Lammps Writer Changes For Updated Topology Class #701

CalCraven · 2022-11-29T00:06:23Z

This PR aims to refactor the current lammpswriter, which was questionably functional in its previous state and not entirely compatible with modern changes to a topology.

In terms of making sure the writer is nice and flexible. I'm pulling out some of the functions for conversions and making those available in the Topology class. That way users can make sure they know what functional forms are being used before writing, and there isn't a lot of conversions happening under the hood, which causes mistakes when people aren't sure how something is working.

See the relevant tests in test_lammpswriter.py for the unit_styles and atom_styles we aim to support. Lot's of different functional forms are technically possible, most of which are actually set in the input lammps file, not in the data file. So we don't currently have in place a lot of testing for them.

Current workflow:

1. Read in topology and forcefield.
2. Apply forcefield to topology.
3. Massage topology using unit and functional form conversions.
4. Write to relevant engine (raising errors if that engine doesn't support the given style).

PR Checklist

…mmpswrite-updates

lgtm-com · 2022-11-29T00:12:25Z

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CalCraven · 2022-11-29T00:13:50Z

Possible method suggested by @daico007 for iterating through atomtypes and connection types. I will test this for the speedups compared to just iterating through all of the connections during the writing step.

# Create an atom type map to do indexing

atypes = list(topology.atom_types())
atypes_map = dict()
for i, uatype in enumerate(unique_atypes):
    matched_idx = list()
    for idx, atype in enumerate(atypes):
        if atype == uatype:
            atypes_map[atype] = i
            matched_idx.append(idx)
    for idx in reversed(matched_idx):
        atypes.pop(idx)

# Make connection types map to extract index later
uc_types = topology.connection_types(PotentialFilters.UNIQUE_NAME_CLASS)
c_types = [ctype for ctype in topology.connection_types]
c_typesmap = dict()
for uc_type in uc_types:
    matched_idx = list()
    for idx, c_type in enumerate(c_types):
        if c_type == uc_type:
            c_typesmap[c_type] = uc_type
            matched_idx.append(idx)
    for idx in reversed(matched_idx):
        c_types.pop(idx)

codecov · 2022-11-29T01:38:19Z

Codecov Report

Patch coverage: 91.45% and project coverage change: -0.07 ⚠️

Comparison is base (2f3c7f3) 91.98% compared to head (27df258) 91.91%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #701      +/-   ##
==========================================
- Coverage   91.98%   91.91%   -0.07%     
==========================================
  Files          67       67              
  Lines        6460     6818     +358     
==========================================
+ Hits         5942     6267     +325     
- Misses        518      551      +33

Impacted Files	Coverage Δ
gmso/formats/mol2.py	`100.00% <ø> (ø)`
gmso/formats/top.py	`88.04% <ø> (ø)`
gmso/utils/decorators.py	`75.00% <10.00%> (-19.12%)`	⬇️
gmso/core/views.py	`89.24% <25.00%> (-6.11%)`	⬇️
gmso/core/topology.py	`96.07% <50.00%> (-0.94%)`	⬇️
gmso/utils/misc.py	`96.36% <66.66%> (-1.75%)`	⬇️
gmso/external/convert_parmed.py	`95.13% <88.88%> (-0.36%)`	⬇️
gmso/utils/conversions.py	`96.40% <94.87%> (-2.15%)`	⬇️
gmso/formats/lammpsdata.py	`95.94% <95.14%> (+0.51%)`	⬆️
gmso/abc/abstract_site.py	`94.66% <100.00%> (+0.07%)`	⬆️
... and 3 more

... and 2 files with indirect coverage changes

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lgtm-com · 2022-11-29T17:20:49Z

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gmso/utils/decorators.py

gmso/core/views.py

gmso/formats/lammpsdata.py

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…ions

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…t matching with lammps output from mbuild writer.

