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makeacluster.py
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makeacluster.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Nov 27 22:57:17 2015
@author: chris
"""
#from __future__ import division
from numpy import *
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import itertools
import numpy
def makeacluster(radius,charges = 0, distance =4,cadmium_term=False,
module = 'nwchem',
removehangeroners = True, surfacepassivation=True,_plot=True):
""" Prepare an xyzfile of cluster of CdS or CdSe with a specified radius and a certain number of point charges around it"""
#########cell vectors in angstroms
a = array([4.16,0,0])
b = 4.16*array([cos(radians(60)),sin(radians(60)),0])
c = array([0,0,6.756])
###### cell vectors in angstroms for CdSe
a = array([4.2985,0,0])
b = 4.2985*array([cos(radians(60)),sin(radians(60)),0])
c = array([0,0,7.0152])
cellvectors = array([a,b,c])
##Atomic positions in fractional coordinates in cell
### For Wurtzite#####
Cdcoord = array([[0,0,0],[0.33,0.333,0.5]])
Scoord = array([[0,0,0.375],[0.3333,0.3333,0.875]])
tetarray = array([[0,0,0.375],[-0.333,-0.333,-0.125],[0.6666,-0.3333,-0.125],[-0.3333,0.6666,-0.125]])
Cdcoord= dot(Cdcoord,cellvectors)
Scoord=dot(Scoord,cellvectors)
Cdcoordlist1 = ndarray((0,3))
Cdcoordlist2 = ndarray((0,3))
Scoordlist1 = ndarray((0,3))
Scoordlist2 = ndarray((0,3))
OHcoordlist=ndarray((0,3))
Hcoordlist=ndarray((0,3))
numbertorepeat = int(radius/b[1])+2
for p in itertools.product(range(-numbertorepeat,numbertorepeat+1),repeat=3):
x= dot(array([p]),cellvectors)+Cdcoord[0]
x2=dot(array([p]),cellvectors)+Cdcoord[1]
y = dot(array([p]),cellvectors)+Scoord[0]
y2 = dot(array([p]),cellvectors)+Scoord[1]
Cdcoordlist1 = append(Cdcoordlist1,x,axis=0)
Cdcoordlist2 = append(Cdcoordlist2,x2,axis=0)
Scoordlist1 = append(Scoordlist1,y,axis=0)
Scoordlist2 = append(Scoordlist2,y2,axis=0)
tetcoord=array([[ -2.08208000e+00, 1.19968767e+00, -8.44500000e-01],
[ -2.08000000e-03, -2.40297801e+00 , -8.44500000e-01],
[ 2.07792000e+00, 1.19968767e+00, -8.44500000e-01],
[ 0.00000000e+00, 0.00000000e+00, 2.53350000e+00]])#ndarray((0,3))
tetcoord2 = array( [[ -2.06544000e+00, -1.19968767e+00, -8.44500000e-01],
[ 1.43520000e-02, 1.08079970e-03, 2.53350000e+00],
[ 1.45600000e-02, 2.40297801e+00, -8.44500000e-01],
[ 2.09456000e+00, -1.19968767e+00, -8.44500000e-01]])
Cdtetcoord1=tetcoord*array([[1,1,-1]])
Cdtetcoord2=tetcoord2*array([[1,1,-1]])
extrashift = (a+b+c)/2
Cdcoordlist1[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist1[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Cdcoordlist2[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist2[:]+=extrashift#array([[radius+extrashift,radius+extrashift,radius+extrashift]])
x= where(numpy.sum(Cdcoordlist1**2,axis=1)<radius**2)[0]
Cdcoordlist1=Cdcoordlist1[x]
x= where(numpy.sum(Cdcoordlist2**2,axis=1)<radius**2)[0]
Cdcoordlist2=Cdcoordlist2[x]
Scoordlist1=Scoordlist1[numpy.sum(Scoordlist1**2,axis=1)<radius**2]
Scoordlist2=Scoordlist2[numpy.sum(Scoordlist2**2,axis=1)<radius**2]
extrashift = 10
Cdcoordlist1[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist1[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Cdcoordlist2[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
Scoordlist2[:]+=array([[radius+extrashift,radius+extrashift,radius+extrashift]])
print '--------------'
if cadmium_term:
"""Cadmium Termination. Still not working"""
