MakeSlab.psm1
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Function Merge-ToSlab{ [CmdletBinding()] Param( [Parameter(Mandatory="True", Position=0)][string]$FirstPOSCAR, [Parameter(Mandatory="True", Position=1)][string]$SecondPOSCAR) Write-Host "Only Cubic and Tetragonal POSCARs are supported. Make sure your POSCARs DO NOT have non-zero xz,yz,zx,zy elements, If so, first rotate POSCAR using Vesta." -ForegroundColor Yellow $data1=(Get-Content $FirstPOSCAR) $data2=(Get-Content $SecondPOSCAR) $lc1=[float]$data1[1] ; $lc2=[float]$data2[1] #lattice constants $x1=[array]($data1[2].split()|Where-Object {$_}) $y1=[array]($data1[3].split()|Where-Object {$_}) $z1=[array]($data1[4].split()|Where-Object {$_}) $x2=[array]($data2[2].split()|Where-Object {$_}) $y2=[array]($data2[3].split()|Where-Object {$_}) $z2=[array]($data2[4].split()|Where-Object {$_}) if([float]$x1[2] -ne 0 -or [float]$y1[2] -ne 0 -or [float]$z1[0] -ne 0 -or [float]$z1[1] -ne 0){ Write-Host "First POSCAR $FirstPOSCAR has any non-zero xz,yz,zx,zy elements, Can't proceed" -ForegroundColor Red break} if([float]$x2[2] -ne 0 -or [float]$y2[2] -ne 0 -or [float]$z2[0] -ne 0 -or [float]$z2[1] -ne 0){ Write-Host "Second $SecondPOSCAR has any non-zero xz,yz,zx,zy elements, Can't proceed" -ForegroundColor Red break} #getting volume and cross-sectional area to find modified (0,0,z) for second POSCAR $V2=([Math]::Pow($lc2,3))*(([float]$x2[0])*([float]$y2[1])*([float]$z2[2])); $Axy1=([Math]::Pow($lc1,2))*(([float]$x1[0])*([float]$y1[1])) $z2_new=[float]$V2/$Axy1 #Make x y same, change z for second slab $totalZ=[float](($lc1*[float]$z1[2])+$z2_new) $factor1=($lc1*[float]$z1[2])/$totalZ $factor2=[float]$z2_new/$totalZ $elem_1= $data1[5].Split()|Where-Object {$_} $total_1=[array]$data1[6].Split()|Where-Object {$_}; $elem_2= $data2[5].Split()|Where-Object {$_} $total_2=[array]$data2[6].Split()|Where-Object {$_} $max_elem_index=[int]([Math]::Max($total_1.Count,$total_2.Count)-1) $total_slab=Foreach($i in 0..$max_elem_index){[int]$total_1[$i]+[int]$total_2[$i]} #index_out_of_range doesnt make problem here. $diff_elem=(Compare-Object -ReferenceObject $elem_1 -DifferenceObject $elem_2 -PassThru) $Elements="$elem_1 $diff_elem" #creates elements in slab $outfile=New-Item -Path ./POSCAR_New.vasp -Force $POSACR_init=@" $($data1[0].Trim()+'/'+$data2[0].Trim()) $("{0:n16}" -f ($lc1*$x1[0])) $("{0,24:N16}" -f 1) $("{0,24:N16}" -f ($x1[1]/$x1[0])) $("{0,24:N16}" -f 0) $("{0,24:N16}" -f ($y1[0]/$x1[0])) $("{0,24:N16}" -f ($y1[1]/$x1[0])) $("{0,24:N16}" -f 0) $("{0,24:N16}" -f 0) $("{0,24:N16}" -f 0) $("{0,24:N16}" -f ($totalZ/($lc1*$x1[0]))) $Elements $total_slab Direct "@ #here-string for Z-only yet. $POSACR_init|Set-Content $outfile #save data in array if($data1[7].StartsWith('S') -or $data2[7].StartsWith('S')){$shift=8;$ii=9}Else{$shift=7;$ii=8} #see if slective dynamics there. $N1=[int]((,$shift+$total_1)|Measure-Object -Sum).Sum $N2=[int]((,$shift+$total_2)|Measure-Object -Sum).Sum $arr1=$data1[$ii..$N1]; $arr2=$data2[$ii..$N2]; #Loops of getting data $start1=0;$stop1=[int]$total_1[0]-1 $start2=0;$stop2=[int]$total_2[0]-1 ForEach($index in 0..$max_elem_index){ if($index -lt $total_1.Count){ ForEach($i in $start1..$stop1){ #Array1 if($i -lt $(($total_1|Measure-Object -Sum).Sum)){ [array]$value=$arr1[$i].Split()|Where-Object {$_} $value_new=([float]$value[2])*$factor1 $line="{0,24:N16}" -f ([float]$value[0]) + "{0,24:N16}" -f ([float]$value[1]) + "{0,24:N16}" -f ($value_new) $line|Add-Content $outfile }} $start1+=[int]$total_1[$index]; $stop1=$start1+ [int]$total_1[$index+1]-1 } if($index -lt $total_2.Count){ ForEach($i in $start2..