mirror of
https://github.com/NehZio/Crystal-MEC
synced 2024-10-19 22:41:50 +02:00
First version of the code
This commit is contained in:
Léo Gaspard
parent
36414f7fc7
commit
60ef46620f
11
README.md
11
README.md
@ -6,6 +6,17 @@ This program need Atomsk to run, you can download it here :
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http://atomsk.univ-lille1.fr/index.php
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http://atomsk.univ-lille1.fr/index.php
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Work still in progress, only work with Sr2IrO4 atm
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You'll also need python 2.7 with numpy installed
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You'll also need python 2.7 with numpy installed
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415
generer.py
Normal file
415
generer.py
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@ -0,0 +1,415 @@
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import numpy as np
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import os
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import operator
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###### CONSTANTS #######
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a = 5.48463
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b = 5.48463
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c = 25.7977
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dr = 0.001
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da = 0.01
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DA = 1.5
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chO = -2.00
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chIr = 4.00
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chSr = 2.00
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dIrO = 2.50
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dSrO = 3.10
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#######################
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def parse(fileName):
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f = open(fileName,'r')
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line = 0
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dataTable = []
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f.readline()
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f.readline()
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while True:
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line = f.readline().strip().split()
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if line == [] :
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break
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line[1] = float(line[1])
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line[2] = float(line[2])
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line[3] = float(line[3])
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dataTable.append(line)
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return dataTable
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def distance(u,v):
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return np.sqrt((u[0]-v[0])**2+(u[1]-v[1])**2+(u[2]-v[2])**2)
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def vect_product(u,v):
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return [u[1]*v[2]-u[2]*v[1],u[2]*v[0]-u[0]*v[2],u[0]*v[1]-u[1]*v[0]]
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def dot_product(u,v):
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return (u[0]*v[0]+u[1]*v[1]+u[2]*v[2])
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def normalize(u):
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norm = np.sqrt(u[0]**2+u[1]**2+u[2]**2)
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return [u[0]/norm, u[1]/norm, u[2]/norm]
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def rot_matrix(oldAxis,newAxis):
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newAxis = normalize(newAxis)
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vp = normalize(vect_product(oldAxis,newAxis))
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angle = np.arccos(dot_product(oldAxis,newAxis))
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rMat = [[np.cos(angle)+vp[0]*vp[0]*(1-np.cos(angle)),vp[0]*vp[1]*(1-np.cos(angle))-vp[2]*np.sin(angle),vp[0]*vp[2]*(1-np.cos(angle))+vp[1]*np.sin(angle)],[vp[0]*vp[1]*(1-np.cos(angle))+vp[2]*np.sin(angle),vp[1]*vp[1]*(1-np.cos(angle))+np.cos(angle),vp[1]*vp[2]*(1-np.cos(angle))-vp[0]*np.sin(angle)],[vp[0]*vp[2]*(1-np.cos(angle))-vp[1]*np.sin(angle),vp[1]*vp[2]*(1-np.cos(angle))+vp[0]*np.sin(angle),np.cos(angle)+vp[2]*vp[2]*(1-np.cos(angle))]]
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##This is the formula for the rotation matrix to change axis
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return rMat
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def rotation(coord, rMat):
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newCoord = []
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for i in range(len(coord)):
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newX = coord[i][0]*rMat[0][0] + coord[i][1]*rMat[1][0] + coord[i][2]*rMat[2][0]
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newY = coord[i][0]*rMat[0][1] + coord[i][1]*rMat[1][1] + coord[i][2]*rMat[2][1]
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newZ = coord[i][0]*rMat[0][2] + coord[i][1]*rMat[1][2] + coord[i][2]*rMat[2][2]
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newCoord.append([newX,newY,newZ])
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return newCoord
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def cut_bath(rBath, coords):
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bath = []
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for i in range(len(coords)):
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if distance([0,0,0],[coords[i][0],coords[i][1],coords[i][2]]) <= rBath:
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bath.append([coords[i][0], coords[i][1], coords[i][2], coords[i][3], 'C'])
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return bath
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def set_pp(rPP,coords):
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pp = []
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for i in range(len(coords)):
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for j in range(len(coords)):
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if coords[i][4] == 'O':
