From d0cf344f0a71297a09e6bd589bd3dc727a159d98 Mon Sep 17 00:00:00 2001
From: James Graham <james@ramos.ecs.soton.ac.uk>
Date: Mon, 9 Oct 2017 13:02:37 +0100
Subject: [PATCH] Give warning when no box size set - resolves #4
---
lib/coordreaders.py | 2 +-
pdb2lmp.py | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/lib/coordreaders.py b/lib/coordreaders.py
index ae968b4..5ef61e2 100644
--- a/lib/coordreaders.py
+++ b/lib/coordreaders.py
@@ -9,7 +9,7 @@ class CoordReader:
def __init__(self):
self.atoms = []
self.molecules = []
- self.cell = []
+ self.cell = [0, 0, 0]
@property
def natoms(self):
diff --git a/pdb2lmp.py b/pdb2lmp.py
index 76a748c..a2b3844 100755
--- a/pdb2lmp.py
+++ b/pdb2lmp.py
@@ -167,6 +167,9 @@ class PDB2LMP:
print("{0:8d} improper types".format(self.nimpropers.types), file=data)
print(file=data)
cell = [val / 2 for val in self.coords.cell]
+ if cell == [0, 0, 0]:
+ print("WARNING: The simulation box/unit cell size is zero.")
+ print(" If this is not intentional, please check your input files.")
print("{0:8.3f} {1:8.3f} xlo xhi".format(-cell[0], cell[0]), file=data)
print("{0:8.3f} {1:8.3f} ylo yhi".format(-cell[1], cell[1]), file=data)
print("{0:8.3f} {1:8.3f} zlo zhi".format(-cell[2], cell[2]), file=data)
--
GitLab