DOS.psm1
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Function Get-DensityHashTable{ #Creates an ordered hashtable to use in plot arguments [ordered]@{textLocation ="[0.05,0.9]"; DOS_Limit ="[0.0,0.6]"; FigureHeight =2.5; E_Limit="[5,-5]"; ProLabels="['Ga','s','p','d']"; ProIndices="[(range(0,1,1)),(0,),(1,2,3,),(4,5,6,7,8,)]";} } $startFile=@' #====No Edit Below Except Last Few Lines of Legend and File Paths in np.loadtxt('Path/To/File')===== #====================Loading Packages============================== import numpy as np import copy import matplotlib as mpl import matplotlib.pyplot as plt from matplotlib import rc import matplotlib.pyplot as plt from matplotlib.gridspec import GridSpec mpl.rcParams['axes.linewidth'] = 0.4 #set the value globally mpl.rcParams['font.serif'] = "STIXGeneral" mpl.rcParams['font.family'] = "serif" mpl.rcParams['mathtext.fontset'] = "stix" left,bottom,top,leg_col=0.15,0.15,0.85,4 text_x,text_y=textLocation; if(FigureWidth <=2): mpl.rc('font', size=8) left,bottom,top,leg_col=0.3,0.2,0.8,2 #====================Loading Files=================================== pdos=np.loadtxt('./pDOS.txt') data_dos=np.loadtxt('./tDOS.txt') D=pdos[:,0]-E_Fermi;TDOS=data_dos[:,1]; eGrid_DOS=int(np.shape(TDOS)[0]); #Energy grid mesh yh=max(E_Limit);yl=min(E_Limit); nField_DOS=int(np.shape(pdos)[1]-1); #Fields in DOS projection #============Calculation of ION(s)+Orbitals-Contribution======= max_index=np.max(np.where(D[:eGrid_DOS] <=yh)); min_index=np.min(np.where(D[:eGrid_DOS] >=yl)) r_data_dos=np.reshape(pdos[:,1:],(-1,eGrid_DOS,nField_DOS)) s_data_dos=np.take(r_data_dos[:,min_index:max_index+1,:],ProIndices[0],axis=0).sum(axis=0) red_dos=np.take(s_data_dos,ProIndices[1],axis=1).sum(axis=1) green_dos=np.take(s_data_dos,ProIndices[2],axis=1).sum(axis=1) blue_dos=np.take(s_data_dos,ProIndices[3],axis=1).sum(axis=1) Elem_dos=red_dos+blue_dos+green_dos; #ION DOS in E_Limit TDOS=TDOS[min_index:max_index+1]; #Updated total DOS D=D[min_index:max_index+1]; #Updated energy in E_limit for DOS #=================Plotting============================ plt.figure(figsize=(FigureWidth,FigureHeight)) gs = GridSpec(1,1) ax1 = plt.subplot(gs[0]) def ax_settings(ax, x_coord,y_coord,Element): ax.tick_params(direction='in', top=True,bottom=True,left=True,right=True,length=4, width=0.3, colors='k', grid_color='k', grid_alpha=0.8) ax.set_ylim([DOS_Limit[0],DOS_Limit[1]]) ax.set_xlim(yl,yh) ax.set_ylabel('Density of States'); ax.set_xlabel(r'$E-E_F$'); ax.text(x_coord,y_coord,r"$\mathrm{%s}^{\mathrm{%s}}$" % (SYSTEM, Element),bbox=dict(edgecolor='white',facecolor='white', alpha=0.6),transform=ax.transAxes,color='red') return None '@ $stack=@' #================StackPlots for DOS==================================== ax1.fill_between(D,TDOS,color=(167/300, 216/300, 222/300),facecolor=(1,1,1),linewidth=0,label='Total'); ax1.fill_between(D,blue_dos+green_dos+red_dos,color=(0,0,1),linewidth=0 ,label=ProLabels[3]); ax1.fill_between(D,green_dos+red_dos,color=(0,1,0),linewidth=0,label=ProLabels[2]); ax1.fill_between(D,red_dos,color=(1,0,0),linewidth=0,label=ProLabels[1]); '@ $area=@' #================AreaPlots for DOS==================================== ax1.fill_between(D,TDOS,color=(167/300, 216/300, 