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Commit 576c7685 authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
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parse MD variables and tons of interatomic potential tables

parent 4c6be9df
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parser/parser-gulp/main.py
+ 116
− 26
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......@@ -225,6 +225,11 @@ class GulpContext(object):
data = self.data
ctable = data.pop('gulp_coordinate_table', None)
if ctable is None:
return # This is probably an MD simulation or something.
# I am sure we will get to suffer because of this relatively arbitrary
# return, but what can you do
symbols = ctable[:, 0]
gulp_labels = ctable[:, 1]
positions = ctable[:, 2:5].astype(float)
......@@ -411,6 +416,8 @@ def get_input_system_sm():
name='input-conf',
sections=['section_system'],
subMatchers=[
SM(r'\s*Formula\s*=\s*(?P<x_gulp_formula>\S+)',
name='formula'),
SM(r'\s*Dimensionality\s*=\s*(?P<x_gulp_pbc>\d+)',
name='pbc'),
SM(r'\s*Symmetry\s*:',
......@@ -537,6 +544,9 @@ def get_header_sm():
name='header',
endReStr=r'\s*Job Started',
subMatchers=[
SM(r'\*\s+.*?\s*\*$',
name='Julian and friends',
repeats=True),
SM(r'\*\*+'),
SM(r'\*\s*Version\s*=\s*(?P<program_version>\S+)',
name='version'),
......@@ -548,7 +558,54 @@ def get_header_sm():
repeats=True,
sections=['x_gulp_section_main_keyword'],
name='mainkw')
])
]),
SM(r'\*\s*(?P<x_gulp_title>.*?)\s*\*$',
name='title')
])
return m
def get_gulp_potential_species_pattern(nspecies):
tokens = []
for i in range(1, nspecies + 1):
tokens.append(r'(?P<x_gulp_forcefield_species_%d>\w+)\s*' % i)
tokens.append(r'(?P<x_gulp_forcefield_speciestype_%d>\S+)\s*' % i)
return ''.join(tokens)
def get_forcefield_table_sm(header, columnheaderpattern, tablepattern, name):
m = SM(header,#r'\s*(General interatomic|Intramolecular|Intermolecular) potentials :',
name=name,
subMatchers=[
SM(columnheaderpattern,#r'\s*Atom\s*Types\s*Potential\s*A*\s*B\s*C\s*D',
#Atom Types Potential A B C D Cutoffs(Ang)
# 1 2 Min Max
# -------------------------------------------------------------------------------
#O s La s Buckingham 0.570E+04 0.299 38.9 0.00 0.000 24.000
subMatchers=[
SM(r'----------+', name='potentials',
endReStr=r'----------+',
subMatchers=[
SM(tablepattern,#''.join(tokens),
#get_gulp_potential_species_pattern(2) +
#r'(?P<x_gulp_forcefield_species_1>\w+)\s*'
#r'(?P<x_gulp_forcefield_speciestype_1>\S+)\s*'
#r'(?P<x_gulp_forcefield_species_2>\S+)\s*'
#r'(?P<x_gulp_forcefield_speciestype_2>\S+)\s*'
# The SRGlue potential is badly written in the table and unparseable.
# Probably a bug. So just ignore it.
#r'(SRGlue|(?P<x_gulp_forcefield_potential_name>\b.{1,14}?)\s*'
#r'(?P<x_gulp_forcefield_parameter_a>\S+)\s*'
#r'(?P<x_gulp_forcefield_parameter_b>\S+)\s*'
#r'(?P<x_gulp_forcefield_parameter_c>\S+)\s*'
# r'(?P<x_gulp_forcefield_parameter_d>\S+)\s*'
# r'(?P<x_gulp_forcefield_cutoff_min>\S+\s*)'
# r'(?P<x_gulp_forcefield_cutoff_max>\S+))$',
name='table',
sections=['x_gulp_section_forcefield'],
repeats=True
),
]),
]),
])
return m
......@@ -567,33 +624,65 @@ def get_general_input_sm():
r'\s*(\S+)\s*(\S+)\s*\d+\s*\S+\s*(\S+)',
r'-------+')
]),
SM(r'\s*General interatomic potentials :',
name='potentials'),
SM(r'\s*Atom\s*Types\s*Potential\s*A*\s*B\s*C\s*D',
#Atom Types Potential A B C D Cutoffs(Ang)
# 1 2 Min Max
# -------------------------------------------------------------------------------
#O s La s Buckingham 0.570E+04 0.299 38.9 0.00 0.000 24.000
