diff --git a/2022_05_Trieste/Fri.PM.Margine/B.pz-vbc.UPF b/2022_05_Trieste/Fri.PM.Margine/B.pz-vbc.UPF new file mode 100644 index 0000000..41a4ad2 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/B.pz-vbc.UPF @@ -0,0 +1,334 @@ + +Generated using ld1 code +Author: P. Giannozzi (?) Generation date: unknown +Info: B LDA 2s2 2p1 VonBarth-Car, l=1 local + 0 The Pseudo was generated with a Non-Relativistic Calculation + 0.00000000000E+00 Local Potential cutoff radius +nl pn l occ Rcut Rcut US E pseu +2S 0 0 2.00 0.00000000000 0.00000000000 0.00000000000 +2P 0 1 1.00 0.00000000000 0.00000000000 0.00000000000 + + + + + 0 Version Number + B Element + NC Norm - Conserving pseudopotential + F Nonlinear Core Correction + SLA PZ NOGX NOGC PZ Exchange-Correlation functional + 3.00000000000 Z valence + 0.00000000000 Total energy + 0.0000000 0.0000000 Suggested cutoff for wfc and rho + 0 Max angular momentum component + 157 Number of points in mesh + 2 1 Number of Wavefunctions, Number of Projectors + Wavefunctions nl l occ + 2S 0 2.00 + 2P 1 1.00 + + + + + + 3.66312777775E-03 3.89937922172E-03 4.15086757474E-03 4.41857553301E-03 + 4.70354917120E-03 5.00690202999E-03 5.32981946727E-03 5.67356328994E-03 + 6.03947668446E-03 6.42898946538E-03 6.84362366233E-03 7.28499946747E-03 + 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0.00000000000E+00 0.00000000000E+00 + 0.00000000000E+00 0.00000000000E+00 0.00000000000E+00 0.00000000000E+00 + + + 1 Number of nonzero Dij + 1 1 2.03126814412E+00 + + + + + +2S 0 2.00 Wavefunction + 9.33461780000E-04 9.93670870000E-04 1.05776430000E-03 1.12599300000E-03 + 1.19862380000E-03 1.27594100000E-03 1.35824740000E-03 1.44586520000E-03 + 1.53913770000E-03 1.63843040000E-03 1.74413240000E-03 1.85665820000E-03 + 1.97644940000E-03 2.10397610000E-03 2.23973930000E-03 2.38427260000E-03 + 2.53814450000E-03 2.70196080000E-03 2.87636710000E-03 3.06205140000E-03 + 3.25974740000E-03 3.47023720000E-03 3.69435470000E-03 3.93298980000E-03 + 4.18709180000E-03 4.45767390000E-03 4.74581790000E-03 5.05267940000E-03 + 5.37949300000E-03 5.72757900000E-03 6.09834920000E-03 6.49331510000E-03 + 6.91409550000E-03 7.36242570000E-03 7.84016720000E-03 8.34931930000E-03 + 8.89203120000E-03 9.47061580000E-03 1.00875660000E-02 1.07455730000E-02 + 1.14475450000E-02 1.21966320000E-02 1.29962500000E-02 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a/2022_05_Trieste/Fri.PM.Margine/Mg.pz-n-vbc.UPF b/2022_05_Trieste/Fri.PM.Margine/Mg.pz-n-vbc.UPF new file mode 100644 index 0000000..50554af --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/Mg.pz-n-vbc.UPF @@ -0,0 +1,444 @@ + +Generated using ld1 code +Author: Stefano de Gironcoli Generation date: before 1998 +Info: Mg LDA 3s2 3p0 VonBarth-Car, l=2 local, core correction + 0 The Pseudo was generated with a Non-Relativistic Calculation + 0.00000000000E+00 Local Potential cutoff radius +nl pn l occ Rcut Rcut US E pseu +3S 0 0 2.00 0.00000000000 0.00000000000 0.00000000000 +3P 0 1 0.00 0.00000000000 0.00000000000 0.00000000000 + + + + + 0 Version Number + Mg Element + NC Norm - Conserving pseudopotential + T Nonlinear Core Correction + SLA PZ NOGX