Source code for jscatter.formel

# -*- coding: utf-8 -*-
# written by Ralf Biehl at the Forschungszentrum Jülich ,
# Jülich Center for Neutron Science 1 and Institute of Complex Systems 1
#    Jscatter is a program to read, analyse and plot data
#    Copyright (C) 2015  Ralf Biehl
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

"""
Physical equations and useful formulas as quadrature of vector functions,
viscosity, compressibility of water, scatteringLengthDensityCalc or sedimentationProfile.
Use scipy.constants for physical constants.

- Each topic is not enough for a single module, so this is a collection.
- Return values are dataArrays were useful. To get only Y values use .Y
- All scipy functions can be used. See http://docs.scipy.org/doc/scipy/reference/special.html.
- Statistical functions http://docs.scipy.org/doc/scipy/reference/stats.html.

Mass and scattering length of all elements in Elements are taken from :
 - Mass: http://www.chem.qmul.ac.uk/iupac/AtWt/
 - Neutron scattering length: http://www.ncnr.nist.gov/resources/n-lengths/list.html

Units converted to amu for mass and nm for scattering length.

"""
from __future__ import division
from __future__ import print_function

import functools
import inspect
import math
import numpy as np
import os
import re
import scipy
import scipy.constants as constants
import scipy.integrate
import scipy.special as special
import sys
import warnings
from collections import deque
from scipy import stats
from scipy.special.orthogonal import p_roots
import pickle
import io

from . import parallel
from .dataarray import dataArray as dA
from .dataarray import dataList as dL
from .libs import ml_internal

_path_=os.path.realpath(os.path.dirname(__file__))

#: Variable to allow printout for debugging as if debug:print('message')
debug=False

# load table with neutron scattering cross sections
with io.open(os.path.join(_path_,'data','Neutronscatteringlengthsandcrosssections.html')) as _f:
    Nscatdat=_f.readlines()

#: Dictionary with coherent and incoherent neutron scattering length.
#: units nm
Nscatlength={}

Hnames={'1H':'h','2H':'d','3H':'t'}
for line in Nscatdat[115+3:486+3]:
    words=[w.strip() for w in line.split('<td>')]
    if words[1] in Hnames.keys():
        Nscatlength[Hnames[words[1]]]=[float(words[3])*1e-6,np.sqrt(float(words[6])/4/np.pi*1e-10)]
    elif words[1][0] not in '0123456789':
        try:
            Nscatlength[words[1].lower()]=[float(words[3])*1e-6,np.sqrt(float(words[6])/4/np.pi*1e-10)]
        except:
            try:
                Nscatlength[words[1].lower()]=[complex(words[3])*1e-6,np.sqrt(float(words[6])/4/np.pi*1e-10)]
            except:
                Nscatlength[words[1].lower()]=[-0,-0]
del words
#  [Z,mass,b_coherent,b_incoherent,name]
#: Elements Dictionary
#: with: { symbol : (electron number; mass; neutron coherent scattering length, neutron incoherent scattering length, name) };
#: units amu for mass and nm for scattering length
Elements={}
# load periodic table perhaps later more of this
with io.open(os.path.join(_path_,'data','elementsTable.dat')) as _f:
    for ele in _f.readlines():
        if ele[0]=='#': continue
        z,symbol,name,mass=ele.split()[0:4]
        try:
            Elements[symbol.lower()]=(int(z),
                                      float(mass),
                                      Nscatlength[symbol.lower()][0],
                                      Nscatlength[symbol.lower()][1],
                                      name)
        except:
            pass
del z,symbol,name,mass

# load table with density parameters accordiing to
# Densities of binary aqueous solutions of 306 inorganic substances
# P. Novotny, O. Sohnel J. Chem. Eng. Data, 1988, 33 (1), pp 49–55 DOI: 10.1021/je00051a018
_aquasolventdensity={}
with open(os.path.join(_path_,'data','aqueousSolutionDensitiesInorganicSubstances.txt')) as _f:
    for ele in _f.readlines():
        if ele[0]=='#': continue
        # substance A*10^-2 -B*10 C*10^3 -D E*10^2 -F*10^4 st*10^2 t Cmax-
        aname,A,B,C,D,E,F,s,Trange,concrange=ele.split()[0:10]
        try:
            _aquasolventdensity[aname.lower()]=(float(A)*1e2,
                                                -float(B)*1e-1,
                                                float(C)*1e-3,
                                                -float(D)*1e0,
                                                float(E)*1e-2,
                                                -float(F)*1e-4,
                                                float(s)/100.,
                                                Trange,
                                                concrange)
        except:
            pass
_aquasolventdensity['c4h11n1o3']=(0.0315602,0.708699)   #: TRIS buffer density    DOI: 10.1021/je900260g
_aquasolventdensity['c8h19n1o6s1']=(0.0774654,0.661610) #: TABS buffer density    DOI: 10.1021/je900260g
del aname,A,B,C,D,E,F,s,Trange,concrange,ele

_bufferDensityViscosity={}
with io.open(os.path.join(_path_,'data','bufferComponents.txt'),'r') as _f:
    for ele in _f.readlines():
        if ele[0]=='#': continue
        # substance
        name,dc0,dc1,dc2,dc3,dc4,dc5,vc0,vc1,vc2,vc3,vc4,vc5,unit,crange=ele.split()
        temp=[float(ss) for ss in [dc0,dc1,dc2,dc3,dc4,dc5,vc0,vc1,vc2,vc3,vc4,vc5] ]
        _bufferDensityViscosity[name.lower()]=tuple(temp)+(unit, crange)
        #except:
        #    pass
del ele,name,dc0,dc1,dc2,dc3,dc4,dc5,vc0,vc1,vc2,vc3,vc4,vc5,unit,crange,temp


felectron=2.8179403267e-6   #: Cross section of electron in nm
kB=0.00831447086363271      #: Boltzmann constant in kJ/(mol⋅K)

def _getFuncCode(func):
    """
    Get code object of a function
    Should work  for python 2 & 3
    """
    try:
        return func.func_code  # python2
    except:
        return func.__code__  # python3

