def do_restart(gl, gver='d'):
comname = os.path.splitext(gl.name)[0] + '.com'
gc = GC(comname)
for atom,xyz in zip(gc.atoms_list, gl.final_geometry):
atom.SetVector(xyz.GetVector())
newcomname = misc.increment_filename(comname)
# reduce scan steps accordingly
steps_done = len(gl.bytedict['orientation:'])-1
print steps_done
if steps_done:
print steps_done
for modred in gc.modreds:
if modred.action == 'S':# this FAILs for multi- scans
modred.scan_num_pts -= steps_done
gc.write_to_file(newcomname)
queue = guess_queue(newcomname)
gsub(newcomname, queue, gver)
def get_args():
"Parse arguments of gau_log2com.py"
parser = argparse.ArgumentParser(
description="""
Reads a structure from a Gaussian Log file and other parameters from a
Gaussian Com file and creates a new Gaussian Com.""",
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('log', help='gaussian log filename')
parser.add_argument('-s', '--scan_step',
help='scan step (default = last = 0)',
default=0,
type=int)
parser.add_argument('-o', '--opt_step',
help='opt step (default = last = 0)',
default=0,
type=int)
parser.add_argument('--new_com',
help='new com name (default = increment template com)',
default='')
parser.add_argument('--template_com',
help='(default = same name as .log)',
default='')
args = parser.parse_args()
if args.template_com == '':
args.template_com = os.path.splitext(args.log)[0] + '.com'
if args.new_com == '':
args.new_com = increment_filename(args.template_com)
if os.path.exists(args.new_com):
sys.stderr.write(
'{0} already exists. Aborting.\n'.format(args.new_com))
sys.exit(2)
args.scan_step -= 1
args.opt_step -= 1
return args
