mirror of https://github.com/NehZio/Crystal-MEC
Delete main.py
This commit is contained in:
Léo
GitHub
parent
c5a5281810
commit
27c15d1f20
163
main.py
163
main.py
|
|
@ -1,163 +0,0 @@
|
|||
import sys
|
||||
import numpy as np
|
||||
|
||||
from src.read_input import *
|
||||
from src.out import *
|
||||
from src.utils import *
|
||||
|
||||
if __name__=='__main__':
|
||||
|
||||
verbose = 2
|
||||
|
||||
if len(sys.argv) == 1:
|
||||
print("Please provide the input file")
|
||||
sys.exit()
|
||||
elif len(sys.argv) == 3 :
|
||||
if sys.argv[2] == 's':
|
||||
verbose = 0
|
||||
elif sys.argv[2] == 'v':
|
||||
verbose = 1
|
||||
elif sys.argv[2] == 'vv':
|
||||
verbose = 2
|
||||
elif sys.argv[2] == 'vvv':
|
||||
verbose = 3
|
||||
else:
|
||||
print("Unknown argument -%s-"%sys.argv[3])
|
||||
elif len(sys.argv) > 3:
|
||||
print("Too much arguments, please provide an input file and a verbose level (v, vv, vvv)")
|
||||
sys.exit()
|
||||
|
||||
inputFile = sys.argv[1]
|
||||
|
||||
# Reads all the parameters from the input file
|
||||
rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translation = read_input(inputFile)
|
||||
|
||||
if verbose > 0:
|
||||
out_input_param(rB , rPP, center, X, Y, Z, symmetry, outputFile, pattern, npattern , atoms, dist, a, b, c, alpha, beta, gamma, showBath, evjen, showFrag, notInPseudo, notInFrag, symGenerator, generator, translation)
|
||||
|
||||
# Converting the angles to radian
|
||||
alpha = alpha * np.pi / 180.0
|
||||
beta = beta * np.pi / 180.0
|
||||
gamma = gamma * np.pi / 180.0
|
||||
|
||||
|
||||
# Computing the number of replications needed in each directions using the interreticular distance
|
||||
# for the planes 100, 010 and 001.
|
||||
#
|
||||
# The condition is : d_{hkl} >= 2*bath_radius + |translation_vector|
|
||||
|
||||
fac = np.sqrt(1-np.cos(alpha)**2-np.cos(beta)**2-np.cos(gamma)**2+2*np.cos(alpha)*np.cos(beta)*np.cos(gamma))
|
||||
|
||||
nA = int(np.ceil(np.sin(alpha)*(2*rB+np.linalg.norm(translation))/(a*fac)))+1
|
||||
nB = int(np.ceil(np.sin(beta)*(2*rB+np.linalg.norm(translation))/(b*fac)))+1
|
||||
nC = int(np.ceil(np.sin(gamma)*(2*rB+np.linalg.norm(translation))/(c*fac)))+1
|
||||
|
||||
if verbose > 1:
|
||||
print("The big cell will be of dimensions %2ix%2ix%2i\n"%(nA,nB,nC))
|
||||
|
||||
coordinates = big_cell(generator,symGenerator,a,b,c,alpha,beta,gamma,nA,nB,nC)
|
||||
|
||||
# Computing the translation vector by addition of the user translation vector and a translation
|
||||
# vector that puts the origin at the center of the big cell
|
||||
t = [-0.5,-0.5,-0.5]
|
||||
M = get_cell_matrix(nA*a,nB*b,nC*c,alpha,beta,gamma)
|
||||
t = np.matmul(M,t)
|
||||
t = [t[0]+translation[0],t[1]+translation[1],t[2]+translation[2]]
|
||||
|
||||
# Translating the coordinates
|
||||
coordinates = translate(t, coordinates)
|
||||
|
||||
# Finding the center and translating the coordinates
|
||||
# If this vector creates a displacment bigger than a, b or c
|
||||
# in any of the abc directions, this might result in an incomplete
|
||||
# sphere later, the user should provide a translation vector
|
||||
# to correct this
|
||||
if center != []:
|
||||
c = find_center(center,coordinates)
|
||||
coordinates = translate(-c,coordinates)
|
||||
|
||||
|
||||
# Orienting the big cell
|
||||
if X != []:
|
||||
k = [1,0,0]
|
||||
|
||||
xVec = find_center(X,coordinates)
|
||||
M = rotation_matrix(k,xVec)
|
||||
|
||||
rotate(M, coordinates)
|
||||
if Y != []:
|
||||
k = [0,1,0]
|
||||
|
||||
yVec = find_center(Y,coordinates)
|
||||
M = rotation_matrix(k,yVec)
|
||||
|
||||
rotate(M, coordinates)
|
||||
if Z != []:
|
||||
k = [0,0,1]
|
||||
|
||||
zVec = find_center(Z,coordinates)
|
||||
M = rotation_matrix(k,zVec)
|
||||
|
||||
rotate(M, coordinates)
|
||||
|
||||
if verbose > 2:
|
||||
print("The big cell contains %5i atoms and will be printed in the file big_cell.xyz\n"%len(coordinates))
|
||||
write_coordinates(coordinates,'big_cell.xyz',3)
|
||||
|
||||
# Cutting the sphere in the big cell
|
||||
coordinates = cut_sphere(coordinates,rB)
|
||||
|
||||
if verbose > 2:
|
||||
print("The sphere contains %5i atoms and will be printed in the file sphere.xyz\n"%len(coordinates))
|
||||
write_coordinates(coordinates,'sphere.xyz',3)
|
||||
|
||||
# Finding the fragment
|
||||
|
||||
nAt, coordinates = find_fragment(coordinates,pattern,npattern,notInFrag)
|
||||
|
||||
if verbose > 2 or showFrag:
|
||||
print("The fragment contains %3i atoms and will be printed in the file fragment.xyz\n"%nAt)
|
||||
write_coordinates(coordinates,'fragment.xyz',4,'O')
|
||||
|
||||
coordinates = find_pseudo(coordinates,rPP,notInPseudo)
|
||||
|
||||
if verbose > 2 or showBath:
|
||||
print("The bath will be printed in the file bath.xyz\n")
|
||||
write_coordinates(coordinates,'bath.xyz',3)
|
||||
print("The bath sorted with the fragment/pseudo/charge will be printed in the file bath_coloured.xyz\n")
|
||||
write_coordinates(coordinates,'bath_coloured.xyz',3,color='yes')
|
||||
|
||||
if evjen:
|
||||
charges = evjen_charges(coordinates,atoms)
|
||||
else:
|
||||
charges = []
|
||||
for i in range(len(coordinates)):
|
||||
li = coordinates[i][3]
|
||||
ii = np.where(atoms=li)[0]
|
||||
charges.append(atoms[ii+1])
|
||||
|
||||
if verbose > 1:
|
||||
print("The total charge fragment+pseudopotential+bath is : % 8.6f\n"%np.sum(charges))
|
||||
|
||||
if symmetry != []:
|
||||
nuc1 = nuclear_repulsion(coordinates,charges)
|
||||
if verbose > 1:
|
||||
print("Nuclear repulsion before the symmetry : % 8.6f\n"%nuc1)
|
||||
|
||||
coordinates,charges,indexList = compute_symmetry(coordinates,charges,symmetry)
|
||||
|
||||
nuc2 = nuclear_repulsion(coordinates,charges)
|
||||
if verbose > 1:
|
||||
print("Nuclear repulsion after the symmetry : % 8.6f\n"%nuc2)
|
||||
print("The total charge fragment+pseudopotential+bath after symmetry is : % 8.6f\n"%np.sum(charges))
|
||||
if verbose > 2:
|
||||
print("The symmetrized coordinates contain %5i atoms \n"%len(indexList))
|
||||
|
||||
else:
|
||||
indexList = [i for i in range(len(coordinates))]
|
||||
|
||||
write_output(outputFile,coordinates,charges,indexList)
|
||||
if verbose > 2:
|
||||
print("The output has been written to %s \n"%outputFile)
|
||||
out_interatomic_distances(coordinates)
|
||||
|
||||
Loading…
Reference in New Issue