### TODO implement this.
print 'terminating the surface with cadmium atoms'
for i in Scoordlist1:
remove = array([])
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
for s in Cdtetcoord1:
if not any(sum((x[:]-s)**2,axis=1)<0.5):
print " adding Cd1 Atom at",[i+s]
Cdcoordlist1= append(Cdcoordlist1,[i+s],axis=0)
for i in Scoordlist2:
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
for s in Cdtetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5):
print " adding Cd2 Atom at",[i+s]
Cdcoordlist2= append(Cdcoordlist2,[i+s],axis=0)
if removehangeroners:
"""removing Cd or S/Se atoms connected by only one bond"""
print '--------------'
print "removing core atoms connected by only one bond"
removefromCd1 = []
removefromCd2 = []
removefromS1 = []
removefromS2 = []
removefromS2_2 = array([])
removefromCd1_2 = array([])
for i in Cdcoordlist1:
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromCd1 = append(removefromCd1,where(all(Cdcoordlist1==i,axis=1))[0])
for i in Cdcoordlist2:
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromCd2 = append(removefromCd2,where(all(Cdcoordlist2==i,axis=1))[0])
for i in Scoordlist1:
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromS1 = append(removefromS1,where(all(Scoordlist1==i,axis=1))[0])
for i in Scoordlist2:
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==1:
removefromS2 = append(removefromS2,where(all(Scoordlist2==i,axis=1))[0])
print " removed", len(removefromCd1), "atoms from Cd1"
print " removed", len(removefromCd2), "atoms from Cd2"
print " removed", len(removefromS1), "atoms from S1"
print " removed", len(removefromS2), "atoms from S2"
Cdcoordlist1 = delete(Cdcoordlist1,removefromCd1,axis=0)
Cdcoordlist2 = delete(Cdcoordlist2,removefromCd2,axis=0)
Scoordlist1 = delete(Scoordlist1,removefromS1,axis=0)
Scoordlist2 = delete(Scoordlist2,removefromS2,axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
alllists = ndarray((0,3))
surface_atoms_count = 0
"""Surface passivation with cations and anions"""
if surfacepassivation:
CdOHbondlength =2.7
for i in Cdcoordlist1:
bondlength=CdOHbondlength
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in tetcoord:
if not any(sum((x[:]-s)**2,axis=1)<0.5):# and not any(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<0.5):
OHcoordlist= append(OHcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
else:
pass
# print min(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1))
for i in Cdcoordlist2:
bondlength=CdOHbondlength ## angstroms
x= append(Scoordlist1,Scoordlist2,axis=0)[numpy.sum((append(Scoordlist1,Scoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in tetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5):# and not any(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<0.5):
OHcoordlist= append(OHcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
else:
pass#print min(sum((OHcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1))
for i in Scoordlist1:
remove = array([])
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in Cdtetcoord1:
if not any(sum((x[:]-s)**2,axis=1)<0.5) and not any(sum((Hcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<2):
Hcoordlist= append(Hcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
for i in Scoordlist2:
bondlength=1.83 ## angstroms
x= append(Cdcoordlist1,Cdcoordlist2,axis=0)[numpy.sum((append(Cdcoordlist1,Cdcoordlist2,axis=0)[:]-i)**2,axis=1)<9]-i
if x.shape[0]==4:
pass
else:
#print 'undercoordinated atom found'
surface_atoms_count +=1
for s in Cdtetcoord2:
if not any(sum((x[:]-s)**2,axis=1)<0.5) and not any(sum((Hcoordlist[:]-(i+s/sqrt(sum(s**2))*bondlength))**2,axis=1)<2):
Hcoordlist= append(Hcoordlist,[i+s/sqrt(sum(s**2))*bondlength],axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
###########Remove Duplicate Atoms
for i in listofcoordlists[0:4]:
