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Option to pass vectors directly as second file #1

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Option to pass vectors directly as second file #1

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0f37e41
Added option to allow second file to be interpreted as vectors to ren…
mokenyi Jun 7, 2019
149df70
read displacements from xyz file
mokenyi Apr 19, 2020
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5 changes: 5 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,11 @@ A Vesta file that contains vectors connecting the initial and final atomic posit
type: string
default: initial.vesta final.vesta

-cd --calculate_displacements
description: If 1, displacement between positions in Vesta files is calculated. Else, second file is assumed to contain vectors to render.
type: int
default: 1

-r --radius
description: vector radius (in angstrom)
type: float
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18 changes: 12 additions & 6 deletions vesta_vectors.py
100644 → 100755
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Expand Up @@ -7,6 +7,7 @@
import numpy as np
import argparse
import re
from copy import deepcopy

def read_in(settings):

Expand All @@ -17,7 +18,7 @@ def read_in(settings):
data = open(filename,'r').read()
combined_data.append(data)

struct_match=re.search(r"STRUC.*THERI",data,flags=re.S)[0]
struct_match=re.search(r"STRUC.*THERI",data,flags=re.S).group(0)
pos_match=re.findall(r"\d+\D+\s+\D+\d+\s+\d+\.\d+\s+(.*?)\s+\d+\D+\s+\d+",struct_match)

if pos_match:
Expand Down Expand Up @@ -86,16 +87,16 @@ def print_to_file(data,settings):
VECTT_str += "{0} {1} {2} {3} {4} 0\n".format(i,settings.radius[0], settings.colour[0], settings.colour[1], settings.colour[2]) # set vector radius and colour
i+=1

ATOMT_match = re.search(r"ATOMT.*SCENE",data["initial_data"],flags=re.S)[0]
ATOMT_match = re.search(r"ATOMT.*SCENE",data["initial_data"],flags=re.S).group(0)
ATOMT_corrected = re.sub(r'([a-zA-Z]+\s+)\d+\.\d+',r"\1 0.0001",ATOMT_match) # this make all atoms reaaaalllly small

SITET_match = re.search(r"SITET.*VECTR",data["initial_data"],flags=re.S)[0]
SITET_match = re.search(r"SITET.*VECTR",data["initial_data"],flags=re.S).group(0)
SITET_corrected = re.sub(r'([a-zA-Z]+\d+\s+)\d+\.\d+',r"\1 0.0001",SITET_match) # this make all atoms reaaaalllly small

BONDP_match = re.search(r"BONDP.*POLYP",data["initial_data"],flags=re.S)[0]
BONDP_match = re.search(r"BONDP.*POLYP",data["initial_data"],flags=re.S).group(0)
BONDP_corrected = re.sub(r'(\d+\s+\d+\s+)\d+\.\d+',r"\1 0.0001",BONDP_match) # this makes all bonds reaaaalllly small

SBOND_match = re.search(r"SBOND.*SITET",data["initial_data"],flags=re.S)[0]
SBOND_match = re.search(r"SBOND.*SITET",data["initial_data"],flags=re.S).group(0)
SBOND_corrected = re.sub(r'(\s+\d\s+\d\s+\d\s+\d\s+\d\s+)\d+\.\d+',r"\1 0.0001",SBOND_match) # make all bonds reaaaalllly small

# substitute the above strings into the output data string
Expand All @@ -121,6 +122,8 @@ def parse_args():
parser.add_argument('--filenames','-f',type=str, nargs=2, required=False,
default=["initial.vesta","final.vesta"], help="name of initial and final vesta files"
)
parser.add_argument('--calculate_displacements','-cd',type=int, nargs='?', required=False,default=1, help="If 1, displacement between positions in Vesta files is calculated. Else, second file is assumed to contain vectors to render."
)
parser.add_argument('--colour','-c',type=int, nargs=3,required=False,
default=[255,0,0], help="vector colour (in RGB)")
parser.add_argument('--radius','-r',type=float, nargs=1, required=False,
Expand Down Expand Up @@ -151,7 +154,10 @@ def parse_args():
if settings.centre_atom:
data = calc_bounds(data)
data = delete_atoms(data)
data = calc_displacement(data)
if settings.calculate_displacements == 1:
data = calc_displacement(data)
else:
data["vectors"]=deepcopy(data["final_positions"])

print ("Printing to file")
print_to_file(data,settings)
Expand Down