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WW_orientation_R5.py
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############################################################################
##This file is used to calculate the WW orientation entropy with respect to
##the each water pair. Firstly, each H2O coordinates were obtained for calculation
##Then, the angle between each H2O pair is obtained (FrameInfor should be take care
##)
##
##
##
##Xianqiang Sun
##TheoChem&Bio
##KTH
##2012-05-28
###########################################################################
#symmetry for the dictionary
import numpy
import sys
import random
sys.path.append('/home/x/xiansu/pfs/program/numpy/lib/python2.6/site-packages')
sys.path.append('/bubo/home/h8/xians/glob/program/python_pkg/lib64/python2.6/site-packages')
from numpy import cos,sin,arccos
from numpy import pi
#from Numeric import *
from datetime import datetime
centreFile=open('optimizedCentre.txt','r')
waterFile=open('waterInforByCentre.txt','r')
allH2OInforFile=open('WW_allCentre_H2O.txt','r')
##conservedH2OInforFile=open('SW_conservedCentre_H2O.txt','r')
angleFile=open('WW_angle.txt','w')
rdfFile=open('rdf_HO_HO.xvg','r')
SorOutput=open('WW_Orien_R5.dat','w')
frameNo=6000
k=1.380648813*(10**(-23)) ## The unit of the boltzmann constant is J/K.
weiH2O=18.0154
mol=6.02214179*(10**23)
pw=0.0331725 ## The unit of this is No. of molecules in per A2.
def getCentreCoord(self):
centreCoord=[]
for centre in self:
centre=centre.split()
centreFloat=[]
for coord in centre:
coord =float(coord)
centreFloat.append(coord)
centreCoord.append(centreFloat)
return centreCoord
##getCentreCoord read the output file from the 'calculatCentre_oop.py'. Read the
##coorditates and save them as list with the float format. The output format is
##the format is:[[x1,y1,z2],[x2,y2,z2]...]
def getWaterInforWithCentre(self):
waterInforWithCentre=[]
for waterInfor in self:
waterInfor=waterInfor.split()
waterInforWithCentre.append(waterInfor)
return waterInforWithCentre
##getWaterInforWithCentre is a function that can be used to read the output waterInfor
##file from 'OptimizeCentre_oop.py'. The water infor were saved as list,[[waterInfor]..]
def orangeWaterInforWithCentre(self,centre):
waterInforAccCentre=[]
for centreNo in range(len(centre)):
eachWaterInforAccCentre=[]
for waterInfor in self:
## print waterInfor[-1]
if waterInfor[-1]==str(centreNo):
eachWaterInforAccCentre.append(waterInfor)
waterInforAccCentre.append(eachWaterInforAccCentre)
return waterInforAccCentre
##getWaterInforWithCentre is organise the water information to lists according the index of
##centres. the water information were saved as[[waterInforInCentre1],[waterInforInCentre1]..].
##WaterInfor in the final result were all saved as list.
def orangeH2OInfor(self):
allH2OInfor=[]
for H2OSet in self:
H2OSetInfor=[]
eachH2O=[]
no=1
for H2O in H2OSet:
if no/3.0==1.0:
eachH2O.append(H2O)
H2OSetInfor.append(eachH2O)
eachH2O=[]
no=1
else:
eachH2O.append(H2O)
no+=1
## for i in H2OSetInfor:
## print i
print 'There were',len(H2OSetInfor), 'in H2OSetInfor!'
allH2OInfor.append(H2OSetInfor)
return allH2OInfor
##orangeH2OInfor can be used to organize a sets of waters which is saved as list H2O informations to sets,
##As there were three atoms in the H2O, therefore, each H2O can be saved as a list. Then, the H2O atom
##lists can be saved as lists. At last the list can be saved according to each centre.
##The output looks like [[[[AtomInfor]...WaterInfor]...CentreInfor]...All H2O]
def removeLessOcuCentre(self,waterInforAccCen,frameNo):
highOcuCentre=[]
for i in range(len(self)):
ocupyNo=len(waterInforAccCen[i])
if (float(ocupyNo)/float(frameNo))>=0.95:
highOcuCentre.append(self[i])
return highOcuCentre
def removeLessOcuWaterInfor(self,waterInforAccCen,frameNo):
highOcuWaterInfor=[]
for i in range(len(self)):
ocupyNo=len(waterInforAccCen[i])
if (float(ocupyNo)/float(frameNo))>=0.95:
highOcuWaterInfor.append(waterInforAccCen[i])
return highOcuWaterInfor
##removeLessOcuCentre is used to obtain the high occupied centre with the ratio>=0.95. The input
##were self: all the centre coordidated; WaterInforAccCen: oranged water information according to
##the centre; frameNo is the total Number of framed you want to calculated.
