From e9d5c8c28d5465dc73b50cbd46c3b7883d65da47 Mon Sep 17 00:00:00 2001
From: Adam Fekete <adam.fekete@kcl.ac.uk>
Date: Mon, 1 Aug 2016 17:46:37 +0100
Subject: [PATCH] styles, coeffs, bug fix (dataSuperContext)
---
parser/parser-lammps/LammpsLogParser.py | 62 ++++++++++++++++++-------
1 file changed, 46 insertions(+), 16 deletions(-)
diff --git a/parser/parser-lammps/LammpsLogParser.py b/parser/parser-lammps/LammpsLogParser.py
index 7d88cb1..547ea1d 100644
--- a/parser/parser-lammps/LammpsLogParser.py
+++ b/parser/parser-lammps/LammpsLogParser.py
@@ -207,8 +207,10 @@ class LammpsMainParser(MainHierarchicalParser):
adHoc=lambda parser: self.adHoc_bond_style(parser)),
SM(r"\s*(?P<x_lammps_dummy_text>angle_style)", forwardMatch=True,
adHoc=lambda parser: self.adHoc_angle_style(parser)),
- SM(r"\s*(?P<x_lammps_dummy_text>dihedral_style)", ),
- SM(r"\s*(?P<x_lammps_dummy_text>improper_style)", ),
+ SM(r"\s*(?P<x_lammps_dummy_text>dihedral_style)", forwardMatch=True,
+ adHoc=lambda parser: self.adHoc_dihedral_style(parser)),
+ SM(r"\s*(?P<x_lammps_dummy_text>improper_style)", forwardMatch=True,
+ adHoc=lambda parser: self.adHoc_improper_style(parser)),
# Atom definition
# There are 3 ways to define atoms in LAMMPS. Read them in from a data or restart file via the read_data
@@ -267,21 +269,21 @@ class LammpsMainParser(MainHierarchicalParser):
SM(r"\s*(?P<x_lammps_dummy_text>velocity)", ),
# settings_force_field_coefficients
- SM(r"\s*(?P<x_lammps_dummy_text>pair_coeff)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>pair_coeff)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_pair_coeff(parser)),
- SM(r"\s*(?P<x_lammps_dummy_text>bond_coeff)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>bond_coeff)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_bond_coeff(parser)),
- SM(r"\s*(?P<x_lammps_dummy_text>angle_coeff)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>angle_coeff)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_angle_coeff(parser)),
- SM(r"\s*(?P<x_lammps_dummy_text>dihedral_coeff)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>dihedral_coeff)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_dihedral_coeff(parser) ),
SM(r"\s*(?P<x_lammps_dummy_text>improper_coeff)", ),
SM(r"\s*(?P<x_lammps_dummy_text>kspace_style)", ),
SM(r"\s*(?P<x_lammps_dummy_text>kspace_modify)", ),
SM(r"\s*(?P<x_lammps_dummy_text>dielectric)", ),
- SM(r"\s*(?P<x_lammps_dummy_text>special_bonds)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>special_bonds)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_special_bonds(parser)),
- SM(r"\s*(?P<x_lammps_dummy_text>pair_modify)", forwardMatch=True,
+ SM(r"\s*(?P<x_lammps_dummy_text>pair_modify)", forwardMatch=True, repeats=True,
adHoc=lambda parser: self.adHoc_pair_modify(parser)),
SM(r"\s*(?P<x_lammps_dummy_text>pair_write)", ),
@@ -690,7 +692,7 @@ class LammpsMainParser(MainHierarchicalParser):
if bondFunctional:
p.addValue('interaction_kind', dihedralFunctional) # functional form of the interaction
- int_index_store = dihedral_dict[i][1]
+ int_index_store = self.dataSuperContext.dihedral_dict[i][1]
interaction_atom_to_atom_type_ref = []
if all(isinstance(elem, list) for elem in int_index_store) == False:
@@ -886,18 +888,18 @@ class LammpsMainParser(MainHierarchicalParser):