[docs]def memoize(**memkwargs): """ A least-recently-used cache decorator to cache expensive function evaluations. Memoize caches results and retrieves from cache if same parameters are used again. This can speedup computation in a model if a part is computed with same parameters several times. During fits it may be faster to calc result for a list of and take from cache. Parameters ---------- function : function Function to evaluate as e.g. f(Q,a,b,c,d) memkwargs : dict Keyword args with substitute values to cache for later interpolation. Empty for normal caching of a function. E.g. memkwargs={'Q':np.r_[0:10:0.1],'t':np.r_[0:100:5]} caches with these values. The needed values can be interpolated from the returned result. See example below. maxsize : int, default 128 maximum size of the cache. Last is dropped. Returns ------- cached function with new methods - last(i) to retrieve the ith evaluation result in cache (last is i=-1). - clear() to clear the cached results. - hitsmisses counts hits and misses. Notes ----- Only keyword arguments for the memoized function are supported!!!! Only one attribute and X are supported for fitting as .interpolate works only for two cached attributes. Examples -------- The example uses a model that computes like I(q,n,..)=F(q)*B(t,n,..). F(q) is cheap to calculate B(t,n,..) not. In the following its better to calc the function for a list of q , put it to cache and take in the fit from there. B is only calculated once. Use it like this:: import jscatter as js import numpy as np # define some data TT=js.loglist(0.01,80,30) QQ=np.r_[0.1:1.5:0.15] # in the data we have 'q' and 'X' data=js.dynamic.finiteZimm(t=TT,q=QQ,NN=124,pmax=100,tintern=10,ll=0.38,Dcm=0.01,mu=0.5,viscosity=1.001,Temp=300) # a short definition for the same as below # makes a unique list of all X values -> interpolation is exact for X tt=list(set(data.X.flatten));tt.sort() # use correct values from data for q -> interpolation is exact for q fZ=js.formel.memoize(q=data.q,t=tt)(js.dynamic.finiteZimm) def fitfunc(Q,Ti,NN,tint,ll,D,mu,viscosity,Temp): res= fZ(t=Ti,q=Q,NN=NN,tintern=tint,ll=ll,Dcm=D,pmax=40,mu=mu,viscosity=viscosity,Temp=Temp) return res.interpolate(q=Q,X=Ti,deg=2)[0] # do the fit data.setlimit(tint=[0.5,40],D=[0,1]) data.makeErrPlot(yscale='l') NN=20 data.fit(fitfunc,{'tint':10,'D':0.1,},{'NN':20,'ll':0.38/(NN/124.)**0.5,'mu':0.5,'viscosity':0.001,'Temp':300},mapNames={'Ti':'X','Q':'q'},) # define the function to memoize, first the long usual way as decorator @js.formel.memoize(Q=np.r_[0:3:0.2],Time=np.r_[0:50:0.5,50:100:5]) def fZ(Q,Time,NN,tintern,ll,Dcm,mu,viscosity,Temp): # finiteZimm accepts t and q as array and returns a dataList with different Q and same X=t res=js.dynamic.finiteZimm(t=Time,q=Q,NN=NN,pmax=20,tintern=tintern,ll=ll,Dcm=Dcm,mu=mu,viscosity=viscosity,Temp=Temp) return res # define the fitfunc def fitfunc(Q,Ti,NN,tint,ll,D,mu,viscosity,Temp): res= fZ(Time=Ti,Q=Q,NN=NN,tintern=tint,ll=ll,Dcm=D,mu=mu,viscosity=viscosity,Temp=Temp) #this is the cached result for the list of Q # interpolate for the single Q value the cached result has again 'q' return res.interpolate(q=Q,X=Ti,deg=2)[0] # do the fit data.setlimit(tint=[0.5,40],D=[0,1]) data.makeErrPlot(yscale='l') data.fit(fitfunc,{'tint':6,'D':0.1,},{'NN':20,'ll':0.38/(20/124.)**0.5,'mu':0.5,'viscosity':0.001,'Temp':300},mapNames={'Ti':'X','Q':'q'}) # the result depends on the interpolation; """ if 'maxsize' in memkwargs: cachesize =memkwargs['maxsize'] del memkwargs['maxsize'] else: cachesize=128 def _memoize(function): function.hitsmisses=[0,0] cache = function.cache = {} deck = function.deck = deque([], maxlen = cachesize) function.last = lambda i=-1:function.cache[function.deck[i]] def clear(): while len(function.deck)>0: del function.cache[function.deck.pop()] function.hitsmisses=[0,0] function.clear=clear @functools.wraps(function) def _memoizer(*args, **kwargs): # make new key=pickle.dumps(args, 1)+pickle.dumps(kwargs, 1) if key in cache: function.hitsmisses[0]+=1 deck.remove(key) deck.append(key) return cache[key] else: function.hitsmisses[1]+=1 cache[key] = function(*args, **dict(kwargs,**memkwargs)) if len(deck)>=cachesize: del cache[deck.popleft()] deck.append(key) return cache[key] return _memoizer return _memoize
#: FibonacciLatticePointsOnSphere; see :py:func:`~.parallel.fibonacciLatticePointsOnSphere` fibonacciLatticePointsOnSphere=parallel.fibonacciLatticePointsOnSphere #: Random points on sphere; see :py:func:`~.parallel.randomPointsOnSphere` randomPointsOnSphere=parallel.randomPointsOnSphere #: Random points in cube; see :py:func:`~.parallel.randomPointsInCube` randomPointsInCube=parallel.randomPointsInCube #: parallel sphereAverage; see :py:func:`~.parallel.psphereAverage` psphereAverage=parallel.psphereAverage
[docs]def loglist(mini=0.1,maxi=5,number=100): """ Log like distribution between mini and maxi with number points. Parameters ---------- mini,maxi : float, default 0.1, 5 Start and endpoint. number : int, default 100 Number of points Returns ------- ndarray """ return np.exp( np.r_[np.log((mini if mini!=0. else 1e-6)):np.log((maxi if maxi!=0 else 1.)):(number if number!=0 else 10)*1j])
[docs]def smooth(data, windowlen=7, window='flat'): """ Smooth data using a window with requested size and type. This method is based on the convolution of a scaled window with the signal. The signal is prepared by introducing reflected copies of the signal (with the window size) in both ends so that transient parts are minimized in the beginning and end part of the output signal. Adapted from SciPy/Cookbook. Parameters ---------- data : array, dataArray Data to smooth. If is dataArray the .Y is smoothed and returned. windowlen : int, default = 7 The length of the smoothing window; should be an odd integer. Smaller 3 returns unchanged data. window : 'hanning', 'hamming', 'bartlett', 'blackman','gaussian', default ='flat' Type of window. - 'flat' will produce a moving average smoothing. - 'gaussian' normalized Gaussian window with sigma=windowlen/7. Returns ------- array (only the smoothed array) Examples -------- :: import jscatter as js import numpy as np t=np.r_[-5:5:0.01] data=np.sin(t)+np.random.randn(len(t))*0.1 y=js.formel.smooth(data) # # smooth dataArray and replace .Y values. data2=js.dA(np.vstack([t,data])) data2.Y=js.formel.smooth(data2, windowlen=40, window='gaussian') p=js.grace() p.plot(t,data) p.plot(t,y) p.plot(data2) p.plot(data2.prune(number=200)) # reduces number of points by real averaging. Notes ----- See numpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve, scipy.signal.gaussian """ windowlen=int(np.ceil(windowlen/2)*2) if hasattr(data,'_isdataArray'): data=data.Y if data.size < windowlen: raise ValueError("Input vector needs to be bigger than window size.") if windowlen<3: return data if not window in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman','gaussian']: raise ValueError("Window is on of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman','gaussian'") s=np.r_[data[windowlen - 1:0:-1], data, data[-1:-windowlen:-1]] if window == 'flat': #moving average w=np.ones(windowlen, 'd') elif window == 'gaussian': # gaussian w=scipy.signal.gaussian(windowlen, std=windowlen/7.) else: w=eval('np.'+window+'(windowlen)') y=np.convolve(w/w.sum(),s,mode='valid') res=y[int((windowlen / 2 - 1)):int(-(windowlen / 2))] return res
[docs]def rotationMatrix(vector,angle): """ Create a rotation matrix corresponding to rotation around vector v by a specified angle. .. math:: R = vv^T + cos(a) (I - vv^T) + sin(a) skew(v) Parameters ---------- vector : array Rotation around a general vector angle : float Angle in rad Returns ------- Rotation matrix Examples -------- :: R=js.formel.rotationMatrix([0,0,1],np.deg2rad(-90)) v=[1,0,0] rv=np.dot(R,v) # # rotate fibonacci Grid qfib=js.formel.fibonacciLatticePointsOnSphere(300,1) qfib=qfib[qfib[:,2]<np.pi/2,:] # select half sphere qfib[:,2]*=(30/90.) # shrink to cone of 30° qfx=js.formel.rphitheta2xyz(qfib) # transform to cartesian R=js.formel.rotationMatrix([0,1,0],np.deg2rad(-90)) # rotation around y axis Rfx=np.einsum('ij,jk->ki',R,qfx.T) # do rotation fig = pyplot.figure() ax = fig.add_subplot(111, projection='3d') sc=ax.scatter(qfx[:,0], qfx[:,1], qfx[:,2], s=2, color='r') sc=ax.scatter(Rfx[:,0], Rfx[:,1], Rfx[:,2], s=2, color='b') ax.scatter(0,0,0, s=55, color='g',alpha=0.5) pyplot.show(block=False) """ d=np.array(vector,dtype=np.float64) d/=np.linalg.norm(d) eye=np.eye(3,dtype=np.float64) ddt=np.outer(d,d) skew=np.array([[0,d[2],-d[1]], [-d[2],0,d[0]], [d[1],-d[0],0]],dtype=np.float64) mtx=ddt+np.cos(angle)*(eye-ddt)+np.sin(angle)*skew return mtx
[docs]def box(x,edges=[0],edgevalue=0, rtol=1e-05, atol=1e-08): """ Box function For equal edges and edge value> 0 the delta function is given. Parameters ---------- x : array edges : list of float, float Edges of the box. If only one number is given the box goes from [-edge:edge] edgevalue : float, default=0 Value to use if x==edge for both edges. rtol,atol : float The relative/absolute tolerance parameter for the edge detection. See numpy.isclose. Returns ------- dataArray Notes ----- Edges may be smoothed by convolution with a Gaussian.:: edge=2 x=np.r_[-4*edge:4*edge:200j] f=js.formel.box(x,edges=edge) res=js.formel.convolve(f,js.formel.gauss(x,0,0.2)) """ edges=np.atleast_1d(edges) if edges.shape[0]<2:edges=np.r_[-abs(edges[0]),abs(edges[0])] v=np.zeros_like(x) v[(x>edges[0]) & (x<edges[1])]=1 v[(np.isclose(x,edges[0])) | (np.isclose(x,edges[1]))]=edgevalue box=dA(np.c_[x,v].T) box.setColumnIndex(iey=None) box.modelname=sys._getframe().f_code.co_name return box
[docs]def gauss(x,mean=1,sigma=1): r""" Normalized Gaussian function. .. math:: g(x)= \frac{1}{sigma\sqrt{2\pi}} e^{-0.5(\frac{x-mean}{sigma})^2} Parameters ---------- x : float Values mean : float Mean value sigma : float 1/e width Returns ------- Gaussian : dataArray """ x=np.atleast_1d(x) result=dA(np.c_[x,np.exp(-0.5*(x-mean)**2/sigma**2)/sigma/np.sqrt(2*np.pi)].T) result.setColumnIndex(iey=None) result.mean=mean result.sigma=sigma result.modelname=sys._getframe().f_code.co_name return result
[docs]def lorentz(x,mean=1,gamma=1): r""" Normalized Lorentz function .. math :: f(x) = \frac{gamma}{\pi((x-mean)^2+gamma^2)} Parameters ---------- gamma : float Half width half maximum mean : float Mean value Returns ------- Lorentz function : dataArray """ x=np.atleast_1d(x) result=dA(np.c_[x,gamma/((x-mean)**2+gamma**2)/np.pi].T) result.setColumnIndex(iey=None) result.mean=mean result.gamma=gamma result.modelname=sys._getframe().f_code.co_name return result
[docs]def lognorm(x,mean=1,sigma=1): r""" Lognormal distribution function. .. math:: f(x>0)= \frac{1}{\sqrt{2\pi}\sigma x }\,e^{ -\frac{(\ln(x)-\mu)^2}{2\sigma^2}} Parameters ---------- x : array x values mean : float mean sigma : float sigma Returns ------- lognorm distribution : dataArray """ mu=math.log(mean**2/(sigma+mean**2)**0.5) nu=(math.log(sigma/mean**2+1))**0.5 distrib=stats.lognorm(s=nu,scale=math.exp(mu)) result=dA(np.c_[x,distrib.pdf(x)].T) result.setColumnIndex(iey=None) result.mean=mean result.sigma=sigma result.modelname=sys._getframe().f_code.co_name return result
