add angle and dihedral restraints in openMM interface and fix UnicodeDecodeError in orca interface

[YingrongChen]

1. add add_angleconstraints and add_dihedralconstraints in openMM interface, with restraints force constant angleforceconstant and dihedralforceconstant. Roughly combined the logic with existing clean_up_constraints_list function to measure current angle and dihedral as the reference for restraints.

2. Fix UnicodeDecodeError when running OpenMM_MD with qmmm theory using orca as the qmtheory

   
   File ~/.conda/envs/ash/lib/python3.10/site-packages/ash/interfaces/interface_ORCA.py:793, in run_orca_SP_ORCApar(orcadir, inpfile, numcores, check_for_warnings, check_for_errors, bind_to_core_option, ignore_ORCA_error)
   792 if check_for_errors:
   --> 793     grab_ORCA_errors(basename+'.out')
   794 if check_for_warnings:

File ~/.conda/envs/ash/lib/python3.10/site-packages/ash/interfaces/interface_ORCA.py:844, in grab_ORCA_errors(filename) 843 for errstring in error_strings: --> 844 error_l = pygrep2(errstring, filename) 845 for e in error_l:

File ~/.conda/envs/ash/lib/python3.10/site-packages/ash/functions/functions_general.py:261, in pygrep2(string, file, print_output) 260 with open(file) as f: --> 261 for line in f: 262 if string in line:

File ~/.conda/envs/ash/lib/python3.10/encodings/ascii.py:26, in IncrementalDecoder.decode(self, input, final) 25 def decode(self, input, final=False): ---> 26 return codecs.ascii_decode(input, self.errors)[0]

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 4231: ordinal not in range(128)

[RagnarB83]

Thank you for contributing. I'm looking things over, looks like we have some conflicts that I will take care of. The changes to deal with UnicodeDecoderror are all good.

Why did you add: md.simulation.minimizeEnergy() to the OpenMM_box_equilibration function? If one wants to minimize before running NPT MD simulations it is better to just call OpenMM_Opt function first.

[YingrongChen]

Hi Dr.Bjornsson,

I apologize for not removing minimizeEnergy() earlier. I added it accidentally because my simulation kept blowing up.

Additionally, I noticed that there are more with open('') calls in interface_orca.py that could cause UnicodeDecodeError. It might be worth reviewing them.

I wanted to ask: is the gpu4pyscf interface ready for QM/MM broken-symmetry DFT? I keep encountering this error: AttributeError: module 'ash.interfaces.interface_pyXscf_mods' has no attribute 'QMMMUKS'

Thank you so much for your help! I’m currently using Ash for Ni-Fe hydrogenase simulations and have found it to be an excellent tool! I am also developing an interface for my own GPU-DFT software.

On Thu, Sep 19, 2024 at 6:04 AM RagnarB83 @.***> wrote:

Thank you for contributing. I'm looking things over, looks like we have some conflicts that I will take care of. The changes to deal with UnicodeDecoderror are all good.

Why did you add: md.simulation.minimizeEnergy() to the OpenMM_box_equilibration function? If one wants to minimize before running NPT MD simulations it is better to just call OpenMM_Opt function first.

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[RagnarB83]

Gotcha. Great to hear, glad you're finding ASH useful. Any contributions and suggestions are welcome.

The gpu4pyscf library is currently not compatible with pointcharge embedding within pyscf. I was trying to figure out how to get around it within ASH (hence the functions in ash.interfaces.interface_pyXscf_mods) but I was not successful yet and have not had time to revisit. You could try to figure out where I got stuck.

Great to hear you are developing an interface for another GPU-DFT code, more GPU-code interfaces in ASH would be a good thing.