store = []
molecule_interaction_atoms = []
molecule_interaction_type = []
- for h in dihedralTypeList:
- for k in dihedralTypeList:
+ for h in self.dataSuperContext.dihedralTypeList:
+ for k in self.dataSuperContext.dihedralTypeList:
store = [ [x[1] - toMoleculeAtomIndex, x[2] - toMoleculeAtomIndex, x[3] - toMoleculeAtomIndex, x[4] - toMoleculeAtomIndex]
- for x in dihedral_interaction_atoms if x[0]==h and x[1] in moleculeTypeInfo[i][2] and x[2] in moleculeTypeInfo[i][2]
+ for x in self.dataSuperContext.dihedral_interaction_atoms if x[0]==h and x[1] in moleculeTypeInfo[i][2] and x[2] in moleculeTypeInfo[i][2]
and x[3] in moleculeTypeInfo[i][2] and x[4] in moleculeTypeInfo[i][2] ]
# store = [ [x[1], x[2], x[3]] for x in bond_interaction_atoms if x[0]==h and x[1] in moleculeTypeInfo[i][2] and x[2] in moleculeTypeInfo[i][2] ]
molecule_interaction_atoms.append(store)
- for l in dihedralTypeList:
- store1 = [ x[0] for x in dihedral_interaction_atoms if x[0]==l
+ for l in self.dataSuperContext.dihedralTypeList:
+ store1 = [ x[0] for x in self.dataSuperContext.dihedral_interaction_atoms if x[0]==l
and x[1] in moleculeTypeInfo[i][2] and x[2] in moleculeTypeInfo[i][2] and x[3] in moleculeTypeInfo[i][2] and x[4] in moleculeTypeInfo[i][2] ]
molecule_interaction_type.append(store1)
@@ -906,7 +908,7 @@ class LammpsMainParser(MainHierarchicalParser):
# print molecule_interaction_type, '#######'
# print molecule_interaction_atoms, '#######'
- for dihedral in dihedralTypeList:
+ for dihedral in self.dataSuperContext.dihedralTypeList:
if dihedral in molecule_interaction_type:
with o(p, 'section_molecule_interaction'):
@@ -919,7 +921,7 @@ class LammpsMainParser(MainHierarchicalParser):
p.addValue('molecule_interaction_kind', dihedralFunctional)
- int_index_store = dihedral_dict[dihedral-1][1]
+ int_index_store = self.dataSuperContext.dihedral_dict[dihedral-1][1]
molecule_interaction_atom_to_atom_type_ref = []
# print int_index_store, '######'
@@ -1297,6 +1299,16 @@ class LammpsMainParser(MainHierarchicalParser):
self.specs_filter.append(line)
return None
+ def adHoc_dihedral_style(self, parser):
+ line = parser.fIn.readline()
+ self.specs_filter.append(line)
+ return None
+ def adHoc_improper_style(self, parser):
+ line = parser.fIn.readline()
+ self.specs_filter.append(line)
+ return None
+
+
def adHoc_thermo_style(self, parser):
line = parser.fIn.readline()
self.specs_filter.append(line)
@@ -1612,6 +1624,24 @@ class LammpsMainParser(MainHierarchicalParser):
def readDihedrals(self, dihedralFunctional):
+ toMass = self.converter.ratioMass
+ toDistance = self.converter.ratioDistance
+ toTime = self.converter.ratioTime
+ toEnergy = self.converter.ratioEnergy
+ toVelocity = self.converter.ratioVelocity
+ toForce = self.converter.ratioForce
+ toTorque = self.converter.ratioTorque
+ toTemp = self.converter.ratioTemp
+ toPress = self.converter.ratioPress
+ toDVisc = self.converter.ratioDVisc
+ toCharge = self.converter.ratioCharge
+ toDipole = self.converter.ratioDipole
+ toEField = self.converter.ratioEField
+ toDensity = self.converter.ratioDensity
+
+ toRadians = 0.0174533 # multiply to convert deg to rad
+
+
dihedral_filt = self.dihedral_coeff
# dihedral_filt = [x for x in storeInput if x.startswith("dihedral_coeff")]
--
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