##These highOcuCentre were saved as list of coordidates. The highOcuWaterInfor were saved according
##to the centre highOcuCentre with the format of [[[waterInforInCentre1],[waterInforInCentre1]]..].
def extractWaterCoor(self):
waterCoor=[]
for waterSet in self:
waterCoorSet=[]
for waterInfor in waterSet:
eachWaterCoor=[]
eachWaterCoorStr=waterInfor[3:-3]
for i in eachWaterCoorStr:
i=float(i)
eachWaterCoor.append(i)
waterCoorSet.append(eachWaterCoor)
waterCoor.append(waterCoorSet)
return waterCoor
##ExtractWaterCoor use the output of function of removeLessOcuWaterInfor.The waterCoord were extracted
##according to each high occupied water coordidate centre. The format of the output is[[waterCoor,waterCoor]
##...]
def getH2OCoord(self):
allH2OCoord=[]
for H2OInforAccCentre in self:
## print len(H2OInforAccCentre)
H2OCoordAccCentre=[]
for H2OInfor in H2OInforAccCentre:
H2OCoord=[]
for H2OAtom in H2OInfor:
H2OAtomCoord=H2OAtom[3:-3]
for number in range(len(H2OAtomCoord)):
H2OAtomCoord[number]=float(H2OAtomCoord[number])
H2OCoord.append(H2OAtomCoord)
H2OCoordAccCentre.append(H2OCoord)
allH2OCoord.append(H2OCoordAccCentre)
print 'The coordinate length in each centre is :',len(H2OCoordAccCentre)
return allH2OCoord
##getH2OCoord is used to extract all the H2O coordidates and save each H2O coordinates
##as list. Then H2O coordinates were saved according to each centre. At last, all
##the H2O coords were saved as a list.
def H2OInforNearbyHighCentre(self,allCentre,conservedH2OInfor,nearbyWaterInfor):
H2OInforAndAround=[]
for conservedCentreNo in range(len(self)):
eachH2OAndAround=[]
eachConservedCentre=self[conservedCentreNo]
eachConservedCentreArray=numpy.array(eachConservedCentre)
eachH2OAndAround.append(conservedH2OInfor[conservedCentreNo])
for allCentreNo in range(len(allCentre)):
aroundCentre=allCentre[allCentreNo]
aroundCentreArray=numpy.array(aroundCentre)
vectorCC=eachConservedCentreArray-aroundCentreArray
vectorCCModulus=numpy.sqrt((vectorCC*vectorCC).sum())
if 5.0>=vectorCCModulus>=1.5:
eachH2OAndAround.append(nearbyWaterInfor[allCentreNo])
if len(eachH2OAndAround)>1:
H2OInforAndAround.append(eachH2OAndAround)
print len(H2OInforAndAround)
return H2OInforAndAround
##H2OInforNearbyHighCentre can be used to find centre around each high occupied centre.The input included
##several information to be calculated. self: the input of the high occupied centre. allcentre: the
##centres for all the optimized centres. conservedH2OInfor inculdes all the H2O infor according to the
##high occupied centre. The nearbyWaterInfor includes all the h2O infors consitant with allCentre
##the output of this functions includes each high occupied H2O infor
##and the H2O infor around each high occupied centre.[[[highOccupiedH2OInfor],[aroundH2OInfor2],[around
##H2OInfor2]],[...]...]. Moreover, the output centre is consistant with centre of findNearByCentre output.
def findNearByWater(self,allCentre,highWaterInfor,waterInfor):
centreAndAround=[]
WWCentreNo=[]
for centreNo in range(len(self)):
eachCentreAndAround=[]
eachCentre=self[centreNo]
eachCentre=numpy.array(eachCentre)
eachCentreAndAround.append(highWaterInfor[centreNo])
no=0
for allCentreNo in range(len(allCentre)):
aroundCentre=allCentre[allCentreNo]
aroundCentre=numpy.array(aroundCentre)
vectorCC=eachCentre-aroundCentre
vectorCCModulus=numpy.sqrt((vectorCC*vectorCC).sum())
if 5.0>=vectorCCModulus>=1.5:
no+=1
eachCentreAndAround.append(waterInfor[allCentreNo])
## print no,'waters arround centre',centreNo
if len(eachCentreAndAround)>1:
WWCentreNo.append(centreNo)
print len(eachCentreAndAround)
centreAndAround.append(eachCentreAndAround)
return centreAndAround
##findNearByWater can be used to find waters around each high occupied centre. The input included
##several information to be calculated. self: the input of the high occupied centre. allcentre: the
##centres for all the optimized centres. The highwaterinfor includes the water informations for all
##the high conserced waters. the output of this functions includes each high occupied water centre
##and the waters around each high occupied centre.[[[highOccupiedCentreInfor1],[aroundWater1],[around
##Water1]],[...]...]
def findNearbyCentre(self,allCentre):
centreNearby=[]
for centreNo in range(len(self)):
eachCentreAndAround=[]
eachCentre=self[centreNo]
eachCentreArray=numpy.array(eachCentre)
eachCentreAndAround.append(eachCentre)
no=0
for allCentreNo in range(len(allCentre)):
aroundCentre=allCentre[allCentreNo]
aroundCentreArray=numpy.array(aroundCentre)
vectorCC=eachCentreArray-aroundCentreArray
vectorCCModulus=numpy.sqrt((vectorCC*vectorCC).sum())
if 5.0>=vectorCCModulus>=1.5:
no+=1
eachCentreAndAround.append(aroundCentre)
## print no,'waters arround centre','centreNo'
if len(eachCentreAndAround)>1:
centreNearby.append(eachCentreAndAround)
## print centreNearby
return centreNearby
##findNearByCentre can be used to find centre around each high occupied centre. The input included
##several information to be calculated. self: the input of the high occupied centre. allcentre: the
##centres for all the optimized centres. the output of this functions includes each high occupied water centre
##and the waters centre around each high occupied centre.[[[highOccupiedCentre1],[aroundCentre2],[around
##centre2]],[...]...]
