import os, sys
import argparse as ap
import numpy as np
parser = ap.ArgumentParser(description = "Add Molecule on surrounding sphere")
parser.add_argument("-i", "--infile", help="Infile from previous step, xyz format")
parser.add_argument("-a", "--add_molecule", help="Molecule to add, xyz format")
parser.add_argument("-o", "--outfile", help="Outfile, xyz format")
group = parser.add_mutually_exclusive_group()
group.add_argument("-r", "--radius_outer", type=float, help="radius from outmost atom to add new molecule at")
group.add_argument("-R", "--radius_center", type=float, help="radius from center to add new molecule at")
args = parser.parse_args()
iterin = xyzt.GetXYZIter(args.infile)
iteradd = xyzt.GetXYZIter(args.add_molecule)
inframe = iterin.get_last_frame()
addframe = iteradd.get_last_frame()
inframe = xyzt.Center(inframe)
addframe = xyzt.Center(addframe)
if args.radius_outer != None:
radius = xyzt.get_extreme_value(inframe['coordinates']) + args.radius_outer
else:
radius = args.radius_center
positioning_vector = np.multiply(np.array([1.0,0.0,0.0]), radius)
parser = ap.ArgumentParser(description="Generate RDF from pairs")
parser.add_argument("-i", "--input", help="Input File, xyz", required=True)
parser.add_argument("-a", "--setaname", help="Set A atom names", nargs="+")
parser.add_argument("-b", "--setbname", help="Set B atom names", nargs="+")
parser.add_argument("-m",
"--setanum",
help="Set A atom indices, zero-based",
nargs="+")
parser.add_argument("-n",
"--setbnum",
help="Set B atom indices, zero-based",
nargs="+")
#parser.add_argument("-f", "--filter" , help="filter function", required=True)
args = parser.parse_args()
xyz_iter = xyzt.GetXYZIter(args.input)
def filter(ec, seta, setb):
outpairs = []
for a in seta:
for b in setb:
if b != (a - 1):
outpairs.append(a)
outpairs.append(b)
return outpairs
seta = []
elem[0], [float(elem[1]),
float(elem[2]),
float(elem[3])]
])
# elif len(elem) == 0:
# pass
else:
raise IOError(
"Line " + str(n) + " in File " + filename +
" : Malformed line. 4 fields (str, float, float, float) expected, "
+ len(elem) + " found.")
inf.close()
return outarray
xyz_iter = xyzt.GetXYZIter(args.Infile)
for n, ec in enumerate(xyz_iter):
if args.box != None:
boxsize = args.box
else:
boxsize = ec['boxvector'][0]
print ec
data = zip(ec['elements'], ec['coordinates'])
write_file(args.Outfile, data, boxsize) #, ElementDict)
#!/usr/bin/env python
import xyzt
import os, sys
import argparse as ap
import numpy as np
parser = ap.ArgumentParser(description = "Define molecule type - Dummy")
parser.add_argument("-i", "--infile", help="infile, xyz format")
args = parser.parse_args()
frame = xyzt.Filter(xyzt.GetXYZIter(args.infile).get_last_frame(), keep=["NN"])
outstring = "1 " * len(frame['elements'])
print outstring
"molecule to center on. Zero-based index, negative indices permitted, default 0",
type=int,
default=None)
group2.add_argument("-C",
"--center_on_coordinates",
help="coordinates to center on. 3 values required",
type=float,
nargs=3,
default=None)
args = parser.parse_args()
#print args
#exit()
frameiterator = xyzt.GetXYZIter(args.input)
moleculespecs = [[]]
if args.types:
for a in args.types:
if a is ",":
moleculespecs.append([])
else:
moleculespecs[-1].append(a)
args.types = moleculespecs
print args.types
#exit()
for f in frameiterator:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os, sys
import xyzt
import argparse as ap
parser = ap.ArgumentParser(description="Center a configuration in its bounding box and output minimum box dimensions")
parser.add_argument("-i", "--infile", help="XYZ input file")
parser.add_argument("-o", "--outfile", help="XYZ output file")
args = parser.parse_args()
xyz_in = xyzt.GetXYZIter(args.infile)
for ec in xyz_in:
xyzt.Write_XYZ(ec, args.outfile, append=True)
#!/usr/bin/env python
import xyzt
import numpy as np
np.set_printoptions(suppress=True)
ipf = xyzt.GetXYZIter("unitvector.xyz")
lf = ipf.get_last_frame()
#print lf
rx = xyzt.rotate_around_origin(lf.copy(), 90, 0, 0)
#print xyzt.rotate_around_origin(lf, 180, 180, 0)
ry = xyzt.rotate_around_origin(lf.copy(), 0, 90, 0)
rz = xyzt.rotate_around_origin(lf.copy(), 0, 0, 90)
print lf['coordinates'][0],
print lf['coordinates'][1],
print lf['coordinates'][2]
print rx['coordinates'][0],
print rx['coordinates'][1],
print rx['coordinates'][2]
print ry['coordinates'][0],
print ry['coordinates'][1],
print ry['coordinates'][2]
print rz['coordinates'][0],
print rz['coordinates'][1],
print rz['coordinates'][2]
print xyzt.get_extreme_value(lf['coordinates'])