problem run the example in the MLP tutorial

my code is just copied from the tutorial:

import mlatom as ml

molDB = ml.data.molecular_database.from_xyz_file(filename = 'H2.xyz')
molDB.add_scalar_properties_from_file('H2_HF.en', 'energy')
molDB.add_xyz_vectorial_properties_from_file('H2_HF.grad', 'energy_gradients')

# Here we define the KREG model for demonstration purposes as it is the fastest
model = ml.models.kreg(model_file='kreg.npz')

the first problem is that the data files contain different numbers of value: the H2.xyz has 361 values while the other two (H2_HF.en and H2_HF.grad) both have 451 values.
so it results in the following error:

Traceback (most recent call last):
  File "/home/ilcpm/MD/mlp/testMLP.py", line 4, in <module>
    molDB.add_scalar_properties_from_file('H2_HF.en', 'energy')
  File "/home/ilcpm/.local/lib/python3.10/site-packages/mlatom/data.py", line 863, in add_scalar_properties_from_file
    self.molecules[ii].__dict__[property_name] = yy
IndexError: list index out of range

it can be solved by use the test_H2.xyz, test_H2_HF.en and test_H2_HF.grad, or just delete the values in H2_HF.en and H2_HF.grad.

then the biggest problem appears:

Traceback (most recent call last):
  File "/home/ilcpm/MD/mlp/testMLP.py", line 8, in <module>
    model = ml.models.kreg(model_file='kreg.npz')
  File "/home/ilcpm/.local/lib/python3.10/site-packages/mlatom/models.py", line 951, in __init__
    from .kreg_api import KREG_API
  File "/home/ilcpm/.local/lib/python3.10/site-packages/mlatom/kreg_api.py", line 5, in <module>
    from .fortran import KREG
ImportError: cannot import name 'KREG' from 'mlatom.fortran' (/home/ilcpm/.local/lib/python3.10/site-packages/mlatom/fortran/__init__.py)

it looks like there should be a python file named KREG.py in the folder mlatom/fortran, but I can't find it

then I try to run the Command-line (input file)

my command is mlatom train_KREG.inp, it can be successfully finish and get the output
then I found the following line in the output:

> /home/ilcpm/.local/lib/python3.10/site-packages/mlatom/MLatomF createMLmodel XYZfile=H2.xyz Yfile=H2_HF.en YgradXYZfile=H2_HF.grad MLmodelOut=kreg.unf sigma=1.0 lambda=1e-06

it seems that there is a binary executable program named MLatomF, so the missing of KREG.py didn't cause problem.

and the values in the three files are not equal:

 <!> File H2_HF.en contains 451 reference values
     but only first 361 will be used

 
    Charge        X            Y            Z
       1     0.000000     0.000000     0.000000
       1     0.000000     0.000000     1.350000
 
  Equilibrium distances: 
1     1-2      1.350000000000
 <!> File H2_HF.en contains 451 reference values
     but only first 361 will be used

 <!> File H2_HF.grad contains 451 reference values
     but only first 361 will be used

Could you consider adding this to the development roadmap? Integrating a PLUMED interface within the molecular dynamics simulation module of the MLAtom project would significantly enhance its sampling capabilities. This integration could streamline the study of complex processes and improve the accuracy of potential energy surface representations. Thank you very much!