OHcoordlist = delete(OHcoordlist,checkduplicates(i,OHcoordlist)[1],axis=0)
Hcoordlist = delete(Hcoordlist,checkduplicates(i,Hcoordlist)[1],axis=0)
listofcoordlists = [Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist]
for i in range(len(listofcoordlists)):
for j in range(i,len(listofcoordlists)):
x = checkduplicates(listofcoordlists[i],listofcoordlists[j],threshold=1)
if x[0].size>0:
if j==i:
# print i,j,x
# print listofcoordlists[i][x[0]]
# print listofcoordlists[i][x[1]]
listofcoordlists[i]=delete(listofcoordlists[i],x[1],axis=0)
print 'duplicate atoms found in same list! THE DUPLICATE ATOMS WERE REMOVED'
else:
print i,j,x
print 'duplicate atoms found! ERROR YOU NEED TO FIX THIS'
(Cdcoordlist1,Cdcoordlist2,Scoordlist1,Scoordlist2,OHcoordlist,Hcoordlist)=listofcoordlists[:]
####################3 add charges aroundthe particls
chargecoordlist=pointsonsphere(charges,radius+distance)+array([[radius,radius,radius]])
###############################
if _plot:
fig=figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,Cdcoordlist1[:,0],Cdcoordlist1[:,1],Cdcoordlist1[:,2],c='b')
Axes3D.scatter(ax,Cdcoordlist2[:,0],Cdcoordlist2[:,1],Cdcoordlist2[:,2],c='b')
Axes3D.scatter(ax,Scoordlist1[:,0],Scoordlist1[:,1],Scoordlist1[:,2],c='r')
Axes3D.scatter(ax,Scoordlist2[:,0],Scoordlist2[:,1],Scoordlist2[:,2],c='r')
Axes3D.scatter(ax,OHcoordlist[:,0],OHcoordlist[:,1],OHcoordlist[:,2],c='y')
Axes3D.scatter(ax,Hcoordlist[:,0],Hcoordlist[:,1],Hcoordlist[:,2],c='k')
Axes3D.scatter(ax,chargecoordlist[:,0],chargecoordlist[:,1],chargecoordlist[:,2],c='k')
numcoreatoms = Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]+Scoordlist1.shape[0]*1+Scoordlist2.shape[0]*1
print 'cadmium atoms:',Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]
print 'sulfur atoms:', Scoordlist1.shape[0]*1+Scoordlist2.shape[0]
print 'negative cations:', OHcoordlist.shape[0]
print 'positive cations:', Hcoordlist.shape[0]
print 'number of core atoms', numcoreatoms
numatoms= Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0]+Scoordlist1.shape[0]*1+Scoordlist2.shape[0]*1+OHcoordlist.shape[0]*1+Hcoordlist.shape[0]*1
print 'num electrons with ECP:', str(10*(Cdcoordlist1.shape[0]+Cdcoordlist2.shape[0])+
8*(Scoordlist1.shape[0]+Scoordlist2.shape[0])+
OHcoordlist.shape[0]*10+
Hcoordlist.shape[0]*0)
print 'num atoms:', numatoms, 'total charge:', str(Cdcoordlist1.shape[0]*2+Cdcoordlist2.shape[0]*2+
Scoordlist1.shape[0]*-2+Scoordlist2.shape[0]*-2+
OHcoordlist.shape[0]*-1+
Hcoordlist.shape[0]*1)
commentline = str('cadmium atoms: '+str(Cdcoordlist1.shape[0]*1+Cdcoordlist2.shape[0])+
', sulfur atoms: '+ str(Scoordlist1.shape[0]*1+Scoordlist2.shape[0])+
', total charge of cluster: '+ str(Cdcoordlist1.shape[0]*2+
+Cdcoordlist2.shape[0]*2
+Scoordlist1.shape[0]*-2
+Scoordlist2.shape[0]*-2
+OHcoordlist.shape[0]*-1
+Hcoordlist.shape[0]*1)+
', number of point charges:'+str(charges)+
' removehangeroners= '+str(removehangeroners)
+'\n')
print 'number of surface atoms counted', surface_atoms_count
with open('/home/chris/Desktop/CdSParticle.xyz','wb') as f:#'+str(numcoreatoms)+'core'+str(charges)+'charges.xyz','wb') as f:
f.write(str(numatoms)+'\n')
f.write(commentline)
for i in append(Cdcoordlist1,Cdcoordlist2,axis=0):
f.write('Cd '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in append(Scoordlist1,Scoordlist2,axis=0):
f.write('S '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in OHcoordlist:
f.write('Cl '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in Hcoordlist:
f.write('H '+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
for i in chargecoordlist:
if module == 'nwchem':
f.write('bq1 '+str(i[0])+' '+str(i[1])+' '+str(i[2])+' charge -1\n')
elif module == 'orca':
f.write('Q -1'+str(i[0])+' '+str(i[1])+' '+str(i[2])+'\n')
f.close()
return None
def pointsonsphere(n,rad):