…nique potential types

Co-authored-by: Co Quach <[email protected]>

… appearance in the topology. Copies of connection types are made, which must be filtered using potential filters to get whatever subset is considered unique.

gmso/formats/lammpsdata.py

daico007

Looks great overall! I only have a few comments about code style for consistency (between units on comment line and actually being written out), and maybe some missing using conversion.
I pulled this PR and reviewed/tested it and things seem to be functional, so I am in favor of merging it soon. There are a few things, as we discussed last time, regarding the necessary of LAMMPS specific harmonic bonds/angles, but I think that can be addressed in a different. Another thing would be using the centralize unit conversing units (since HOOMD and GROMACS is using same/similar functionality.

gmso/utils/conversions.py

daico007 · 2023-05-23T16:03:57Z

gmso/core/topology.py

+        for potStr in exp_unitsDict:
+            potContainer = getattr(self, potStr + "_types")


It seems like this method only convert all the potentials. Should we also convert the atoms' position too?

I think the initial goal for this method was just to be used on the parameters of the potential expressions, which is why it's missing things. Pairpotentials come to mind as an example of that. However, I ended up converting the expressions on writing out, instead of upfront in the lammpswriter, and mostly relying on methods that are living in lammpsdata.py because of that. I still think the best way to do the conversion would be:

Grab the set of base UnitSystem. Presumably, this would be from a library, or passed directly to whatever function by the user. I can see a useful added input of also passing units specific to parameters in the topology, such as: {"angle_types":{"theta":u.degrees}}, which would override the value for that UnitSystem.

Determine if the unit changes should happen in place or to a copy of the topology. This would be mostly for speedups, and prevent issues with overwriting whatever you pass to the function.

Iterate through all components of the topology. Each component should be passed to a generic unit_conversion method with the base units and the conversion should be done. These components include: [box, sites, atomtypes, bondtypes, angletypes, dihedraltypes, impropertypes, pairpotentials]. Each of these may have their own specific methods, but should be accessible through a single api.

Once the conversions are made, then the topology attributes can be written out directly as floats with the to_value() method. Rounding should also occur on writing.

To summarize, I think this function is not used currently at all. I can either delete it, or leave it as a starting place for the next PR that looks to normalize and standardize all of the unit handling in GMSO.

daico007 · 2023-05-23T16:15:56Z

gmso/tests/test_top.py

        for site in top.sites:
-            site.atom_type = ff.atom_types[site.name]
-
-        top.update_atom_types()
+            site.atom_type = ff.atom_types[site.atom_type.name]

        for bond in top.bonds:
            bond.bond_type = bond.connection_type = ff.bond_types[
                "opls_111~opls_112"
            ]

-        top.update_bond_types()
-


I think we could remove this section completely at this point. It was there when the apply method was not yet available.

gmso/tests/test_conversions.py

daico007 · 2023-05-23T17:52:01Z

gmso/formats/lammpsdata.py

+reg = UnitRegistry()
+dim = u.dimensions.current_mks * u.dimensions.time
+conversion = 1 * getattr(u.physical_constants, "elementary_charge").value
+reg.add(
+    "elementary_charge",
+    base_value=conversion,
+    dimensions=dim,
+    tex_repr=r"\rm{e}",
+)
+conversion = 1 * getattr(u.physical_constants, "boltzmann_constant_mks").value
+dim = u.dimensions.energy / u.dimensions.temperature
+reg.add(
+    "kb", base_value=conversion, dimensions=dim, tex_repr=r"\rm{kb}"
+)  # boltzmann temperature
+conversion = (
+    4
+    * np.pi
+    * getattr(u.physical_constants, "reduced_planck_constant").value ** 2
+    * getattr(u.physical_constants, "eps_0").value
+    / (
+        getattr(u.physical_constants, "electron_charge").value ** 2
+        * getattr(u.physical_constants, "electron_mass").value
+    )
+)
+dim = u.dimensions.length
+reg.add(
+    "a0", base_value=conversion, dimensions=dim, tex_repr=r"\rm{a0}"
+)  # bohr radius
+conversion = (
+    getattr(u.physical_constants, "reduced_planck_constant").value ** 2
+    / u.Unit("a0", registry=reg).base_value ** 2
+    / getattr(u.physical_constants, "electron_mass").value
+)
+dim = u.dimensions.energy
+reg.add(
+    "Ehartree", base_value=conversion, dimensions=dim, tex_repr=r"\rm{Ehartree}"
+)  # Hartree energy
+conversion = np.sqrt(
+    10**9 / (4 * np.pi * getattr(u.physical_constants, "eps_0").value)
+)
+dim = u.dimensions.charge
+reg.add(
+    "Statcoulomb_charge",
+    base_value=conversion,
+    dimensions=dim,
+    tex_repr=r"\rm{Statcoulomb_charge}",
+)  # Static charge