NOGC PZ Exchange-Correlation functional + 2.00000000000 Z valence + 0.00000000000 Total energy + 0.0000000 0.0000000 Suggested cutoff for wfc and rho + 1 Max angular momentum component + 171 Number of points in mesh + 2 2 Number of 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1.49126032066E-28 2.00640872576E-30 + diff --git a/2022_05_Trieste/Fri.PM.Margine/epw1.in b/2022_05_Trieste/Fri.PM.Margine/epw1.in new file mode 100644 index 0000000..1e3b9d4 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/epw1.in @@ -0,0 +1,64 @@ +-- +&inputepw + prefix = 'mgb2', + amass(1) = 24.305, + amass(2) = 10.811 + outdir = './' + dvscf_dir = './save' + + ep_coupling = .true. + elph = .true. + epwwrite = .true. + epwread = .false. + + etf_mem = 1 + + wannierize = .true. + nbndsub = 5 + + num_iter = 500 + dis_froz_max= 8.8 + proj(1) = 'B:pz' + proj(2) = 'f=0.5,1.0,0.5:s' + proj(3) = 'f=0.0,0.5,0.5:s' + proj(4) = 'f=0.5,0.5,0.5:s' + + iverbosity = 2 + + fsthick = 0.2 ! eV + degaussw = 0.05 ! eV + + fermi_plot = .true. + ephwrite = .true. + + eliashberg = .true. + + laniso = .true. + limag = .true. + lpade = .true. + + nsiter = 500 + conv_thr_iaxis = 1.0d-3 + wscut = 0.5 + muc = 0.05 + + nstemp = 2 + temps = 10 20 + + nk1 = 6 + nk2 = 6 + nk3 = 6 + + nq1 = 2 + nq2 = 2 + nq3 = 2 + + mp_mesh_k = .true. + nkf1 = 20 + nkf2 = 20 + nkf3 = 20 + + nqf1 = 10 + nqf2 = 10 + nqf3 = 10 + / diff --git a/2022_05_Trieste/Fri.PM.Margine/epw2.in b/2022_05_Trieste/Fri.PM.Margine/epw2.in new file mode 100644 index 0000000..bd78e20 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/epw2.in @@ -0,0 +1,65 @@ +-- +&inputepw + prefix = 'mgb2', + amass(1) = 24.305, + amass(2) = 10.811 + outdir = './' + dvscf_dir = './save' + + ep_coupling = .false. + elph = .false. + epwwrite = .false. + epwread = .true. + + etf_mem = 1 + + wannierize = .false. + nbndsub = 5 + + num_iter = 500 + dis_froz_max= 8.8 + proj(1) = 'B:pz' + proj(2) = 'f=0.5,1.0,0.5:s' + proj(3) = 'f=0.0,0.5,0.5:s' + proj(4) = 'f=0.5,0.5,0.5:s' + + iverbosity = 2 + + fsthick = 0.2 ! eV + degaussw = 0.05 ! eV + + fermi_plot = .false. + ephwrite = .false. + + eliashberg = .true. + imag_read = .true. + + laniso = .true. + limag = .true. + lpade = .false. + + nsiter = 500 + conv_thr_iaxis = 1.0d-3 + wscut = 0.5 + muc = 0.05 + + nstemp = 6 + temps = 10 30 40 50 60 70 + + nk1 = 6 + nk2 = 6 + nk3 = 6 + + nq1 = 2 + nq2 = 2 + nq3 = 2 + + mp_mesh_k = .true. + nkf1 = 20 + nkf2 = 20 + nkf3 = 20 + + nqf1 = 10 + nqf2 = 10 + nqf3 = 10 + / diff --git a/2022_05_Trieste/Fri.PM.Margine/epw3.in b/2022_05_Trieste/Fri.PM.Margine/epw3.in new file mode 100644 index 0000000..de37671 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/epw3.in @@ -0,0 +1,67 @@ +-- +&inputepw + prefix = 'mgb2', + amass(1) = 24.305, + amass(2) = 10.811 + outdir = './' + dvscf_dir = './save' + + ep_coupling = .false. + elph = .false. + epwwrite = .false. + epwread = .true. + + etf_mem = 1 + + wannierize = .false. + nbndsub = 5 + + num_iter = 500 + dis_froz_max= 8.8 + proj(1) = 'B:pz' + proj(2) = 'f=0.5,1.0,0.5:s' + proj(3) = 'f=0.0,0.5,0.5:s' + proj(4) = 'f=0.5,0.5,0.5:s' + + iverbosity = 2 + + fsthick = 0.2 ! eV + degaussw = 0.05 ! eV + + fermi_plot = .false. + ephwrite = .false. + + eliashberg = .true. + imag_read = .false. + + fila2f = 'mgb2.a2f' + + liso = .true. + limag = .true. + lpade = .false. + + nsiter = 500 + conv_thr_iaxis = 1.0d-3 + wscut = 0.5 + muc = 0.05 + + nstemp = 18 + temps = 1 35 + + nk1 = 6 + nk2 = 6 + nk3 = 6 + + nq1 = 2 + nq2 = 2 + nq3 = 2 + + mp_mesh_k = .true. + nkf1 = 20 + nkf2 = 20 + nkf3 = 20 + + nqf1 = 10 + nqf2 = 10 + nqf3 = 10 + / diff --git a/2022_05_Trieste/Fri.PM.Margine/nscf.in b/2022_05_Trieste/Fri.PM.Margine/nscf.in new file mode 100644 index 0000000..353ed72 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/nscf.in @@ -0,0 +1,250 @@ + &control + calculation = 'nscf', + restart_mode = 'from_scratch', + prefix = 'mgb2', + pseudo_dir = './', + outdir = './', + / + &system + ibrav = 4, + celldm(1) = 5.8260252227888, + celldm(3) = 1.1420694129095, + nat = 3, + ntyp = 2, + ecutwfc = 40 + occupations = 'smearing' + smearing = 'mp' + degauss = 0.05 + nbnd = 16 + / + &electrons + diagonalization = 'david' + mixing_mode = 'plain' + mixing_beta = 0.7 + conv_thr = 1.0d-9 + / + ATOMIC_SPECIES + Mg 24.305 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nq2 = 2, + nq3 = 2, + tr2_ph = 1.0d-12 + / diff --git a/2022_05_Trieste/Fri.PM.Margine/pp.py b/2022_05_Trieste/Fri.PM.Margine/pp.py new file mode 100644 index 0000000..3a41ba4 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/pp.py @@ -0,0 +1,230 @@ +#!/usr/bin/env python3 +# +# Post-processing script from of PH data in format used by EPW +# 14/07/2015 - Creation of the script - Samuel Ponce +# 14/03/2018 - Automatically reads the number of q-points - Michael Waters +# 14/03/2018 - Detect if SOC is included in the calculation - Samuel Ponce +# 05/06/2019 - Removed SOC for xml detection instead - Felix Goudreault +# +from __future__ import print_function +try: + from builtins import input +except ImportError: + print('Install future. e.g. "pip install --user future"') +# import numpy as np + +import os +import re +from xml.dom import minidom + + +# Return the number of q-points in the IBZ +def get_nqpt(prefix): + fname = '_ph0/' + prefix + '.phsave/control_ph.xml' + + fid = open(fname, 'r') + lines = fid.readlines() + # these files are relatively small so reading the whole thing shouldn't + # be an issue + fid.close() + + line_number_of_nqpt = 0 + while 'NUMBER_OF_Q_POINTS' not in lines[line_number_of_nqpt]: + # increment to line of interest + line_number_of_nqpt += 1 + line_number_of_nqpt += 1 # its on the next line after that text + + nqpt = int(lines[line_number_of_nqpt]) + + return nqpt + + +# Check if the calculation include SOC +def hasSOC(prefix): + fname = prefix+'.save/data-file-schema.xml' + + xmldoc = minidom.parse(fname) + item = xmldoc.getElementsByTagName('spinorbit')[0] + lSOC = item.childNodes[0].data + + return lSOC + + +# Check if the calculation includes PAW +def hasPAW(prefix): + fname = prefix+'.save/data-file-schema.xml' + + xmldoc = minidom.parse(fname) + item = xmldoc.getElementsByTagName('paw')[0] + lPAW = (item.childNodes[0].data == 'true') + + return lPAW + + +# Check if the calculation used .fc or .fc.xml files +def hasfc(prefix): + fname = str(prefix)+'.fc.xml' + if (os.path.isfile(fname)): + lfc = True + else: + fname_no_xml = re.sub('\.xml$', '', fname) + if (os.path.isfile(fname_no_xml)): + lfc = True + else: + lfc = False + + return lfc + + +# check if calculation used xml files (irrelevant of presence of SOC) +def hasXML(prefix): + # check for a file named prefix.dyn1.xml + # if it exists => return True else return False + fname = os.path.join(prefix + ".dyn1.xml") + if os.path.isfile(fname): + return True + # check if the other without .xml extension exists + # if not raise an error + fname_no_xml = re.sub('\.xml$', '', fname) + + class FileNotFoundError(Exception): + pass + if not os.path.isfile(fname_no_xml): + raise FileNotFoundError( + "No dyn0 file found cannot tell if xml format was used.") + return False + + +# Check if the calculation was done in sequential +def isSEQ(prefix): + fname = '_ph0/'+str(prefix)+'.dvscf' + if (os.path.isfile(fname)): + lseq = True + else: + lseq = False + + return lseq + + +# Enter the number of irr. q-points +user_input = input( + 'Enter the prefix used for PH calculations (e.g. diam)\n') +prefix = str(user_input) + +# # Test if SOC +# SOC = hasSOC(prefix) +# Test if '.xml' files are used +XML = hasXML(prefix) + +# Test if PAW +PAW = hasPAW(prefix) + +# Test if fc +fc = hasfc(prefix) + +# Test if seq. or parallel run +SEQ = isSEQ(prefix) + +if True: # this gets the nqpt from the outputfiles + nqpt = get_nqpt(prefix) + +else: + # Enter the number of irr. q-points + user_input = input( + 'Enter the number of irreducible q-points\n') + nqpt = user_input + try: + nqpt = int(user_input) + except ValueError: + raise Exception('The value you enter is not an integer!') + +os.system('mkdir save 2>/dev/null') + +for iqpt in range(1, nqpt+1): + label = str(iqpt) + + # Case calculation in seq. + if SEQ: + # Case with XML files + if XML: + os.system('cp '+prefix+'.dyn0 '+prefix+'.dyn0.xml') + os.system('cp '+prefix+'.dyn'+str(iqpt)+'.xml save/'+prefix + + '.dyn_q'+label+'.xml') + if (iqpt == 1): + os.system('cp _ph0/'+prefix+'.dvscf* save/'+prefix+'.dvscf_q' + + label) + os.system('cp -r _ph0/'+prefix+'.phsave save/') + if fc: + os.system('cp '+prefix+'.fc.xml save/ifc.q2r.xml') + if PAW: + os.system('cp _ph0/'+prefix+'.dvscf_paw* save/'+prefix + + '.dvscf_paw_q'+label) + else: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf* save/'+prefix+'.dvscf_q'+label) + os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*') + if PAW: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf_paw* save/'+prefix+'.dvscf_paw_q'+label) + # Case without XML files + else: + os.system('cp '+prefix+'.dyn'+str(iqpt)+' save/'+prefix+'.dyn_q' + + label) + if (iqpt == 1): + os.system('cp _ph0/'+prefix+'.dvscf save/'+prefix+'.dvscf_q' + + label) + os.system('cp -r _ph0/'+prefix+'.phsave save/') + if fc: + os.system('cp '+prefix+'.fc save/ifc.q2r') + if PAW: + os.system('cp _ph0/'+prefix+'.dvscf_paw save/'+prefix + + '.dvscf_paw_q'+label) + else: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf save/'+prefix+'.dvscf_q'+label) + os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*') + if