Issue with writing virtual sites via a lone pair #755
Description
For forcefields such as tip4p, we can read the forcefield, and virtual sites are treated just the same as a site. The virtual site is then assigned an atomtype just the same via the forcefield, and this is great. However, for our writers, these virtual sites need to be identified (and differentiated from coarse grained systems) in order to be handled specially. For example, Gromacs has a [ dummies ] section that needs to be written if a lone pair is included. Currently, since we have no special implementation for it, the top writer will throw an error.
We need to add some logic into the writers that can handle virtual sites, potentially some changes logic into the gmso.Site to assist with that, and make sure any readers that could have virtual sites would also properly bring that into a gmso.Topology.
import mbuild
from gmso.parameterization import apply
OPC_XML = 'OPC4_GMSO.xml'
opc_wat = mb.load('OPC.mol2')
N_COMPOUNDS=100
X_LENGTH = 5.15
startingBox=mb.fill_box(compound=opc_wat ,n_compounds=2,box=[5,5,5])
top = startingBox.to_gmso()
gmso_ff = gmso.ForceField('OPC4_GMSO.xml')
parameterized_top = apply(top, gmso_ff, identify_connections=True, remove_untyped=True)
parameterized_top.save('init_gmso.gro', overwrite=True)
parameterized_top.save('init_gmso.top', overwrite=True)Errors as:
UnexpectedCharacters Traceback (most recent call last)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lexer.py:486, in ContextualLexer.lex(self, lexer_state, parser_state)
485 last_token = lexer_state.last_token # Save last_token. Calling root_lexer.next_token will change this to the wrong token
--> 486 token = self.root_lexer.next_token(lexer_state, parser_state)
487 raise UnexpectedToken(token, e.allowed, state=parser_state, token_history=[last_token], terminals_by_name=self.root_lexer.terminals_by_name)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lexer.py:398, in TraditionalLexer.next_token(self, lex_state, parser_state)
397 allowed = {"<END-OF-FILE>"}
--> 398 raise UnexpectedCharacters(lex_state.text, line_ctr.char_pos, line_ctr.line, line_ctr.column,
399 allowed=allowed, token_history=lex_state.last_token and [lex_state.last_token],
400 state=parser_state, terminals_by_name=self.terminals_by_name)
402 value, type_ = res
UnexpectedCharacters: No terminal matches '_' in the current parser context, at line 1 col 2
[_LP;X1][O;X3](H)(H)
^
Expected one of:
* BANG
* SEMICOLON
* LABEL
* "R"
* "$("
* COMMA
* LPAR
* X
* RPAR
* R
* LSQB
* RSQB
* NUM
* STAR
* AMPERSAND
* SYMBOL
* HASH
Previous tokens: Token('LSQB', '[')
During handling of the above exception, another exception occurred:
UnexpectedCharacters Traceback (most recent call last)
Cell In[23], line 46
44 print(f"Found {len(parameterized_top.atom_types)} in topology")
45 parameterized_top.save('init_gmso.gro', overwrite=True)
---> 46 parameterized_top.save('init_gmso.top', overwrite=True)
File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gmso/gmso/core/topology.py:1490, in Topology.save(self, filename, overwrite, **kwargs)
1487 from gmso.formats import SaversRegistry
1489 saver = SaversRegistry.get_callable(filename.suffix)
-> 1490 saver(self, filename, **kwargs)
File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gmso/gmso/formats/top.py:102, in write_top(top, filename, top_vars)
81 out_file.write(
82 "[ atomtypes ]\n"
83 "; name\t"
(...)
89 "epsilon\n"
90 )
92 for atom_type in top.atom_types(PotentialFilters.UNIQUE_NAME_CLASS):
93 out_file.write(
94 "{0:12s}"
95 "{1:4s}"
96 "{2:12.5f}"
97 "{3:12.5f}\t"
98 "{4:4s}"
99 "{5:12.5f}"
100 "{6:12.5f}\n".format(
101 atom_type.name,
--> 102 str(_lookup_atomic_number(atom_type)),
103 atom_type.mass.in_units(u.amu).value,
104 atom_type.charge.in_units(u.elementary_charge).value,
105 "A",
106 atom_type.parameters["sigma"].in_units(u.nanometer).value,
107 atom_type.parameters["epsilon"]
108 .in_units(u.Unit("kJ/mol"))
109 .value,
110 )
111 )
113 # Define unique molecule by name only
114 unique_molecules = _get_unique_molecules(top)
File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gmso/gmso/formats/top.py:381, in _lookup_atomic_number(atom_type)
379 """Look up an atomic_number based on atom type information, 0 if non-element type."""