[docs]def voigt(x, center=0, fwhm=1,lg=1,asym=0, amplitude=1): """ Voigt function for peak analysis (normalized). The Voigt function is a convolution of gaussian and lorenzian shape peaks for peak analysis. The Lorenzian shows a stronger contribution outside FWHM with a sharper peak. Asymmetry of the shape can be added by a sigmoidal change of the FWHM [2]_. Parameters ---------- x : array Axis values. center : float Center of the distribution. fwhm : float Full width half maximum of the Voigt function. lg : float, default = 1 Lorenzian/gaussian fraction of both FWHM, describes the contributions of gaussian and lorenzian shape. - lorenzian/gaussian >> 1 lorenzian, - lorenzian/gaussian ~ 1 central part gaussian, outside lorenzian wings - lorenzian/gaussian << 1. gaussian asym : float, default=0 asymmetry factor in sigmoidal as :math:`2*fwhm/(1+np.exp(asym*(x-center)))` For a=0 the Voigt is symmetric with fwhm. amplitude : float, default = 1 amplitude Returns ------- Voigt function : dataArray .center .sigma .gamma .fwhm .asymmetry .lorenzianOverGaussian References ---------- .. [1] https://en.wikipedia.org/wiki/Voigt_profile .. [2] Aaron L. Stancik, Eric B. Brauns A simple asymmetric lineshape for fitting infrared absorption spectra Vibrational Spectroscopy 47 (2008) 66–69 """ ln2=math.log(2) # calc the fwhm in gauss and lorenz to get the final FWHM in the Voigt function with an accuracy of 0.02% # as given in Olivero, J. J.; R. L. Longbothum (February 1977). # Empirical fits to the Voigt line width: A brief review". Journal of Quantitative Spectroscopy and Radiative Transfer. 17 (2): 233–236. # doi:10.1016/0022-4073(77)90161-3 FWHM=fwhm/(0.5346*lg+(0.2166*lg**2+1)**0.5) z =lambda fwhm: ( (x-center)+ 1j* lg * fwhm/2. )/math.sqrt(2) / (fwhm/(2*np.sqrt(2*ln2))) # the sigmoidal fwhm for asymmetry afwhm=lambda fwhm,a: 2*fwhm/(1+np.exp(a*(x-center))) # calc values with asymmetric FWHM val = amplitude / (afwhm(FWHM,asym)/ (2*np.sqrt(2*ln2))) / math.sqrt(2*np.pi) * special.wofz(z(afwhm(FWHM,asym))).real sigma=(FWHM/ (2*np.sqrt(2*ln2))) gamma=FWHM/2. result=dA(np.c_[x,val].T) result.setColumnIndex(iey=None) result.center=center result.sigma=sigma result.gamma=gamma result.fwhm=fwhm result.asymmetry=asym result.lorenzianOverGaussian=lg result.modelname=sys._getframe().f_code.co_name return result
[docs]def Ea(z,a,b=1): r""" Mittag-Leffler function for real z and real a,b with 0<a, b<0. Evaluation of the Mittag-Leffler (ML) function with 1 or 2 parameters by means of the OPC algorithm [1]. The routine evaluates an approximation Et of the ML function E such that :math:`|E-Et|/(1+|E|) \approx 10^{-15}` Parameters ---------- z : real array Values a : float, real positive Parameter alpha b : float, real positive, default=1 Parameter beta Returns ------- array Notes ----- - Mittag Leffler function defined as .. math:: E(x,a,b)=\sum_{k=0}^{\inf} \frac{z^k}{\Gamma(b+ak)} - The code uses code from K.Hinsen at https://github.com/khinsen/mittag-leffler which is a Python port of `Matlab implementation <https://se.mathworks.com/matlabcentral/fileexchange/48154-the-mittag-leffler-function>`_ of the generalized Mittag-Leffler function as described in [1]_. Examples -------- :: import numpy as np import jscatter as js from scipy import special x=np.r_[-10:10:0.1] # tests np.all(js.formel.Ea(x,1,1)-np.exp(x)<1e-10) z = np.linspace(0., 2., 50) np.allclose(js.formel.Ea(np.sqrt(z), 0.5), np.exp(z)*special.erfc(-np.sqrt(z))) z = np.linspace(-2., 2., 50) np.allclose(js.formel.Ea(z**2, 2.), np.cosh(z)) References ---------- .. [1] R. Garrappa, Numerical evaluation of two and three parameter Mittag-Leffler functions, SIAM Journal of Numerical Analysis, 2015, 53(3), 1350-1369 """ if a<=0 or b<=0: raise ValueError('a and b must be real and positive.') g=1 # only use gamma=1 log_epsilon = np.log(1.e-15) # definition through Laplace transform inversion # we use for this the code from K.Hinsen, see header in ml_internal _eaLPI = lambda z : np.vectorize(ml_internal.LTInversion,[np.float64])(1,z,a,b,g,log_epsilon) res = np.zeros_like(z,dtype=np.float64) eps=1.e-15 choose=np.abs(z)<=eps res[ choose]=1/special.gamma(b) res[~choose]=_eaLPI(z[~choose]) return res
[docs]def boseDistribution(w,temp): r""" Bose distribution for integer spin particles in non-condensed state (hw>0). .. math:: n(w) &= \frac{1}{e^{hw/kT}-1} &\ hw>0 &= 0 &\: hw=0 \: This is not real just for convenience! Parameters ---------- w : array Frequencies in units 1/ns temp : float Temperature in K Returns ------- dataArray """ h=constants.h k=constants.k bose=np.piecewise(w,[w==0], [0,1/(np.exp(h*w[w!=0]*1e9/(k*temp))-1)] ) result=dA(np.c_[w,bose].T) result.setColumnIndex(iey=None) result.columnname='w; n' result.temperature=temp result.modelname=sys._getframe().f_code.co_name return result
######################################################################## # quadrature
[docs]class AccuracyWarning(Warning): pass
def _cached_p_roots(n): """ Cache p_roots results to speed up calls of the fixed_quad function. """ #scipy.integrate.quadrature if n in _cached_p_roots.cache: return _cached_p_roots.cache[n] _cached_p_roots.cache[n] = p_roots(n) return _cached_p_roots.cache[n] _cached_p_roots.cache = dict()
[docs]def parQuadratureFixedGauss(func, lowlimit, uplimit, parname, n=5, weights=None, **kwargs): """ Compute a definite integral using fixed-order Gaussian quadrature . Integrate func over parname from a to b using Gauss-Legendre quadrature [1]_ of order `n` for all .X. If function returns ndarray all is integrated and returned as ndarray. If function returns dataArray, only the .Y values is integrated and returned as dataArray. Parameters ---------- func : callable A Python function or method returning a vector array of dimension 1. If func returns dataArray .Y is integrated. lowlimit : float Lower limit of integration. uplimit : float Upper limit of integration. parname : string Name of the integration variable which should be a scalar. after evaluation the correspinding attribute has the mean value with weights. weights : ndarray shape(2,N),default=None - Weights for integration along parname e.g. a Gaussian with a<weights[0]<b and weights[1] contains weight values - Missing values are linear interpolated (faster). If None equal weights are used. kwargs : dict, optional Extra keyword arguments to pass to function, if any. n : int, optional Order of quadrature integration. Default is 5. ncpu : int,default=1, optional Number of cpus in the pool. Set this to zero if the integated function uses multiprocessing to avoid errors. - 0 -> all cpus are used - int>0 min (ncpu, mp.cpu_count) - int<0 ncpu not to use Returns ------- array or dataArray Examples -------- :: t=np.r_[1:100] gg=js.formel.gauss(t,50,10) js.formel.parQuadratureFixedGauss(js.formel.gauss,0,100,'x',mean=50,sigma=10,n=50) Notes ----- Reimplementation of scipy.integrate.quadrature.fixed_quad to work with vector output of the integrand function and weights . References ---------- .. [1] https://en.wikipedia.org/wiki/Gaussian_quadrature """ x, w = _cached_p_roots(n) x = np.real(x) if np.isinf(lowlimit) or np.isinf(uplimit): raise ValueError("Gaussian quadrature is only available for finite limits.") y = (uplimit - lowlimit) * (x + 1) / 2.0 + lowlimit if weights is not None: wy=np.interp(y,weights[0],weights[1]) normfactor=np.trapz(weights[1],weights[0]) parmean=np.trapz(weights[1]*weights[0],weights[0])/normfactor else: wy=np.ones_like(y) normfactor= uplimit - lowlimit parmean= (uplimit + lowlimit) / 2 # set default for ncpu to use only one process. if 'ncpu' not in kwargs: kwargs.update({'ncpu':1,'output':False}) # calc the function values res=parallel.doForList(func,looplist=y,loopover=parname,**kwargs) # res = [func(**dict(kwargs, **{parname: yy})) for yy in y] # single cpu if isinstance(res[0],dA): Y=[r.Y for r in res] res[0].Y= (uplimit - lowlimit) / 2.0 * np.sum(w * wy * np.atleast_2d(Y).T, axis=-1) res[0].weightNormFactor=normfactor setattr(res[0],parname,parmean) return res[0] else: return (uplimit - lowlimit) / 2.0 * np.sum(w * wy * np.atleast_2d(res).T, axis=-1)
pQFG=parQuadratureFixedGauss
[docs]def parQuadratureAdaptiveGauss(func, lowlimit, uplimit, parname, weights=None, tol=1.e-8, rtol=1.e-8, maxiter=50, miniter=8, **kwargs): """ Compute a definite integral using fixed-tolerance Gaussian quadrature for vector output. Adaptive integration of func from `a` to `b` using Gaussian quadrature adaptivly increasing number of points by 8. If function returns ndarray each element is integrated and returned as ndarray of same dimension. If function returns dataArray, only the .Y values is integrated and returned as dataArray. Parameters ---------- func : function A Python function or method to integrate. lowlimit : float Lower limit of integration. uplimit : float Upper limit of integration. parname : string name of the integration variable which should be a scalar. weights : ndarray shape(2,N),default=None - Weights for integration along parname e.g. a Gaussian with a<weights[0]<b and weights[1] contains weight values - Missing values are linear interpolated (faster). If None equal weights are used. kwargs : dict, optional Extra keyword arguments to pass to function, if any. tol, rtol : float, optional Iteration stops when error between last two iterates is less than `tol` OR the relative change is less than `rtol`. maxiter : int, default 50, optional Maximum order of Gaussian quadrature. miniter : int, default 8, optional Minimum order of Gaussian quadrature. ncpu : int, optional Number of cpus in the pool. Set this to zero if the integated function uses multiprocessing to avoid errors. - not given or 0 -> all cpus are used - int>0 min (ncpu, mp.cpu_count) - int<0 ncpu not to use Returns ------- val : float Gaussian quadrature approximation (within tolerance) to integral for all vector elements. err : float Difference between last two estimates of the integral. Examples -------- :: t=np.r_[1:100] gg=js.formel.gauss(t,50,10) js.formel.parQuadratureAdaptiveGauss(js.formel.gauss,0,100,'x',mean=50,sigma=10) Notes ----- Reimplementation of scipy.integrate.quadrature.quadrature to work with vector output of the integrand function. References ---------- .. [1] https://en.wikipedia.org/wiki/Gaussian_quadrature """ val = np.inf err = np.inf maxiter = max(miniter+1, maxiter) for n in range(maxiter ,miniter, -8)[::-1]: result = parQuadratureFixedGauss(func, lowlimit, uplimit, parname, n,weights, **kwargs) if isinstance(result,dA): newval=result.Y else: newval=result err = abs(newval-val) val = newval if np.all(err < tol) or np.all(err < rtol*abs(val)): break else: warnings.warn("maxiter (%d) exceeded in %s. Latest maximum abs. error %e and rel error = %e" % (maxiter, _getFuncCode(func).co_name, err.flatten().max(), np.max(abs(err) / abs(val))), AccuracyWarning) if isinstance(result,dA): result.IntegralErr_funktEval=err,n return result
pQAG=parQuadratureAdaptiveGauss
