Initial population. Packege setup. Nothing working yet.

qeutil/__init__.py

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+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+"""This module defines an interface to Quantum-Espresso.
+http://www.quantum-espresso.org/
+"""
+
+
+
+from ase import Atom, Atoms
+import os
+from glob import glob
+from os.path import join, isfile, islink
+
+import numpy as np
+
+from ase.data import atomic_numbers
+from ase.units import Bohr, Hartree, Rydberg, fs
+from ase.data import chemical_symbols
+from ase.calculators.calculator import FileIOCalculator, Parameters, kpts2mp, ReadError
+
+from quantumespresso.io import *
+
+
+class QuantumEspresso(FileIOCalculator):
+    """Class for doing Quantum Espresso calculations.
+
+    The default parameters are very close to those that 
+    the QE Fortran code would use.  These are the exceptions::
+
+    """
+
+    implemented_properties = ['energy', 'forces', 'stress']
+
+    pass
+
+

qeutil/analyzers.py

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+def get_EOS(d, comment=""):
+    # Fitting functions
+    def BMEOS(v,v0,b0,b0p):
+        return (b0/b0p)*(pow(v0/v,b0p) - 1)
+    fitfunc = lambda p, x: [BMEOS(xv,p[0],p[1],p[2]) for xv in x]
+    errfunc = lambda p, x, y: fitfunc(p, x) - y
+
+    pv=array([d[:,0]**3,d[:,1]]).T
+
+    # Estimate the initial guess assuming b0p=1
+    # Limiting volumes
+    v1=min(pv[:,0])
+    v2=max(pv[:,0])
+    # The pressure is falling with the growing volume
+    p2=min(pv[:,1])
+    p1=max(pv[:,1])
+    b0=(p1*v1-p2*v2)/(v2-v1)
+    v0=v1*(p1+b0)/b0
+    # Initial guess
+    p0=[v0,b0,1]
+    #Fitting
+    #print p0
+    fit, succ = optimize.leastsq(errfunc, p0[:], args=(pv[:,0],pv[:,1]))
+
+    # Ranges - the ordering in pv is not guarateed at all!
+    # In fact it may be purely random.
+    x=numpy.array([min(pv[:,0]),max(pv[:,0])])
+    y=numpy.array([min(pv[:,1]),max(pv[:,1])])
+
+    # Plot the P(V) curves and points for the crystal
+    # Plot the points
+    plot(pv[:,0]**1/3,pv[:,1],'.',label='Calc. '+comment)
+
+    # Mark the center P=0 V=V0
+    axvline(fit[0]**1/3,ls='--')
+    axhline(0,ls='--')
+
+    # Plot the fitted B-M EOS through the points
+    xa=numpy.linspace(x[0],x[-1],20)
+    plot(xa**1/3,fitfunc(fit,xa),'-', label="B-M fit:\n$V_0$=%f ($A_0$=%f),\n$B_0$=%f kBar,\n$B'_0$=%f  " 
+         % (fit[0], fit[0]**(1.0/3), fit[1], fit[2]) )
+    legend()
+    ylabel('Pressure (kBar)')
+    xlabel('Lattice constant ($\mathrm{\AA}$)')
+    draw();
+    return fit, pv
+
+
+def analize_dir(idx, ex=True, bdir='/home/jochym/Desktop/Fizyka/', 
+                qp=array([G1,X,G2,L]), lbl=None, ax=None, castep=False):
+    s=0
+    t=[]
+    for x in [0]+map(norm,qp[1:]-qp[:-1]):
+        s+=x
+        t.append(s)
+
+    par=calcData[idx]
+
+    try:
+        frq=loadtxt(bdir + idx +'/'+par['prefix']+'.freq.gp')
+    except IOError :
+        print "Cannot open frequency file in", wd
+        return
+    if ax :
+        ax1=ax[0]
+    else :
+        ax1=subplot2grid([1,4],[0,3],colspan=1)
+
+    phdos=loadtxt(bdir+idx+'/'+params['prefix']+'.dos')
+    clr=ax1.plot(phdos[:,1],cminv2meV*phdos[:,0])[0].get_color()
+    ax1.yaxis.set_label_position("right")
+    ax1.yaxis.tick_right()
+    ax1.xaxis.tick_top()
+
+    if ax :
+        ax2=ax[1]
+    else :
+        ax2=subplot2grid([1,4],[0,0],colspan=3,sharey=ax1)
+
+
+    clr=None
+
+    if lbl :
+        lbltxt=", ".join(["%s" % (l,) for l in lbl if not (l in par.keys())])
+        lbltxt+=", ".join(["%s" % (par[l],) for l in lbl if l in par.keys()])
+    else :
+        lbltxt=idx    
+
+    for i in range(frq.shape[1]-1):
+        if clr :
+            ax2.plot(frq[1:,0], cminv2meV*frq[1:,i+1],'.',color=clr)
+        else :
+            clr=ax2.plot(frq[1:,0], cminv2meV*frq[1:,i+1],'.',label=lbltxt)[0].get_color()
+
+
+    if ex :
+        frqexp1=loadtxt('thO2-phon.png.dat')
+        clr=ax2.plot(frqexp1[:,0],frqexp1[:,1],'o')[0].get_color();
+        frqexp2=loadtxt('thO2-phon-2.dat')
+        ax2.plot(t[2]-frqexp2[:,0],frqexp2[:,1],'o',color=clr)[0];
+        frqexp3=loadtxt('thO2-phon-3.dat')
+        ax2.plot(t[2]+frqexp3[:,0],frqexp3[:,1],'o',color=clr,label='Experiment')[0];
+    if castep :
+        frqexp4=loadtxt('castep-take2.csv')
+        ax2.plot((t[3]-t[0])*frqexp4[:,0], frqexp4[:,1],'o', label='CASTEP')
+
+
+    title("M-P grid (e.s.): %(kx)dx%(ky)dx%(kz)d (phon): %(nq)d^3" % par)
+    xlim(0,max(frq[1:,0]))
+    ylim(0,ylim()[1])
+    #xticks(t,[u'Γ','X',u'Γ','L'])
+    vlines(xticks()[0][1:-1],ylim()[0],ylim()[1],linestyles='--')
+    ylabel('Energy (meV)')
+    subplots_adjust(wspace=0)
+    return [ax1,ax2]