def MOTD():
utils.ff_print_source(False)
utils.ff_use_colours(fancy_format_colours)
utils.ff_print_time(False)
os.system('color 07')
features = [
'Loading molecules from xyz files or alternatively download from pubchem.',
'Visualising molecules as a ball-and-stick model or as a wireframe model.',
'Algorithms for guessing atom types, bonds, and bond orders.',
'Support for STO-nG basis set for atomic/molecular orbital visualtions and calculations.',
'Crude extended-Hückel method for calculation of molecular orbitals.'
]
planned_features = [
'Improvements to extended-Hückel and molecular integrals.',
'Marching cubes algorithm to visualise orbitals as iso-volumes instead of current random-dot style.'
]
utils.message(f'Welcome, this project so far supports the following:',
colour='blue')
[utils.message(f'-- {f}', colour='blue') for f in features]
utils.message(f'Planned features:', colour='blue')
[utils.message(f'-- {f}', colour='blue') for f in planned_features]
print()
'Improvements to extended-Hückel and molecular integrals.',
'Marching cubes algorithm to visualise orbitals as iso-volumes instead of current random-dot style.'
]
utils.message(f'Welcome, this project so far supports the following:',
colour='blue')
[utils.message(f'-- {f}', colour='blue') for f in features]
utils.message(f'Planned features:', colour='blue')
[utils.message(f'-- {f}', colour='blue') for f in planned_features]
print()
MOTD()
utils.ff_print_source(fancy_format_source)
utils.ff_use_colours(fancy_format_colours)
utils.ff_print_time(fancy_format_time)
utils.ff_verbosity(verbosity)
if colour_map == None:
colour_map = cmap.BlueRed(posneg_mode=True)
#viewer setup
pg.init()
screen = scr.Screen3D(resolution, bkgr_colour=background_colour)
mol = mol6.Molecule(molecule, basis_set_type=basis_set, repeat=repeats)
if add_hydrogens:
mol.add_hydrogens()
atoms = mol.atoms
import modules.minimizer as mini
import modules.moldynamics as md
import os, math, copy
import numpy as np
from subprocess import check_output
# def printer(m):
# for a1, a2 in m.get_unique_bonds():
# print(a1, a2, a1.distance_to(a2))
# for a1, a2, a3, angle in m.get_unique_bond_angles():
# print(a1,a2,a3,angle)
utils.ff_print_source(False)
utils.ff_use_colours(False)
utils.ff_print_time(False)
ff = uff.ForceField()
ethane = mol.Molecule('butane.pcp')
a = ethane.atoms
# md.perform_md(ethane)
# ethane2 = mol.Molecule('benzene2')
p = plot.Plot()
# e1 = ff.get_energy(ethane,verbosity=1)*4.18
# e2 = ff.get_energy(ethane2,verbosity=1)*4.18
# print((e2-e1)/0.001)
# print((44.67307-44.64240)/0.001)