[docs]def parQuadratureSimpson(funktion, lowlimit, uplimit, parname, weights=None, tol=1e-6, rtol=1e-6, dX=None, **kwargs): """ Integrate a function over one of its parameters with weights using the adaptive Simpson rule. Integrate by adaptive Simpson integration for all .X values at once. Only .Y values are integrated and checked for tol criterion. Attributes and non .Y columns correspond to the weighted mean of parname. Parameters ---------- funktion : function Function returning dataArray or array lowlimit,uplimit : float Interval borders to integrate parname : string Parname to integrate weights : ndarray shape(2,N),default=None - Weights for integration along parname e.g. a Gaussian with a<weights[0]<b and weights[1] contains weight values - Missing values are linear interpolated (faster). If None equal weights are used. tol,rtol : float, default=1e-6 | Relative error or absolute error to stop integration. Stop if one is full filled. | Tol is divided for each new interval that the sum of tol is kept. | .IntegralErr_funktEvaluations in dataArray contains error and number of points in interval. dX : float, default=None Minimal distance between integration points to determine a minimal step for integration variable. kwargs : Additional parameters to pass to funktion. If parname is in kwargs it is overwritten. Returns ------- dataArray or array dataArrays have additional parameters as error and weights. Notes ----- What is the meaning of tol in simpson method? If the error in an interval exceeds tol, the algorithm subdivides the interval in two equal parts with each :math:`tol/2` and applies the method to each subinterval in a recursive manner. The condition in interval i is :math:`error=|f(ai,mi)+f(mi,bi)-f(ai,bi)|/15 < tol`. The recursion stops in an interval if the improvement is smaller than tol. Thus tol is the upper estimate for the total error. Here we use a absolute (tol) and relative (rtol) criterion: :math:`|f(ai,mi)+f(mi,bi)-f(ai,bi)|/15 < rtol*fnew` with :math:`fnew= ( f(ai,mi)+f(mi,bi) + [f(ai,mi)+f(mi,bi)-f(ai,bi)]/15 )` as the next improved value As this is tested for all .X the **worst** case is better than tol, rtol. The algorithm is efficient as it memoizes function evaluation at each interval border and reuses the result. This reduces computing time by about a factor 3-4. Different distribution can be found in scipy.stats. But any distribution given explicitly can be used. E.g. triangular np.c_[[-1,0,1],[0,1,0]].T Examples -------- :: import jscatter as js import numpy as np import scipy # testcase: integrate over x of a function # area under normalized gaussian is 1 js.formel.parQuadratureSimpson(js.formel.gauss,-10,10,'x',mean=0,sigma=1) # # normal distribtion of parameter D with width ds t=np.r_[0:150:0.5] D=0.3 ds=0.1 diff=js.dynamic.simpleDiffusion(t=t,q=0.5,D=D) distrib =scipy.stats.norm(loc=D,scale=ds) x=np.r_[D-5*ds:D+5*ds:30j] pdf=np.c_[x,distrib.pdf(x)].T diff_g=js.formel.parQuadratureSimpson(js.dynamic.simpleDiffusion,-3*ds+D,3*ds+D,parname='D',weights=pdf,tol=0.01,q=0.5,t=t) # compare it p=js.grace() p.plot(diff,le='monodisperse') p.plot(diff_g,le='polydisperse') p.xaxis(scale='l') p.legend() References ---------- .. [1] https://en.wikipedia.org/wiki/Adaptive_Simpson's_method """ # We have to deal with return values as arrays and dataArrays if lowlimit==uplimit: # return function with parname=a ; to be consistent result=funktion(**dict(kwargs, **{parname:lowlimit})) if isinstance(result,dA): result.weightNormFactor=1 return result if lowlimit>uplimit: lowlimit, uplimit= uplimit, lowlimit def _memoize(f): """ avoid multiple calculations of same values at borders in each interation saves factor 3-4 in time """ f.memo={} def _helper(x): if x not in f.memo: # this overwrites the kwargs[parname] with x Y=f(**dict(kwargs,**{parname:x})) if isinstance(Y,dA): # calc the function value f.memo[x]=Y.Y else: f.memo[x]=Y if weights is not None: # weight of value f.memo[x]*=np.interp(x,weights[0],weights[1]) return f.memo[x] return _helper stack=[[lowlimit, uplimit, tol]] if dX is None: dX=2*(uplimit-lowlimit) funkt=_memoize(funktion) Integral=0 Err=0 nn=0 # do adaptive integration while stack : # is not empty [x1,x2,err]=stack.pop() m=(x1+x2)/2. I1=(funkt(x1)+4*funkt(m)+funkt(x2))*(x2-x1)/6. # Simpson rule. mleft=(x1+m)/2. Ileft=(funkt(x1)+4*funkt(mleft)+funkt(m))*(m-x1)/6. # Simpson rule. mright=(m+x2)/2. Iright=(funkt(m)+4*funkt(mright)+funkt(x2))*(x2-m)/6. # Simpson rule. # does the new point improve better than interval err on relative scale if (np.all(np.abs(Ileft+Iright-I1)<15*rtol*(Ileft+Iright+(Ileft+Iright-I1)/15.)) or \ np.all(np.abs((Ileft+Iright-I1))<15*err)) and\ (x2-x1) < dX: # good enough in this interval Integral+=(Ileft+Iright+(Ileft+Iright-I1)/15.) Err+=abs((Ileft+Iright-I1)/15.) nn+=1 else: # split interval to improve with new points stack.append([x1,m,err/2]) stack.append([m,x2,err/2]) # calc final result with normalized weights if weights is not None: normfactor=np.trapz(weights[1],weights[0]) parmean=np.trapz(weights[1]*weights[0],weights[0])/normfactor else: normfactor= uplimit - lowlimit parmean= (lowlimit + uplimit) / 2 result=funktion(**dict(kwargs,**{parname:parmean})) if not isinstance(result,dA): return Integral result.Y=Integral result.IntegralErr_funktEvaluations=max(Err),nn result.weightNormFactor=normfactor return result
pQS=parQuadratureSimpson
[docs]def simpleQuadratureSimpson(funktion, lowlimit, uplimit, parname, weights=None, tol=1e-6, rtol=1e-6, **kwargs): """ Integrate a scalar function over one of its parameters with weights using the adaptive Simpson rule. Integrate by adaptive Simpson integration for scalar function. Parameters ---------- funktion : function function to integrate lowlimit,uplimit : float interval to integrate parname : string parname to integrate weights : ndarray shape(2,N),default=None - Weights for integration along parname e.g. a Gaussian with a<weights[0]<b and weights[1] contains weight values - Missing values are linear interpolated (faster). If None equal weights are used. tol,rtol : float, default=1e-6 | Relative error for intervals or absolute integral error to stop integration. kwargs : additional parameters to pass to funktion if parname is in kwargs it is overwritten Returns ------- float Notes ----- What is the meaning of tol in simpson method? See parQuadratureSimpson. Examples -------- :: distrib =scipy.stats.norm(loc=1,scale=0.2) x=np.linspace(0,1,1000) pdf=np.c_[x,distrib.pdf(x)].T # define function f1=lambda x,p1,p2,p3:js.dA(np.c_[x,x*p1+x*x*p2+p3].T) # calc the weighted integral result=js.formel.parQuadratureSimpson(f1,0,1,parname='p2',weights=pdf,tol=0.01,p1=1,p3=1e-2,x=x) # something simple should be 1 js.formel.simpleQuadratureSimpson(js.formel.gauss,-10,10,'x',mean=0,sigma=1) References ---------- .. [1] https://en.wikipedia.org/wiki/Adaptive_Simpson's_method """ if lowlimit==uplimit: # return function with parname=a ; to be consistent result=funktion(**dict(kwargs, **{parname:lowlimit})) return result if lowlimit>uplimit: lowlimit, uplimit= uplimit, lowlimit def _memoize(f): """ avoid multiple calculations of same values at borders in each interation saves factor 3-4 in time """ f.memo={} def _helper(x): if x not in f.memo: # this overwrites the kwargs[parname] with x Y=f(**dict(kwargs,**{parname:x})) if isinstance(Y,dA):Y=Y.Y f.memo[x]=Y if weights is not None: f.memo[x]*=np.interp(x,weights[0],weights[1]) return f.memo[x] return _helper stack=[[lowlimit, uplimit, tol]] funkt=_memoize(funktion) Integral=0 Err=0 # do adaptive integration while stack: # is not empty [x1,x2,err]=stack.pop() m=(x1+x2)/2. I1=(funkt(x1)+4*funkt(m)+funkt(x2))*(x2-x1)/6. # Simpson rule. mleft=(x1+m)/2. Ileft=(funkt(x1)+4*funkt(mleft)+funkt(m))*(m-x1)/6. # Simpson rule. mright=(m+x2)/2. Iright=(funkt(m)+4*funkt(mright)+funkt(x2))*(x2-m)/6. # Simpson rule. # does the new point improve better than interval err on relative scale if np.all(np.abs(Ileft+Iright-I1)<15*rtol*(Ileft+Iright+(Ileft+Iright-I1)/15.)) or \ np.all(np.abs((Ileft+Iright-I1))<15*err): # good enough in this interval Integral+=(Ileft+Iright+(Ileft+Iright-I1)/15.) Err+=abs((Ileft+Iright-I1)/15.) else: # split interval to improve with new points stack.append([x1,m,err/2]) stack.append([m,x2,err/2]) return Integral
sQS=simpleQuadratureSimpson
[docs]def convolve(A,B,mode='same',normA=False,normB=False): r""" Convolve A and B with proper tracking of the output X axis. Approximate the convolution integral as the discrete, linear convolution of two one-dimensional sequences. Missing values are linear interpolated to have matching steps. Values outside of X ranges are set to zero. Parameters ---------- A,B : dataArray, ndarray To be convolved arrays (length N and M). - dataArray convolves Y with Y values - ndarray A[0,:] is X and A[1,:] is Y normA,normB : bool, default False Determines if A or B should be normalised that :math:`\int_{x_{min}}^{x_{max}} A(x) dx = 1`. mode : 'full','same','valid', default 'same' See example for the difference in range. - 'full' Returns the convolution at each point of overlap, with an output shape of (N+M-1,). At the end-points of the convolution, the signals do not overlap completely, and boundary effects may be seen. - 'same' Returns output of length max(M, N). Boundary effects are still visible. - 'valid' Returns output of length M-N+1. Returns ------- dataArray (with attributes from A) Notes ----- - :math:`A\circledast B (t)= \int_{-\infty}^{\infty} A(x) B(t-x) dx = \int_{x_{min}}^{x_{max}} A(x) B(t-x) dx` - If A,B are only 1d array use np.convolve. - If attributes of B are needed later use .setattr(B,'B-') to prepend 'B-' for B attributes. Examples -------- Demonstrate the difference between modes :: import jscatter as js;import numpy as np s1=3;s2=4;m1=50;m2=10 G1=js.formel.gauss(np.r_[0:100.1:0.1],mean=m1,sigma=s1) G2=js.formel.gauss(np.r_[-30:30.1:0.2],mean=m2,sigma=s2) p=js.grace() p.title('Convolution of Gaussians (width s mean m)') p.subtitle(r's1\S2\N+s2\S2\N=s_conv\S2\N ; m1+m2=mean_conv') p.plot(G1,le='mean 50 sigma 3') p.plot(G2,le='mean 10 sigma 4') ggf=js.formel.convolve(G1,G2,'full') p.plot(ggf,le='full') gg=js.formel.convolve(G1,G2,'same') p.plot(gg,le='same') gg=js.formel.convolve(G1,G2,'valid') p.plot(gg,le='valid') gg.fit(js.formel.gauss,{'mean':40,'sigma':1},{},{'x':'X'}) p.plot(gg.modelValues(),li=1,sy=0,le='fit m=$mean s=$sigma') p.legend(x=100,y=0.1) p.xaxis(max=150,label='x axis') p.yaxis(min=0,max=0.15,label='y axis') References ---------- .. [1] Wikipedia, "Convolution", http://en.wikipedia.org/wiki/Convolution. """ # convert to array if hasattr(A,'_isdataArray'): AY=A.Y AX=A.X else: AX=A[0,:] AY=A[1,:] if normA: AY=AY/np.trapz(AY,AX) if hasattr(B,'_isdataArray'): BY=B.Y BX=B.X else: BX=B[0,:] BY=B[1,:] if normB: BY=BY/np.trapz(BY,BX) # create a combined x scale dx=min(np.diff(AX).min(),np.diff(BX).min()) ddx=0.1*dx # this accounts for the later >= BX.min() to catch problems with numerical precision XX=np.r_[min(AX.min(),BX.min()):max(AX.max(),BX.max())+dx:dx] # interpolate missing values #if x scale is equal this is nearly no overhead AXX = XX[(XX >= AX.min()-ddx) & (XX <= AX.max()+ddx)] AY_xx = np.interp(AXX, AX, AY, left=0, right=0) BXX = XX[(XX >= BX.min()-ddx) & (XX <= BX.max()+ddx)] BY_xx = np.interp(BXX, BX, BY, left=0, right=0) if len(AXX)<len(BXX): # AXX always the larger one; this is also done in C source AXX,BXX=BXX,AXX # convolve res = np.convolve(AY_xx, BY_xx, mode=mode) * dx # define x scale # n,nleft,nright,length to reproduce C-source of convolve n=BXX.shape[0] l=AXX.shape[0] xx = np.r_[AX.min() + BX.min():AX.max() + BX.max()+dx:dx] if mode=='full': # length=l+n-1 nleft=0 nright=l+n-1 elif mode=='valid': # length=l-n+1 nleft=n-1 nright=l else: # mode=='same' # length=l nleft=(n-1)//2 nright=nleft+l xx=xx[nleft:nright] result=dA(np.c_[xx,res].T) result.setattr(A) return result