if n ==0:
return ndarray((0,3))
golden_angle = numpy.pi * (3 - numpy.sqrt(5))
theta = golden_angle * numpy.arange(n)
z = numpy.linspace(1 - 1.0 / n, 1.0 / n - 1, n)
radius = numpy.sqrt(1 - z * z)
points = numpy.zeros((n, 3))
points[:,0] = radius * numpy.cos(theta)
points[:,1] = radius * numpy.sin(theta)
points[:,2] = z
points = numpy.zeros((n, 3))
points[:,0] = radius * numpy.cos(theta)*rad
points[:,1] = radius * numpy.sin(theta)*rad
points[:,2] = z*rad
# ax = fig.add_subplot(111, projection='3d')
return points
def perm(n, seq):
coordlist = ndarray((0,3))
for p in itertools.product(seq, repeat=n):
coordlist = append(coordlist,array([p]),axis=0)
return coordlist
def rotate(vector, aroundvector, bydegrees):
if all(vector == 0):
return vector
bydegrees = radians(bydegrees)
apar = dot(vector,aroundvector)*aroundvector/sum(aroundvector**2)**2
aper = vector - apar
w = numpy.cross(aroundvector,aper)
aperrot = sqrt(sum(aper**2))*(cos(bydegrees)*aper/sqrt(sum(aper**2))+sin(bydegrees)*w/sqrt(sum(w**2)))
return aperrot+apar
def symmetrizeC3(geometry,angle):
##### Now symmetrize to C3V by taking the average of the rotated clusters
center = mean(geometry,axis=0)
geometry[:]-=center
geometryrot = ndarray(geometry.shape)
geometryrot2 = ndarray(geometry.shape)
for i in geometry:
rotatedatom = rotate(i,array([0,0,1]),120)
if min(sum((geometry[:]-array([rotatedatom]))**2, axis = 1))>0.01:
print "symmetry error detected"
closestatom = argmin(sum((geometry[:]-array([rotatedatom]))**2, axis = 1))
geometryrot[closestatom] = rotatedatom
for i in geometry:
rotatedatom = rotate(i,array([0,0,1]),240)
closestatom = argmin(sum((geometry[:]-array([rotatedatom]))**2, axis = 1))
geometryrot2[closestatom] = rotatedatom
geometry_mean = (geometry+geometryrot+geometryrot2)/3
with open('/home/chris/Desktop/rotatedgeo.xyz', 'wb') as f:
f.write('66\nrotetateclsuter\n')
for i in range(66):
if i<33:
f.write('Cd '+str(geometry_mean[i][0])+' '+str(geometry_mean[i][1])+' '+str(geometry_mean[i][2])+'\n')
else:
f.write('S '+str(geometry_mean[i][0])+' '+str(geometry_mean[i][1])+' '+str(geometry_mean[i][2])+'\n')
f.close()
print geometry_mean-geometry
print checkduplicates(geometry_mean, geometry_mean)
return 0
def addMePA(xyzfile):
allatoms = array([[ 3.73479929, 4.70148859, 1.08453093],
[ -0.45777444, 5.46389693, 1.4292281],
[ 3.99256744, 1.42776590, 0.17101104],
[ -3.23253881, 2.73557278, 0.17389669],
[ 0.00277074, -0.00738694, -0.25202305],
[ 0.00013075, -0.01651818, 6.38550475],
[ 4.95224596, -2.34187282, 1.40722903],
[ -5.94120956, 0.87524543, 1.07437676],
[ -4.49880283, -3.12964705, 1.41125120],
[ -0.75991343, -4.18114040, 0.15674939],
[ 2.20650584, -5.59236598, 1.05533723],
[ 0.96252338, 4.36198028, -1.42717920],
[ 4.81764990, 3.19485539, -2.77622069],
[ -1.73138701, 4.16471485, -3.46626689],
[ -2.55306625, 2.91594904, 4.51767596],
[ 1.50206160, 1.89218763, -4.09811156],
[ 0.98329346, 2.34564526, 3.59745292],
[ 4.46454220, -0.56369361, -3.4747580],
[ 3.80849139, 0.73094006, 4.51682402],
[ -5.17525966, 2.60395011, -2.77772471],
[ -2.37975873, 0.36837952, -4.07698444],
[ -2.53045715, -0.33540920, 3.59449188],
[ 0.88144546, -2.23348348, -4.09931249],
[ 1.54175224, -2.03600240, 3.58132334],
[ 3.31038688, -3.02228474, -1.45695989],
[ -4.27528734, -1.35796536, -1.44852313],
[ -2.72513737, -3.56991001, -3.48209886],
[ -1.25794100, -3.68787964, 4.50492503],
[ 0.35261163, -5.75579556, -2.79552608],
[ 0.74123700, 4.43697518, -4.02956973],
[ -0.64622546, 4.44077927, 3.74595547],
[ 4.18920378, 1.70873805, -4.66166552],
[ 3.47773976, 2.51701231, 2.54165082],
[ -3.55947851, 2.79106662, -4.65228042],
[ -3.92545305, 1.73860005, 2.54076867],
[ -0.00271263, 0.01013464, -5.02518153],
[ -0.00332939, -0.00785361, 2.48730355],
[ 3.46776368, -2.83946171, -4.05736012],
[ 4.17115409, -1.67896151, 3.73089394],