222/300),linewidth=0,label='Total'); ax1.fill_between(D,red_dos,color=(1,0,0,0.4),linewidth=0,label=ProLabels[1]); ax1.plot(D,red_dos, 'r',linewidth=0.3) ax1.fill_between(D,green_dos,color=(0,1,0,0.4),linewidth=0,label=ProLabels[2]); ax1.plot(D,green_dos, 'g',linewidth=0.3) ax1.fill_between(D,blue_dos,color=(0,0,1,0.4),linewidth=0 ,label=ProLabels[3]); ax1.plot(D,blue_dos, 'b',linewidth=0.3) '@ $line=@' #================LinePlots for DOS==================================== ax1.plot(D,TDOS,'k',linewidth=0.5,linestyle='dashed',label='Total'); ax1.plot(D,red_dos, 'r',linewidth=0.6,label=ProLabels[1]) ax1.plot(D,green_dos, 'g',linewidth=0.6,label=ProLabels[2]) ax1.plot(D,blue_dos, 'b',linewidth=0.6,label=ProLabels[3]) '@ $endFile=@' #==========Adjust Settings======================================== ax_settings(ax1,textLocation[0],textLocation[1],ProLabels[0]) gs.update(left=left,bottom=bottom,top=top,wspace=0.0, hspace=0.0) # set the spacing between axes. leg=ax1.legend(fontsize='small',frameon=False,handletextpad=0.5,handlelength=1.5,columnspacing=1,ncol=leg_col, bbox_to_anchor=(0, 1), loc='lower left'); #===================Name it & Save=============================== ProLabels=[prolabel.replace("$","").replace("_","").replace("^","") for prolabel in ProLabels]; #Remove $ and _ characters in path atom_index_range=','.join(str(ProIndices[0][i]+1) for i in range(np.shape(ProIndices[0])[0])); #creates a list of projected atoms if(ProLabels[0]=='' or ProLabels[0]==' '): #check if this projection of whole composite. atom_index_range='All' name=str('Ions'+'_'+ProLabels[0]+'['+atom_index_range+']'+'('+str(ProLabels[1])+')('+str(ProLabels[2])+')('+str(ProLabels[3])+')'+'_D'); #A for All,B for Bnads, D for DOS. plt.savefig(str(name+'.pdf'),transparent=True) '@ Function Get-DensityPlot{ #Plots of different types [CmdletBinding()] Param([Parameter()][switch]$HalfColumnWide, [Parameter()][switch]$AreaPlot, [Parameter()][switch]$LinePlot, #[Parameter()][switch]$ProjectedDOS, [Parameter()][switch]$StackPlot,#[Parameter()][switch]$DOS, [hashtable]$PlotArguments) #Get Hashtable from function Get-PlotArguments if(-not (Test-Path .\tDOS.txt)){Write-Host "Required files not found. Generating using 'Export-VaspRun' ..." -ForegroundColor Green; Export-VaspRun;} if($(Test-Path .\tDOS.txt)){ #checks if file generated. Write-Host "Files now exist. Plotting ..." -ForegroundColor Yellow; #making a plot file in order $variablesList=@(); $(Foreach($key in $PlotArguments.Keys){ $xxx="$($key) =$($PlotArguments.$key);" $variablesList+=$xxx}); $variablesList=$($variablesList|Sort-Object) -join "`n" $consoleInput=@" $variablesList "@ if($HalfColumnWide.IsPresent){$Width=1.7}Else{$Width=3.4} $PlotInput=$line # Default plot if no selection made. if($AreaPlot.IsPresent){$PlotInput=$area} if($LinePlot.IsPresent){$PlotInput=$line} if($StackPlot.IsPresent){$PlotInput=$stack} $head=(Get-Content .\tDOS.txt)[0].Split('#') $pythonFileContent=@" #=================Input Variables===================== $($consoleInput) FigureWidth=$($Width); SYSTEM='$($head[-3])'; $($head[-1]); $($startFile) $($PlotInput) $($endFile) "@ $pythonFileContent|Set-Content .\DOS.py python .\DOS.py #strat plotting } #if block ends } Export-ModuleMember -Function "Get-DensityHashTable" Export-ModuleMember -Function "Get-DensityPlot" |