380 try:
--> 381 element = element_by_atom_type(atom_type)
382 return element.atomic_number
383 except GMSOError:
File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gmso/gmso/core/element.py:313, in element_by_atom_type(atom_type, verbose)
311 matched_element = element_by_symbol(atom_type.name, verbose=verbose)
312 if matched_element is None and atom_type.definition:
--> 313 matched_element = element_by_smarts_string(
314 atom_type.definition, verbose=verbose
315 )
317 if matched_element is None:
318 raise GMSOError(
319 f"Failed to find an element from atom type"
320 "{atom_type} with "
(...)
323 "definition: {atom_type.definition}"
324 )
File ~/Dropbox/Mac/Documents/Vanderbilt/Research/MoSDeF/gmso/gmso/core/element.py:260, in element_by_smarts_string(smarts_string, verbose)
256 SMARTS = foyer.smarts.SMARTS
258 PARSER = SMARTS()
--> 260 symbols = PARSER.parse(smarts_string).iter_subtrees_topdown()
262 first_symbol = None
263 for symbol in symbols:
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/foyer/smarts.py:86, in SMARTS.parse(self, smarts_string)
84 def parse(self, smarts_string):
85 """Convert SMARTS string to parsed grammar object."""
---> 86 return self.PARSER.parse(smarts_string)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lark.py:581, in Lark.parse(self, text, start, on_error)
563 def parse(self, text, start=None, on_error=None):
564 """Parse the given text, according to the options provided.
565
566 Parameters:
(...)
579
580 """
--> 581 return self.parser.parse(text, start=start, on_error=on_error)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/parser_frontends.py:106, in ParsingFrontend.parse(self, text, start, on_error)
104 stream = text if self.skip_lexer else LexerThread(self.lexer, text)
105 kw = {} if on_error is None else {'on_error': on_error}
--> 106 return self.parser.parse(stream, chosen_start, **kw)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/parsers/lalr_parser.py:41, in LALR_Parser.parse(self, lexer, start, on_error)
39 def parse(self, lexer, start, on_error=None):
40 try:
---> 41 return self.parser.parse(lexer, start)
42 except UnexpectedInput as e:
43 if on_error is None:
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/parsers/lalr_parser.py:171, in _Parser.parse(self, lexer, start, value_stack, state_stack, start_interactive)
169 if start_interactive:
170 return InteractiveParser(self, parser_state, parser_state.lexer)
--> 171 return self.parse_from_state(parser_state)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/parsers/lalr_parser.py:188, in _Parser.parse_from_state(self, state)
186 except NameError:
187 pass
--> 188 raise e
189 except Exception as e:
190 if self.debug:
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/parsers/lalr_parser.py:178, in _Parser.parse_from_state(self, state)
176 try:
177 token = None
--> 178 for token in state.lexer.lex(state):
179 state.feed_token(token)
181 end_token = Token.new_borrow_pos('$END', '', token) if token else Token('$END', '', 0, 1, 1)
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lexer.py:489, in ContextualLexer.lex(self, lexer_state, parser_state)
487 raise UnexpectedToken(token, e.allowed, state=parser_state, token_history=[last_token], terminals_by_name=self.root_lexer.terminals_by_name)
488 except UnexpectedCharacters:
--> 489 raise e
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lexer.py:478, in ContextualLexer.lex(self, lexer_state, parser_state)
476 while True:
477 lexer = self.lexers[parser_state.position]
--> 478 yield lexer.next_token(lexer_state, parser_state)
479 except EOFError:
480 pass
File ~/miniconda3/envs/gmso-dev/lib/python3.11/site-packages/lark/lexer.py:398, in TraditionalLexer.next_token(self, lex_state, parser_state)
396 if not allowed:
397 allowed = {"<END-OF-FILE>"}
--> 398 raise UnexpectedCharacters(lex_state.text, line_ctr.char_pos, line_ctr.line, line_ctr.column,
399 allowed=allowed, token_history=lex_state.last_token and [lex_state.last_token],
400 state=parser_state, terminals_by_name=self.terminals_by_name)
402 value, type_ = res
404 if type_ not in self.ignore_types:
UnexpectedCharacters: No terminal matches '_' in the current parser context, at line 1 col 2
[_LP;X1][O;X3](H)(H)
^
Expected one of:
* BANG
* R
* LABEL
* "R"
* STAR
* "$("
* X
* SYMBOL
* HASH
Previous tokens: Token('LSQB', '[')