[docs]def sphereAverage(function,relError=300,*args,**kwargs): """ Spherical average - non-parallel A Fibonacci lattice or Monte Carlo integration with pseudo random grid is used. Parameters ---------- function : function Function to evaluate returning a list of return values (all are integrated) function gets cartesian coordinate of point on unit sphere as first argument relError : float, default 300 Determines how points on sphere are selected for integration - >=1 Fibonacci Lattice with relError*2+1 points (min 15 points) - 0<1 Pseudo random points on sphere (see randomPointsOnSphere). Stops if relative improvement in mean is less than relError (uses steps of 20*ncpu new points). Final error is (stddev of N points) /sqrt(N) as for Monte Carlo methods. even if it is not a correct 1-sigma error in this case. args,kwargs : Forwarded to function Returns ------- array like : Values from function and appended Monte Carlo error estimates. Examples -------- :: def f(x,r): return [js.formel.xyz2rphitheta(x)[1:].sum()*r] js.formel.sphereAverage(f,relError=500,r=1) js.formel.sphereAverage(f,relError=0.01,r=1) """ if relError<0: relError=abs(relError) if relError==0: print('Try again with relError > 0') return elif 0<relError<1: steps=40 points=rphitheta2xyz(randomPointsOnSphere(NN=steps,skip=0)) npoints = steps results=np.r_[[np.array(function(point,*args,**kwargs),ndmin=1) for point in points]] prevmean=results.mean(axis=0).real #prevstd=results.std(axis=0).real while 1: points=rphitheta2xyz(randomPointsOnSphere(NN=steps,skip=npoints)) npoints+=steps result=np.r_[[np.array(function(point,*args,**kwargs),ndmin=1) for point in points]] results=np.r_[results,np.array(result,ndmin=1)] mean=results.mean(axis=0).real #std=results.std(axis=0).real if np.all( abs(mean-prevmean) < relError*abs(mean) ) : # np.all(std / mean / (results.shape[0] - 1) ** 0.5 < relError): # MC error break prevmean = mean #prevstd = std elif relError>=1: qfib=fibonacciLatticePointsOnSphere(max(relError,7),1) points=rphitheta2xyz(qfib) # to cartesian results=np.r_[[np.array(function(point,*args,**kwargs),ndmin=1) for point in points]] return np.r_[results.mean(axis=0),results.std(axis=0)/np.sqrt(results.shape[0]-1)]
[docs]def parDistributedAverage(funktion, sig, parname, type='normal', nGauss=30, **kwargs): """ Average a function assuming a parameter is distributed with width sig. Function average over a parameter with weights determined from probability distribution. Adaptive integration over given distribution or summation with weights is used. Parameters ---------- funktion : function Function to integrate with distribution weight. Function needs to return dataArray. sig : float width parameter of the distribution, see Notes parname : string Name of the parameter of funktion which shows a distribution type : 'normal','lognorm','gamma','lorentz','uniform','poisson','duniform', default 'normal' Type of the distribution kwargs : parameters Any additonal kword parameter to pass to function. The value of parname will be the mean value of the distribution. nGauss : float , default=30 Order of quadrature integration as number of intervals in Gauss–Legendre quadrature over distribution. Distribution is integrated in probability interval [0.001..0.999]. ncpu : int, optional Number of cpus in the pool. Set this to zero if the integated function uses multiprocessing to avoid errors. - not given or 0 -> all cpus are used - int>0 min (ncpu, mp.cpu_count) - int<0 ncpu not to use Returns ------- dataArray as returned from function with - .parname_mean = mean of parname - .parname_std = standard deviation of parname Notes ----- The used distributions are from scipy.stats. Choose the distribution according to the problem. mean is the value in kwargs[parname]. mean and sig are used as: * norm : | mean , std | stats.norm(loc=mean,scale=sig) * lognorm : | mean and sig evaluate to mean and std | mu=math.log(mean**2/(sig+mean**2)**0.5) | nu=(math.log(sig/mean**2+1))**0.5 | stats.lognorm(s=nu,scale=math.exp(mu)) * gamma : | mean and sig evaluate to mean and std | stats.gamma(a=mean**2/sig**2,scale=sig**2/mean) * lorentz = cauchy: | mean and std are not defined. Use FWHM instead to describe width. | sig=FWHM | stats.cauchy(loc=mean,scale=sig)) * uniform : | sig is width | stats.uniform(loc=mean-sig/2.,scale=sig)) * poisson: stats.poisson(mu=mean,loc=sig) * duniform: | sig>1 | stats.randint(low=mean-sig, high=mean+sig) For more distribution look into this source code and use it appropriate with scipy.stats. Examples -------- :: import jscatter as js p=js.grace() q=js.loglist(0.1,5,500) sp=js.ff.sphere(q=q,radius=5) p.plot(sp,sy=[1,0.2],legend='single radius') p.yaxis(scale='l',label='I(Q)') p.xaxis(scale='n',label='Q / nm') sig=0.2 p.title('radius distribution with width %.g' %(sig)) sp2=js.formel.pDA(js.ff.sphere,sig,'radius',type='normal',q=q,radius=5,nGauss=100) p.plot(sp2,li=[1,2,2],sy=0,legend='normal 100 points Gauss ') sp4=js.formel.pDA(js.ff.sphere,sig,'radius',type='normal',q=q,radius=5,nGauss=30) p.plot(sp4,li=[1,2,3],sy=0,legend='normal 30 points Gauss ') sp5=js.formel.pDA(js.ff.sphere,sig,'radius',type='normal',q=q,radius=5,nGauss=5) p.plot(sp5,li=[1,2,5],sy=0,legend='normal 5 points Gauss ') sp3=js.formel.pDA(js.ff.sphere,sig,'radius',type='lognormal',q=q,radius=5) p.plot(sp3,li=[3,2,4],sy=0,legend='lognormal') sp6=js.formel.pDA(js.ff.sphere,sig,'radius',type='gamma',q=q,radius=5) p.plot(sp6,li=[2,2,6],sy=0,legend='gamma ') # an unrealistic example sp7=js.formel.pDA(js.ff.sphere,1,'radius',type='poisson',q=q,radius=5) p.plot(sp7,li=[1,2,6],sy=0,legend='poisson ') sp8=js.formel.pDA(js.ff.sphere,1,'radius',type='duniform',q=q,radius=5) p.plot(sp8,li=[1,2,6],sy=0,legend='duniform ') p.legend() """ mean=kwargs[parname] # define the distribution with parameters if type=='poisson': distrib=stats.poisson(mu=mean,loc=sig) elif type=='duniform': sigm=max(sig,1) distrib = stats.randint(low=mean-sigm, high=mean+sigm) elif type=='lognorm': mu=math.log(mean**2/(sig+mean**2)**0.5) nu=(math.log(sig/mean**2+1))**0.5 distrib=stats.lognorm(s=nu,scale=math.exp(mu)) elif type=='gamma': distrib=stats.gamma(a=mean**2/sig**2,scale=sig**2/mean) elif type=='lorentz' or type=='cauchy': distrib=stats.cauchy(loc=mean,scale=sig) elif type=='uniform': distrib=stats.uniform(loc=mean-sig/2.,scale=sig) else:# type=='norm' default distrib=stats.norm(loc=mean,scale=sig) # get starting and end values for integration a=distrib.ppf(0.001) b=distrib.ppf(0.999) if type in ['poisson','duniform']: # discrete distributions x=np.r_[int(a):int(b+1)] w=distrib.pmf(x) result=[funktion(**dict(kwargs, **{parname: xi})) for xi in x] if isinstance(result[0],dA): result[0].Y=np.sum([result[i].Y*wi for i,wi in enumerate(w)],axis=0)/w.sum() else: result[0] = np.sum([result[i] * wi for i, wi in enumerate(w)], axis=0) / w.sum() result=result[0] else : # here we use the fixedGauss for integration x=np.linspace(a,b,1000) pdf=np.c_[x,distrib.pdf(x)].T # calc the weighted integral result=parQuadratureFixedGauss(funktion, a, b, parname=parname, n=nGauss, weights=pdf, **kwargs) normfactor=np.trapz(pdf[1],pdf[0]) if isinstance(result,dA): result.Y/=normfactor else: result /= normfactor if isinstance(result,dA): # calc mean and std and store in result setattr(result,parname+'_mean',distrib.mean()) setattr(result,parname+'_std',distrib.std()) if type=='lorentz' or type=='cauchy': setattr(result,parname+'_FWHM',2*sig) return result
pDA=parDistributedAverage
[docs]def viscosity(mat='h2o',T=293.15): """ Viscosity of pure solvents. For buffer solvents use bufferviscosity. Parameters ---------- mat : string 'h2o','d2o','toluol','methylcyclohexan', default h2o Solvent T : float Temperature T in Kelvin default 293K Returns ------- float : viscosity in Pa*s water H2O ~ 0.001 Pa*s =1 cPoise # Poise=0.1 Pa*s References ---------- .. [1] The Viscosity of Toluene in the Temperature Range 210 to 370 K M. J. Assael, N.K. Dalaouti, J.H., Dymond International Journal of Thermophysics, Vol. 21,291 No. 2, 2000 # accuracy +- 0.4 % laut paper Max error von Experiment data .. [2] Thermal Offset Viscosities of Liquid H2O, D2O, and T2O C. H. Cho, J. Urquidi, S. Singh, and G. Wilse Robinson J. Phys. Chem. B 1999, 103, 1991-1994 """ temp=T if re.match('^'+mat,'toluol'): # print 'Material Toluol Temperatur', temp , ' Viscosity in mPas (=cP) ', Tc,ck0,ck1,ck2,ck3,ck4=591.75,34.054,-219.46,556.183,-653.601,292.762 # critical temperature and coefficients T=temp/Tc vis29315=0.0005869 # Pas vis=vis29315*math.exp(ck0+ck1*T+ck2*T*T+ck3*T*T*T+ck4*T*T*T*T) return vis*1000 elif re.match('^'+mat,'methylcyclohexan'): # print 'Material Methylcyclohexan Temperatur', temp , ' Viscosity in mPas (=cP)' vis=0.001*math.exp(-4.48+1217./temp) return vis*1000 elif re.match('^'+mat,'d2o'): # print 'Material D2O Temperatur', temp , ' Viscosity in mPas (=cP) ', T0=231.832 # reference Temperature ck0=0.0 ck1=1.0 ck2=2.7990E-3 # Koeffizienten ck3=-1.6342E-5 ck4=2.9067E-8 gamma=1.55255 dT=temp-T0 vis231832=885.60402 # cPK^gamma vis=vis231832*(ck0+ck1*dT+ck2*dT**2+ck3*dT**3+ck4*dT**4)**(-gamma) # print vis return vis*1e-3 else: # print 'Material H2O Temperatur', temp , ' Viscosity in mPas (=cP) ', T0=225.334 # reference Temperature ck0=0.0 ck1=1.0 ck2=3.4741E-3 # Koeffizienten ck3=-1.7413E-5 ck4=2.7719E-8 gamma=1.53026 dT=temp-T0 vis225334=802.25336 # cPK^gamma vis=vis225334*1/((ck0+ck1*dT+ck2*dT**2+ck3*dT**3+ck4*dT**4)**gamma) # print vis return vis*1e-3
def _convertfromUltrascan(): """ Internal usage to document how bufferComponents.txt was generated Get xml file from ultrascan and convert to ascii file to read on module load (faster than xmltree) We use only the fields we need here. Ultrascan is released under GNU Lesser General Public License, version 3. See notice in bufferComponents.txt """ import xml.etree.ElementTree buffers = xml.etree.ElementTree.parse('bufferComponents.xml').getroot() bl=[] # new bufferlines bl+=['# buffer coefficients for density (dci) and viscosity (vci) as read from Ultrascan 3 '+'\n'] content=['name']+['dc0','dc1','dc2','dc3','dc4','dc5']+['vc0','vc1','vc2','vc3','vc4','vc5']+['unit','range'] bl+=['# '+' '.join(content)+'\n'] for buff in buffers: name=buff.attrib['name'].title().replace(' ','').replace('-','') if name[0].isdigit():name=name[1:]+name[0] line=[name] line += [buff[0].attrib[attrib] for attrib in ['c0','c1','c2','c3','c4','c5']] line += [buff[1].attrib[attrib] for attrib in ['c0', 'c1', 'c2', 'c3', 'c4', 'c5']] line += [buff.attrib[attrib].strip().replace(' ', '_') for attrib in ['unit', 'range']] bl+=[' '.join(line)+'\n'] bl.sort() with io.open(os.path.join(_path_,'data','bufferComponents.txt'),'w') as _f: _f.writelines(bl)