[ -4.20196677, -1.57060486, -4.04933515],
[ -3.53060015, -2.79614465, 3.73504438],
[ -0.62463325, -4.46372023, -4.67635054],
[ 0.44748177, -4.28341329, 2.52481152],
[ 1.79334057, 6.15314947, 0.33208226],
[ 5.55303831, 3.65754425, -0.46937522],
[ -1.77455171, 4.68869481, -0.74204629],
[ 1.74568849, 1.79694051, -1.26045912],
[ 1.94632660, 1.65173243, 6.00004182],
[ 4.95599592, -0.80678637, -0.75922862],
[ -5.94441654, 2.98322195, -0.46759778],
[ -2.43853084, 0.59877699, -1.25432294],
[ -2.41524712, 0.83987083, 5.99734552],
[ 0.69721678 ,-2.42073954, -1.26854049],
[ 0.46924459, -2.53096433, 5.98775239],
[ 4.43666586, -4.63906404, 0.30520008],
[ -6.23050849, -1.53090073, 0.31876024],
[ -3.17891818, -3.89146035, -0.76368896],
[ 0.38866467, -6.64405085, -0.49626228]])
atomcenter = sum(allatoms,axis=0)
atomcenter = array([0,0,0])
# C -1.4255400000 2.275800,0000 0.1498900000
# P -2.0727700000 0.8165500000 -0.7496400000
# H -0.3427600000 2.2060900000 0.0812300000
# H -1.8434700000 3.0857900000 -0.4746900000
# H -1.8709200000 2.2658600000 1.1464000000
# O -1.4521900000 1.1860200000 -2.1113400000
# O -3.5385700000 1.1054100000 -0.4997000000
# O -1.5251800000 -0.4706000000 -0.1678200000
MePAvecs = array([[ -1.4255400000,2.2758000000,0.1498900000],
[ -2.0727700000 ,0.8165500000,-0.7496400000 ],
[ -0.3427600000 , 2.2060900000, 0.0812300000 ],
[ -1.8434700000 , 3.0857900000, -0.4746900000 ],
[-1.8709200000 , 2.2658600000, 1.1464000000 ],
[ -1.4521900000 , 1.1860200000, -2.1113400000 ],
[-3.5385700000 , 1.1054100000, -0.4997000000 ],
[ -1.5251800000, -0.4706000000, -0.1678200000 ]])
MePAvecs-=MePAvecs[1] ### put phosphorous at center
CPvec = MePAvecs[0]
Cdtarget = array([-1.2579410000 , -3.6878796400 , 4.5049250300 ])
Pposition = (Cdtarget)/sqrt(sum((Cdtarget)**2))
rotationaround = numpy.cross(CPvec,Pposition)
#bydegrees = np.degrees(np.arcsin(sqrt(sum(rotationaround**2))/sqrt(sum(CPvec**2))/sqrt(sum(Pposition**2))))
bydegrees=np.degrees(np.arccos(np.dot(CPvec,Pposition)/sqrt(np.dot(CPvec,CPvec)*np.dot(Pposition,Pposition))))
print bydegrees
rotatedvecs = np.ndarray((0,3))
print '___________________'
for i in MePAvecs:
print i
rotatedvecs = append(rotatedvecs, [rotate(i,rotationaround,bydegrees)+3*Pposition + Cdtarget],axis = 0)
print rotatedvecs
#rotatedvecs[:]+=3*Pposition + Cdtarget
print numpy.cross(rotatedvecs[0],Pposition)
# return 0
# finalP = 3*Pposition + Cdtarget + atomcenter
# v = numpy.cross(CPvec, Pposition)
# s = sqrt(sum(v**2))#/sqrt(sum(CPvec**2))/sqrt(sum(Pposition**2))
#
# c = numpy.dot(CPvec, Pposition)#/sqrt(sum(CPvec**2))/sqrt(sum(Pposition**2))
# print degrees(arcsin(s)), degrees(arccos(c))
# if c<0:
# c+=pi
# vx = array([[0,-v[2],v[1]],
# [v[2],0,-v[0]],
# [-v[1],v[0],0]])
# I = array([[1,0,0],[0,1,0],[0,0,1]])
# rotationmatrix = I + vx + np.dot(vx,vx)*(1-c)/s**2
#
# rotatedvecs =transpose(np.dot(rotationmatrix,transpose(MePAvecs)))
# #shift= rotatedvecs[1]-wherePshouldendup
# rotatedvecs[:]+=finalP
# # rotatedvecs[:]+=atomcenter#-=shift
with open('/home/chris/Desktop/addMePa.xyz','wb') as f:#'+str(numcoreatoms)+'core'+str(charges)+'charges.xyz','wb') as f:
f.write('66\n')
f.write('MePA\n')
f.write('''Cd 3.73479929 4.70148859 1.08453093
Cd -0.45777444 5.46389693 1.42922813
Cd 3.99256744 1.42776590 0.17101104
Cd -3.23253881 2.73557278 0.17389669
Cd 0.00277074 -0.00738694 -0.25202305
Cd 0.00013075 -0.01651818 6.38550475
Cd 4.95224596 -2.34187282 1.40722903
Cd -5.94120956 0.87524543 1.07437676
Cd -4.49880283 -3.12964705 1.41125120
Cd -0.75991343 -4.18114040 0.15674939
Cd 2.20650584 -5.59236598 1.05533723
Cd 0.96252338 4.36198028 -1.42717920
Cd 4.81764990 3.19485539 -2.77622069
Cd -1.73138701 4.16471485 -3.46626689
Cd -2.55306625 2.91594904 4.51767596
Cd 1.50206160 1.89218763 -4.09811156
Cd 0.98329346 2.34564526 3.59745292
