From 6f7bd78ea2352a406e7627c229a47a365b25b60b Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Wed, 29 Nov 2017 01:02:04 -0500
Subject: [PATCH] Fixes issue #701
PyLammps now supports thermo_style entries such as c_msd[4]
---
python/lammps.py | 26 +++++++++++++++++++++++++-
1 file changed, 25 insertions(+), 1 deletion(-)
diff --git a/python/lammps.py b/python/lammps.py
index 944eaeabf5..ee6e461d33 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -603,6 +603,30 @@ class Atom2D(Atom):
self.lmp.eval("fy[%d]" % self.index))
+class variable_set:
+ def __init__(self, name, variable_dict):
+ self._name = name
+ array_pattern = re.compile(r"(?P<arr>.+)\[(?P<index>[0-9]+)\]")
+
+ for key, value in variable_dict.items():
+ m = array_pattern.match(key)
+ if m:
+ g = m.groupdict()
+ varname = g['arr']
+ idx = int(g['index'])
+ if varname not in self.__dict__:
+ self.__dict__[varname] = {}
+ self.__dict__[varname][idx] = value
+ else:
+ self.__dict__[key] = value
+
+ def __str__(self):
+ return "{}({})".format(self._name, ','.join(["{}={}".format(k, self.__dict__[k]) for k in self.__dict__.keys() if not k.startswith('_')]))
+
+ def __repr__(self):
+ return self.__str__()
+
+
def get_thermo_data(output):
""" traverse output of runs and extract thermo data columns """
if isinstance(output, str):
@@ -630,7 +654,7 @@ def get_thermo_data(output):
elif line.startswith("Loop time of "):
in_run = False
columns = None
- thermo_data = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
+ thermo_data = variable_set('ThermoData', current_run)
r = {'thermo' : thermo_data }
runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
elif in_run and len(columns) > 0:
--
GitLab