Talk:Mod:Hunt Research Group/Dcreate EEF coms
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This code generates a collection of Gaussian input .com files with fields of varying strengths
and directions based on a provided .com file.
The user can specify the fields that use the keyword format Field=M+\-N where M describes a multipole (e.g x, y, z, xx, xy, xyz, etc) and N describes the magnitude of the field where N*0.0001 is the field strength in atomic units (au).
Running Dcreate_EEF_coms.py
To use, first create a .com file for the molecule you want to apply fields to. To run this script:
python generate_EEF_coms.py template_com_file
Please note no file extensions
"""
import os
import sys
import re
# User-editable parameters
FIELD_DIRECTIONS = ["x","y"]
FIELD_STRENGTHS = [200,250]
FIELD_SIGNS = [1, -1]
def update_chk_line(lines, suffix):
"""
Modify %chk= line to have the updated file name.
Parameters
----------
lines : list
list of every string in the file
suffix : string
string containing the suffix to be appended to the template file name
Returns
-------
new_lines : list
list of every string in the file with the updated .chk file name.
"""
new_lines = []
chk_updated = False
# Goes through line by line looking for a %chk line, and updates with
# the new file name if found.
for line in lines:
if line.strip().lower().startswith("%chk="):
chk_base = line.strip().split("=")[1]
base_name, ext = os.path.splitext(chk_base)
new_chk = f"%chk={base_name}_{suffix}.chk\n"
new_lines.append(new_chk)
chk_updated = True
else:
new_lines.append(line)
# If no %chk line found, add one at top
if not chk_updated:
new_lines.insert(0, f"%chk=job_{suffix}.chk\n")
return new_lines
def update_field_line(lines, field_spec):
"""
Adds the Field= keyword to the .com file if not present, or replaces it
with the updated field if present.
Parameters
----------
lines : list
list of every string in the file.
field_spec : str
argument for the field keyword e.g 'x+50'.
Returns
-------
new_lines : list
list of every string in the file with the updated/added field keyword.
"""
new_lines = []
field_inserted = False
for line in lines:
# If Field= already present, replace it
if "field=" in line:
line = re.sub(r"field=[^\s]+", f"field={field_spec}", line)
field_inserted = True
new_lines.append(line)
elif not field_inserted and line.strip() == "":
# If Field= isn't present in the methodd, insert Field= right before
# first blank after method section
if any("#" in l for l in new_lines):
new_lines.append(f" field={field_spec}\n")
field_inserted = True
new_lines.append(line)
else:
new_lines.append(line)
if not field_inserted:
print("Warning: Keyword 'Field="+field_spec+"' failed to be added to corrosponding file.",
"Please check .com files are correctly formatted")
return new_lines
def generate_field_files(filename):
"""
Generates a new .com file for each combination of field strength and direction.
The resulting files have the following naming format:
templatefilename_directionstrength.com
e.g if the template filename is "emim_opt.com", then the files for field=+\-50 are
emim_opt_x50.com
emim_opt_x-50.com
Parameters
----------
filename : str
Name of template .com file excluding extension.
"""
filename_ext = filename + ".com"
if not os.path.exists(filename_ext):
print(f"Error: File '{filename}' not found.")
sys.exit(1)
with open(filename_ext, "r") as f:
lines = f.readlines()
base_name = filename
ext=".com"
for direction in FIELD_DIRECTIONS:
for strength in FIELD_STRENGTHS:
for sign in FIELD_SIGNS:
field_value = sign * strength
if sign >= 0:
field_spec = f"{direction}+{strength}"
else:
field_spec = f"{direction}-{strength}"
suffix = f"{direction}{field_value}"
new_lines = update_chk_line(lines, suffix)
new_lines = update_field_line(new_lines, field_spec)
new_filename = f"{base_name}_{suffix}{ext}"
with open(new_filename, "w") as f:
f.writelines(new_lines)
print(f"Created: {new_filename}")
if __name__ == "__main__":
if len(sys.argv) != 2:
print("Usage: python generate_EEF_coms.py template_com_file")
sys.exit(1)
generate_field_files(sys.argv[1])