[docs]def bufferviscosity(composition, T=293.15, show=False): """ Viscosity of water with inorganic substances as used in biological buffers. Solvent with composition of H2O and D2O and additional components at temperature T. Ternary solutions allowed. Units are mol; 1l h2o = 55.50843 mol Based on data from ULTRASCAN3 [1]_ supplemented by the viscosity of H2O/D2O mixturees for conc=0. Parameters ---------- composition : list of compositional strings Compositional strings of chemical name as 'float'+'name' First float is content in Mol followed by component name as 'h2o' or 'd2o' light and heavy water were mixed with prepended fractions. ['1.5urea','0.1sodiumchloride','2h2o','1d2o'] for 1.5 M urea + 100 mM NaCl in a 2:1 mixture of h2o/d2o. By default '1h2o' is assumed. T : float, default 293.15 Temperature in K show : bool, default False Show composition and validity range of components and result in mPas. Returns ------- float viscosity in Pa*s Notes ----- - Viscosities of H2O/D2O mixtures mix by linear interpolation between concentrations (accuracy 0.2%) [2]_. - The change in viscosity due to components is added based on data from Ultrascan3 [1]_. - Multicomponent mixtures are composed of binary mixtures. - Glycerol%" is in unit "%weight/weight" for range="0-32%, here the unit is changed to weight% insthead of M. - Propanol1, Propanol2 are 1-Propanol, 2-Propanol References ---------- .. [1] http://www.ultrascan3.uthscsa.edu/ .. [2] Viscosity of light and heavy water and their mixtures Kestin Imaishi Nott Nieuwoudt Sengers, Physica A: Statistical Mechanics and its Applications 134(1):38-58 .. [3] Thermal Offset Viscosities of Liquid H2O, D2O, and T2O C. H. Cho, J. Urquidi, S. Singh, and G. Wilse Robinson J. Phys. Chem. B 1999, 103, 1991-1994 availible components:: h2o1 d2o1 """ if isinstance(composition,str): composition=[composition] cd2o=0 ch2o=0 nwl={} # nonwaterlist # decompose composition for compo in composition: compo=compo.lower() decomp=re.findall('\d+\.\d+|\d+|\D+',compo) if not re.match('\d',decomp[0]): raise KeyError('Component %s missing concentration ' %compo) component=''.join(decomp[1:]) conc=float(decomp[0]) # in Mol if component in ['h2o1','h2o' ]: ch2o+=conc elif component in ['d2o1','d2o']: cd2o+=conc else: nwl[component]=(conc,)+(_bufferDensityViscosity[component][6:14]) if ch2o==0 and cd2o==0: # default if no water composition was given ch2o=1 # # temperature dependent viscosity of h20/d2o mixture as basis in mPas (Ultrascan units for below) ch2od2o=(ch2o + cd2o) ch2o = ch2o / ch2od2o cd2o = cd2o / ch2od2o visc=(ch2o*viscosity(mat='h2o',T=T)+cd2o*viscosity(mat='d2o',T=T))*1000. # coefficints all for c=0 give water viscosity (which is not always correct!!) # coefficients[i>0] give increase from conc =0 # so add them up vc=np.r_[0.].repeat(6) # sum coefficients ff=np.r_[1.,1e-3,1e-2,1e-3,1e-4,1e-6] # standard powers for k,v in nwl.items(): c=v[0] # concentration (converted to mM) coefficients=v[1:7] # coefficients range=v[8] # validity range cp=np.r_[0,c**0.5,c,c*c,c**3,c**4] # concentration powers if show: print('%20s %12.3f M valid: %20s' %(k,c,range)) vc+=coefficients*cp if show: print(' h2o %.3f d2o %.3f => visc %.3f mPas' %(ch2o,cd2o, visc)) visc=visc+np.sum(vc*ff) # multiply by standard powers if show: print(' mixture => %.3f mPas' %(visc)) return visc/1000. # return use Pa*s
# complete the docstring from above _avlist=sorted(_bufferDensityViscosity.keys()) _i=0 while _i<len(_avlist): bufferviscosity.__doc__+=' '+''.join([' %-25s'%cc for cc in _avlist[_i:_i+3]])+'\n' _i+=3 bufferviscosity.__doc__+='\n'
[docs]def waterdensity(composition,T=293.15,units='mol',showvalidity=False): """ Density of water with inorganic substances (salts). Solvent with composition of H2O and D2O and additional inorganic components at temperature T. Ternary solutions allowed. Units are mol; 1l h2o = 55.50843 mol Parameters ---------- composition : list of compositional strings | Compositional string of chemical formula as 'float'+'chemical char' + integer | First float is content in mol (is later normalised to sum of contents) | chemical letter + number of atoms in formula (single atoms append 1 ,fractional numbers allowed) | e.g. | 'h2o1' or 'd2o1' light and heavy water with 'd1' for deuterium | 'c3h8o3' or 'c3h1d7o3' partial deuterated glycerol | ['55.55h2o','2.5Na1Cl1'] for 2.5 mol NaCl added to 1l h2o (55.55 mol) | ['20H2O1','35.55D2O1','0.1Na1Cl1'] h2o/d2o mixture with 100mMol NaCl units : default='mol' Anything except 'mol' unit is mass fraction 'mol' units is mol and mass fraction is calculated as mass=[mol]*mass_of_molecule e.g. 1l Water with 123mM NaCl ['55.5H2O1','0.123Na1Cl1'] T : float, default=293.15 temperature in K showvalidity : bool, default False Show additionally validity range for temperature and concentration according to [4]_. - Temperature range in °C - concentration in wt % or up to a saturated solution (satd) - error in 1/100 % see [4]_. Returns ------- float in g/ml Notes ----- - D2O maximum density 1.10596 at T=273.15+11.23 K [1]_ . - For mixtures of H2O/D2O molar volumes add with an accuracy of about 2e-4 cm**3/mol compared to 18 cm**3/mol molar volume [3]_. - Additional densities of binary aqueous solutions [4]_. References ---------- .. [1] The dilatation of heavy water K. Stokland, E. Ronaess and L. Tronstad Trans. Faraday Soc., 1939,35, 312-318 DOI: 10.1039/TF9393500312 .. [2] Effects of Isotopic Composition, Temperature, Pressure, and Dissolved Gases on the Density of Liquid Water George S. Kell JPCRD 6(4) pp. 1109-1131 (1977) .. [3] Excess volumes for H2O + D2O liquid mixtures Bottomley G Scott R Australian Journal of Chemistry 1976 vol: 29 (2) pp: 427 .. [4] Densities of binary aqueous solutions of 306 inorganic substances P. Novotny, O. Sohnel J. Chem. Eng. Data, 1988, 33 (1), pp 49–55 DOI: 10.1021/je00051a018 availible components:: h2o1 d2o1 TRIS c4h11n1o3 TABS c8h19n1o6s1 """ mw=18.01528 # mol weight water T-=273.15 wdensity=lambda T,a0,a1,a2,a3,a4,a5,b:(a0+a1*T+a2*T**2+a3*T**3+a4*T**4+a5*T**5)/(1+b*T)/1000. # 5-100 °C # D2O max density 1.10596 at T=11,23°C from Stokeland Trans. Faraday Soc., 1939,35, 312-31 # we use here 1104.633 instead of the original 1104.7056 of Kell to get the max density correct cD2O=[1104.633,28.88152,-7.652899e-3,-136.61854e-6,534.7350e-9,-1361.843e-12,25.91488e-3] # 0-150 K cH2O=[999.84252,16.945227,-7.9870641e-3,-46.170600e-6,105.56334e-9,-280.54337e-12,16.879850e-3] # additional density due to added inorganic components def _getadddensity(c,TT,decompp): pp=_aquasolventdensity[decompp] if decompp=='c4h11n1o3': return pp[0]*c**pp[1] elif decompp=='c8h19n1o6s1': return pp[0]*c**pp[1] else: if showvalidity: print(decompp,': Temperaturerange: ',pp[7],' concentration: ',pp[8],' error %:',pp[6]) return (pp[0]*c+pp[1]*c*TT+pp[2]*c*TT*TT+pp[3]*c**(3/2.)+pp[4]*c**(3/2.)*TT+pp[5]*c**(3/2.)*TT*TT)*1e-3 cd2o=0 ch2o=0 nonwaterlist={} adddensity=0 if isinstance(composition,str): composition=[composition] for compo in composition: compo=compo.lower() decomp=re.findall('\d+\.\d+|\d+|\D+',compo) if not re.match('\d',decomp[0]): # add a 1 as concentration in front if not there decomp=[1]+decomp if not re.match('\d+\.\d+|\d+',decomp[-1]): raise KeyError('last %s Element missing following number '%decomp[-1]) mass=np.sum([Elements[ele][1]*float(num) for ele,num in zip(decomp[1:][::2],decomp[1:][1::2])]) if units.lower()!='mol': # we convert here from mass to mol concentration=float(decomp[0])/mass else: concentration=float(decomp[0]) # concentration of this component decomp1=''.join(decomp[1:]) if decomp1=='h2o1': ch2o+=concentration elif decomp1=='d2o1': cd2o+=concentration else: nonwaterlist[decomp1]=concentration wff=(1000/mw)/(ch2o+cd2o) for k,v in nonwaterlist.items(): # additional density due to components adddensity+=_getadddensity(v*wff,T,k) density=cd2o/(cd2o+ch2o)*wdensity(T,cD2O[0],cD2O[1],cD2O[2],cD2O[3],cD2O[4],cD2O[5],cD2O[6]) density+=ch2o/(cd2o+ch2o)*wdensity(T,cH2O[0],cH2O[1],cH2O[2],cH2O[3],cH2O[4],cH2O[5],cH2O[6]) return density+adddensity
# complete the docstring from above _aqlist=sorted(_aquasolventdensity.keys()) _i=0 while _i<len(_aqlist): waterdensity.__doc__+=' '+''.join([' %-12s'%cc for cc in _aqlist[_i:_i+6]])+'\n' _i+=6 waterdensity.__doc__+='\n'
[docs]def scatteringLengthDensityCalc(composition,density=None,T=293,units='mol',mode='all'): """ Scattering length density of composites and water with inorganic components for xrays and neutrons. Parameters ---------- composition : list of concentration + chemical formula A string with chemical formula as letter + number and prepended concentration in mol or mmol. E.g. '0.1C3H8O3' or '0.1C3H1D7O3' for glycerol and deuterated glycerol ('D' for deuterium). - For single atoms append 1 to avoid confusion. Fractional numbers allowed, but think of meaning (Isotope mass fraction??) - For compositions use a list of strings preceded by mass fraction or concentration in mol of component. This will be normalized to total amount Examples: - ['4.5H2O1','0.5D2O1'] mixture of 10% heavy and 90% light water. - ['1.0h2o','0.1c3h8o3'] for 10% mass glycerol added to 100% h2o with units='mass' - ['55000H2O1','50Na3P1O4','137Na1Cl1'] for a 137mMol NaCl +50mMol phophate H2O buffer (1l is 55000 mM H2O) - ['1Au1'] gold with density 19.302 g/ml Remember to adjust density. density : float, default=None Density in g/cm**3 = g/ml. If not given function waterdensity is tried to calculate the solution density with inorganic components. In this case 'h2o1' and/or 'd2o1' need to be in composition. Otherwise measure by weighting a volume from pipette (lower accuracy) or densiometry (higher accuracy). units : 'mol' Anything except 'mol' prepended unit is mass fraction (default). 'mol' prepended units is mol and mass fraction is calculated as mass=[mol]*mass_of_molecule e.g. 1l Water with 123mmol NaCl ['55.5H2O1','0.123Na1Cl1'] mode : - 'xsld' xray scattering length density in nm**-2 - 'edensity' electron density in e/nm**3 - 'ncohsld' coherent scattering length density in nm**-2 - 'incsld' incoherent scattering length density in nm**-2 - 'all' [xsld, edensity, ncohsld, incsld, masses, masses full protonated, masses full deuterated, d2o/h2o fraction in composition] T : float, default=293 Temperature in °K Returns ------- sld : float or list of float corresponding to mode Notes ----- - edensity=be*massdensity/weightpermol*sum_atoms(numberofatomi*chargeofatomi) - be = scattering length electron =µ0*e**2/4/pi/m=2.8179403267e-6 nm - masses, masses full protonated, masses full deuterated for each chemical in composition. - In mode 'all' the masses can be used to calc the deuterated density if same volume is assumed. e.g. fulldeuterated_density=protonated_density/massfullprotonated*massfulldeuterated For density reference of H2O/D2O see waterdensity. Examples -------- :: # 5% D2O in H2O with 10% mass NaCl js.formel.scatteringLengthDensityCalc(['9.5H2O1','0.5D2O1','1Na1Cl1'],units='mass') # protein NaPi buffer in D2O prevalue in mmol; 55000 mmol H2O is 1 liter. js.formel.scatteringLengthDensityCalc(['55000D2O1','50Na3P1O4','137Na1Cl1']) # silica js.formel.scatteringLengthDensityCalc('1Si1O2',density=2.65) # gold js.formel.scatteringLengthDensityCalc(['1Au1'],density=19.32) # PEG1000 js.formel.scatteringLengthDensityCalc(['1C44H88O23'],density=1.21) """ edensity=[] bcdensity=[] bincdensity=[] total=0 totalmass=0 d2o=0 h2o=0 massfullprotonated=[] massfulldeuterated=[] totalmass=[] if not isinstance(density,(float,int,np.ndarray)): density=waterdensity(composition,T=T,units=units) density=float(density) if isinstance(composition,str): composition=[composition] for compo in composition: compo=compo.lower() # decompose in numbers and characters decomp=re.findall('\d+\.