def findNearbyCentreNo(self,allCentre):
WWCentreNo=[]
for centreNo in range(len(self)):
eachCentreAndAround=[]
eachCentre=self[centreNo]
eachCentreArray=numpy.array(eachCentre)
eachCentreAndAround.append(eachCentre)
no=0
for allCentreNo in range(len(allCentre)):
aroundCentre=allCentre[allCentreNo]
aroundCentreArray=numpy.array(aroundCentre)
vectorCC=eachCentreArray-aroundCentreArray
vectorCCModulus=numpy.sqrt((vectorCC*vectorCC).sum())
if 5.0>=vectorCCModulus>=1.5:
no+=1
eachCentreAndAround.append(aroundCentre)
## print no,'waters arround centre','centreNo'
if len(eachCentreAndAround)>1:
WWCentreNo.append(centreNo)
print WWCentreNo
return WWCentreNo
##findNearByCentreNo can be used to find centre around each high occupied centre. The input included
##several information to be calculated. self: the input of the high occupied centre. allcentre: the
##centres for all the optimized centres. the output of this functions includes each high occupied water centre
##and the waters centre around each high occupied centre.[[[highOccupiedCentre1],[aroundCentre2],[around
##centre2]],[...]...]
def findNearbyCentreAndAroundNo(self,allCentre):
WWCentreNo=[]
for centreNo in range(len(self)):
eachCentreNoAndAround=[]
eachCentre=self[centreNo]
eachCentreArray=numpy.array(eachCentre)
eachCentreNoAndAround.append(centreNo)
no=0
for allCentreNo in range(len(allCentre)):
aroundCentre=allCentre[allCentreNo]
aroundCentreArray=numpy.array(aroundCentre)
vectorCC=eachCentreArray-aroundCentreArray
vectorCCModulus=numpy.sqrt((vectorCC*vectorCC).sum())
if 5.0>=vectorCCModulus>=1.5:
no+=1
eachCentreNoAndAround.append(allCentreNo)
print allCentreNo
print no,'waters arround centre',centreNo
if len(eachCentreNoAndAround)>1:
WWCentreNo.append(eachCentreNoAndAround)
print 'each CenterNo and around:',WWCentreNo
return WWCentreNo
##findNearByCentreAndAroundNo can be used to find centre around each high occupied centre. The input included
##several information to be calculated. self: the input of the high occupied centre. allcentre: the
##centres for all the optimized centres. the output of this functions includes each high occupied water centre
##and the waters centre around each high occupied centre.[[[highOccupiedCentre1No,aroundCentreNo1,aroundCentreNo2],
##[...]...]
def extractWaterCoor(self):
waterCoor=[]
for waterSet in self:
waterCoorSet=[]
for waterInfor in waterSet:
eachWaterCoor=[]
eachWaterCoorStr=waterInfor[3:-3]
## print eachWaterCoorStr
for i in eachWaterCoorStr:
## print i
i=float(i)
eachWaterCoor.append(i)
waterCoorSet.append(eachWaterCoor)
waterCoor.append(waterCoorSet)
return waterCoor
##ExtractWaterCoor use the output of function of removeLessOcuWaterInfor.The waterCoord were extracted
##according to each high occupied water coordidate centre. The format of the output is[[waterCoor,waterCoor]
##...]
def extractWaterCoorAround(self):
waterCoordAround=[]
for eachWaterCentre in waterInforAroundCentre:
## print len(eachWaterCentre)
eachWaterCoordAround=extractWaterCoor(eachWaterCentre)
waterCoordAround.append(eachWaterCoordAround)
## print len(waterCoordAround)
return waterCoordAround
##ExtractWaterCoorAround use mainly use the function of ExtractWaterCoor to extract the water coordinates
##Around each centre. This function read the output of 'findNearByWater' and then the save each waterCoordnate
##according to each high occupied water coordidate centre. The highly accupied centre was saved as the first
##item in each sublist. The waters around this centre were saved as the following items
##The format of the output is[[[centreWaterCoorList],[waterCoorAroundCentre],[waterCoorAroundCentre]..]..]
def calculateGR(self,centre,frameNo):
gr=[]
waterDensPerA2=0.0331725
constant1=(4/3.0)*pi
for centreNo in range(len(centre)):
grNo=range(24)
waterCoorSet=self[centreNo]
## frameNo=len(waterCoorSet)
centreCoor=centre[centreNo]
centreCoor=numpy.array(centreCoor)
for no in range(len(grNo)):
grNo[no]=0
## print grNo
for waterCoor in waterCoorSet:
## print waterCoor, centreCoor
waterCoor=numpy.array(waterCoor)
dist=numpy.linalg.norm(waterCoor-centreCoor)
## print dist
for number in range(24):
nextNumber=number+1
if nextNumber*0.05>dist>=number*0.05:
grNo[number]+=1
## print waterCoor, centreCoor, dist, number
elif dist==24*0.05:
grNo[23]+=1
## print grNo
for number in range(len(grNo)):
prevNumber=number+1
grNo[number]=round(grNo[number]/(constant1*(((prevNumber*0.05)**3)-((number*0.05)**3)))/waterDensPerA2/frameNo,3)
## print grNo
gr.append(grNo)
return gr
##calculateGR is used to calculate the g(r) distribution of each coordidate centre
##the input include : (1),self: the water coordidate sets according to the centre
##(2)Centre:each centre for calculation. (3) frameNo: total frames for the
##calculation. The frameNo information should be included to calculate the
##water density at each centre. The output of this function is list of g(r)
##According to each centre. Moreover, as we have to calculate the g(r) according
##to the distance between the centre and the oxygen coordidated in each frame.