Cd 4.46454220 -0.56369361 -3.47475802
Cd 3.80849139 0.73094006 4.51682402
Cd -5.17525966 2.60395011 -2.77772471
Cd -2.37975873 0.36837952 -4.07698444
Cd -2.53045715 -0.33540920 3.59449188
Cd 0.88144546 -2.23348348 -4.09931249
Cd 1.54175224 -2.03600240 3.58132334
Cd 3.31038688 -3.02228474 -1.45695989
Cd -4.27528734 -1.35796536 -1.44852313
Cd -2.72513737 -3.56991001 -3.48209886
Br -1.25794100 -3.68787964 4.50492503
Cd 0.35261163 -5.75579556 -2.79552608
S 0.74123700 4.43697518 -4.02956973
S -0.64622546 4.44077927 3.74595547
S 4.18920378 1.70873805 -4.66166552
S 3.47773976 2.51701231 2.54165082
S -3.55947851 2.79106662 -4.65228042
S -3.92545305 1.73860005 2.54076867
S -0.00271263 0.01013464 -5.02518153
S -0.00332939 -0.00785361 2.48730355
S 3.46776368 -2.83946171 -4.05736012
S 4.17115409 -1.67896151 3.73089394
S -4.20196677 -1.57060486 -4.04933515
S -3.53060015 -2.79614465 3.73504438
S -0.62463325 -4.46372023 -4.67635054
S 0.44748177 -4.28341329 2.52481152
S 1.79334057 6.15314947 0.33208226
S 5.55303831 3.65754425 -0.46937522
S -1.77455171 4.68869481 -0.74204629
S 1.74568849 1.79694051 -1.26045912
S 1.94632660 1.65173243 6.00004182
S 4.95599592 -0.80678637 -0.75922862
S -5.94441654 2.98322195 -0.46759778
S -2.43853084 0.59877699 -1.25432294
S -2.41524712 0.83987083 5.99734552
S 0.69721678 -2.42073954 -1.26854049
S 0.46924459 -2.53096433 5.98775239
S 4.43666586 -4.63906404 0.30520008
S -6.23050849 -1.53090073 0.31876024
S -3.17891818 -3.89146035 -0.76368896
S 0.38866467 -6.64405085 -0.49626228\n''')
f.write('C '+str(rotatedvecs[0,0])+' '+str(rotatedvecs[0,1])+' '+str(rotatedvecs[0,2])+'\n')
f.write('P '+str(rotatedvecs[1,0])+' '+str(rotatedvecs[1,1])+' '+str(rotatedvecs[1,2])+'\n')
f.write('H '+str(rotatedvecs[2,0])+' '+str(rotatedvecs[2,1])+' '+str(rotatedvecs[2,2])+'\n')
f.write('H '+str(rotatedvecs[3,0])+' '+str(rotatedvecs[3,1])+' '+str(rotatedvecs[3,2])+'\n')
f.write('H '+str(rotatedvecs[4,0])+' '+str(rotatedvecs[4,1])+' '+str(rotatedvecs[4,2])+'\n')
f.write('O '+str(rotatedvecs[5,0])+' '+str(rotatedvecs[5,1])+' '+str(rotatedvecs[5,2])+'\n')
f.write('O '+str(rotatedvecs[6,0])+' '+str(rotatedvecs[6,1])+' '+str(rotatedvecs[6,2])+'\n')
f.write('O '+str(rotatedvecs[7,0])+' '+str(rotatedvecs[7,1])+' '+str(rotatedvecs[7,2])+'\n')
f.close()
return rotatedvecs
def checkduplicates(a,b,threshold=0.001):
infirstarray = array([],dtype = int)
insecondarray = array([],dtype=int)
if all(a==b):
for x in range(a.shape[0]):
r= where(sum((b[:][x+1:]-a[x])**2, axis = -1)<threshold)[0]+x+1
if r.size>2:
print "ERROR IN CHECK DUPLICATES. TRIPLICATE FOUND"
insecondarray=numpy.append(insecondarray,r)
if r.size>0:
infirstarray=numpy.append(infirstarray,x)
else:
for x in range(a.shape[0]):
#print x
r= where(sum((b[:]-a[x])**2, axis = -1)<threshold)[0]
if r.size>2:
print "ERROR IN CHECK DUPLICATES. TRIPLICATE FOUND"
#print r
insecondarray=numpy.append(insecondarray,r)
if r.size>0:
infirstarray=numpy.append(infirstarray,x)
return (infirstarray,insecondarray)
def prepdftcharged(charges,chargemag,totalcharge,d=0):
"""used to create input files for nwchem for Cd29S29 clusters with point charges"""
z=array([[3.73479929,4.70148859,1.08453093],
[-0.45777444,5.46389693,1.42922813],
[3.99256744,1.42776590,0.17101104],
[-3.23253881,2.73557278,0.17389669],
[0.00277074,-0.00738694,-0.25202305],
[0.00013075,-0.01651818,6.38550475],
[4.95224596, -2.34187282,1.40722903],
[-5.94120956,0.87524543,1.07437676],
[-4.49880283,-3.12964705,1.41125120],
[-0.75991343,-4.18114040,0.15674939],
[2.20650584,-5.59236598,1.05533723],
[0.96252338,4.36198028,-1.42717920],
[4.81764990,3.19485539,-2.77622069],
[-1.73138701,4.16471485,-3.46626689],
[-2.55306625,2.91594904,4.51767596],
[1.50206160,1.89218763,-4.09811156],
[0.98329346,2.34564526,3.5974529],
[4.46454220,-0.56369361,-3.47475802],
[3.80849139,0.73094006,4.51682402],