\d+|\d+|\D+',compo) if not re.match('\d',decomp[0]): # add a 1 as concentration in front if not there decomp=[1]+decomp mass=np.sum([Elements[ele][1]*float(num) for ele,num in zip(decomp[1:][::2],decomp[1:][1::2])]) if units.lower() is 'mol': ##if units=mol we convert here from mol to mass fraction massfraction=float(decomp[0])*mass else: massfraction=float(decomp[0]) sumZ=0 b_coherent=0 b_incoherent=0 # check for completeness at end if not re.match('\d+\.\d+|\d+',decomp[-1]): raise KeyError('last %s Element missing following number '%decomp[-1]) massfullprotonated+=[0] massfulldeuterated+=[0] for ele,num in zip(decomp[1:][::2],decomp[1:][1::2]): if ele in Elements.keys(): num=float(num) sumZ+=Elements[ele][0]*num massfullprotonated[-1]+=(Elements['h'][1]*num) if ele in ['h','d'] else (Elements[ele][1]*num) massfulldeuterated[-1]+=(Elements['d'][1]*num) if ele in ['h','d'] else (Elements[ele][1]*num) b_coherent+=Elements[ele][2]*num b_incoherent+=Elements[ele][3]*num else: print('decomposed to \n',decomp) raise KeyError('"%s" not found in Elements'%ele) # density[g/cm^3] / mass[g/mol]= N in mol/cm^3 --> N*Z is charge density if ''.join(decomp[1:])=='h2o1': h2o+=massfraction if ''.join(decomp[1:])=='d2o1': d2o+=massfraction edensity.append(massfraction*density*(constants.N_A/1e21)/mass*sumZ) bcdensity.append(massfraction*density*(constants.N_A/1e21)/mass*b_coherent) bincdensity.append(massfraction*density*(constants.N_A/1e21)/mass*b_incoherent) totalmass+=[mass] total+=massfraction if mode[0]=='e': return sum(edensity)/total elif mode[0]=='x': return sum(edensity)/total*felectron elif mode[0]=='n': return sum(bcdensity)/total elif mode[0]=='i': return sum(bincdensity)/total else: return sum(edensity)/total*felectron,\ sum(edensity)/total,\ sum(bcdensity)/total,\ sum(bincdensity)/total,\ totalmass,\ massfullprotonated,\ massfulldeuterated,\ d2o/(h2o+d2o) if h2o+d2o!=0 else 0
[docs]def watercompressibility(d2ofract=1,T=278,units='psnmg'): """ Isothermal compressibility of H2O and D2O mixtures. Compressibility in units ps^2*nm/(g/mol) or in 1/bar. Linear mixture according to d2ofract. Parameters ---------- d2ofract : float, default 1 Fraction D2O T : float, default 278K Temperature in K units : string 'psnmg' ps^2*nm/(g/mol) or 1/bar Returns ------- float Notes ----- To get kT*compressibility =compr*k_B/Nav*300/cm**3 in hwater 1.91e-24 cm**3 at 20°C References ---------- .. [1] Isothermal compressibility of Deuterium Oxide at various Temperatures Millero FJ and Lepple FK Journal of chemical physics 54,946-949 (1971) http://dx.doi.org/10.1063/1.1675024 .. [2] Precise representation of volume properties of water at one atmosphere G. S. Kell J. Chem. Eng. Data, 1967, 12 (1), pp 66–69 http://dx.doi.org/10.1021/je60032a018 """ t=T-273.15 h2o=lambda t:1e-6*(50.9804-0.374957*t+7.21324e-3*t**2-64.1785e-6*t**3+0.343024e-6*t**4-0.684212e-9*t**5) d2o=lambda t:1e-6*(53.61-0.4717*t+0.009703*t**2-0.0001015*t**3+0.0000005299*t**4) comp_1overbar=d2ofract*d2o(t)+(1-d2ofract)*h2o(t) # MMTK units ps, nm, g/mol if units=='psnmg': # factor=1e-8*m*s**2/(g/Nav) factor=1e-8*1e9*1e12**2# /(6.0221366999999997e+23/6.0221366999999997e+23) else: factor=1 compressibility_psnmgUnits=comp_1overbar*factor return compressibility_psnmgUnits
[docs]def dielectricConstant(material='d2o',T=293.15,conc=0,delta=5.5): r""" Dielectric constant of H2O and D2O buffer solutions. Dielectric constant :math:`\epsilon` of H2O and D2O (error +- 0.02) with added buffer salts. .. math:: \epsilon (c)=\epsilon (c=0)+2c\: delta\; for\; c<2M Parameters ---------- material : string 'd2o' (default) or 'h2o' Material 'd2o' (default) or 'h2o' T : float Temperature in °C conc : float Salt concentration in mol/l. delta : float Total excess polarisation dependent on the salt and presumably on the temperature! Returns ------- dielectric constant : float Notes ----- ====== ========== =========================== Salt delta(+-1) deltalambda (not used here) ====== ========== =========================== HCl -10 0 LiCI 7 -3.5 NaCI 5.5 -4 default KCl 5 -4 RbCl 5 -4.5 NaF 6 -4 KF 6.5 -3.5 NaI -7.5 -9.5 KI -8 -9.5 MgCI, -15 -6 BaCl2 -14 -8.5 LaCI. -22 -13.5 NaOH -10.5 -3 Na2SO. -11 -9.5 ====== ========== =========================== References ---------- .. [1] The dielectric constant of water and heavy water between 0 and 40.degree. J. Phys. Chem., 1967, 71 (3), pp 656–662 http://dx.doi.org/10.1021/j100862a028 .. [2] Dielectric Constant of Deuterium Oxide C.G Malmberg, Journal of Research of National Bureau of Standards, Vol 60 No 6, (1958) 2874 http://nvlpubs.nist.gov/nistpubs/jres/60/jresv60n6p609_A1b.pdf .. [3] Dielectric Properties of Aqueous Ionic Solutions. Parts I and II Hasted et al. J Chem Phys 16 (1948) 1 http://link.aip.org/link/doi/10.1063/1.1746645 """ if material=='h2o': diCo=lambda t:10**(1.94404-1.991e-3*T) return diCo(T)+2*delta*conc elif material=='d2o': diCo=lambda t:87.48-0.40509*(t-273.15)+9.638e-4*(t-273.15)**2-1.333e-6*(t-273.15)**3 return diCo(T)+2*delta*conc
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[docs]def cstar(Rg,Mw): r""" Overlap concentration :math:`c^*` for a polymer. .. math:: c^* = \frac{ 3M_w }{ 4N_A \pi R_g^3 } Parameters ---------- Rg : float in nm radius of gyration Mw : float molecular weight Returns ------- Concentration % w/vol References ---------- .. [1] Overlap concentration of macromolecules in solution Ying, Q. & Chu, B. Macromolecules 20, 362–366 (1987) """ cstar=3.*Mw/(constants.Avogadro*4*np.pi*(Rg*1E-9)**3)/1000 # in g/l return cstar
[docs]def Dtrans(Rh,Temp=273.15,solvent='h2o',visc=None): """ Translational diffusion of a sphere. Parameters ---------- Rh : float Hydrodynamic radius in nm. Temp : float Temperature in K. solvent : float Solvent type as in viscosity; used if visc==None. visc : float Viscosity in Pas => H2O ~ 0.001 Pas =1 cPoise. If visc=None the solvent viscosity is calculated from function viscosity(solvent ,temp) with solvent eg 'h2o' (see viscosity). Returns ------- Translational diffusion coefficient : float in nm^2/ns. """ kT=Temp*kB if visc is None: visc=viscosity(solvent,Temp)*6.0221367e+23/1e9/1e9 # conversion from Pa*s= kg/m/s=u/nm/ns D0=kT/(6*math.pi*visc*Rh)*1000 return D0
D0=Dtrans
[docs]def Drot(Rh,Temp=273.15,solvent='h2o',visc=None): """ Rotational diffusion of a sphere. Parameters ---------- Rh : float Hydrodynamic radius in nm. Temp : float Temperature in K. solvent : float Solvent type as in viscosity; used if visc==None. visc : float Viscosity in Pas => H2O ~ 0.001 Pa*s =1 cPoise. If visc=None the solvent viscosity is calculated from function viscosity(solvent ,temp) with solvent eg 'h2o'. Returns ------- Rotational diffusion coefficient in 1/ns. """ kT=Temp*kB if visc is None: visc=viscosity(solvent,Temp)*6.0221367e+23/1e9/1e9 # conversion from Pa*s= kg/m/s=u/nm/ns D0=kT/(8*math.pi*visc*Rh**3) return D0
[docs]def molarity(objekt,c,total=None): """ Calculates the molarity. Parameters ---------- objekt : object,float Objekt with method .mass() or molecular weight in Da. c : float Concentration in g/ml -> mass/Volume total : float, default None Total volume in milliliter [ml] Concentration is calculated by c[g]/total[ml] if given. Returns ------- molarity : float in mol/liter (= mol/1000cm^3) """ if c>1: print( 'c limited to 1') c=1. if hasattr(objekt,'mass'): mass=objekt.mass() else: mass=objekt if total is not None: c=abs(float(c)/(float(total))) # pro ml (cm^^3) water density =1000g/liter if c>1: print( 'concentration c has to be smaller 1 unit is g/ml') return weightPerl=c*1000 # weight per liter numberPerl=(weightPerl/(mass/constants.N_A)) molarity=numberPerl/constants.N_A return molarity
[docs]def xyz2rphitheta(XYZ,transpose=False): """ Transformation cartesian coordinates [X,Y,Z] to spherical coordinates [r,phi,theta]. Parameters ---------- XYZ : array Nx3 Coordinates with [x,y,z] ( XYZ.shape[1]==3). transpose : bool Transpose XYZ before transformation. Returns ------- rphitheta : array Nx3 Coordinates with [r,phi,theta] - phi : float azimuth -pi < phi < pi - theta : float polar angle 0 < theta < pi - r : float length Examples -------- Single coordinates :: js.formel.xyz2rphitheta([1,0,0]) Transform Fibonacci lattice on sphere to xyz coordinates :: fib=js.formel.fibonacciLatticePointsOnSphere(10,1) js.formel.xyz2rphitheta(fib) Tranformation 2D X,Z coordinates in plane to r,phi coordinates (Z=0) :: rp=js.formel.xyz2rphitheta([data.X,data.Z,abs(data.X*0)],transpose=True) )[:,:2] """ xyz=np.array(XYZ,ndmin=2) if transpose: xyz=xyz.T assert xyz.shape[1]==3 , 'XYZ second dimension should be 3. Transpose it?' rpt=np.zeros(xyz.shape) rpt[:,0]=(xyz**2).sum(axis=1)**0.5 rpt[:,1]=np.arctan2(xyz[:,1],xyz[:,0]) # arctan2 is special function for this purpose rpt[:,2]=np.arctan2((xyz[:,:-1]**2).sum(axis=1)**0.5,xyz[:,2]) return np.array(rpt.squeeze(),ndmin=np.ndim(XYZ))
[docs]def rphitheta2xyz(RPT,transpose=False): """ Transformation spherical coordinates [r,phi,theta] to cartesian coordinates [x,y,z]. Parameters ---------- RPT : array Nx3 Coordinates with [r,phi,theta] - r : float length - phi : float azimuth -pi < phi < pi - theta : float polar angle 0 < theta < pi transpose : bool Transpose RPT before transformation. Returns ------- xyz : array Nx3 with [x,y,z] coordinates """ rpt=np.array(RPT,ndmin=2) if transpose: xyz=xyz.T assert rpt.shape[1]==3 , 'RPT second dimension should be 3. Transpose it?' xyz=np.zeros(rpt.shape) xyz[:,0]=rpt[:,0]*np.cos(rpt[:,1])*np.sin(rpt[:,2]) xyz[:,1]=rpt[:,0]*np.sin(rpt[:,1])*np.sin(rpt[:,2]) xyz[:,2]=rpt[:,0]*np.cos(rpt[:,2]) return np.array(xyz.squeeze(),ndmin=np.ndim(RPT))
[docs]def T1overT2(tr=None,Drot=None,F0=20e6,T1=None,T2=None): r""" Calculates the T1/T2 from a given rotational correlation time tr or Drot for proton relaxation measurement. tr=1/(6*D_rot) with rotational diffusion D_rot and correlation time tr. Parameters ---------- tr : float Rotational correlation time. Drot : float If given tr is calculated from Drot. F0 : float NMR frequency e.g. F0=20e6 Hz=> w0=F0*2*np.pi is for Bruker Minispec with B0=0.47 Tesla T1 : float NMR T1 result in s T2 : float NMR T2 resilt in s to calc t12 directly Returns ------- T1/T2 : float Notes ----- :math:`J(\omega)=\tau/(1+\omega^2\tau^2)` :math:`T1^{-1}=\frac{\sigma}{3} (2J(\omega_0)+8J(2\omega_0))` :math:`T2^{-1}=\frac{\sigma}{3} (3J(0)+ 5J(\omega_0)+2J(2\omega_0))` :math:`tr=T1/T2` References ---------- .. [1] Intermolecular electrostatic interactions and Brownian tumbling in protein solutions. Krushelnitsky A Physical chemistry chemical physics 8, 2117-28 (2006) .. [2] The principle of nuclear magnetism A. Abragam Claredon Press, Oxford,1961 """ w0=F0*2*np.pi J=lambda w,tr:tr/(1+w**2*tr**2) if Drot is not None: # noinspection PyUnusedLocal tr=tr=1./(6*Drot) t1sig3=1./(2.*J(w0,tr)+8.*J(2*w0,tr)) t2sig3=1./(3.*tr+5*J(w0,tr)+J(2*w0,tr)) if T1 is not None: print( 'T1: %(T1).3g sigma = %(sigma).4g'%{'T1':T1,'sigma':t1sig3*3./T1}) if T2 is not None: print( 'T2: %(T2).3g sigma = %(sigma).4g'%{'T2':T2,'sigma':t2sig3*3./T2}) return t1sig3/t2sig3