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if coords[j][4] == 'C' and coords[j][3] != 'O':
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if distance([coords[i][0],coords[i][1],coords[i][2]],[coords[j][0],coords[j][1],coords[j][2]]) <= rPP:
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coords[j][4] == 'Cl'
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pp.append(j)
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for i in pp:
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coords[i][4] = 'Cl'
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return coords
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def find_frag(coords):
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for i in coords:
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if distance(i,[0,0,0]) < 1:
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i[4] = 'O'
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for j in range(len(coords)):
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if distance(i,coords[j]) != 0 and distance(i,coords[j]) < 2.00:
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coords[j][4] = 'O'
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for k in range(len(coords)):
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if distance(coords[j],coords[k]) != 0 and distance(coords[j],coords[k]) < 2.06:
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coords[k][4] = 'O'
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return coords
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def eivgen(coords):
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charges = []
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for i in coords:
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nIr = 0
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nSr = 0
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nO = 0
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for j in coords:
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if i[3] == 'Ir' and j[3] == 'O' and distance(i,j) < dIrO:
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nO += 1
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elif i[3] == 'Sr' and j[3] == 'O' and distance(i,j) < dSrO:
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nO += 1
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if i[3] == 'Ir':
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charges.append(chIr*(nO/6.00))
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if i[3] == 'Sr':
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charges.append(chSr*(nO/9.00))
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typeO = 0
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if i[3] == 'O':
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for j in coords:
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if j[3] == 'Ir' and distance(i,j) < dIrO:
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nIr += 1
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if distance(i,j) < 2.00:
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typeO = 1
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elif j[3] == 'Sr' and distance(i,j) < dSrO:
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nSr += 1
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if typeO == 0:
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charges.append(chO*((chSr*nSr+chIr*nIr)/(5*chSr+chIr)))
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else:
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charges.append(chO*((chSr*nSr+chIr*nIr)/(4*chSr+2*chIr)))
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coords = [[coords[i][0],coords[i][1],coords[i][2],coords[i][3],coords[i][4],charges[i]] for i in range(len(coords))]
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return coords
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def symmetry(coord,atoms,charges, operations):
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newCoord = []
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while coord != []:
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toDel = []
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newCoord.append(coord[0]) #Add the atom to a new list
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name = atoms[0]
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a = newCoord[-1][:] #label a = E
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b = [-a[0],a[1],a[2]] #label b = yOz mirror plan
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c = [-a[0],-a[1],a[2]] #label c = C2 rotation around z
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d = [a[0],-a[1],a[2]] #label d = xOz mirror plan
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e = [a[0],a[1],-a[2]] #label e = xOy mirror plan
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f = [-a[0],a[1],-a[2]] #label f = C2 rotation around y
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g = [a[0],-a[1],-a[2]] #label g = C2 rotation around x
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h = [-a[0],-a[1],-a[2]] #label h = i
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newCoord[-1].append(name+"a")
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newCoord[-1].append(charges[0])
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del atoms[0] #Delete from old list
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del coord[0]
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del charges[0]
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for t in coord:
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index = coord.index(t)
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if name == atoms[index]: #Check if it is the same atom
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if distance(t,a) == 0:
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print("ERROR : Twice the same atom")
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if 'xOz' in operations:
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if distance(t,d) <= da:
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newCoord.append(d)
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newCoord[-1].append(name+'d')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,d) and distance(t,d) < DA:
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print "Error : This atom should not be there",distance(t,d),t,d,a,charges[index]
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print "Are you sure about the xOz symmetry operation ?"
