示例#1
0
文件: pvt_shrink.py 项目: cdknorow/MD
    def PVvsV_correlation():
        global counter
        ax1 = get_plot()
        #ax1 = get_plot()
        TP = []
        NV = []
        Z = []
        Z_var = []
        for i in range(len(Volume)):
            TP = []
            for j in range(len(temperature[i])):
                TP.append(pressure[i][j]*Volume[i]/(temperature[i][j]*N))
            NV.append(N/(Volume[i]))
            Z.append(sum(TP)/len(TP))
            var = 0
            for i in range(len(TP)):
                var += (TP[i]- Z[-1])**2/len(TP)
            Z_var.append(var**2)
            #print Z[-1], Z_var[-1], Z_var[-1]/Z[-1]*100
        NV[0] = 0
        Z[0] = 1
        Z_var[0]=0

        ax1.errorbar(NV,Z,yerr=Z_var,fmt='x%c'%colors[counter],label=title)
        #peos.modifiedstarling_fit_all(ax1,np.array(Z),np.array(NV),colors[counter])
        peos.viralexpansion_3(ax1,np.array(Z),np.array(NV),colors[counter],show=True)
        #plt.semilogx()
        #plt.semilogy()
        ax1.set_xlabel(u'$\eta$')
        ax1.set_ylabel('PV/NkT')
示例#2
0
文件: pvt_shrink.py 项目: cdknorow/MD
    def ZvsZpot_gamma(pfit_fe_coef=[],fmin=9,fmax=-1, set_fe = True):
        if set_fe:
            if n == 6.25:
                pfit_fe_coef =[-0.123471,3.112000,3.320848,0.083388]
            if n == 7:
                pfit_fe_coef = [-0.051930 ,2.703564 ,3.246362,0.379012]
            if n == 8:
                pfit_fe_coef = [-0.112304,2.741619 ,2.576233, 0.984856]
            if n == 9:
                pfit_fe_coef = [-0.282307, 3.300624 ,1.358420, 1.786398]
            if n == 10:
                pfit_fe_coef = [-0.626243, 4.208299, -0.225634, 2.708868]
            if n == 11:
                pfit_fe_coef = [-0.764629, 5.146447 ,-1.897390, 3.667005]
            if n == 12:
                pfit_fe_coef = [-0.951805, 6.005817, -3.441567, 4.552962]
            if n == 13:
                pfit_fe_coef = [-2.138254, 9.811643, -7.846507,6.339112]
            if n == 14:
                pfit_fe_coef = [-1.857837,9.347776,-8.089134,6.768926]
        global counter
        gamma=[]
        NV = []
        Z = []
        Z_potential = []
        r_cut = float(os.getcwd().split('/')[-1].split('_')[-2])
        print 'N is ',N
        Z_potential_no = []
        for i in range(len(Volume)):
            gamma.append(N/Volume[i]*temperature_avg[i]**(-3/n))
            # rho
            NV.append(N/(Volume[i]))
            # (Z - 1) / rho
            Z.append((pressure_avg[i]*Volume[i]/(N*temperature_avg[i])-1))
            # (2 * Beta Phi_T / N ) / rho
            DE  = N*NV[-1]*2*math.pi/((n-3)*r_cut**(n-3))
            #print 'Delta DE', DE/potential_avg[i]
            Z_potential.append(n/3*((potential_avg[i]+DE)/(N*temperature_avg[i])))
            Z_potential_no.append(n/3*((potential_avg[i])/(N*temperature_avg[i])))

        fit_Z = []
        fit_ZFE = []
        ax1 = get_plot()
        print "potential"
        fit_Z_potential = peos.viralexpansion_3(ax1, Z_potential[fmin:fmax], np.array(gamma[fmin:fmax]),'r',show=True)
        print "potential w/o correction"
        fit_Z_potential_no = peos.viralexpansion_3(ax1,
                Z_potential_no[fmin:fmax],
                np.array(gamma[fmin:fmax]),'r',show=False)
        ax1.set_ylabel(r'Z-1')
        ax1.set_xlabel(r'$\gamma$')
        plt.show()
        print "Free Energy"
        print 'a=%f,c1=%f,c2=%f,c3=%f'%(pfit_fe_coef[0],pfit_fe_coef[1],pfit_fe_coef[2],pfit_fe_coef[3])
        #fit_Z_pressure = peos.viralexpansion_3(ax1, Z[fmin:fmax], np.array(gamma[fmin:fmax]),'r',show=True) 
        PvsV(fit_Z_potential,fit_Z_potential_no,pfit_fe_coef,fmin=fmin)
示例#3
0
文件: pvt_shrink.py 项目: cdknorow/MD
    def Z_gamma():
        global counter
        ax1 = get_plot()
        ax1.set_xlabel(r'$\gamma$')
        ax1.set_ylabel('Z-1')
        r_cut = float(os.getcwd().split('/')[-1].split('_')[-2])
        NV = [0]
        Z_potential = [0]
        Z_potentialm = [0]
        for i in range(len(Volume)):
            # rho
            NV.append(N/(Volume[i]))
            # Z - 1
            #Z.append((pressure_avg[i]*Volume[i]/(N*temperature_avg[i])-1)/NV[-1])
            # 2 * Beta Phi_T / N 
            DE  = N*NV[-1]*2*math.pi/((n-3)*r_cut**(n-3))
            Z_potential.append(n/3*((potential_avg[i]+DE)/(N*temperature_avg[i]*NV[-1])))
            Z_potentialm.append(n/3*((potential_avg[i]+DE)/(N*temperature_avg[i])))

