Adding DPD System initialization

[StephMcCallum]

Attempting to incorporate the code in PhantomWalk into flowerMD so that we can use the modular class resources. PhantomWalk is a two step packing routine, first a non-self avoiding random walk, then a dpd relaxation simulation which runs in a loop checking energy cutoffs.

As a first pass, it made the most sense to me to put the RandomWalk at the system level, and DPD simulation at the simulation level. I attempted to use the gmso ff file instead of coding the DPD_FF as a class. But, since this file is gmso and not foyer, I was running into some issues. This is where I'm stopping today. The RandomWalk placement seems to be working, but I have not verified.

In tutorials, I'm debugging the workflow in notebook 7. Focusing on getting CG linear mono-disperse systems working.

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[StephMcCallum]

@chrisjonesBSU
This random walk is similar to yours in path class. I'm not sure if it would be better to loop that in here instead. But I think here we should be able to translate the monomer units if the flowermd molecule is all-atom

[chrisjonesBSU]

I'd suggest leaving this one as a simpler RW implementation. It will be straight forward to either make a different system class that uses a different RW approach, or just go straight from mBuild to flower.

[StephMcCallum]

Error from tutorial notebook 7, cell 6. When I try to pass in a gmso xml to BaseXMLForcefield, I get an invalid document error. I think that this function is expecting a Foyer xml file. I tried adding an option for loading a gmso xml, so that the filepath doesn't go to Foyer, then to gmso, but am still getting the same error. @chrisjonesBSU

---------------------------------------------------------------------------
DocumentInvalid                           Traceback (most recent call last)
Cell In[6], line 1
----> 1 system.apply_forcefield(force_field=Bead_Spring_DPD(),r_cut=1.15)

Cell In[5], line 7, in Bead_Spring_DPD.__init__(self, forcefield_files)
      6 def __init__(self, forcefield_files=f"{FF_DIR}/hoomd-dpd-hhp.xml"):
----> 7     super(Bead_Spring_DPD, self).__init__(forcefield_files=forcefield_files,gmso_xml=True)
      8     self.description = "DPD forcefield loaded from an XML file."

File ~/Desktop/cmelab/forks/flowerMD/flowermd/base/forcefield.py:12, in BaseXMLForcefield.__init__(self, forcefield_files, name, gmso_xml)
     11 def __init__(self, forcefield_files=None, name=None,gmso_xml=False):
---> 12     super(BaseXMLForcefield, self).__init__(
     13         forcefield_files=forcefield_files, name=name
     14     )
     15     if gmso_xml==True:
     16         self.gmso_ff = ForceField(forcefield_files or name)

File ~/miniconda3/envs/flowermd-dev/lib/python3.12/site-packages/foyer/forcefield.py:526, in Forcefield.__init__(self, forcefield_files, name, validation, debug)
    524 if validation:
    525     for ff_file_name in preprocessed_files:
--> 526         Validator(ff_file_name, debug)
    527 super(Forcefield, self).__init__(*preprocessed_files)
    529 if len(preprocessed_files) == 1:

File ~/miniconda3/envs/flowermd-dev/lib/python3.12/site-packages/foyer/validator.py:29, in Validator.__init__(self, ff_file_name, debug)
     26 preprocessed_ff_file_name = preprocess_forcefield_files([ff_file_name])
     28 ff_tree = etree.parse(preprocessed_ff_file_name[0])
---> 29 self.validate_xsd(ff_tree)
     31 self.atom_type_names = ff_tree.xpath("/ForceField/AtomTypes/Type/@name")
     32 self.atom_types = ff_tree.xpath("/ForceField/AtomTypes/Type")

File ~/miniconda3/envs/flowermd-dev/lib/python3.12/site-packages/foyer/validator.py:74, in Validator.validate_xsd(ff_tree, xsd_file)
     71     return ValidationError(error_text, keyword, line)
     73 try:
---> 74     xmlschema.assertValid(ff_tree)
     75 except DocumentInvalid as ex:
     76     message = ex.error_log.last_error.message

File src/lxml/etree.pyx:3813, in lxml.etree._Validator.assertValid()

DocumentInvalid: Element 'FFMetaData': This element is not expected., line 2

[StephMcCallum]

The fix to BaseXMLForcefield seems to be working. However, the dpd xml is not the correct formatting. See tutorial 7 notebook for the latest error, can't match AtomType expression to accepted potentials (although equation is listed under potentials). The AtomType must have an expression