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break
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if 'yOz' in operations:
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if distance(t,b) <= da:
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newCoord.append(b)
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newCoord[-1].append(name+'b')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,b) and distance(t,b) < DA:
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print "Error : This atom should not be there",distance(t,b),t,b,a,charges[index]
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print "Are you sure about the yOz symmetry operation ?"
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break
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if 'C2z' in operations:
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if distance(t,c) <= da:
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newCoord.append(c)
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newCoord[-1].append(name+'c')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,c) and distance(t,c) < DA:
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print "Error : This atom should not be there",distance(t,c),t,c,a,charges[index]
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print "Are you sure about the C2z axis ?"
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break
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if 'xOy' in operations:
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if distance(t,e) <= da:
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newCoord.append(e)
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newCoord[-1].append(name+'e')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,e) and distance(t,e) < DA:
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print "Error : This atom should not be there",distance(t,e),t,e,a,charges[index]
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print "Are you sure about the xOy operation ?"
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break
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if 'C2y' in operations:
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if distance(t,f) <= da:
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newCoord.append(f)
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newCoord[-1].append(name+'f')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,f) and distance(t,f) < DA:
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print "Error : This atom should not be there",distance(t,f),t,f,a,charges[index]
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print "Are you sure about the C2y axis ?"
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break
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if 'C2x' in operations:
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if distance(t,g) <= da:
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newCoord.append(g)
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newCoord[-1].append(name+'g')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,g) and distance(t,g) < DA:
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print "Error : This atom should not be there",distance(t,g),t,g,a,charges[index]
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print "Are you sure about the C2x axis ?"
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break
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if 'i' in operations:
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if distance(t,h) <= da:
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newCoord.append(h)
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newCoord[-1].append(name+'h')
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newCoord[-1].append(charges[index])
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toDel.append(index)
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elif da < distance(t,h) and distance(t,h) < DA:
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print "Error : This atom should not be there",distance(t,h),t,h,a,charges[index]
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print "Are you sure about the i operation ?"
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break
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for m in range(len(toDel)): #We delete the atoms seen in the simmetry
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del coord[toDel[m]-m]