##Each g(r) were saved as list. the form of the output looks like
##[[g(0~0.1),g(0.1~0.2)...g(1.1~1.2)]......]
def calculateGRTheta(self,centre,frameNo):
grTheta=[]
## thetaDensity=frameNo/20.0
reference=numpy.array([0,0,1])
referenceModulus=numpy.sqrt((reference*reference).sum())
for centreNo in range(len(centre)):
grThetaNo=range(20)
waterCoorSet=self[centreNo]
centreCoor=centre[centreNo]
centreCoor=numpy.array(centreCoor)
# frameNo=len(waterCoorSet)
thetaDensity=frameNo/20.0
for no in range(len(grThetaNo)):
grThetaNo[no]=0
for waterCoor in waterCoorSet:
## print waterCoor, centreCoor
waterCoor=numpy.array(waterCoor)
orientation=waterCoor-centreCoor
orientationModulus=numpy.sqrt((orientation*orientation).sum())
dot=numpy.dot(orientation,reference)
cosAngle=dot/referenceModulus/orientationModulus
angle=numpy.arccos(cosAngle)
## print 'the angle of Phi is',angle
for number in range(20):
nextNumber=number+1
if nextNumber*pi/20.0>angle>=number*pi/20.0:
## print 'the angle of Phi is',waterCoor, centreCoor, angle, number
grThetaNo[number]+=1
elif angle==pi:
grThetaNo[19]+=1
## print 'the angle distri bution',grThetaNo
for number in range(len(grThetaNo)):
nextNumber=number+1
grThetaNo[number]=(grThetaNo[number]/(cos(number*pi/20.0)-cos(nextNumber*pi/20.0)))/(frameNo/2.0)
grTheta.append(grThetaNo)
## print grTheta
return grTheta
####????????????????????????????????????????????Maybe A question here
##calculateGRTheta is used to calculate the g(theta) distribution of each coordidate centre
##the input include : (1),self: the water coordidate sets according to the centre
##(2)Centre:each centre for calculation. (3) frameNo: total frames for the
##calculation. The frameNo information should be included to calculate the
##water density at each centre. The output of this function is list of g(theta)
##According to each centre. Moreover, as we have to calculate the g(theta) according
##to the reference oritentation[0, 0,1 ] and the oritentation between the centre and the oxygen coordidated
##in each frame.Each g(theta) were saved as list. the form of the output looks like
##[[g(0~*pi/20.0),g(pi/20.0~2*pi/20.0)...g(pi~19*pi/20.0)]......]
def calculateGRPhi(self,centre,frameNo):
grPhi=[]
## phiDensity=frameNo/20.0
referenceZ=numpy.array([0,0,1])
referenceZModulus=numpy.sqrt((referenceZ*referenceZ).sum())
referenceX=numpy.array([1,0,0])
referenceXModulus=numpy.sqrt((referenceX*referenceX).sum())
for centreNo in range(len(centre)):
grPhiNo=range(40)
waterCoorSet=self[centreNo]
centreCoor=centre[centreNo]
centreCoorArray=numpy.array(centreCoor)
# frameNo=len(waterCoorSet)
phiDensity=frameNo/40.0
for no in range(len(grPhiNo)):
grPhiNo[no]=0
for waterCoor in waterCoorSet:
waterCoorArray=numpy.array(waterCoor)
orientation=waterCoorArray-centreCoorArray
orientationModulus=numpy.sqrt((orientation*orientation).sum())
dot1=numpy.dot(orientation,referenceZ)
cosAngle1=dot1/referenceZModulus/orientationModulus
zReflection=orientationModulus*cosAngle1
waterCoorCopy=[]
waterCoorCopy.extend(waterCoor)
waterCoorCopy[2]=waterCoorCopy[2]-zReflection
newWaterCoorArray=numpy.array(waterCoorCopy)
newOrientation=newWaterCoorArray-centreCoorArray
newOrientationModulus=numpy.sqrt((newOrientation*newOrientation).sum())
dot2=numpy.dot(newOrientation,referenceX)
cosAngle2=dot2/referenceXModulus/newOrientationModulus
angle=numpy.arccos(cosAngle2)
if newOrientation[1]<0:
angle=2*pi-angle
for number in range(40):
nextNumber=number+1
if nextNumber*pi/20.0>angle>=number*pi/20.0:
grPhiNo[number]+=1
elif angle==2*pi:
grPhiNo[39]+=1
print 'the angle distri bution grPhiNo',centreNo, grPhiNo
for number in range(len(grPhiNo)):
grPhiNo[number]=grPhiNo[number]/phiDensity
grPhi.append(grPhiNo)
print 'the angle distri bution grPhiNo',centreNo, grPhiNo
## print grPhi
return grPhi
####????????????????????????????????????????????Maybe A question here
##calculateGRPhi is used to calculate the g(Phi) distribution of each coordidate centre
##the input include : (1),self: the water coordidate sets according to the centre
##(2)Centre:each centre for calculation. (3) frameNo: total frames for the
##calculation. The frameNo information should be included to calculate the
##water density at each centre. The output of this function is list of g(Phi)
##According to each centre. We first calculate the cos(theta) according to [1,0,0]. According to cos(theta)
##The reflection of water Coordidate on XOY plane was found. Therefore, cos(theta) were obtained according to
##the reference oritentation[0,0,1] and the oritentation between the centre and reflection on XOY
##in each frame.Each g(Phi) were saved as list. the form of the output looks like
##[[g(0~*pi/20.0),g(pi/20.0~2*pi/20.0)...g(pi~19*pi/20.0)]......]