        #ax1.errorbar(NV,Z,yerr=Z_var,fmt='x%c'%colors[counter],label=title)
        #peos.modifiedstarling_fit_all(ax1,np.array(Z_potential),np.array(NV),colors[counter],show=True)
        #peos.viralexpansion_3(ax1,np.array(Z_potential),np.array(NV),colors[counter],show=True)
        A = peos.viralexpansion_3(ax1,np.array(Z_potentialm),np.array(NV),colors[counter],show=True)
        #peos.viralexpansion_3(ax1,np.array(Z_potentialm),np.array(NV),colors[counter],show=True)
        g=.1
        init =A[1]*g+.5*A[2]*g**2+A[3]*g**3/3.
        print init
示例#4
0
文件: pvt_shrink.py 项目: cdknorow/MD
    def FreeEnergy():
        global counter
        global n
        # Fit to Z-1 from N/V = 0 to g
        #if n==6.:
        #    c1=3.586511
        #    c2=6.1187979
        #    c1= 3.630785
        #    c2=5.919866
        #    g=.1
        #if n==7.:
        #    c1= 3.139660
        #    c2 = 6.038275
        #    g=.1
        #if n==8:
        #    c1 = 2.889490
        #    c2=5.810482
        #    g=.1
        #if n==9:
        #    c1= 2.748766
        #    c2=5.428522
        #    g=.1
        #if n ==10:
        #    c1= 2.098992
        #    c2=7.387928
        #    g=.1
        #if n ==11.:
        #    c1= 2.434736
        #    c2=5.788083
        #    g=.1
        #if n ==12.:
        #    a=2.549678
        #    c1= 3.993234
        #    c2=2.712819
        #    c3=3.469902
        #    g=.1
        #if n ==13.:
        #    a=1.000000
        #    c1= 2.532850
        #    c2=3.437891
        #    c3=4.843509
        #    g=.1
        #if n ==14.:
        #    a  = 1.000000
        #    c1 = 2.482896
        #    c2 = 3.367217
        #    c3 = 4.901456
        #    g  = .1
        #if n == 6.25:
        #    a  = 1.000000
        #    c1 = 3.525116
        #    c2 = 5.409153
        #    c3 = 1.469899
        #    g  = .1
        #try:
        #    init =a*g+.5*c1*g**2+c2/3.*g**3+c3/4.*g**4
        #except:
        #    init =c1*g+c2/2.*g**2
        if n==6.:
            init = .398
            g=.1
        if n == 6.25:
            init = .385
            g  = .1
        if n==7.:
            init = .352
            g=.1
        if n==8:
            init = .324
            g=.1
        if n==9:
            init = .306
            g=.1
        if n ==10:
            init = 0.293
            g = .1
        if n ==11.:
            init = 0.283
            g  = .1
        if n ==12.:
            init = 0.276
            g  = .1
        if n ==13.:
            init=.271
            g=.1
        if n ==14.:
            init=.265
            g  = .1
        print 'free energy from fit',init
        r_cut = float(os.getcwd().split('/')[-1].split('_')[-2])
        NV = []
        Z = []
        Z_potential = []
        Z_potential_no = []
        gamma2 = []
        for i in range(len(temperature_avg)):
            temperature_avg[i]=1.0
        for i in range(len(Volume)):
            # rho
            NV.append(N/(Volume[i]))
            # Z - 1
            Z.append((pressure_avg[i]*Volume[i]/(N*temperature_avg[i])-1)/NV[-1])
            # 2 * Beta Phi_T / N 
            DE  = N*NV[-1]*2*math.pi/((n-3)*r_cut**(n-3))
            Z_potential.append(n/3*((potential_avg[i]+DE)/(N*temperature_avg[i]*NV[-1])))
            Z_potential_no.append(n/3*((potential_avg[i])/(N*temperature_avg[i]*NV[-1])))
            ##
            gamma2.append(NV[-1]/2**0.5*(1/temperature_avg[i])**0.5)
        #peos.viralexpansion(ax1,np.array(Z_potential[0:5]),np.array(NV[0:5]),colors[counter],show=True)
        #peos.modifiedstarling_fit_all(ax1,np.array(Z_potential),np.array(NV),colors[counter])
        ax1 = get_plot()
        print NV[:4]
        #Integrate To get the Free Energy 
        #F_excess_Z, gamma = simpson_integration_min(Z, NV,
        #       initial=init,int_min=g)
        F_excess_potential, NV = simpson_integration_min(Z_potential, NV,
               initial=init,int_min=g)
        print NV[:4]
        print F_excess_potential[:4]
        gamma = []