[-5.17525966,2.60395011,-2.77772471],
[-2.37975873,0.36837952,-4.07698444],
[-2.53045715,-0.33540920,3.59449188],
[0.88144546,-2.23348348,-4.09931249],
[1.54175224,-2.03600240,3.58132334],
[3.31038688,-3.02228474,-1.45695989],
[-4.27528734,-1.35796536,-1.44852313],
[-2.72513737,-3.56991001,-3.48209886],
[-1.25794100,-3.68787964,4.50492503],
[0.35261163,-5.75579556,-2.79552608],
[0.74123700,4.43697518,-4.02956973],
[-0.64622546,4.44077927,3.74595547],
[4.18920378,1.70873805,-4.66166552],
[3.47773976,2.51701231,2.54165082],
[-3.55947851,2.79106662,-4.65228042],
[-3.92545305,1.73860005,2.54076867],
[-0.00271263,0.01013464,-5.02518153],
[-0.00332939,-0.00785361,2.48730355],
[3.46776368,-2.83946171,-4.05736012],
[4.17115409,-1.67896151,3.73089394],
[-4.20196677,-1.57060486,-4.04933515],
[-3.53060015,-2.79614465,3.73504438],
[-0.62463325,-4.46372023,-4.67635054],
[0.44748177,-4.28341329,2.52481152],
[1.79334057,6.15314947,0.33208226],
[5.55303831,3.65754425,-0.46937522],
[-1.77455171,4.68869481,-0.74204629],
[1.74568849,1.79694051,-1.26045912],
[1.94632660,1.65173243,6.00004182],
[4.95599592,-0.80678637,-0.75922862],
[-5.94441654,2.98322195,-0.46759778],
[-2.43853084,0.59877699,-1.25432294],
[-2.41524712,0.83987083,5.99734552],
[0.69721678,-2.42073954,-1.26854049],
[0.46924459,-2.53096433,5.98775239],
[4.43666586,-4.63906404,0.30520008],
[-6.23050849,-1.53090073,0.31876024],
[-3.17891818,-3.89146035,-0.76368896],
[0.38866467,-6.64405085,-0.49626228]])
print z.shape
# z = numpy.loadtxt('/home/chris/Desktop/q16_cd29/Cd29.xyz',skiprows = 2, usecols = (1,2,3), delimiter = ' ',unpack=False)
chargemag = float(totalcharge)/charges
print "number of charges",charges
print 'total charge', totalcharge
print 'magnitude of each charge', chargemag
(x1,y1,z1) = tuple(numpy.mean(z,axis=0))
center = numpy.mean(z,axis=0)
minradius = max(sqrt(sum((z[:]-center)**2,axis = 1)))
radius = minradius + d
chargecoordlist = pointsonsphere(charges,radius) + center
# with open('/home/chris/Desktop/q16_cd29/Cd29.xyz','rb') as r:
# xyzcoords = r.read()[3:]
# r.close()
totalcharge = str(totalcharge)
print totalcharge
newfolder = 'Q'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29S29'
try:
os.mkdir('/home/chris/Desktop/charges/'+newfolder)
except:
pass
outputfilename = str('/home/chris/Desktop/charges/'+newfolder+'/'+newfolder+'.nw')
newfolder = 'Q'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29S29'
print "newfolder name", newfolder
print "saving as", outputfilename
with open(outputfilename,'wb') as f:
f.write('''start "'''+newfolder+'''"
echo
memory total 4096 mb
charge 0
geometry
Cd 3.73479929 4.70148859 1.08453093
Cd -0.45777444 5.46389693 1.42922813
Cd 3.99256744 1.42776590 0.17101104
Cd -3.23253881 2.73557278 0.17389669
Cd 0.00277074 -0.00738694 -0.25202305
Cd 0.00013075 -0.01651818 6.38550475
Cd 4.95224596 -2.34187282 1.40722903
Cd -5.94120956 0.87524543 1.07437676
Cd -4.49880283 -3.12964705 1.41125120
Cd -0.75991343 -4.18114040 0.15674939
Cd 2.20650584 -5.59236598 1.05533723
Cd 0.96252338 4.36198028 -1.42717920
Cd 4.81764990 3.19485539 -2.77622069
Cd -1.73138701 4.16471485 -3.46626689
Cd -2.55306625 2.91594904 4.51767596
Cd 1.50206160 1.89218763 -4.09811156
Cd 0.98329346 2.34564526 3.59745292
Cd 4.46454220 -0.56369361 -3.47475802
Cd 3.80849139 0.73094006 4.51682402
Cd -5.17525966 2.60395011 -2.77772471
Cd -2.37975873 0.36837952 -4.07698444
Cd -2.53045715 -0.33540920 3.59449188
Cd 0.88144546 -2.23348348 -4.09931249
Cd 1.54175224 -2.03600240 3.58132334
Cd 3.31038688 -3.02228474 -1.45695989
Cd -4.27528734 -1.35796536 -1.44852313
Cd -2.72513737 -3.56991001 -3.48209886
Cd -1.25794100 -3.68787964 4.50492503
Cd 0.35261163 -5.75579556 -2.79552608
S 0.74123700 4.43697518 -4.02956973
S -0.64622546 4.44077927 3.74595547
S 4.18920378 1.70873805 -4.66166552
