Dear Angus,
I have been calculating the system using your input file.
No error, no segmentation fault, so far.
test-7.3]$ grep achiev gaaso.out
convergence has been achieved in 10 iterations
convergence has been achieved in 8 iterations
convergence has been achieved in 9 iterations
test-7.3]$ grep bfgs gaaso.out
number of bfgs steps = 0
number of bfgs steps = 1
number of bfgs steps = 2
test-7.3]$ grep '! total energy' gaaso.out
! total energy = -22477.13808906 Ry
! total energy = -22551.10067194 Ry
! total energy = -22646.03611011 Ry
Dear Angus,
It is now the 3rd step in the vc-relaxation process.
Now I will have to stop the calculation since it consumes
very large computer resources.
Here I used the cutoff of 'ecutwfc = 40' since the value 100 Ry you
specified is very large for this test calculation.
Also I used the NC pseudopotentials at the pseudo-dojo.
At what computational step did you encounter the segmentation fault?
Was it at the first scf cycle before entering the vc-relaxation?
> 2024/06/05 20:02、Angus Gentles <[email protected]>のメール:
>
> Dear Kazume Nishdate,
>
> I have already changed this in my compilation, its set to 50 in my version.
> Thanks for the comment though.
>
> Kind regards,
> Angus Gentles
> ams-OSRAM
> Intitute of Microelectronics, TU WienFrom: Kazume NISHIDATE
> <[email protected]>
> Sent: 05 June 2024 12:46 PM
> To: Angus Gentles <[email protected]>; Quantum ESPRESSO users Forum
> <[email protected]>
> Subject: Re: [QE-users] Segmentation fault in qe-7.3 with DFT+U
> [You don't often get email from [email protected]. Learn why this is
> important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Dear Angus Gentles,
>
>
> Just a note.
>
> You should check the source file 'Modules/parameters.f90'.
> It is sates that
>
> > INTEGER, PARAMETER :: ntypx = 10
> > !! max number of different types of atom
> > INTEGER, PARAMETER :: nsx = ntypx
>
> so you can handle up to 10 different kinds of atom.
>
> However, you specify the ntype as
> > ntyp = 20
>
> in your input file, and this is two times larger than the default
> value.
>
> I think, you should try to re-compile QE with increasing the value of
> ntypx in the 'Modules/parameters.f90'. And then, you can calculate
> your system without the limitation of the 'ntype'.
>
>
>
> > 2024/06/05 17:05、Angus Gentles via users
> > <[email protected]>のメール:
> >
> > Dear all,
> >
> > I am getting a segmentation fault error when using DFT+U calculations as
> > below.
> >
> > [n3511-027:2614825] 127 more processes have sent help message
> > help-mpi-btl-openib.txt / error in device init
> > [n3511-027:2614825] Set MCA parameter "orte_base_help_aggregate" to 0 to
> > see all help / error messages
> > [n3511-027:2614833:0:2614833] Caught signal 11 (Segmentation fault: address
> > not mapped to object at address 0xffffffff80a1adb8)
> > ==== backtrace (tid:2614833) ====
> > 0 /lib64/libucs.so.0(ucs_handle_error+0x2dc) [0x14bef008cedc]
> > 1 /lib64/libucs.so.0(+0x2b0bc) [0x14bef008d0bc]
> > 2 /lib64/libucs.so.0(+0x2b28a) [0x14bef008d28a]
> > 3
> > /home/fs71766/waldhoer02/data/tools/vsc5/base_libs/install/openmpi-4.1.1/lib/libmpi.so.40(MPI_Bcast+0x58)
> > [0x14bf04d4e598]
> > 4
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_blacs_openmpi_lp64.so.2(MKLMPI_Bcast+0xdd)
> > [0x14bf0c5a6dfd]
> > 5
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(PB_CpgemmMPI+0x1097)
> > [0x14bf0c1bbad7]
> > 6
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdgemm_+0xda7)
> > [0x14bf0c21ff07]
> > 7
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdlaed1_+0x7cd)
> > [0x14bf0bcc6dbd]
> > 8
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdlaed0_+0x9a1)
> > [0x14bf0bcc6551]
> > 9
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdstedc_+0x639)
> > [0x14bf0bcd0f19]
> > 10
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(mkl_pzheevd0_+0xf99)
> > [0x14bf0bf377c9]
> > 11
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(mkl_pzheevdm_+0xb99)
> > [0x14bf0bf36379]
> > 12
> > /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pzheevd_+0x3ca)
> > [0x14bf0bf3553a]
> > 13 pw.x() [0xbb9d5a]
> > 14 pw.x() [0xb9bb82]
> > 15 pw.x() [0x71de4b]
> > 16 pw.x() [0x5a03a9]
> > 17 pw.x() [0x5a47c4]
> > 18 pw.x() [0x412a44]
> > 19 pw.x() [0x41caf9]
> > 20 pw.x() [0x4f955b]
> > 21 pw.x() [0x40688c]
> > 22 pw.x() [0x4065cd]
> > 23 /lib64/libc.so.6(__libc_start_main+0xe5) [0x14bf033d8d85]
> > 24 pw.x() [0x40660e]
> > =================================
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x14bf033ecb4f in ???