get_forcefield_table_sm(r'\s*(General interatomic|Intramolecular) potentials :',
r'\s*Atom\s*Types\s*Potential\s*A*\s*B\s*C\s*D',
get_gulp_potential_species_pattern(2) +
r'(SRGlue|'
r'(?P<x_gulp_forcefield_potential_name>\b.{1,14}?)\s*'
r'(?P<x_gulp_forcefield_parameter_a>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_b>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_c>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_d>\S+)\s*'
r'(?P<x_gulp_forcefield_cutoff_min>\S+\s*)'
r'(?P<x_gulp_forcefield_cutoff_max>\S+)$)',
name='interatomic'),
get_forcefield_table_sm(r'\s*(Intermolecular) potentials :', # Basically a copy of the one just above
r'\s*Atom\s*Types\s*Potential\s*A*\s*B\s*C\s*D',
get_gulp_potential_species_pattern(2) +
r'(SRGlue|(?P<x_gulp_forcefield_potential_name>\b.{1,14}?)\s*'
r'(?P<x_gulp_forcefield_parameter_a>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_b>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_c>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_d>\S+)\s*'
r'(?P<x_gulp_forcefield_cutoff_min>\S+\s*)'
r'(?P<x_gulp_forcefield_cutoff_max>\S+))$',
name='intermolecular'),
get_forcefield_table_sm(r'\s*General Three-body potentials :',
r'\s*Atom\s*Atom\s*Atom\s*Force Constants\s*Theta',
get_gulp_potential_species_pattern(3) +
r'(?P<x_gulp_forcefield_threebody_1>\S+)\s*'
r'(?P<x_gulp_forcefield_threebody_2>\S+)\s*'
r'(?P<x_gulp_forcefield_threebody_3>\S+)\s*'
r'(?P<x_gulp_forcefield_threebody_theta>\S+)\s*',
name='3-body'),
get_forcefield_table_sm(r'\s*General Four-body potentials :',
r'\s*Atom Types\s*Force cst\s*Sign\s*Phase\s*Phi0',
get_gulp_potential_species_pattern(4) +
r'(?P<x_gulp_forcefield_fourbody_force_constant>\S+)\s*'
r'(?P<x_gulp_forcefield_fourbody_sign>\S+)\s*'
r'(?P<x_gulp_forcefield_fourbody_phase>\S+)\s*'
r'(?P<x_gulp_forcefield_fourbody_phi0>\S+)\s*',
name='3-body'),
])
return m
def get_md_sm():
m = SM(r'\*\s*Molecular Dynamics',
name='md',
subMatchers=[
SM(r'\s*Molecular dynamics production :',
name='mdstep',
subMatchers=[
SM(r'----------+', name='potentials',
endReStr=r'----------+',
SM(r'\s*\*\*\s*Time :\s*(?P<x_gulp_md_time__ps>\S+)\s*ps :',
sections=['section_system', 'section_single_configuration_calculation'],
repeats=True,
subMatchers=[
SM(r'(?P<x_gulp_forcefield_species_1>\w+)\s*'
r'(?P<x_gulp_forcefield_speciestype_1>\S+)\s*'
r'(?P<x_gulp_forcefield_species_2>\S+)\s*'
r'(?P<x_gulp_forcefield_speciestype_2>\S+)\s*'
# The SRGlue potential is badly written in the table and unparseable.
# Probably a bug. So just ignore it.
r'(SRGlue|(?P<x_gulp_forcefield_potential_name>\b.{1,14}?)\s*'
r'(?P<x_gulp_forcefield_parameter_a>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_b>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_c>\S+)\s*'
r'(?P<x_gulp_forcefield_parameter_d>\S+)\s*\S+\s*\S+$)',
name='forcefield',
sections=['x_gulp_section_forcefield'],
repeats=True
),
]),
SM(r'\s*Kinetic energy\s*\(eV\)\s*=\s*(?P<x_gulp_md_kinetic_energy__eV>\S+)'),
SM(r'\s*Potential energy\s*\(eV\)\s*=\s*(?P<x_gulp_md_potential_energy__eV>\S+)'),
SM(r'\s*Total energy\s*\(eV\)\s*=\s*(?P<x_gulp_md_total_energy__eV>\S+)'),
SM(r'\s*Temperature\s*\(K\)\s*=\s*(?P<x_gulp_md_temperature__K>\S+)'),
SM(r'\s*Pressure\s*\(GPa\)\s*=\s*(?P<x_gulp_md_pressure__GPa>\S+)'),
])
])
])
return m
......@@ -610,6 +699,7 @@ infoFileDescription = SM(
get_general_input_sm(),
get_output_config_sm(),
get_optimise_sm(), # note British spelling
get_md_sm(),
SM(r'x^',
name='impossible') # 'Parse' the whole file
])
......
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