From e96bce2db2e9d38e6a071f3ff1f811f1594f5316 Mon Sep 17 00:00:00 2001
From: James Gebbie-Rayet <james.gebbie@stfc.ac.uk>
Date: Mon, 23 Apr 2018 15:38:30 +0100
Subject: [PATCH] Issue #86

Fix for files provided in LAMMPS input files when they appear as part of
more complex input parameters. Bug and example code provided by Anders
Johansson which was worked into the original LAMMPS plugin.
---
 AUTHORS.rst            |  4 +++-
 longbow/apps/lammps.py | 37 +++++++++++++++++++++++--------------
 2 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/AUTHORS.rst b/AUTHORS.rst
index 4d2ac73..a65f8bd 100644
--- a/AUTHORS.rst
+++ b/AUTHORS.rst
@@ -12,4 +12,6 @@ Prof Charles A. Laughton (University of Nottingham)
 Contributors:
 #############
 
-Developers with accepted contributions should include their name below.
\ No newline at end of file
+Developers with accepted contributions should include their name below.
+
+Anders Johansson - The University of Oslo - Contributed code to the LAMMPS plugin.
\ No newline at end of file
diff --git a/longbow/apps/lammps.py b/longbow/apps/lammps.py
index e20e40d..953b709 100644
--- a/longbow/apps/lammps.py
+++ b/longbow/apps/lammps.py
@@ -93,8 +93,15 @@ def file_parser(filename, path, files, substitutions=None):
 
         files.append(addfile)
 
-        # Create a dict for any variable substitutions and define keywords.
-        keywords = ['read_data', 'read_restart', 'read_dump', 'include']
+        # List of LAMMPS output commands, these will be used to mask against
+        # keywords that shouldn't used to detect files for transfer.
+        output_commands = ["print", "dump", "log", "restart", "write_dump",
+                           "write_restart", "pair_write", "write_coeff",
+                           "ave/time", "ave/chunk", "bond_write",
+                           "ave/histo/weight", "saed/vtk", "ave/histo",
+                           "write_data"]
+
+        # Setup variables to be substituted.
         variables = {} if not substitutions else substitutions
 
         fil = _fileopen(path, addfile)
@@ -114,28 +121,30 @@ def file_parser(filename, path, files, substitutions=None):
 
             else:
 
-                words = line[:len(line)].split()
+                words = line.split()
 
             if len(words) > 0:
 
                 _internalsubstitutions(variables, words)
 
-                # If this line is reading in an input file.
-                if words[0].lower() in keywords:
+                # Does this line contain an output command?
+                if set(words).isdisjoint(output_commands):
 
-                    newfile = words[-1]
+                    for word in words:
 
-                    # Do variable substitutons
-                    newfile = _variablesubstitutions(newfile, variables)
+                        if os.path.isfile(os.path.join(path, word)):
 
-                    # Deduce the location of newfile.
-                    newpath = path
+                            newfile = word
 
-                    # Check newfile.
-                    newfile = _newfilechecks(addfile, newfile, path)
+                            # Do variable substitutons
+                            newfile = _variablesubstitutions(newfile,
+                                                             variables)
 
-                    # Recursive function.
-                    file_parser(newfile, newpath, files, substitutions)
+                            # Check newfile.
+                            newfile = _newfilechecks(addfile, newfile, path)
+
+                            # Recursive function.
+                            file_parser(newfile, path, files, substitutions)
 
         fil.close()