        for i in NV:
            gamma.append(i*(sum(temperature_avg)/len(temperature_avg))**(-3/6.))
        gamma = np.array(gamma)
        ax1.plot(gamma,F_excess_potential, '-',label=title+' FE Potential')

        #FIT OF Free Energy
        print len(NV)
        fmin= delta # Min Cutoff of fit
        print 'fmin =',fmin, 'fit range', NV[fmin],'-',NV[-1]
        fitted = peos.viralexpansion_3(ax1, F_excess_potential[fmin:],
                np.array(gamma[fmin:]),'r',show=False)

        ## fitted function ##
        fit_FE = []
        for g in gamma:
            fit_FE.append(fitted[0]+fitted[1]*g+fitted[2]*g**2+fitted[3]*g**3)
        ax1.plot(gamma,fit_FE, '-x',label=title+' fit')


        #fcc calculated trvsst
        fcc_excess = np.zeros((gamma.shape[0]))
        energy_excess = np.zeros((gamma.shape[0]))
        if n == 6:
            a_fcc = 3.6131
            b_fcc = 3.6982
            g_L = 2.36
            g_fcc = 2.39
        if n == 6.25:
            a_fcc = 3.4247505
            b_fcc = 3.7851997
            g_L = 2.36
            g_fcc = 2.39
        if n == 7:
            a_fcc = 2.9754654
            b_fcc = 4.0185839
            g_L = 2.05
            g_fcc = 2.08
        if n == 8:
            a_fcc = 2.5402261
            b_fcc = 4.2753817
            g_L = 1.7
            g_fcc = 1.73
        if n == 9:
            a_fcc = 2.2083911
            b_fcc = 4.4821760
            g_L = 1.49
            g_fcc = 1.52
        if n == 10:
            a_fcc = 1.9388997
            b_fcc = 4.6487343
            g_L = 1.4
            g_fcc = 1.43
        if n == 11:
            a_fcc = 1.7118338
            b_fcc = 4.7823161
            g_L = 1.25
            g_fcc = 1.28
        if n == 12:
            a_fcc = 1.5164850
            b_fcc = 4.8884526
            g_L = 1.16
            g_fcc = 1.19
        if n == 13:
            a_fcc = 1.3461175
            b_fcc = 4.9714449
            g_L = 1.10
            g_fcc = 1.13
        if n == 14:
            a_fcc = 1.1964035
            b_fcc = 5.0346944
            g_L = 1.0
            g_fcc = 1.03

        for i,g in enumerate(gamma):
            fcc_excess[i] = a_fcc*g**(n/3.) + b_fcc + (n/2.)*math.log(g)
            energy_excess[i] = a_fcc*g**(n/3.) + 3
        ax1.plot(gamma, fcc_excess, '-',label='fcc phonon')
        ax1.set_xlabel(u'$\gamma_{%i}$'%int(n))
        ax1.set_ylabel('Excess Free Energy of Liquid')
        coex_fcc  =  a_fcc*g_fcc**(n/3.) + b_fcc + (n/2.)*math.log(g_fcc)
        coex_liq  = fitted[0]+fitted[1]*g_L+fitted[2]*g_L**2+fitted[3]*g_L**3
        print 'Df = ', - coex_fcc + coex_liq
        ax1.set_xlim([g_L-.2,g_fcc+.02])
        ax1.set_ylim([coex_fcc-4,coex_liq+2])
        plt.legend(loc=2)
        plt.show()
        ZvsZpot_gamma(pfit_fe_coef=fitted,fmin=fmin*2, set_fe = False)