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Entries missing from input_parameters #104

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Entries missing from input_parameters #104

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31 changes: 29 additions & 2 deletions atomisticparsers/gromacs/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
# limitations under the License.
#
import os

import numpy as np
import logging
import re
Expand Down Expand Up @@ -49,6 +50,7 @@
GeometryOptimizationMethod,
GeometryOptimizationResults,
)

from .metainfo.gromacs import (
x_gromacs_section_control_parameters,
x_gromacs_section_input_output_files,
Expand All @@ -66,7 +68,7 @@
def to_float(string):
try:
value = float(string)
except ValueError:
except (ValueError, TypeError):
value = None
return value

Expand Down Expand Up @@ -199,22 +201,31 @@ def init_quantities(self):
def str_to_input_parameters(val_in):
re_array = re.compile(r"\s*([\w\-]+)\[[\d ]+\]\s*=\s*\{*(.+)")
re_scalar = re.compile(r"\s*([\w\-]+)\s*[=:]\s*(.+)")
re_comment = re.compile(r"^\S+?(?=[\s;])")
parameters = dict()
val = [line.strip() for line in val_in.splitlines()]
for val_n in val:
val_scalar = re_scalar.match(val_n)
if val_scalar:
parameters[val_scalar.group(1)] = val_scalar.group(2)
val_scalar_group2 = val_scalar.group(2)
inline_comment = re_comment.match(val_scalar_group2)
if inline_comment:
parameters[val_scalar.group(1)] = inline_comment.group(1)
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try this:

parameters[val_scalar.group(1)] = inline_comment.group()

else:
parameters[val_scalar.group(1)] = val_scalar.group(2)
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this is not functional, but just to avoid calling the group() twice: parameters[val_scalar.group(1)] = val_scalar_group2

continue
val_array = re_array.match(val_n)
if val_array:
# print("val_array", val_array)
parameters.setdefault(val_array.group(1), [])
value = [
to_float(v) for v in val_array.group(2).rstrip("}").split(",")
]
parameters[val_array.group(1)].append(
value[0] if len(value) == 1 else value
)
# print("\nTEST:", parameters)

return parameters

self._quantities = [
Expand Down Expand Up @@ -1065,6 +1076,7 @@ def parse_method(self):
self.parse_interactions(interactions, sec_model)

input_parameters = self.input_parameters
# print("input_parameters", input_parameters)
sec_force_calculations = ForceCalculations()
sec_force_field.force_calculations = sec_force_calculations
sec_neighbor_searching = NeighborSearching()
Expand All @@ -1075,6 +1087,12 @@ def parse_method(self):
int(nstlist) if nstlist else None
)
rlist = to_float(input_parameters.get("rlist", None))
# rlist = (
# to_float(value)
# if (value := input_parameters.get("rlist")) is not None
# else None
# )

sec_neighbor_searching.neighbor_update_cutoff = (
rlist * ureg.nanometer if rlist else None
)
Expand Down Expand Up @@ -1197,6 +1215,12 @@ def get_barostat_parameters(self):
)
return barostat_parameters

# TODO: implement
def get_umbrella_sampling_parameters(self):
umbrella_sampling_parameters = {}
umbrella_sampling = self.input_parameters.get("pull", "")
# print("test", umbrella_sampling)

def get_free_energy_calculation_parameters(self):
free_energy_parameters = {}
free_energy = self.input_parameters.get("free-energy", "")
Expand Down Expand Up @@ -1241,7 +1265,9 @@ def get_free_energy_calculation_parameters(self):

atoms_info = self.traj_parser._results["atoms_info"]
atoms_moltypes = np.array(atoms_info["moltypes"])
# print("atoms_moltypes", atoms_moltypes)
couple_moltype = self.input_parameters.get("couple-moltype", "").split()
print("couple_moltype", self.input_parameters.get("couple-moltype", ""))
n_atoms = len(atoms_moltypes)
indices = []
if len(couple_moltype) == 1 and couple_moltype[0].lower() == "system":
Expand Down Expand Up @@ -1507,6 +1533,7 @@ def parse_input(self):
sec_run.x_gromacs_section_control_parameters = sec_control_parameters
input_parameters = self.input_parameters
input_parameters.update(self.info.get("header", {}))
# print("input_parameters: ", input_parameters)
for key, val in input_parameters.items():
key = (
"x_gromacs_inout_control_%s"
Expand Down
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