> > #1 0x14bf04d4e598 in ompi_comm_invalid
> > at ../../../../ompi/communicator/communicator.h:341
> > #2 0x14bf04d4e598 in PMPI_Bcast
> > at
> > /home/fs71766/waldhoer02/data/tools/vsc5/base_libs/build/openmpi-4.1.1/ompi/mpi/c/profile/pbcast.c:72
> > #3 0x14bf0c5a6dfc in ???
> > #4 0x14bf0c1bbad6 in ???
> > #5 0x14bf0c21ff06 in ???
> > #6 0x14bf0bcc6dbc in ???
> > #7 0x14bf0bcc6550 in ???
> > #8 0x14bf0bcd0f18 in ???
> > #9 0x14bf0bf377c8 in ???
> > #10 0x14bf0bf36378 in ???
> > #11 0x14bf0bf35539 in ???
> > #12 0xbb9d59 in __zhpev_module_MOD_pzheevd_drv
> > at /home/fs71287/gentles/tools/sc-qe-7.3/LAXlib/zhpev_drv.f90:1562
> > #13 0xb9bb81 in laxlib_pcdiaghg_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/LAXlib/cdiaghg.f90:587
> > #14 0x71de4a in pcegterg_
> > at
> > /home/fs71287/gentles/tools/sc-qe-7.3/KS_Solvers/Davidson/cegterg.f90:944
> > #15 0x5a03a8 in diag_bands_k
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:1030
> > #16 0x5a03a8 in diag_bands_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:322
> > #17 0x5a47c3 in c_bands_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:132
> > #18 0x412a43 in electrons_scf_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/electrons.f90:689
> > #19 0x41caf8 in electrons_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/electrons.f90:192
> > #20 0x4f955a in run_pwscf_
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/run_pwscf.f90:189
> > #21 0x40688b in pwscf
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/pwscf.f90:85
> > #22 0x4065cc in main
> > at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/pwscf.f90:40
> >
> > I have been using 128 atom supercells with DFT+U calculations, Using
> > InGaAsSb. The version is qe-7.3. I have seen a few previous versions having
> > similar problems, but I am not sure if their fixes will be a appropriate
> > given the changes in the DFT+U codes. It seems to be a problem with loading
> > the environment. I am using supercomputers with 128 processors. The input
> > file is:
> >
> > &CONTROL
> > calculation = 'vc-relax',
> > disk_io = 'low',
> > etot_conv_thr = 1d-05,
> > forc_conv_thr = 0.001,
> > outdir = './tmp_In0.0Ga1.0As0.75Sb0.25_4x4x4',
> > prefix = 'In0.0Ga1.0As0.75Sb0.25_4x4x4',
> > pseudo_dir = '/home/fs71287/gentles/data/pseudos/',
> > restart_mode = 'from_scratch',
> > verbosity = 'low',
> > /
> > &SYSTEM
> > celldm(1) = 43.6265,
> > degauss = 0.0001,
> > ecutwfc = 100,
> > ibrav = 2,
> > lspinorb = .TRUE.,
> > nat = 128,
> > nbnd = 1792,
> > noncolin = .TRUE.,
> > ntyp = 20,
> > occupations = 'smearing',
> > /
> > &ELECTRONS
> > conv_thr = 1d-05,
> > mixing_beta = 0.65,
> > /
> > &IONS
> > /
> > &CELL
> > cell_dofree = 'ibrav',
> > /
> > ATOMIC_SPECIES
> > As1 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> > As0 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> > As2 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> > As3 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> > As4 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> > Ga1 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> > Ga0 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> > Ga2 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> > Ga3 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> > Ga4 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> > In1 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> > In0 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> > In2 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> > In3 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> > In4 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> > Sb1 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> > Sb0 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> > Sb2 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> > Sb3 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> > Sb4 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> > ATOMIC_POSITIONS crystal