Would it be cleaner to put this inside _unit_style_factory?

Upon chatting with @daico007, I think all of this is going to get moved to the units module in an upcoming PR. So, I'll leave this here for now, as it's not worth the effort to move this right before it will all get moved again.

gmso/formats/lammpsdata.py

daico007

Looks great overall! I only have a few comments about code style for consistency (between units on comment line and actually being written out), and maybe some missing using conversion.
I pulled this PR and reviewed/tested it and things seem to be functional, so I am in favor of merging it soon (after addressing the failing test and comments above). There are a few things, as we discussed last time, regarding the necessity of LAMMPS specific harmonic bonds/angles json, but I think that can be addressed in a different. Another thing would be using the centralize unit conversing units (since HOOMD and GROMACS is using same/similar functionality.

daico007 · 2023-05-23T19:29:26Z

Note: we still have one failing tests at

___ TestLammpsWriter.test_lammps_vs_parmed_by_mol[typed_methylnitroaniline] ____
  
      def compare_lammps_files(fn1, fn2, skip_linesList=[]):
          """Check for line by line equality between lammps files, by any values."""
          with open(fn1, "r") as f:
              line1 = f.readlines()
          with open(fn2, "r") as f:
              line2 = f.readlines()
          for lnum, (l1, l2) in enumerate(zip(line1, line2)):
              print(l1, l2)
              print("###############")
              for arg1, arg2 in zip(l1.split(), l2.split()):
                  try:
                      comp1 = float(arg1)
                      comp2 = float(arg2)
                  except ValueError:
                      comp1 = str(arg1)
                      comp2 = str(arg2)
                  if isinstance(comp1, float):
  >                   assert np.isclose(
                          comp1, comp2, 1e-3
                      ), f"The following two lines have not been found to have equality {l1} and {l2}"
  E                   AssertionError: The following two lines have not been found to have equality 18 dihedral types
  E                      and 23 dihedral types
  E                     
  E                   assert False
  E                    +  where False = <function isclose at 0x7ff1877b4d30>(18.0, 23.0, 0.001)
  E                    +    where <function isclose at 0x7ff1877b4d30> = np.isclose
  
  /Users/runner/work/gmso/gmso/gmso/tests/test_lammps.py:37: AssertionError

gmso/formats/lammpsdata.py

daico007 · 2023-05-29T02:58:49Z

gmso/formats/lammpsdata.py

+                _parameter_converted_to_float(
+                    improper_type.parameters["k"], base_unyts, cfactorsDict
+                ),
+                improper_type.parameters["chieq"]


Suggested change

improper_type.parameters["chieq"]

improper_type.parameters["phi_eq"]

Currently, in the PeriodicImproperPotential json, the three variables are k (energy), n (dimensionless) and phi_eq (angle). I think the chieq could be a typo. Also, why don't the n get written out somewhere?

I guess, this is supposed to write out harmonic improper, in which case, we need to adjust the list in _accepted_potential

Looking at the docs (https://docs.lammps.org/improper_style.html), looks like our PeriodicImproper is called fourier in lammps?