$stop2){ #Array2 if($i -lt $(($total_2|Measure-Object -Sum).Sum)){ [array]$value=$arr2[$i].Split()|Where-Object {$_} $value_new=([float]$value[2])*$factor2+$factor1 $line="{0,24:N16}" -f ([float]$value[0]) + "{0,24:N16}" -f ([float]$value[1]) + "{0,24:N16}" -f ($value_new) $line|Add-Content $outfile }} $start2+=[int]$total_2[$index]; $stop2=$start2+ [int]$total_2[[int]($index+1)]-1 } } Write-Host "File [POSCAR_New.vasp] created." -ForegroundColor Green } Function Enable-SelectiveDynamics{ [CmdletBinding()] Param( [Parameter(Mandatory="True", Position=0)][string]$InputPOSCAR, [Parameter(Position=1)][array]$SelectSitesNumber=@()) $data=Get-Content $InputPOSCAR if($data[7].StartsWith('S')){$shift=8;$ii=9}Else{$shift=7;$ii=8} #see if slective dynamics there. $N=([array]$data[6].Split()|Where-Object {$_}|Measure-Object -Sum).Sum+$shift $data_New=$data[$ii..$N]; $outFile=New-Item ./POSCAR_eSD.vasp -Force $($data[0..6])|Set-Content $outFile $POSCAR_init=@" Selective dynamics Direct "@ $POSCAR_init|Add-Content $outFile ForEach($i in 0..($data_New.Count-1)){ if ($SelectSitesNumber.Contains($($i-(-1)))){$pattern=" T T T"; }Else{$pattern=" F F F"} $value=($data_New[$i].Replace('F','').Replace('T','').TrimEnd()) "$value $pattern"|Add-Content $outFile} Write-Host "File [POSCAR_eSD.vasp] is created." -ForegroundColor Green } Function Select-SitesInLayers{ [CmdletBinding()] Param( [Parameter(Mandatory="True", Position=0)][string]$InputPOSCAR, [Parameter(Mandatory="True", Position=1)][array]$Array_2Decimal=@()) $data=Get-Content $InputPOSCAR $SelectLayersPosition=@($Array_2Decimal) if($data[7].StartsWith('S')){$shift=8;$ii=9}Else{$shift=7;$ii=8} #see if slective dynamics there. $N=([array]$data[6].Split()|Where-Object {$_}|Measure-Object -Sum).Sum+$shift $data_New=$data[$ii..$N]; $X=@();$Y=@();$Z=@(); #arrays of elements in 3D ForEach($i in 0..($data_New.Count-1)){ [array]$value=($data_New[$i].Split()|Where-Object {$_}); [string]$value2=$value[2];[string]$value1=$value[1];[string]$value0=$value[0]; [string]$nV2=(($value2.split('.')[0],$value2.split('.')[1].Substring(0,2)) -join '.') [string]$nV1=(($value1.split('.')[0],$value1.split('.')[1].Substring(0,2)) -join '.') [string]$nV0=(($value0.split('.')[0],$value0.split('.')[1].Substring(0,2)) -join '.') if ($SelectLayersPosition -contains $nV0){$X+=$($i+1)} if ($SelectLayersPosition -contains $nV1){$Y+=$($i+1)} if ($SelectLayersPosition -contains $nV2){$Z+=$($i+1)} } [pscustomobject]@{XY_PlaneSites=[array]($Z|Sort-Object);YZ_PlaneSites=[array]($X|Sort-Object);ZX_PlaneSites=[array]($Y|Sort-Object)} #output custom Object } Function Disable-SelectiveDynamics{ [CmdletBinding()] Param([Parameter(Mandatory="True",Position=0)][string]$InputPOSCAR) $read1=(Get-Content $InputPOSCAR|Where-Object {$_ -notmatch 'elective'})[0..6] $read2=(Get-Content $InputPOSCAR|Select-Object -Skip 7|Where-Object {$_ -notmatch 'elective'}).Replace('F','').Replace('T','').TrimEnd()|Where-Object {$_} $outFile =New-Item POSCAR_dSD.vasp -Force ($read1,$read2)|Set-Content $outFile -Force Write-Host "File [POSCAR_dSD.vasp] created." } Function Show-LayersInfo{ [CmdletBinding()] Param([Parameter(Mandatory="True",Position=0)][string]$InputPOSCAR) $data=(Get-Content $InputPOSCAR|Where-Object {$_ -notmatch 'elective'}) $nAtoms=[int]($data[6].Split(" ")|Where-Object {$_}|Measure-Object -sum).sum $coords=$data[8..($nAtoms+7)] $z_coord=@();$x_coord=@();$y_coord=@(); Foreach($coord in $coords){ [array]$value=$coord.split()|Where-Object {$_} [string]$value2=$value[2];[string]$value1=$value[1];[string]$value0=$value[0]; $z_coord+=(($value2.split('.')[0],$value2.split('.')[1].Substring(0,2)) -join '.') $y_coord+=(($value1.split('.')[0],$value1.split('.')[1].Substring(0,2)) -join '.') $x_coord+=(($value0.split('.')[0],$value0.split('.')[1].Substring(0,2)) -join '.') } [pscustomobject]@{ X_AtLayers=[array]($x_coord|Select-Object -Unique|Sort-Object); Y_AtLayers=[array]($y_coord|Select-Object -Unique|Sort-Object); Z_AtLayers=[array]($z_coord|Select-Object -Unique|Sort-Object)} #output custom Object } Export-ModuleMember -Function 'Merge-ToSlab' Export-ModuleMember -Function 'Enable-SelectiveDynamics' Export-ModuleMember -Function 'Select-SitesInLayers' Export-ModuleMember -Function 'Disable-SelectiveDynamics' Export-ModuleMember -Function 'Show-LayersInfo' |