> > Ga4 0.000000 0.000000 0.000000
> > As4 0.062500 0.062500 0.062500
> > Ga3 0.000000 0.000000 0.250000
> > As4 0.062500 0.062500 0.312500
> > Ga4 0.000000 0.000000 0.500000
> > As4 0.062500 0.062500 0.562500
> > Ga4 0.000000 0.000000 0.750000
> > As4 0.062500 0.062500 0.812500
> > Ga4 0.000000 0.250000 0.000000
> > As4 0.062500 0.312500 0.062500
> > Ga4 0.000000 0.250000 0.250000
> > As4 0.062500 0.312500 0.312500
> > Ga2 0.000000 0.250000 0.500000
> > Sb4 0.062500 0.312500 0.562500
> > Ga2 0.000000 0.250000 0.750000
> > As4 0.062500 0.312500 0.812500
> > Ga4 0.000000 0.500000 0.000000
> > As4 0.062500 0.562500 0.062500
> > Ga4 0.000000 0.500000 0.250000
> > As4 0.062500 0.562500 0.312500
> > Ga1 0.000000 0.500000 0.500000
> > Sb4 0.062500 0.562500 0.562500
> > Ga3 0.000000 0.500000 0.750000
> > As4 0.062500 0.562500 0.812500
> > Ga4 0.000000 0.750000 0.000000
> > As4 0.062500 0.812500 0.062500
> > Ga2 0.000000 0.750000 0.250000
> > Sb4 0.062500 0.812500 0.312500
> > Ga2 0.000000 0.750000 0.500000
> > As4 0.062500 0.812500 0.562500
> > Ga4 0.000000 0.750000 0.750000
> > As4 0.062500 0.812500 0.812500
> > Ga4 0.250000 0.000000 0.000000
> > As4 0.312500 0.062500 0.062500
> > Ga3 0.250000 0.000000 0.250000
> > As4 0.312500 0.062500 0.312500
> > Ga4 0.250000 0.000000 0.500000
> > As4 0.312500 0.062500 0.562500
> > Ga4 0.250000 0.000000 0.750000
> > As4 0.312500 0.062500 0.812500
> > Ga3 0.250000 0.250000 0.000000
> > As4 0.312500 0.312500 0.062500
> > Ga4 0.250000 0.250000 0.250000
> > As4 0.312500 0.312500 0.312500
> > Ga2 0.250000 0.250000 0.500000
> > Sb4 0.312500 0.312500 0.562500
> > Ga2 0.250000 0.250000 0.750000
> > Sb4 0.312500 0.312500 0.812500
> > Ga4 0.250000 0.500000 0.000000
> > As4 0.312500 0.562500 0.062500
> > Ga4 0.250000 0.500000 0.250000
> > As4 0.312500 0.562500 0.312500
> > Ga1 0.250000 0.500000 0.500000
> > Sb4 0.312500 0.562500 0.562500
> > Ga2 0.250000 0.500000 0.750000
> > As4 0.312500 0.562500 0.812500
> > Ga4 0.250000 0.750000 0.000000
> > As4 0.312500 0.812500 0.062500
> > Ga2 0.250000 0.750000 0.250000
> > Sb4 0.312500 0.812500 0.312500
> > Ga2 0.250000 0.750000 0.500000
> > As4 0.312500 0.812500 0.562500
> > Ga4 0.250000 0.750000 0.750000
> > As4 0.312500 0.812500 0.812500
> > Ga4 0.500000 0.000000 0.000000
> > As4 0.562500 0.062500 0.062500
> > Ga3 0.500000 0.000000 0.250000
> > As4 0.562500 0.062500 0.312500
> > Ga4 0.500000 0.000000 0.500000
> > As4 0.562500 0.062500 0.562500
> > Ga4 0.500000 0.000000 0.750000
> > As4 0.562500 0.062500 0.812500
> > Ga3 0.500000 0.250000 0.000000
> > As4 0.562500 0.312500 0.062500
> > Ga4 0.500000 0.250000 0.250000
> > As4 0.562500 0.312500 0.312500
> > Ga2 0.500000 0.250000 0.500000
> > Sb4 0.562500 0.312500 0.562500
> > Ga1 0.500000 0.250000 0.750000
> > Sb4 0.562500 0.312500 0.812500
> > Ga4 0.500000 0.500000 0.000000
> > As4 0.562500 0.562500 0.062500
> > Ga3 0.500000 0.500000 0.250000
> > Sb4 0.562500 0.562500 0.312500
> > Ga0 0.500000 0.500000 0.500000
> > Sb4 0.562500 0.562500 0.562500
> > Ga2 0.500000 0.500000 0.750000
> > As4 0.562500 0.562500 0.812500
> > Ga4 0.500000 0.750000 0.000000
> > As4 0.562500 0.812500 0.062500
> > Ga1 0.500000 0.750000 0.250000
> > Sb4 0.562500 0.812500 0.312500
> > Ga2 0.500000 0.750000 0.500000
> > As4 0.562500 0.812500 0.562500
> > Ga4 0.500000 0.750000 0.750000
> > As4 0.562500 0.812500 0.812500
> > Ga4 0.750000 0.000000 0.000000
> > As4 0.812500 0.062500 0.062500
> > Ga3 0.750000 0.000000 0.250000
> > As4 0.812500 0.062500 0.312500
> > Ga4 0.750000 0.000000 0.500000