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del atoms[toDel[m]-m]
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del charges[toDel[m]-m]
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return newCoord
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def write_input(fragCoord,ppCoord,bathCoord,fileName, sym):
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g = open(fileName,'w')
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if sym == 'y':
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for i in range(len(fragCoord)):
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if fragCoord[i][3][-1] == 'a':
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g.write('%4s % 5.3f % 5.3f % 5.3f angstrom\n' %(fragCoord[i][3].replace('a','')+str(i+1),fragCoord[i][0],fragCoord[i][1],fragCoord[i][2]))
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g.write("\n\n")
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for i in range(len(ppCoord)):
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if ppCoord[i][3][-1] == 'a':
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g.write('%4s % 5.3f % 5.3f % 5.3f angstrom\n' %(ppCoord[i][3].replace('a','')+str(i+1),ppCoord[i][0],ppCoord[i][1],ppCoord[i][2]))
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g.write("\n\n")
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for i in range(len(bathCoord)):
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if bathCoord[i][3][-1] == 'a':
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g.write('% 5.3f % 5.3f % 5.3f % 5.3f 0. 0. 0. \n'%(bathCoord[i][0],bathCoord[i][1],bathCoord[i][2],bathCoord[i][4]))
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if sym == 'n':
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for i in range(len(fragCoord)):
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g.write('%4s % 5.3f % 5.3f % 5.3f angstrom\n' %(fragCoord[i][3]+str(i+1),fragCoord[i][0],fragCoord[i][1],fragCoord[i][2]))
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g.write('\n\n')
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for i in range(len(ppCoord)):
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g.write('%4s % 5.3f % 5.3f % 5.3f angstrom\n' %(ppCoord[i][3]+str(i+1),ppCoord[i][0],ppCoord[i][1],ppCoord[i][2]))
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g.write('\n\n')
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for i in range(len(bathCoord)):
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g.write('% 5.3f % 5.3f % 5.3f % 5.3f 0. 0. 0. \n' %(bathCoord[i][0],bathCoord[i][1],bathCoord[i][2], bathCoord[i][4]))
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g.close()
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def translation(vec, coords):
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for i in range(len(coords)):
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coords[i][0] -= vec[0]
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coords[i][1] -= vec[1]
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coords[i][2] -= vec[2]
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return coords
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def main():
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fileName = raw_input("Name of the cif file : ")
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rBath = input("Chose the bath radius (in Angstrom) : ")
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rPP = input("Chose the pseudopotential radius (in Angstrom) : ")
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nA = int(np.floor(2*rBath/a)+2) #We chose the number of time we need to replicate
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nB = int(np.floor(2*rBath/b)+2) #to be able to cut the bath
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nC = int(np.floor(2*rBath/c)+2)
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cmd = 'atomsk '+ fileName + ' ' + '-duplicate ' + str(nA) + ' ' + str(nB) + ' ' + str(nC) + ' ' + fileName.replace('cif','xyz') + ' -v 0'
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os.system(cmd)
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data = parse(fileName.replace('cif','xyz')) #Read the data from the xyz file
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coords = [[data[i][1],data[i][2],data[i][3]] for i in range(len(data))]
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labels = [data[i][0] for i in range(len(data))]
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coords = [[coords[i][0],coords[i][1],coords[i][2],labels[i]] for i in range(len(coords))]
