git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9180 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
326
tools/moltemplate/src/lttree_postprocess.py
Executable file
326
tools/moltemplate/src/lttree_postprocess.py
Executable file
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#!/usr/bin/env python
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"""
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lttree_postprocess.py
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This is a stand-alone python script which checks the files created by
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lttree.py to insure that the standard instance-variables ($variables)
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have all been defined. This script performs a task which is very similar
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to the task performed by lttree_check.py. This script attempts to detect
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mistakes in the names of $atom, $bond, $angle, $dihedral, $improper, & $mol
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variables.
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"""
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import sys
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from lttree_styles import *
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from ttree_lex import ExtractCatName
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g_program_name = 'lttree_postprocess.py'
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atom_style = 'full'
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ttree_assignments_fname = 'ttree_assignments.txt'
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defined_mols = set([])
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defined_atoms = set([])
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defined_bonds = set([])
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defined_angles = set([])
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defined_dihedrals = set([])
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defined_impropers = set([])
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g_no_check_msg = \
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'(To override this error, run moltemplate using the \"-nocheck\" argument.)\n'
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if len(sys.argv) > 1:
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for i in range(0,len(sys.argv)):
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if ((sys.argv[i].lower() == '-atomstyle') or
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(sys.argv[i].lower() == '-atom-style') or
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(sys.argv[i].lower() == '-atom_style')):
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if i+1 >= len(sys.argv):
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raise InputError('Error('+g_program_name+'): The '+sys.argv[i]+' flag should be followed by a LAMMPS\n'
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' atom_style name (or single quoted string containing a space-separated\n'
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' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
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atom_style = sys.argv[i+1]
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elif ((sys.argv[i].lower() == '-ttreeassignments') or
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(sys.argv[i].lower() == '-ttree-assignments') or
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(sys.argv[i].lower() == '-ttree_assignments')):
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if i+1 >= len(sys.argv):
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raise InputError('Error('+g_program_name+'): The '+sys.argv[i]+' flag should be followed by \n'
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' a file containing the variable bindings created by ttree/moltemplate.\n')
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ttree_assignments_fname = sys.argv[i+1]
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else:
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pass # ignore other arguments (they are intended for lttree.py)
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atom_column_names = AtomStyle2ColNames(atom_style)
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i_atomid = 0
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i_molid = -1
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for i in range(0,len(atom_column_names)):
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if atom_column_names[i].lower() == 'atom-id':
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i_atomid = i
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elif atom_column_names[i].lower() == 'molecule-id':
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i_molid = i
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i_max_column = max(i_atomid, i_molid)
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# The following variables are defined in "lttree_styles.py"
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#data_atoms="Data Atoms"
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#data_masses="Data Masses"
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#data_velocities="Data Velocities"
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#data_bonds="Data Bonds"
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#data_angles="Data Angles"
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#data_dihedrals="Data Dihedrals"
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#data_impropers="Data Impropers"
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g_program_name = 'lttree_postprocess.py'
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g_version_str = '0.4'
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g_date_str = '2012-12-12'
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sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
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try:
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# ------------ defined_atoms ------------
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try:
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f = open(data_atoms+'.template', 'r')
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except:
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raise InputError('Error('+g_program_name+'): Unable to open file\n'+
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'\"'+data_atoms+'.template\"\n'
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' for reading. (Do your files lack a \"'+data_atoms+'\" section?)\n'
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+g_no_check_msg+'\n')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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else:
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line = line_orig.rstrip('\n')
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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elif len(tokens) <= i_max_column:
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raise InputError('Error('+g_program_name+'): The following line from\n'
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' "\"'+data_atoms+'.template\" has bad format:\n\n'
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+line_orig+'\n'
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' This my probably an internal error. (Feel free to contact the developer.)\n'
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+g_no_check_msg+'\n')
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else:
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defined_atoms.add(tokens[i_atomid])
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if i_molid != -1:
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defined_mols.add(tokens[i_molid])
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f.close()
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# ------------ defined_bonds ------------
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try:
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f = open(data_bonds+'.template', 'r')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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else:
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line = line_orig.rstrip('\n')
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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elif len(tokens) < 4:
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raise InputError('Error('+g_program_name+'): The following line from\n'
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' "\"'+data_bonds+'.template\" has bad format:\n\n'
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+line_orig+'\n'
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' This my probably an internal error. (Feel free to contact the developer.)\n'
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+g_no_check_msg+'\n')
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else:
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defined_bonds.add(tokens[0])
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f.close()
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except:
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pass # Defining bonds (stored in the data_bonds file) is optional
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# ------------ defined_angles ------------
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try:
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f = open(data_angles+'.template', 'r')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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else:
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line = line_orig.rstrip('\n')
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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elif len(tokens) < 5:
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raise InputError('Error('+g_program_name+'): The following line from\n'
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' "\"'+data_angles+'.template\" has bad format:\n\n'
