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

@@ -12,4 +12,6 @@ Prof Charles A. Laughton (University of Nottingham)
 Contributors:
 #############
 
-Developers with accepted contributions should include their name below.
+Developers with accepted contributions should include their name below.
+
+Anders Johansson - The University of Oslo - Contributed code to the LAMMPS plugin.

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()