> > As4 0.812500 0.062500 0.562500
> > Ga4 0.750000 0.000000 0.750000
> > As4 0.812500 0.062500 0.812500
> > Ga3 0.750000 0.250000 0.000000
> > As4 0.812500 0.312500 0.062500
> > Ga4 0.750000 0.250000 0.250000
> > As4 0.812500 0.312500 0.312500
> > Ga2 0.750000 0.250000 0.500000
> > Sb4 0.812500 0.312500 0.562500
> > Ga1 0.750000 0.250000 0.750000
> > Sb4 0.812500 0.312500 0.812500
> > Ga4 0.750000 0.500000 0.000000
> > As4 0.812500 0.562500 0.062500
> > Ga3 0.750000 0.500000 0.250000
> > As4 0.812500 0.562500 0.312500
> > Ga1 0.750000 0.500000 0.500000
> > Sb4 0.812500 0.562500 0.562500
> > Ga2 0.750000 0.500000 0.750000
> > As4 0.812500 0.562500 0.812500
> > Ga4 0.750000 0.750000 0.000000
> > As4 0.812500 0.812500 0.062500
> > Ga2 0.750000 0.750000 0.250000
> > Sb4 0.812500 0.812500 0.312500
> > Ga2 0.750000 0.750000 0.500000
> > As4 0.812500 0.812500 0.562500
> > Ga4 0.750000 0.750000 0.750000
> > As4 0.812500 0.812500 0.812500
> > K_POINTS automatic
> > 3 3 3 0 0 0
> >
> > HUBBARD (atomic)
> > U In0-5p -2.24
> > U Ga0-4p -2.04
> > U As0-4p 4.02
> > U Sb0-5p 4.43
> > U In1-5p -2.2575000000000003
> > U Ga1-4p -2.39
> > U As1-4p 4.5424999999999995
> > U Sb1-5p 4.7825
> > U In2-5p -2.2750000000000004
> > U Ga2-4p -2.74
> > U As2-4p 5.0649999999999995
> > U Sb2-5p 5.135
> > U In3-5p -2.2925
> > U Ga3-4p -3.09
> > U As3-4p 5.5875
> > U Sb3-5p 5.4875
> > U In4-5p -2.31
> > U Ga4-4p -3.44
> > U As4-4p 6.11
> > U Sb4-5p 5.84
> >
> > The output file gets through several optimisation steps and then stalls at
> > an scf iteration, as below:
> >
> > Number of occupied Hubbard levels = 615.3045
> >
> > total cpu time spent up to now is 166039.0 secs
> >
> > total energy = -22879.33720322 Ry
> > estimated scf accuracy < 0.00963404 Ry
> >
> > iteration # 2 ecut= 100.00 Ry beta= 0.65
> > Davidson diagonalization with overlap
> > ethr = 5.38E-07, avg # of iterations = 6.0
> >
> > total cpu time spent up to now is 172245.2 secs
> >
> > total energy = -22879.33685019 Ry
> > estimated scf accuracy < 0.03584310 Ry
> >
> > iteration # 3 ecut= 100.00 Ry beta= 0.65
> > Davidson diagonalization with overlap
> >
> > I am relatively confident that this isn't a problem with the memory of the
> > computer being overcome. I get problems on smaller cells and bands
> > calculations. Any help is appreciated.
> >
> >
> > With kind regards, I am
> > Angus Gentles
> > ams-OSRAM
> > Intitute of Microelectronics, TU Wien
> >
> >
> > _______________________________________________
> > The Quantum ESPRESSO community stands by the Ukrainian
> > people and expresses its concerns about the devastating
> > effects that the Russian military offensive has on their
> > country and on the free and peaceful scientific, cultural,
> > and economic cooperation amongst peoples
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX
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>
>
> 西館数芽
> Kazume NISHIDATE Ph.D
>
> Department of Systems Innovation Engineering,
> Graduate School of Science and Engineering, Iwate University
> 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
> Phone:+81-19-621-6391
> [email protected], [email protected]
> https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fnisidatelab%2F&data=05%7C02%7C%7Cdadb2905ea4545a700bc08dc854cd65b%7Cec1ca250c2344d56a76b7dfb9eee0c46%7C0%7C0%7C638531815451870160%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C40000%7C%7C%7C&sdata=06Tb%2FdWAL2rfExfPCGov9qOKWrlp7HOMpaInUF4i%2B0c%3D&reserved=0
西館数芽
Kazume NISHIDATE Ph.D
Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
[email protected], [email protected]
https://sites.google.com/site/nisidatelab/
_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
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