From 576c7685835ea05261d87fe117b7b41443e80e35 Mon Sep 17 00:00:00 2001
From: Ask Hjorth Larsen <asklarsen@gmail.com>
Date: Mon, 10 Oct 2016 15:44:35 +0200
Subject: [PATCH] parse MD variables and tons of interatomic potential tables
---
parser/parser-gulp/main.py | 142 ++++++++++++++++++++++++++++++-------
1 file changed, 116 insertions(+), 26 deletions(-)
diff --git a/parser/parser-gulp/main.py b/parser/parser-gulp/main.py
index cdf3162..9f0ee54 100644
--- a/parser/parser-gulp/main.py
+++ b/parser/parser-gulp/main.py
@@ -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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