def calculateGReachCentre(self,nearbyCentre,frameNo):
grCentreAndAround=[]
for eachWaterNo in range(len(self)):
eachCentre=nearbyCentre[eachWaterNo]
eachWater=self[eachWaterNo]
eachGr=calculateGR(eachWater,eachCentre,frameNo)
grCentreAndAround.append(eachGr)
return grCentreAndAround
##calculateGReachCentre is used to calculate the Gr of for all the centre waters and the arounded waters.
##The input included self: water coordinates which is saved as list of waters and arounded waters. This can be the
##output of function 'extractWaterCoorAround'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(waterCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGr],[aroundWatrer1 Gr]...]......]
def calculateGThetaeachCentre(self,nearbyCentre,frameNo):
gthetaCentreAndAround=[]
for eachWaterNo in range(len(self)):
eachCentre=nearbyCentre[eachWaterNo]
eachWater=self[eachWaterNo]
eachGtheta=calculateGRTheta(eachWater,eachCentre,frameNo)
gthetaCentreAndAround.append(eachGtheta)
return gthetaCentreAndAround
##calculateGThetaeachCentre is used to calculate the GTheta of for all the centre waters and the arounded waters.
##The input included self: water coordinates which is saved as list of waters and arounded waters. This can be the
##output of function 'extractWaterCoorAround'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(waterCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGTheta],[aroundWatrer1 GTheta]...]......]
def calculateGPhieachCentre(self,nearbyCentre,frameNo):
gphiCentreAndAround=[]
for eachWaterNo in range(len(self)):
eachCentre=nearbyCentre[eachWaterNo]
eachWater=self[eachWaterNo]
eachGphi=calculateGRPhi(eachWater,eachCentre,frameNo)
gphiCentreAndAround.append(eachGphi)
return gphiCentreAndAround
##calculateGPhieachCentre is used to calculate the Gphi of for all the centre waters and the arounded waters.
##The input included self: water coordinates which is saved as list of waters and arounded waters. This can be the
##output of function 'extractWaterCoorAround'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(waterCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGPhi],[aroundWatrer1 GPhi]...]......]
def getRdfOO(self):
rdf=[]
for line in self:
line=line.split()
for No in range(len(line)):
eachElement=line[No]
line[No]=float(eachElement)
line[0]=line[0]*10
rdf.append(line)
## print rdf
return rdf
##getRdfOO is used to get the RDF distribution of water with Oxy-Oxy paris.
##the input self is the rdf file and the output is the rdf distribution as lists.
def calculateGRInhTrans(self,rdfOO):
print rdfOO
waterDensPerA2=0.0331725
constant1=(4/3.0)*pi
grInhTrans=[]
for setNo in range(len(self)):
grInhTransSet=[0]
centreSet=self[setNo]
## waterCoordSet=waterCoordAround[setNo]
## print waterCoordSet
## print 'there were :',len(waterCoordSet),'sets in waterCoordSet'
totalNo=len(centreSet)
referenceCentre=centreSet[0]
referenceCentreArray=numpy.array(referenceCentre)
for aroundNo in range(totalNo):
if aroundNo>=1:
aroundCentre=centreSet[aroundNo]
aroundCentreArray=numpy.array(aroundCentre)
distanceVector=referenceCentreArray-aroundCentreArray
distanceModulus=numpy.sqrt((distanceVector*distanceVector).sum())
## print distanceModulus
for line in rdfOO:
## print line
OOdistan=line[0]-distanceModulus
## print line[0]
if OOdistan<=0.015:
grAround=line[1]
## waterCoorNo=len(waterCoordSet[aroundNo])
#### print waterCoorNo
## print distanceModulus
## grAround=round(waterCoorNo/(constant1*((distanceModulus+1.2)**3-(distanceModulus-1.2)**3))/waterDensPerA2/frameNo,3)
print grAround
grAround=numpy.log(grAround)*grAround-grAround+1
grInhTransSet.append(grAround)
grInhTrans.append(grInhTransSet)
print grInhTrans
return grInhTrans
##?????????????????????????Problem in determinning the 0.025
##calculateGRInhTrans is used to calculate the G(r,r) translocation redical distribution function used fir WW translocation entropy
##the input of this function includes self: the output of 'findNearbyCentre' as self: including all the reference centre and centers
##around reference. Therefore, it is a set of centres looks like[[[highOccupiedCentre1],[aroundCentre2],[around
##centre2]],[...]...]. The other input is the water coordinates which includes all the coordinates saved according to the self(centres)
##the output of the fromat is [[G(r1,r1)=0,G(r1,r2),G(r1,r3)...],...].