[docs]def DrotfromT12(t12=None,Drot=None,F0=20e6,Tm=None,Ts=None,T1=None,T2=None): """ Rotational correlation time from T1/T2 or T1 and T2 from NMR proton relaxation measurement. Allows to rescale by temperature and viscosity. Parameters ---------- t12 : float T1/T2 from NMR with unit seconds Drot : float !=None means output Drot instead of rotational correlation time. F0 : float Resonance frequency of NMR instrument. For Hydrogen F0=20 MHz => w0=F0*2*np.pi Tm f: float Temperature of measurement in K. Ts : float Temperature needed for Drot -> rescaled by visc(T)/T. T1 : float NMR T1 result in s T2 : float NMR T2 result in s to calc t12 directly remeber if the sequence has a factor of 2 Returns ------- Correlation time or Drot : float Notes ----- See T1overT2 """ if T1 is not None and T2 is not None and t12 is None: t12=T1/T2 if Tm is None: Tm=293 if Ts is None: Ts=Tm if t12 is not None: diff=lambda tr,F0:T1overT2(tr=tr,Drot=None,F0=F0,T1=None,T2=None)-t12 # find tr where diff is zero to invert the equation trr=scipy.optimize.brentq(diff,1e-10,1e-5,args=(F0,)) # rescale with visc(T)/T tr=trr*(Tm/viscosity('d2o',T=Tm))/(Ts/viscosity('d2o',T=Ts)) print( 'tau_rot: %(trr).3g at Tm=%(Tm).5g \ntau_rot: %(tr).5g at Ts=%(Ts).3g \n (scalled by Tm/viscosity(Tm)/(T/viscosity(T)) = %(rv).4g'%{ 'trr':trr,'Tm':Tm,'tr':tr,'Ts':Ts,'rv':tr/trr}) else: raise Exception('give t12 or T1 and T2') temp=T1overT2(trr,F0=F0,T1=T1,T2=T2) print('D_rot= : %(drot).4g '%{'drot':1/(6*tr)}) if Drot is not None: Drot=1/(6*tr) print( 'returns Drot') return Drot return tr
[docs]def sedimentationProfileFaxen(t=1e3,rm=48,rb=85,number=100,rlist=None,c0=0.01,s=77,Dt=1.99e-11,w=246, Rh=None,visc='h2o',temp=293,densitydif=None): """ Faxen solution to the Lamm equation of sedimenting particles in centrifuge; no bottom part. Bottom equillibrium distribution is not in Faxen solution included. Results in particle distribution along axis for time t. Parameters ---------- t : float Time after start in seconds. If list, results at these times is given as dataList. rm : float Axial position of meniscus in mm. rb : float Axial position of bottom in mm. number : integer Number of points between rm and rb to calculate. c0 : float Initial concentration in cell; just a scaling factor. s : float Sedimentation coefficient in Svedberg; 77 S is r=10 nm particle in H2O. Dt : float Translational diffusion coefficient in m**2/s; 1.99e-11 is r=10 nm particle. w : float Radial velocity rounds per second; 246 rps=2545 rad/s is 20800g in centrifuge fresco 21. Rh : float Hydrodynamic radius in nm ; if given Dt and s are calculated from Rh. visc : float, 'h2o','d2o' Viscosity in units Pas. If 'h2o' or 'd2o' the corresponding viscosity at given temperature is used. densitydif : float Density difference between solvent and particle in g/ml; protein in 'h2o'=> is used =>1.35-1.= 0.35 g/cm**3 Returns ------- Concentration distribution : dataArray, dataList .pelletfraction is the content in pellet as fraction already diffused out .rmeniscus Notes ----- Default values are for Heraeus Fresco 21 at 21000g. References ---------- .. [1] Über eine Differentialgleichung aus der physikalischen Chemie. Faxén, H. Ark. Mat. Astr. Fys. 21B:1-6 (1929) """ # get solvent viscosity if visc in ['h2o','d2o']: visc=viscosity(visc,temp) if densitydif is None: densitydif=0.35 # protein - water densitydif*=1e3# to kg/m³ timelist=dL() if Rh is not None: kT=temp*kB Dt=kT/(6*math.pi*visc*Rh*1e9) S=2./9./visc*densitydif*(Rh*1e-9)**2/1e-13 svedberg=1e-13 s*=svedberg rm/=1000. rb/=1000.# end r=np.r_[rm:rb:number*1j] # nn points if rlist is not None: rm=min(rlist) rb=max(rlist) # not used here r=rlist/1000. w=w*2*np.pi for tt in np.atleast_1d(t): ct=(0.5*c0*np.exp(-2.*s*w**2*tt)) cr=(1-scipy.special.erf((rm*(w**2*s*tt+np.log(rm)-np.log(r)))/(2.*np.sqrt(Dt*tt)))) timelist.append(dA(np.c_[r*1000,cr*ct].T)) timelist[-1].time=tt timelist[-1].rmeniscus=rm timelist[-1].w=w timelist[-1].Dt=Dt timelist[-1].c0=c0 timelist[-1].viscosity=visc timelist[-1].sedimentation=s/svedberg timelist[-1].pelletfraction=1-scipy.integrate.simps(y=timelist[-1].Y,x=timelist[-1].X)/(max(r)*1000*c0) timelist[-1].modelname=inspect.currentframe().f_code.co_name if Rh is not None: timelist[-1].Rh=Rh if len(timelist)==1: return timelist[0] return timelist
[docs]def sedimentationProfile(t=1e3,rm=48,rb=85,number=100,rlist=None,c0=0.01,S=None,Dt=None,omega=246, Rh=10,temp=293,densitydif=0.41,visc='h2o'): """ Approximate solution to the Lamm equation of sedimenting particles in centrifuge including bottom equilibrium distribution. Bottom equilibrium distribution is not in faxen solution. Results in particle concentration profile between rm and rb for time t Parameters ---------- t : float or list Time after start in seconds. If list, results at these times is given as dataList. rm : float Axial position of meniscus in mm. rb : float Axial position of bottom in mm. number : int Number of points between rm and rb to calculate. rlist : list of float Explicit list of positions where to calculate eg to zoom bottom. c0 : float Initial concentration in cell; just a scaling factor. S : float Sedimentation coefficient in Svedberg; 77 S is r=10 nm particle in H2O. Dt : float Translational diffusion coefficient in m**2/s; 1.99e-11 is r=10 nm particle. omega : float Radial velocity rounds per second; 246 rps=2545 rad/s is 20800g in centrifuge fresco 21. Rh : float Hydrodynamic radius in nm ; if given the Dt and s are calculated from this. densitydif : float Density difference between solvent and particle in g/ml; Protein in 'h2o'=> is used =>1.41-1.= 0.41 g/cm**3. visc : float, 'h2o', 'd2o' Viscosity of the solvent in Pas. (H2O ~ 0.001 Pa*s =1 cPoise) If 'h2o' or 'd2o' the corresponding viscosity at given temperature is used. Returns ------- concentration profile : dataArray, dataList Columns [position in [mm]; ; conc_meniscus_part; conc_bottom_part] Notes ----- From [1]_:"The deviations from the expected results are smaller than 1% for simulated curves and are valid for a great range of molecular masses from 0.4 to at least 7000 kDa. The presented approximate solution, an essential part of LAMM allows the estimation of s and D with an accuracy comparable to that achieved using numerical solutions, e.g the program SEDFIT of Schuck et al." Default values are for Heraeus Fresco 21 at 21000g. Examples -------- Sedimentation (up concentration) of unilamellar liposomes of DOPC. The density of DOPC is about 1.01 g/ccm in water with 1 g/ccm. Lipid volume fraction is 33% for 50nm radius (10% for 200 nm) for a bilayer thickness of 6.5 nm. :: import numpy as np import jscatter as js t1=np.r_[100:6e3:11j] # time in seconds # open plot() p=js.grace(1.5,1.5) p.multi(2,1) # calculate sedimentation profile for two different particles # data correspond to Fresco 21 with dual rotor # default is solvent='h2o',temp=293 Rh2=150 # nm g=21000. # g # RZB number omega=g*246/21000 D100nm=js.formel.sedimentationProfile(t=t1,Rh=50,c0=0.05,omega=omega,rm=58,rb=85,densitydif=0.0033) D400nm=js.formel.sedimentationProfile(t=t1,Rh=200,c0=0.05,omega=omega,rm=58,rb=85,densitydif=0.001) # plot it p[0].plot(D100nm,li=[1,2,-1],sy=0,legend='%s nm-> t=$time s' ) p[1].plot(D400nm,li=[1,2,-1],sy=0,legend='%s nm-> t=$time s' ) # pretty up p[0].yaxis(min=0,max=0.2,label='concentration') p[1].yaxis(min=0,max=0.2,label='concentration') p[1].xaxis(label='position mm') p[0].xaxis(label='') p[0].text(x=70,y=0.15,string='D=100 nm') p[1].text(x=70,y=0.15,string='D=400 nm') p[0].legend(x=50,y=0.2,charsize=0.5) p[1].legend(x=50,y=0.2,charsize=0.5) p[0].title('Concentration profile in first 6000s') p[0].subtitle('at 21000g ') References ---------- .. [1] A new approximate whole boundary solution of the Lamm equation for the analysis of sedimentation velocity experiments J. Behlke, O. Ristau Biophysical Chemistry 95 (2002) 59–68 """ # make here all in SI units if visc in ['h2o','d2o']: # in Pa*s visc=viscosity(visc,temp) densitydif*=1e3 # to kg/m³ if isinstance(t,(int,float)): t=np.r_[t] timelist=dL() if Rh is not None: kT=temp*kB Dt=kT/(6*math.pi*visc*Rh*1e9) S=2./9./visc*densitydif*(Rh*1e-9)**2/1e-13 svedberg=1e-13 S*=svedberg rm/=1000.# meniscus in m rb/=1000.# bottom in m r=np.r_[rm:rb:number*1j] # nn points in m if rlist is not None: # explicit given list between meniscus and bottom r=rlist/1000. # create variables for calculation omega=omega*2*np.pi # in rad taulist=2*S*omega**2*np.atleast_1d(t) # timevariable for moving boundary # x=(r/rm)**2 # not used # meniscus part eps=2*Dt/(S*omega**2*rm**2) w=2*(r/rm-1) b=1-0.5*eps # bottom part epsb=2*Dt/(S*omega**2*rb**2) d=1-epsb/2. z=2*(r/rb-1) # use scipy and numpy functions erfc=scipy.special.erfc erfcx = scipy.special.erfcx exp=np.exp sqrt=np.sqrt # moving meniscus part # one makes errors dependent on values , to resolve this i had to change as decribed # i have to test more examples to see if the c3 solution is needed also for c2 c1=lambda tau:erfc((exp(tau/2.)-0.5*w-1+0.25*eps*(exp(-tau/2.)-exp(tau/2.)))/sqrt(eps*(exp(tau)-1))) c2=lambda tau:-(exp(b*w/eps)/(1-b))*erfc( (w+2*b*(exp(tau/2.)-1))/(2*sqrt(2*eps*(exp(tau/2.)-1))) ) # c2 error: exp(b*w/eps) goes infinity even if erfc is zero -> so exp of log to compensate before exp is taken #c2=lambda tau:-1./(1-b)*exp((b*w/eps)+np.log(erfc((w+2*b*(exp(tau/2.)-1))/(2*sqrt(2*eps*(exp(tau/2.)-1)))))) # same here #c3=lambda tau:(2-b)/(1-b)*exp( (w+2*(exp(tau/2.)-1)*(1-b))/eps)* erfc( (w+2*(exp(tau/2.)-1)*(2-b)) / (2*sqrt(2*eps*(exp(tau/2.)-1))) ) #c3=lambda tau:(2-b)/(1-b)*exp(((w+2*(exp(tau/2.)-1)*(1-b))/eps)+np.log(erfc( (w+2*(exp(tau/2.)-1)*(2-b)) / (2*sqrt(2*eps*(exp(tau/2.)-1)))))) def c3(tau): # to avoid RuntimeWarning in c3: divide by zero encountered in log for np.log( erfc(xxerfc) # i use erfcx and take the additional exp(-xxerfc) in front of log xxerfc=(w + 2 * (exp(tau / 2.) - 1) * (2 - b)) / (2 * sqrt(2 * eps * (exp(tau / 2.) - 1))) res=(2 - b) / (1 - b) * exp( ((w + 2 * (exp(tau / 2.) - 1) * (1 - b)) / eps) + -xxerfc**2 + np.log( erfcx(xxerfc) ) ) return res # bottom part cexptovercfax=lambda tau:c1(tau)+c2(tau)+c3(tau) c4=lambda tau:-erfc((d*tau-z)/(2*sqrt(epsb*tau))) c5=lambda tau:-exp(d*z/epsb)/(1-d)*erfc((-z-d*tau)/(2*sqrt(epsb*tau))) c6=lambda tau:(2-d)/(1-d)*exp(((1-d)*tau+z)/epsb)*erfc((-z-(2-d)*tau)/(2*sqrt(epsb*tau))) # add both cexptovercbottom=lambda tau:c4(tau)+c5(tau)+c6(tau) for tau in taulist: timelist.append(dA(np.c_[r*1000,(cexptovercfax(tau)+cexptovercbottom(tau))*c0/2./exp(tau)].T)) timelist[-1].time=tau/(2*S*omega**2) timelist[-1].rmeniscus=rm timelist[-1].rbottom=rb timelist[-1].w=w timelist[-1].Dt=Dt timelist[-1].c0=c0 timelist[-1].viscosity=visc timelist[-1].sedimentation=S/svedberg timelist[-1].modelname=inspect.currentframe().f_code.co_name # timelist[-1].pelletfraction=1-scipy.integrate.simps(y=timelist[-1].Y, x=timelist[-1].X)/(max(r)*1000*c0) if Rh is not None: timelist[-1].Rh=Rh timelist[-1].columnname='position; concentration; conc_meniscus_part; conc_bottom_part' if len(timelist)==1: timelist[0].setColumnIndex(iey=None) return timelist[0] timelist.setColumnIndex(iey=None) return timelist