Yeah so the naming is slightly weird, that's on of the reasons I was tagging things with LAMMPS as the potential template name.
As far as I can tell:
GMSO PeriodicImproperPotential = lammps modified improper_style CVFF (not sure if there's a 1-1 conversion here
GMSO HarmonicImproperPotential = 1/2* LAMMPS improper_style harmonic
GMSO FourierTorsionPotential != LAMMPS improper_style fourier (we would probably just need a separate template for it).

The equations for PeriodicImproper and and lammps improper_style fourier, are similar, but missing the phi_eq term.

So I am looking back here: https://github.com/mosdef-hub/mbuild/blob/main/mbuild/formats/lammpsdata.py.
It seems like that the current mbuild version support LAMMPS improper harmonic (coming fromstructure.impropers) and cvff (coming from structure.dihedrals where dihedral.improper == True). So I think, in GMSO, that would map GMSO harmonic --> LAMMPS harmonic and GMSO periodic --> LAMMPS cvff.

Need to add a test for this, for some reason it's not being caught at all.

jaclark5

Nice work, I only read through the code and made comments. I'll download and perform testing when it passes the tests.

gmso/core/box.py

jaclark5 · 2023-06-15T13:21:22Z

gmso/core/topology.py

+        Parameters
+        ----------
+        expressionMap : dict, default={}
+            map with keys of the potential type and the potential to change to


This is a little confusing and only made sense after looking at the example. Maybe:
Map where the keys represent the current potential type and the corresponding values represent the desired potential type.

jaclark5 · 2023-06-15T13:23:27Z

gmso/core/topology.py

+        """
+        from gmso.utils.conversions import convert_topology_expressions
+
+        return convert_topology_expressions(self, expressionMap)


Why make a method for convert_potential_styles instead of just using convert_topology_expressions. Regardless of whether this method remains, the import should be at the top of the module considering that it is an in-package import and not an optional external dependency.

After discussing with @daico007, all of this will get refactored so that the 3 engine writers are using similar methods. This method is analagous to what HOOMD and GROMACS Top writers are currently using locally, so that code will end up being extracted to this topology method.

gmso/core/topology.py

gmso/formats/lammpsdata.py

jaclark5 · 2023-06-15T15:46:03Z

gmso/formats/lammpsdata.py

+            ) * get_units(unit_style, "length")
+            type_list[i].parameters["epsilon"] = float(
+                pair.split()[1]
+            ) * get_units(unit_style, "energy")
        elif len(pair.split()) == 4:
            warnings.warn("Currently not reading in mixing rules")


Do you think this should be added then?

Unfortunately, there seems to be no direct way to get this from the lammpsdata file. It is usually set in the lammps simulation input file.
pair_style lj/cut rcut
pair_modify mix combining_rule
read_data data.lammps

So I think we're handcuffed here, I think this warning could be changed though to tell the user they need to manually specify the mixing rule as topology.combining_rule = "geometric" or "lorentz". The default in GMSO is lorentz.

This len(pair.split()) == 4 bit is actually referring to the pair_style lj/cut if a specific cutoff is given for the pair https://docs.lammps.org/pair_lj.html. GMSO does not keep track of rcut values as of now, as that is typically part of the input file, not the topology files.

I'm going to raise this as an issue, to see if someone would want to make a site specific or pair potential with these parameters for them.

jaclark5 · 2023-06-15T16:10:15Z

gmso/formats/lammpsdata.py

+        )
+    )
+    out_file.write("{:d} atoms\n".format(top.n_sites))
+    if atom_style in ["full", "molecular"]:


How will this handle hybrid atom_styles that add bonds and angles to styles such as DPD or ellipsoid (the former from personal use and the latter is in the example directory for lammps).
Also "bond", "angle", and "amoeba" have native bond and angle capability so the lists here need to be updated.