def calculateGRConstant(self,rdfOO):
print rdfOO
waterDensPerA2=0.0331725
constant1=(4/3.0)*pi
grInhTrans=[]
for setNo in range(len(self)):
grInhTransSet=[0]
centreSet=self[setNo]
## waterCoordSet=waterCoordAround[setNo]
## print waterCoordSet
## print 'there were :',len(waterCoordSet),'sets in waterCoordSet'
totalNo=len(centreSet)
referenceCentre=centreSet[0]
referenceCentreArray=numpy.array(referenceCentre)
for aroundNo in range(totalNo):
if aroundNo>=1:
aroundCentre=centreSet[aroundNo]
aroundCentreArray=numpy.array(aroundCentre)
distanceVector=referenceCentreArray-aroundCentreArray
distanceModulus=numpy.sqrt((distanceVector*distanceVector).sum())
## print distanceModulus
for line in rdfOO:
## print line
OOdistan=line[0]-distanceModulus
## print line[0]
if OOdistan<=0.015:
grAround=line[1]
## waterCoorNo=len(waterCoordSet[aroundNo])
#### print waterCoorNo
## print distanceModulus
## grAround=round(waterCoorNo/(constant1*((distanceModulus+1.2)**3-(distanceModulus-1.2)**3))/waterDensPerA2/frameNo,3)
print grAround
## grAround=numpy.log(grAround)*grAround-grAround+1
grInhTransSet.append(grAround)
grInhTrans.append(grInhTransSet)
print grInhTrans
return grInhTrans
##?????????????????????????Problem in determinning the 0.025
##calculateGRInhTrans is used to calculate the G(r,r) translocation redical distribution function used fir WW translocation entropy
##the input of this function includes self: the output of 'findNearbyCentre' as self: including all the reference centre and centers
##around reference. Therefore, it is a set of centres looks like[[[highOccupiedCentre1],[aroundCentre2],[around
##centre2]],[...]...]. The other input is the water coordinates which includes all the coordinates saved according to the self(centres)
##the output of the fromat is [[G(r1,r1)=0,G(r1,r2),G(r1,r3)...],...].
def getH2OEulerTheta(self,frameNo):
referenceH1=numpy.array([0.79079641377315202, 0.61207926934631729, 0.0])
referenceH2=numpy.array([-0.79079641377315202, 0.61207926934631729, 0.0])
referenceZ=numpy.array([0.0,0.0,1.0])
eulerTheta=[]
## eulerThetaDensity=frameNo/20.0
CentreNo=0
for H2OCoordSet in self:
eulerThetaNo=range(10)
# frameNo=len(H2OCoordSet)
eulerThetaDensity=frameNo/10.0
CentreNo+=1
for no in range(len(eulerThetaNo)):
eulerThetaNo[no]=0
for H2OCoord in H2OCoordSet:
H1=numpy.array(H2OCoord[1])
H2=numpy.array(H2OCoord[2])
OT=numpy.array(H2OCoord[0])
H1=H1-OT
H2=H2-OT
ZH2O=numpy.cross(H1,H2)
ZH2OModulus=numpy.sqrt((ZH2O*ZH2O).sum())
dot1=numpy.dot(referenceZ,ZH2O)
cosAngleTheta=dot1/ZH2OModulus
angleTheta=numpy.arccos(cosAngleTheta)
## print angleTheta
for number in range(10):
nextNumber=number+1
if nextNumber*pi/10.0>angleTheta>=number*pi/10.0:
eulerThetaNo[number]+=1
elif angleTheta==pi:
eulerThetaNo[9]+=1
# print 'the euler Theta No is:',CentreNo, eulerThetaNo
for number in range(len(eulerThetaNo)):
nextNumber=number+1
eulerThetaNo[number]=(eulerThetaNo[number]/(cos(number*pi/10.0)-cos(nextNumber*pi/10.0)))/(frameNo/2.0)
eulerTheta.append(eulerThetaNo)
# print 'the euler Theta No is:',CentreNo,eulerThetaNo
return eulerTheta
##getH2OEulerTheta is used to calculate the Euler distrubution of all the waters.
##The water coordinates were saved as lists with both Oxygen, and Hydeogen atoms.
##The coordinates looks like[[[OxygenCoord],[Hydgrogen1 coordinate],[Hydrogen2 Coordinate]....]...]
##the output of the Euler angle is very similar with other functions. the distribution is
##divided into 20 intergration spaces. The output is [[g(0~*pi/20.0),g(pi/20.0~2*pi/20.0)...g(pi~19*pi/20.0)]......]