S 3.47773976 2.51701231 2.54165082
S -3.55947851 2.79106662 -4.65228042
S -3.92545305 1.73860005 2.54076867
S -0.00271263 0.01013464 -5.02518153
S -0.00332939 -0.00785361 2.48730355
S 3.46776368 -2.83946171 -4.05736012
S 4.17115409 -1.67896151 3.73089394
S -4.20196677 -1.57060486 -4.04933515
S -3.53060015 -2.79614465 3.73504438
S -0.62463325 -4.46372023 -4.67635054
S 0.44748177 -4.28341329 2.52481152
S 1.79334057 6.15314947 0.33208226
S 5.55303831 3.65754425 -0.46937522
S -1.77455171 4.68869481 -0.74204629
S 1.74568849 1.79694051 -1.26045912
S 1.94632660 1.65173243 6.00004182
S 4.95599592 -0.80678637 -0.75922862
S -5.94441654 2.98322195 -0.46759778
S -2.43853084 0.59877699 -1.25432294
S -2.41524712 0.83987083 5.99734552
S 0.69721678 -2.42073954 -1.26854049
S 0.46924459 -2.53096433 5.98775239
S 4.43666586 -4.63906404 0.30520008
S -6.23050849 -1.53090073 0.31876024
S -3.17891818 -3.89146035 -0.76368896
S 0.38866467 -6.64405085 -0.49626228
end
bq\n''')
for i in chargecoordlist:
f.write(str(i[0])+' '+str(i[1])+' '+str(i[2])+' ' +str(chargemag) + '\n')
f.write('''
end
basis
Cd library "LANL2DZ ECP"
S library "LANL2DZ ECP"
end
ecp
Cd library "LANL2DZ ECP"
S library "LANL2DZ ECP"
end
dft
xc b3lyp
direct
mult 1
iterations 200
convergence energy 1E-5 density 5E-6 gradient 5e-5 ncysh 200
end
dplot
TITLE LUMO
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;262
output lumo.cube
end
task tddft gradient
task dplot
dplot
TITLE HOMO
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;261
output homo.cube
end
task dplot''')
f.close()
if False:
fig=figure()
ax = fig.add_subplot(111, projection='3d')
Axes3D.scatter(ax,z[:,0],z[:,1],z[:,2],c='b')
Axes3D.scatter(ax,chargecoordlist[:,0],chargecoordlist[:,1],chargecoordlist[:,2],c='r')
return None
def CdSetddftcharged(charges,chargemag,totalcharge,d=0):
#### d distance of charges from surface in is in angstrom
z = numpy.loadtxt('/home/chris/Desktop/CdSe29_finalgeometry.xyz',skiprows = 2, usecols = (1,2,3), delimiter = ' ',unpack=False)
if z.shape[0]!=58:
return 0
chargemag = float(totalcharge)/charges
print "number of charges",charges
print 'total charge', totalcharge
print 'magnitude of each charge', chargemag
(x1,y1,z1) = tuple(numpy.mean(z,axis=0))
center = numpy.mean(z,axis=0)
minradius = max(sqrt(sum((z[:]-center)**2,axis = 1)))
radius = minradius + d
chargecoordlist = pointsonsphere(charges,radius) + center
# with open('/home/chris/Desktop/CdSe29_finalgeometry.xyz','rb') as r:
# xyzcoords = r.read()[3:]
# r.close()
totalcharge = str(totalcharge)
print totalcharge
newfolder = 'tddftQ'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29Se29'
try:
os.mkdir('/home/chris/Desktop/charges/'+newfolder)
except:
pass
outputfilename = str('/home/chris/Desktop/charges/'+newfolder+'/'+newfolder+'.nw')
newfolder = 'tddftQ'+totalcharge+'d'+str(charges)+'r'+str(d)+'_Cd29Se29'
print "newfolder name", newfolder
print "saving as", outputfilename
with open(outputfilename,'wb') as f:
f.write('''start "'''+newfolder+'''"
echo
memory total 4096 mb
charge 0
geometry
symmetry c1\n''')
for i in range(z.shape[0]):
if i<29: f.write('Cd '+str(z[i,0])+' '+str(z[i,1])+' '+str(z[i,2])+'\n')
elif i>30: f.write('Se '+str(z[i,0])+' '+str(z[i,1])+' '+str(z[i,2])+'\n')
f.write('''end
bq\n''')
for i in chargecoordlist:
f.write(str(i[0])+' '+str(i[1])+' '+str(i[2])+' ' +str(chargemag) + '\n')
f.write('''
end
basis
Cd library "LANL2DZ ECP"
Se library "LANL2DZ ECP"
end
ecp
Cd library "LANL2DZ ECP"
Se library "LANL2DZ ECP"
end
dft
xc b3lyp
direct
mult 1
iterations 200
convergence energy 1E-5 density 5E-6 gradient 5e-5 ncysh 200
end
tddft
nroots 10
civecs
notriplet
end
dplot
TITLE LUMO
GAUSSIAN
vectors ./'''+newfolder+'''.movecs
LimitXYZ
-10 10 50
-10 10 50
-10 10 50
orbitals view;1;262
output lumo.cube
end
task tddft energy
task dplot
dplot