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coords = translation([nA*a/2,nB*b/2,nC*c/2],coords) #Putting the origin at the center of the cell
|
||||||
|
|
||||||
|
################ SPECIFIC FOR THE WANTED FRAG ###################
|
||||||
|
|
||||||
|
labels = [i[3] for i in coords]
|
||||||
|
|
||||||
|
nearestIridium = [100,100,100]
|
||||||
|
for i in coords:
|
||||||
|
if i[3] == 'Ir':
|
||||||
|
if distance([0,0,0],[i[0],i[1],i[2]]) < distance([0,0,0],nearestIridium) and distance([0,0,0],[i[0],i[1],i[2]]) > 1:
|
||||||
|
nearestIridium = i
|
||||||
|
nearestIridium = [np.absolute(nearestIridium[0]), nearestIridium[1], nearestIridium[2]]
|
||||||
|
|
||||||
|
rMat = rot_matrix([1,0,0],nearestIridium)
|
||||||
|
coords = rotation(coords, rMat)
|
||||||
|
print("Rotated to a new X axis")
|
||||||
|
|
||||||
|
coords = translation([0.5*distance([0,0,0],nearestIridium),0,0],coords)
|
||||||
|
|
||||||
|
print("Translation ok")
|
||||||
|
|
||||||
|
|
||||||
|
nearestOxygen = [100,100,100]
|
||||||
|
for i in range(len(labels)):
|
||||||
|
if labels[i] == 'O':
|
||||||
|
if distance([0,0,0],[coords[i][0],coords[i][1],coords[i][2]]) < distance([0,0,0],nearestOxygen) :
|
||||||
|
nearestOxygen = coords[i]
|
||||||
|
|
||||||
|
rMat = rot_matrix([0,0,1],nearestOxygen)
|
||||||
|
coords = rotation(coords,rMat)
|
||||||
|
print("Rotated to a new Z axis")
|
||||||
|
coords = [[coords[i][0],coords[i][1],coords[i][2],labels[i]] for i in range(len(coords))]
|
||||||
|
|
||||||
|
#################################################################a
|
||||||
|
|
||||||
|
|
||||||
|
coords = cut_bath(rBath,coords)
|
||||||
|
coords = find_frag(coords)
|
||||||
|
coords = set_pp(rPP,coords)
|
||||||
|
|
||||||
|
|
||||||
|
coords = eivgen(coords)
|
||||||
|
ch = 0
|
||||||
|
for i in range(len(coords)):
|
||||||
|
ch += coords[i][5]
|
||||||
|
print("Total charge : % 8.5f"%ch)
|
||||||
|
sym = 'x'
|
||||||
|
|
||||||
|
os.system('rm '+fileName.replace('cif','xyz'))
|
||||||
|
|
||||||
|
while sym != 'y' and sym != 'n':
|
||||||
|
sym = raw_input("Do you want to treat the symmetry ? (y/n) ")
|
||||||
|
|
||||||
|
|
||||||
|
frag = sorted([i for i in coords if i[4] == 'O'],key=operator.itemgetter(3))
|
||||||
|
pp = sorted([i for i in coords if i[4] == 'Cl'],key=operator.itemgetter(3))
|
||||||
|
bath = sorted([i for i in coords if i[4] == 'C'],key=operator.itemgetter(3))
|
||||||
|
|
||||||
|
if sym == 'y':
|
||||||
|
operation = raw_input("What are the symmetry operations you'd like to treat ? (C2(x,y,z), xOy xOz yOz, i) ").split()
|
||||||
|
rep = 0
|
||||||
|
for i in range(len(coords)-1):
|
||||||
|
for j in range(i+1,len(coords)):
|
||||||
|
rep += (coords[i][5]*coords[j][5])/distance(coords[i],coords[j])
|
||||||
|
print("Nuclear repulsion before symmetry : %f"%rep)
|
||||||
|
|
||||||
|
frag = symmetry([[i[0],i[1],i[2]] for i in frag],[i[3] for i in frag], [i[5] for i in frag], operation)
|
||||||
|
pp = symmetry([[i[0],i[1],i[2]] for i in pp],[i[3] for i in pp], [i[5] for i in pp], operation)
|
||||||
|
bath = symmetry([[i[0],i[1],i[2]] for i in bath],[i[3] for i in bath], [i[5] for i in bath], operation)
|
||||||
|
|
||||||
|
coords = frag+pp+bath
|
||||||
|
|
||||||
|
rep = 0
|
||||||
|
for i in range(len(coords)-1):
|
||||||
|
for j in range(i+1,len(coords)):
|
||||||
|
rep += (coords[i][4]*coords[j][4])/distance(coords[i],coords[j])
|
||||||
|
|
||||||
|
print("Nuclear repulsion after symmetry : %f"%rep)
|
||||||
|
|
||||||
|
if sym == 'n':
|
||||||
|
frag = [[i[0],i[1],i[2],i[3],i[5]] for i in frag]
|
||||||
|
pp = [[i[0],i[1],i[2],i[3],i[5]] for i in pp]
|
||||||
|
bath = [[i[0],i[1],i[2],i[3],i[5]] for i in bath]
|
||||||
|
fileName = raw_input("What name do you wish yo give to your file ? ")
|
||||||
|
|
||||||
|
write_input(frag,pp,bath,fileName,sym)
|
||||||
|
|
||||||
|
if raw_input("Do you want to visualize the bath ? (y/n) ") == 'y':
|
||||||
|
coords = frag+pp+bath
|
||||||
|
if sym == 'y':
|
||||||
|
for i in coords:
|
||||||
|
l = ['a','b','c','d','e','f','g','h']
|
||||||
|
if i[3][-1] in l:
|
||||||
|
i[3] = i[3][:-1]
|
||||||
|
g = open('tmp.xyz','w')
|
||||||
|
g.write('%i \n \n'%len(coords))
|
||||||
|
for i in coords:
|
||||||
|
g.write('%s % 5.3f % 5.3f % 5.3f \n'%(i[3],i[0],i[1],i[2]))
|
||||||
|
g.close()
|
||||||
|
os.system('avogadro tmp.xyz')
|
||||||
|
os.system('rm tmp.xyz')
|
||||||
|
|
||||||
|
|
||||||
|
main()
|
||||||
Loading…
Reference in New Issue
Block a user