def getH2OEulerPhi(self,frameNo):
referenceH1=numpy.array([0.79079641377315202, 0.61207926934631729, 0.0])
referenceH2=numpy.array([-0.79079641377315202, 0.61207926934631729, 0.0])
referenceZ=numpy.array([0.0,0.0,1.0])
referenceY=numpy.array([0.0,1.0,0.0])
referenceX=numpy.array([1.0,0.0,0.0])
revReferenceY=numpy.array([0.0,-1.0,0.0])
eulerPhi=[]
## eulerPhiDensity=frameNo/20.0
CentreNo=0
for H2OCoordSet in self:
eulerPhiNo=range(10)
# frameNo=len(H2OCoordSet)
eulerPhiDensity=frameNo/10.0
CentreNo+=1
for no in range(len(eulerPhiNo)):
eulerPhiNo[no]=0
for H2OCoord in H2OCoordSet:
H1=numpy.array(H2OCoord[1])
H2=numpy.array(H2OCoord[2])
OT=numpy.array(H2OCoord[0])
H1=H1-OT
H2=H2-OT
ZH2O=numpy.cross(H1,H2)
ZH2OOnXY=numpy.copy(ZH2O)
ZH2OOnXY[2]=0.0
ZH2OOnXYModulus=numpy.sqrt((ZH2OOnXY*ZH2OOnXY).sum())
dot1=numpy.dot(revReferenceY,ZH2OOnXY)
cosAnglePhi=dot1/ZH2OOnXYModulus
anglePhi=numpy.arccos(cosAnglePhi)
if ZH2OOnXY[0]<0:
anglePhi=2*pi-anglePhi
for number in range(10):
nextNumber=number+1
if nextNumber*pi/5.0>anglePhi>=number*pi/5.0:
eulerPhiNo[number]+=1
elif anglePhi==2*pi:
eulerPhiNo[9]+=1
# print 'the euler phi No is:',CentreNo, eulerPhiNo
for number in range(len(eulerPhiNo)):
eulerPhiNo[number]=eulerPhiNo[number]/eulerPhiDensity
eulerPhi.append(eulerPhiNo)
# print 'the euler phi No is:',CentreNo, eulerPhiNo
return eulerPhi
##getH2OEulerPhi is used to calculate the Euler distrubution of all the waters.
##The water coordinates were saved as lists with both Oxygen, and Hydeogen atoms.
##The coordinates looks like[[[OxygenCoord],[Hydgrogen1 coordinate],[Hydrogen2 Coordinate]....]...]
##the output of the Euler angle is very similar with other functions. the distribution is
##divided into 20 intergration spaces. The output is [[g(0~*pi/20.0),g(pi/20.0~2*pi/20.0)...g(pi~19*pi/20.0)]......]
def getH2OEulerPsi(self,frameNo):
referenceH1=numpy.array([0.79079641377315202, 0.61207926934631729, 0.0])
referenceH2=numpy.array([-0.79079641377315202, 0.61207926934631729, 0.0])
referenceZ=numpy.array([0.0,0.0,1.0])
referenceY=numpy.array([0.0,1.0,0.0])
revReferenceY=numpy.array([0.0,-1.0,0.0])
eulerPsi=[]
## eulerPsiDensity=frameNo/20.0
CentreNo=0
for H2OCoordSet in self:
# frameNo=len(H2OCoordSet)
eulerPsiDensity=frameNo/10.0
eulerPsiNo=range(10)
CentreNo+=1
for no in range(len(eulerPsiNo)):
eulerPsiNo[no]=0
for H2OCoord in H2OCoordSet:
H1=numpy.array(H2OCoord[1])
H2=numpy.array(H2OCoord[2])
OT=numpy.array(H2OCoord[0])
H1=H1-OT
H2=H2-OT
YH2O=numpy.add(H1,H2)
ZH2O=numpy.cross(H1,H2)
XH2O=numpy.cross(YH2O,ZH2O)
ZH2OOnXY=numpy.copy(ZH2O)
ZH2OOnXY[2]=0.0
crossLine=numpy.cross(referenceZ,ZH2O)
XH2OModulus=numpy.sqrt((XH2O*XH2O).sum())
crossLineModulus=numpy.sqrt((crossLine*crossLine).sum())
## print crossLineModulus
dot1=numpy.dot(crossLine,XH2O)
cosAnglePsi=dot1/XH2OModulus/crossLineModulus
## print cosAnglePsi
anglePsi=numpy.arccos(cosAnglePsi)
## print anglePsi
if XH2O[2]<0:
anglePsi=2*pi-anglePsi
for number in range(10):
nextNumber=number+1
if nextNumber*pi/5.0>anglePsi>=number*pi/5.0:
eulerPsiNo[number]+=1
elif anglePsi==2*pi:
eulerPsiNo[9]+=1
# print 'the euler Psi No is:',CentreNo, eulerPsiNo
for number in range(len(eulerPsiNo)):
eulerPsiNo[number]=eulerPsiNo[number]/eulerPsiDensity
eulerPsi.append(eulerPsiNo)
# print 'the euler Psi No is:',CentreNo, eulerPsiNo
return eulerPsi
##getH2OEulerPsi is used to calculate the Euler distrubution of all the waters.
##The water coordinates were saved as lists with both Oxygen, and Hydeogen atoms.
##The coordinates looks like[[[OxygenCoord],[Hydgrogen1 coordinate],[Hydrogen2 Coordinate]....]...]
##the output of the Euler angle is very similar with other functions. the distribution is
##divided into 20 intergration spaces. The output is [[g(0~*pi/20.0),g(pi/20.0~2*pi/20.0)...g(pi~19*pi/20.0)]......]
def getH2OCoordForWW(self):
H2OCoordForWW=[]
for H2OInforCenAndAround in self:
H2OCoordCentre=getH2OCoord(H2OInforCenAndAround)
H2OCoordForWW.append(H2OCoordCentre)
return H2OCoordForWW
##self is all the H2OinforForWW. therefore, I use the function getH2OCoord to extract all the H2O coordidates. the output of the
##function looks like the output of 'H2OInforNearbyHighCentre' the output:[[[highOccupiedH2OCoord],[aroundH2OCoord2],[around
##H2OCoord2]],[...]...]. Moreover, the output centre is consistant with centre of findNearByCentre output.
def calculateEulerThetaReachCentre(self,nearbyCentre,frameNo):
eulerThetaEacCentreAndAround=[]
for eachH2ONo in range(len(self)):
eachCentre=nearbyCentre[eachH2ONo]
eachH2O=self[eachH2ONo]
eacheulerTheta=getH2OEulerTheta(eachH2O,frameNo)
eulerThetaEacCentreAndAround.append(eacheulerTheta)
return eulerThetaEacCentreAndAround
##calculateEulerThetaReachCentre is used to calculate the gEulerTheta of for all the centre H2O and the arounded H2Os.