Also "bond", "angle", and "amoeba" have native bond and angle capability so the lists here need to be updated.

The only atom styles supported at this point are the ones we supported in the mbuild lammpswriter. So for now, we just have these from the doc string:

atom_style : str, optional, default='full' Defines the style of atoms to be saved in a LAMMPS data file. The following atom styles are currently supported: 'full', 'atomic', 'charge', 'molecular' see http://lammps.sandia.gov/doc/atom_style.html for more information on atom styles.

How will this handle hybrid atom_styles that add bonds and angles to styles such as DPD or ellipsoid (the former from personal use and the latter is in the example directory for lammps).

Hybrid is going to be interesting, to say the least. According to the lammps read_data docs, hybrid will look like:
atom-ID atom-type x y z sub-style1 sub-style2
So the way to handle that would be for something in the full topology:

if len(atom_style) > 0 and atom_style[0] == "hybrid": style_formatsList = get_styleformats(atom_style[1:], top, section_type) sectionStr = "" # or put default info here for style_format in style_formatsList: sectionStr+=style_format(top) out_file.write(sectionStr)

Something that you iterate through the topology for might look like:

if len(atom_style) > 0 and atom_style[0] == "hybrid": style_formatsList = get_styleformats(atom_style[1:], top, section_type) for site in top.sites: sectionStr = "" for style_format in style_formatsList: sectionStr+=style_format(site) out_file.write(style_format(site))

where atom_style isn't a string, but a list of styles you pass to the writer function.
i.e. atom_style = ["hybrid", "charge", "full"]

I think this is something that can be added as we add some of these specific styles into the writer.

jaclark5 · 2023-06-15T16:14:37Z

gmso/formats/lammpsdata.py

+def _write_site_data(out_file, top, atom_style, base_unyts, cfactorsDict):
+    """Write atomic positions and charges to LAMMPS file.."""
+    out_file.write("\nAtoms\n\n")
+    if atom_style == "atomic":


what about other styles (e.g. DPD)

Will be addressed in later PR's on a case by case basis.

jaclark5 · 2023-06-15T16:20:07Z

gmso/tests/test_conversions.py

+        expected_units_dim = dict(
+            zip(["c0", "c1", "c2", "c3", "c4", "c5"], ["energy"] * 6)
+        )
+        base_units = u.UnitSystem("atomic", "Å", "mp", "fs", "nK", "rad")


Will a user ever need to type the symbol, Å? if so, using this nonstandard character could be a concern.

The string: "angstrom" should work just as well here and provide equivalency. So we shouldn't run into the issue of being forced to use the Å to create the unyt.Unit.

…ort locations from conversions.py

…ing, added ljunitclass that will always be unitless

gmso/formats/lammpsdata.py

…on degrees regardless of unitsystem.

gmso/formats/lammpsdata.py

…nding to the units conversion

gmso/external/convert_parmed.py

gmso/tests/test_lammps.py

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daico007

I think this PR is ready for now. There several changes that would optimize/clean things up a bit, but those make more sense in follow up PRs per ongoing discussions.

CalCraven added 3 commits November 21, 2022 13:35

Initial commit for lammpswriter testing

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LAMMPS writer refactor for updated topology class

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Merge branch 'main' of https://github.com/mosdef-hub/gmso into 700-la…

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Order bonds, angles, and dihedrals consistently for lammpsdata files mosdef-hub/mbuild#1070

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Co-authored-by: Co Quach <[email protected]>

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Improvements to LAMMPS writer #320

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Increase unit support in Lammpswriter #458

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		for potStr in exp_unitsDict:
		potContainer = getattr(self, potStr + "_types")

	improper_type.parameters["chieq"]
	improper_type.parameters["phi_eq"]

Lammps Writer Changes For Updated Topology Class #701

Lammps Writer Changes For Updated Topology Class #701

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CalCraven commented Nov 29, 2022 •

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