Merge pull request #2 from m-bone/PathSearchMethod

Path search method

Author: m-bone

AtomMapping.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+##############################################################################
+# Developed by: Matthew Bone
+# Last Updated: 16/06/2021
+# Updated by: Matthew Bone
+#
+# Contact Details:
+# Bristol Composites Institute (BCI)
+# Department of Aerospace Engineering - University of Bristol
+# Queen's Building - University Walk
+# Bristol, BS8 1TR
+# U.K.
+# Email - matthew.bone@bristol.ac.uk
+#
+# File Description:
+# This wrapper is used to call all the AutoMapper family of tools from a command
+# line. Linux users can consider adding the location of this repo to their PATH
+# so that this wrapper can be called from anywhere.
+##############################################################################
+
+import argparse
+from LammpsUnifiedCleaner import file_unifier
+from LammpsToMolecule import lammps_to_molecule
+from LammpsToMoleculePartial import lammps_to_molecule_partial
+from LammpsToLammpsPartial import lammps_to_lammps_partial
+from PathSearch import map_from_path
+
+# Init the parser
+parser = argparse.ArgumentParser(description='Run preprocessing tools for LAMMPS simulation using fix bond/react')
+
+# List of arguments for command line
+parser.add_argument('directory', metavar='directory', type=str, nargs=1, help='Directory of file(s), can be found in bash with . or $PWD')
+parser.add_argument('tool', metavar='tool', type=str, nargs=1, choices=['clean', 'molecule', 'molecule-partial', 'lammps-partial', 'map'], help='Name of tool to be used. Possible tools: clean, molecule, molecule-partial, lammps-partial, map')
+parser.add_argument('data_files', metavar='data_files', nargs='+', help='Name of file(s) to be acted on. If tool is "map" then this must be two files ordered as pre-bond post-bond. If "clean" this can be a list of files in any order')
+parser.add_argument('--coeff_file', metavar='coeff_file', nargs=1, help='Argument for the "clean" tool: a coefficients file to be cleaned')
+parser.add_argument('--save_name', metavar='save_name', nargs=1, help='Argument for "molecule", "molecule-partial" and "lammps-partial" tools: a prefix that is added to "molecule.data" for the file name of the new file')
+parser.add_argument('--ba', metavar='bonding_atoms', nargs=2, help='Argument for "molecule", "molecule-partial" and "lammps-partial" tools: atom IDs of the atoms that will be involved in creating a new bond, separated by white space. Order of atoms must be the same between molecule files, when mapping.')
+parser.add_argument('--ebt', metavar='elements_by_type', nargs='+', help='Argument for "molecule-partial", "lammps-partial" and "map" tools: series of elements symbols in the same order as the types specified in the data file and separated with a whitespace')
+parser.add_argument('--da', metavar='delete_atoms', nargs='+', help='An optional argument for "molecule", "molecule-partial" and "lammps-partial" tools: atom IDs of the atoms that will be deleted after the bond has formed, separated by white space')
+parser.add_argument('--debug', action='store_true', help='Argument for "map": prints debugging statements highlighting which parts of the path search determine a mapped atom pair')
+
+# Get arguments from parser
+args = parser.parse_args()
+# Take compulsory args out of list - other args done later
+tool = args.tool[0]
+directory = args.directory[0]
+
+
+# Throw errors if arguments are missing from certain tools
+if tool == 'clean' and (args.coeff_file is None):
+    parser.error('"clean" tool requries --coeff_file')
+
+if tool == 'molecule' and (args.save_name is None or args.ba is None):
+    parser.error('"molecule" tool requries --save_name and --ba (bonding atoms) arguments')
+
+if 'partial' in tool and (args.save_name is None or args.ba is None or args.ebt is None):
+    parser.error('"molecule-partial" or "lammps-partial" tools require --save_name, --ba (bonding atoms) and --ebt (elements by type) arguments')
+
+if tool != 'clean' and tool != 'map' and len(args.data_files) > 1:
+    parser.error('This tool can only take 1 data_file as input')
+
+if tool == 'map' and (len(args.data_files) != 2 or args.ebt is None):
+    parser.error('Map tool requires 2 data_files and --ebt (elements by type) arguments')
+
+# Unified data file clean
+if tool == "clean":  
+    print(f'DataFiles List: {args.data_files}')
+    file_unifier(directory, args.coeff_file[0], args.data_files)
+
+# Produce molecule data file
+elif tool == "molecule":
+    lammps_to_molecule(directory, args.data_files[0], args.save_name[0], args.ba, args.da)
+
+# Produce partial molecule data file
+elif tool == "molecule-partial":
+    lammps_to_molecule_partial(directory, args.data_files[0], args.save_name[0], args.ebt, args.ba, args.da)
+
+# Produce partial lammps data file
+elif tool == "lammps-partial":
+    lammps_to_lammps_partial(directory, args.data_files[0], args.save_name[0], args.ebt, args.ba, args.da)
+
+elif tool == 'map':
+    map_from_path(directory, args.data_files[0], args.data_files[1], args.ebt, args.debug)