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+line_orig+'\n'
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' This my probably an internal error. (Feel free to contact the developer.)\n'
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+g_no_check_msg+'\n')
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else:
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defined_angles.add(tokens[0])
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f.close()
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except:
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pass # Defining angles (stored in the data_angles file) is optional
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# ------------ defined_dihedrals ------------
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try:
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f = open(data_dihedrals+'.template', 'r')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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else:
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line = line_orig.rstrip('\n')
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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elif len(tokens) < 6:
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raise InputError('Error('+g_program_name+'): The following line from\n'
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' "\"'+data_dihedrals+'.template\" has bad format:\n\n'
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+line_orig+'\n'
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' This my probably an internal error. (Feel free to contact the developer.)\n'
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+g_no_check_msg+'\n')
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else:
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defined_dihedrals.add(tokens[0])
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f.close()
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except:
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pass #Defining dihedrals (stored in the data_dihedrals file) is optional
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# ------------ defined_impropers ------------
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try:
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f = open(data_impropers+'.template', 'r')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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else:
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line = line_orig.rstrip('\n')
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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elif len(tokens) < 6:
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raise InputError('Error('+g_program_name+'): The following line from\n'
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' "\"'+data_impropers+'.template\" has bad format:\n\n'
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+line_orig+'\n'
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' This my probably an internal error. (Feel free to contact the developer.)\n'
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+g_no_check_msg+'\n')
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else:
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defined_impropers.add(tokens[0])
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f.close()
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except:
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pass #Defining impropers (stored in the data_impropers file) is optional
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# ---- Check ttree_assignments to make sure variables are defined ----
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try:
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f = open(ttree_assignments_fname, 'r')
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except:
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raise InputError('Error('+g_program_name+'): Unable to open file\n'+
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'\"'+ttree_assignments_fname+'\"\n'
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' for reading. (Do your files lack a \"'+data_atoms+'\" section?)\n'
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+g_no_check_msg+'\n')
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for line_orig in f:
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ic = line_orig.find('#')
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if ic != -1:
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line = line_orig[:ic]
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usage_location_str = 'near ' + line_orig[ic+1:]
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else:
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line = line_orig.rstrip('\n')
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usage_location_str = ''
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tokens = line.strip().split()
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if len(tokens) == 0:
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pass
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if len(tokens) > 0:
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# This file contains a list of variables of the form:
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#
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# @/atom:MoleculeType1:C 1
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# @/atom:MoleculeType2:N 2
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# :
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# $/atom:molecule1141:C2 13578
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# $/atom:molecule1142:N1 13579
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#
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# We only care about instance variables (which use the '$' prefix)
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# Lines in this file with a different prefix ('@') which don't
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# contain '$' should be ignored.
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i_prefix = tokens[0].find('$')
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if i_prefix != -1:
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descr_str = tokens[0][i_prefix+1:]
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cat_name = ExtractCatName(descr_str)
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if ((cat_name == 'atom') and
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(tokens[0] not in defined_atoms)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
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' Reference to undefined $atom:\n\n'
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that atom belongs to a molecule (or other subunit), make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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elif ((cat_name == 'bond') and
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(tokens[0] not in defined_bonds)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
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' Reference to undefined $bond:\n\n'
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that bond belongs to a molecule (or other subunit), make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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elif ((cat_name == 'angle') and
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(tokens[0] not in defined_angles)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
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' Reference to undefined $angle:\n\n'+
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that angle belongs to a molecule (or other subunit), make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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elif ((cat_name == 'dihedral') and
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(tokens[0] not in defined_dihedrals)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n\n'+
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' Reference to undefined $dihedral:\n\n'
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that dihedral belongs to a molecule (or other subunit), make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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elif ((cat_name == 'improper') and
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(tokens[0] not in defined_impropers)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
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' Reference to undefined $improper:\n\n'
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that improper belongs to a molecule (or other subunit), make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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elif ((cat_name == 'mol') and
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(tokens[0] not in defined_mols)):
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raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
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' Reference to undefined $mol (molecule-ID) variable:\n\n'
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' '+tokens[0]+' (<--full name)\n\n'+
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' (If that molecule is part of a larger molecule, then make sure that\n'+
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' you specified the correct path which leads to it (using / and ..))\n\n'+
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g_no_check_msg)
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f.close()
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sys.stderr.write(g_program_name+': -- No errors detected. --\n')
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exit(0)
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except (ValueError, InputError) as err:
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sys.stderr.write('\n'+str(err)+'\n')
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sys.exit(1)
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