##The input included self: H2O coordinates which is saved as list of H2O and arounded H2O. This can be the
##output of function 'getH2OCoordForWW'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(H2OCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGEularTheta],[aroundH2O GEularTheta]...]......]
def calculateEulerPhiReachCentre(self,nearbyCentre,frameNo):
eulerPhiEacCentreAndAround=[]
for eachH2ONo in range(len(self)):
eachCentre=nearbyCentre[eachH2ONo]
eachH2O=self[eachH2ONo]
eacheulerPhi=getH2OEulerPhi(eachH2O,frameNo)
eulerPhiEacCentreAndAround.append(eacheulerPhi)
return eulerPhiEacCentreAndAround
##calculateEulerPhiReachCentre is used to calculate the gEulerPhi of for all the centre H2O and the arounded H2Os.
##The input included self: H2O coordinates which is saved as list of H2O and arounded H2O. This can be the
##output of function 'getH2OCoordForWW'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(H2OCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGEularPhi],[aroundH2O GEularPhi]...]......]
def calculateEulerPsiReachCentre(self,nearbyCentre,frameNo):
eulerPsiEacCentreAndAround=[]
for eachH2ONo in range(len(self)):
eachCentre=nearbyCentre[eachH2ONo]
eachH2O=self[eachH2ONo]
eacheulerPsi=getH2OEulerPsi(eachH2O,frameNo)
eulerPsiEacCentreAndAround.append(eacheulerPsi)
return eulerPsiEacCentreAndAround
##calculateEulerPsiReachCentre is used to calculate the gEulerTheta of for all the centre H2O and the arounded H2Os.
##The input included self: H2O coordinates which is saved as list of H2O and arounded H2O. This can be the
##output of function 'getH2OCoordForWW'. nearbycentre is all the centres for the calculation. The centre
##information should be consistant with the self(H2OCoordinate). Morover, it can read the output of function
##'findNearbyCentre'. The output of this function looks like[[[centreGEularPsi],[aroundH2O GEularPsi]...]......]
def intgGr(self):
sumGr=0
for eachGrNo in range(len(self)):
eachGr=self[eachGrNo]
nextNo=eachGrNo+1
eachGr=eachGr*(((nextNo*0.05)**3)-((eachGrNo*0.05)**3))/3.0
sumGr+=eachGr
## print sumGr
return sumGr
##intgGr is used to do the integration of GR according to the integral of 0.05. The input is a list a GR
##along the distance R. The output of this function is sum(gr*dr)
def intgGtheta(self):
sumGtheta=0
for gthetaNo in range(len(self)):
eachGtheta=self[gthetaNo]
angle1=gthetaNo*pi/20.0
angle2=(gthetaNo+1)*pi/20.0
eachGtheta=eachGtheta*(cos(angle1)-cos(angle2))
sumGtheta+=eachGtheta
return sumGtheta
##intgGtheta is used to do the integration of Gtheta according to the integral of pi/20.0. The input is a list a Gtheta
##along each angle. The output of this function is sum(gtheta*sinTheta*dTheta).
def intgGangle(self):
sumGangle=0
for eachGangle in self:
eachGangle=eachGangle*pi/20.0
sumGangle+=eachGangle
return sumGangle
##intgGangle is used to do the integration of Gangle according to the integral of pi/20.0. The input is a list a Gangle
##along each angle. The output of this function is sum(gangle*dangle)
def getWforWW(self,nearbyCentre,waterCoordAroundCentre,frameNo):
WforWW=[] #single terms for WW entropy calculation
## for centreSetNo in range(len(self)):
## grOOSet=self[centreSetNo]
## OcoordSet=waterCoordAroundCentre[centreSetNo]
## H2OCoordSet=H2OCoordForWW[centreSetNo]
gr=calculateGReachCentre(waterCoordAroundCentre,nearbyCentre,frameNo)
grtheta=calculateGThetaeachCentre(waterCoordAroundCentre,nearbyCentre,frameNo)
grphi=calculateGPhieachCentre(waterCoordAroundCentre,nearbyCentre,frameNo)
## gEtheta=calculateEulerThetaReachCentre(H2OCoordForWW,nearbyCentre,frameNo)
## gEphi=calculateEulerPhiReachCentre(H2OCoordForWW,nearbyCentre,frameNo)
## gEpsi=calculateEulerPsiReachCentre(H2OCoordForWW,nearbyCentre,frameNo)
for centreSetNo in range(len(self)):
WforWWEachCentreAndAround=[]
gRconstantSet=self[centreSetNo]
grSet=gr[centreSetNo]
grthetaSet=grtheta[centreSetNo]