PAW: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf_paw save/'+prefix+'.dvscf_paw_q'+label) + else: + # Case with XML format + if XML: + os.system('cp '+prefix+'.dyn0 '+prefix+'.dyn0.xml') + os.system('cp '+prefix+'.dyn'+str(iqpt)+'.xml save/'+prefix + + '.dyn_q'+label+'.xml') + if (iqpt == 1): + os.system('cp _ph0/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q' + + label) + os.system('cp -r _ph0/'+prefix+'.phsave save/') + if fc: + os.system('cp '+prefix+'.fc.xml save/ifc.q2r.xml') + if PAW: + os.system('cp _ph0/'+prefix+'.dvscf_paw1 save/'+prefix + + '.dvscf_paw_q'+label) + else: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf1 save/'+prefix+'.dvscf_q'+label) + os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*') + if PAW: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf_paw1 save/'+prefix+'.dvscf_paw_q'+label) + # Case without XML format + else: + os.system('cp '+prefix+'.dyn'+str(iqpt)+' save/'+prefix+'.dyn_q' + + label) + if (iqpt == 1): + os.system('cp _ph0/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q' + + label) + os.system('cp -r _ph0/'+prefix+'.phsave save/') + if fc: + os.system('cp '+prefix+'.fc save/ifc.q2r') + if PAW: + os.system('cp _ph0/'+prefix+'.dvscf_paw1 save/'+prefix + + '.dvscf_paw_q'+label) + else: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf1 save/'+prefix+'.dvscf_q'+label) + os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*') + if PAW: + os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix + + '.dvscf_paw1 save/'+prefix+'.dvscf_paw_q'+label) diff --git a/2022_05_Trieste/Fri.PM.Margine/scf.in b/2022_05_Trieste/Fri.PM.Margine/scf.in new file mode 100644 index 0000000..07a89c0 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/scf.in @@ -0,0 +1,33 @@ + &control + calculation = 'scf', + restart_mode = 'from_scratch', + prefix = 'mgb2', + pseudo_dir = './', + outdir = './', + / + &system + ibrav = 4, + celldm(1) = 5.8260252227888, + celldm(3) = 1.1420694129095, + nat = 3, + ntyp = 2, + ecutwfc = 40 + occupations = 'smearing' + smearing = 'mp' + degauss = 0.05 + / + &electrons + diagonalization = 'david' + mixing_mode = 'plain' + mixing_beta = 0.7 + conv_thr = 1.0d-9 + / + ATOMIC_SPECIES + Mg 24.305 Mg.pz-n-vbc.UPF + B 10.811 B.pz-vbc.UPF + ATOMIC_POSITIONS crystal + Mg 0.000000000 0.000000000 0.000000000 + B 0.333333333 0.666666667 0.500000000 + B 0.666666667 0.333333333 0.500000000 + K_POINTS AUTOMATIC + 8 8 8 0 0 0 diff --git a/2022_05_Trieste/Fri.PM.Margine/script_gap0_imag b/2022_05_Trieste/Fri.PM.Margine/script_gap0_imag new file mode 100644 index 0000000..ed4ae52 --- /dev/null +++ b/2022_05_Trieste/Fri.PM.Margine/script_gap0_imag @@ -0,0 +1,6 @@ +#!/bin/tcsh + +awk 'FNR==2 {print FILENAME,$0}' mgb2.imag_iso_* | awk '{print $1 " " $4*1000}' > mgb2.imag_iso_gap0 +sed -i 's/mgb2.imag_iso_//' mgb2.imag_iso_gap0 + +exit diff --git a/2022_05_Trieste/Fri.PM.Margine/tutorial_Fri_PM_Margine.pdf b/2022_05_Trieste/Fri.PM.Margine/tutorial_Fri_PM_Margine.pdf new file mode 100644 index 0000000..d1b2fee Binary files /dev/null and b/2022_05_Trieste/Fri.PM.Margine/tutorial_Fri_PM_Margine.pdf differ