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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
Expand Down
66 changes: 40 additions & 26 deletions vesta_vectors.py
100644 → 100755
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Expand Up @@ -7,29 +7,33 @@
import numpy as np
import argparse
import re
from copy import deepcopy
import xyz
import os

def read_in(settings):

combined_positions = []
combined_data = []

for filename in [settings.filenames[0], settings.filenames[1]]:
data = open(filename,'r').read()
combined_data.append(data)

struct_match=re.search(r"STRUC.*THERI",data,flags=re.S)[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:
positions = [[float(y) for y in x.split()] for x in pos_match]
else:
raise ValueError("Invalid file format (I am only able to parse Vesta files)")


for i,filename in enumerate(settings.filenames):
if i==0 or os.path.splitext(filename)[1]=='.vesta':
data = open(filename,'r').read()
combined_data.append(data)

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:
positions = [[float(y) for y in x.split()] for x in pos_match]
else:
raise ValueError("Invalid Vesta file!")
elif os.path.splitext(filename)[1]=='.xyz':
positions,ignore=xyz.read(filename)
positions=positions.tolist()
combined_positions.append(positions)

data = {"initial_data": combined_data[0],
"final_data": combined_data[1],
"initial_positions": combined_positions[0], # positions in fractional coordinates
"final_positions": combined_positions[1], # positions in fractional coordinates
}
Expand Down Expand Up @@ -86,32 +90,35 @@ 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
data["output_data"] = re.sub(r'(VECTR\n)',VECTR_str,data["initial_data"])
data["output_data"] = re.sub(r'(VECTT\n)',VECTT_str,data["output_data"])
data["output_data"] = re.sub(r'(ATOMT.*SCENE)',ATOMT_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(BONDP.*POLYP)',BONDP_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(SBOND.*SITET)',SBOND_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(SITET.*VECTR)',SITET_corrected,data["output_data"],flags=re.S)

if settings.hide_atoms == 1:
data["output_data"] = re.sub(r'(ATOMT.*SCENE)',ATOMT_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(BONDP.*POLYP)',BONDP_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(SBOND.*SITET)',SBOND_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(SITET.*VECTR)',SITET_corrected,data["output_data"],flags=re.S)
data["output_data"] = re.sub(r'(VECTS).*(FORMP)',r"\1 {} \n \2".format(settings.scale_factor[0]),data["output_data"],flags=re.S) # set vector scale factor
if settings.centre_atom: # centre the output structure around a particular atom
data["output_data"] = re.sub(r'(BOUND).*(SBOND)',r"\1 \n {0} {1} {2} {3} {4} {5} \n 0 0 0 0 0 \n \2".format(data["min_bound"][0],data["max_bound"][0],data["min_bound"][1],data["max_bound"][1],data["min_bound"][2],data["max_bound"][2]),data["output_data"],flags=re.S)

file_out = open('vectors.vesta','w+')
file_out = open(settings.outname,'w+')
file_out.write(data["output_data"])
file_out.close()


def parse_args():

Expand All @@ -121,6 +128,8 @@ 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 All @@ -135,7 +144,9 @@ def parse_args():
default=[1.0], help='scale all vector moduli by this fixed amount')
parser.add_argument('--centre_atom', '-ca', type=int, nargs=1, required=False,
default=None, help='the output vesta structure is centred around an atom in the initial structure, specified by this index position (indexing from one)')

parser.add_argument('--hide_atoms', '-ha', type=int, nargs='?', required=False, default=0, help="hide atoms")
parser.add_argument('--outname','-o',type=str,nargs='?',required=False,
default='vectors.vesta',help="output file name")
args = parser.parse_args()

return args
Expand All @@ -151,8 +162,11 @@ 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)
print ("All done.")
print ("Saved output to {0}".format(os.path.abspath(settings.outname))