[Pw_forum] question about pseudopotential generation by ld1.x
Dear All, I am trying to generate a pseudopotential by ld1.x code in espresso. I have two questions about this process. First, in a example to generate Pt pseudopotential in atomic_doc, the configuration of pseudo is specified as following 7 5D 3 2 4.00 0.00 2.10 2.40 1.50 5D 3 2 0.00 -0.20 2.10 2.40 1.50 5D 3 2 4.00 0.00 2.10 2.40 2.50 5D 3 2 0.00 -0.20 2.10 2.40 2.50 6P 2 1 0.00 -0.00 3.30 3.30 0.50 6P 2 1 0.00 -0.00 3.40 3.40 1.50 6S 1 0 2.00 0.00 2.60 2.60 0.50 I don't know why, for example, 5D orbitals need four lines? I am confused because I think I can put quantum numbers, occupation and match radius in one line Moreover, what does the last number (1.50, 2.50...) represent? Secondly, after plotting logarithmic derivatives, I found some 'sparks', both in atomic and pseudo wave functions. I would like to know if this is a sign of trouble? For atomic wave functions, I have a 'spark' in deep place (negative energy), and for pseudo wave function, I have a 'spark' at energy 0. I appreciate any help and thank you in advance. Best Wishes jia -- Jia Chen Dept of Chemistry Princeton University Princeton, NJ 08544
[Pw_forum] OpenMPI / QE INSTALLATION ISSUES
Dear Edmund Formerly I had installed PWscf on CentOS and there was not any main problem. Please be sure that your gfortran works well and note that "--with-tm" option is generally only necessary if the TM headers and libraries are not in default compiler/linker search paths. I have installed the Openmpi without "--with-tm". Did you install proper libraries on your system ? Best Wishes Masoud Nahali SUT > > Hi, > I am in the process of installing Quantum espresso but, am > experiencing issues compiling my OpenMPI. I get the error "configure: > error: could not run a simple Fortran 77 program. Aborting." > > Am using gcc-4.2.2 and OpenMPI-1.4.2 on CentOS-5.4. The configure > instruction isssued appears as below: > ./configure --prefix=/opt/openmpi/1.4.2 --with-tm=/opt/torque/2.5.1 > CC=gcc CXX=g++ F77=gfortran FC=gfortran > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100819/94509e82/attachment.htm
[Pw_forum] Band Structure of Graphite
00.420.0093
0.000.430.0094
0.000.440.0095
0.000.450.0096
0.000.460.0097
0.000.470.0098
0.000.480.0099
0.000.490.00100
0.000.500.00101
0.0066670.4966670.00102
0.010.490.00103
0.020.490.00104
0.020.480.00105
0.030.480.00106
0.040.480.00107
0.040.470.00108
0.050.470.00109
0.050.460.00110
0.060.460.00111
0.070.460.00112
0.070.450.00113
0.080.450.00114
0.0933320.4533320.00115
0.090.440.00116
0.100.440.00117
0.1133320.4433320.00118
0.110.430.00119
0.1266650.4366650.00120
0.120.420.00121
0.130.420.00122
0.1466650.4266650.00123
0.1533320.4233320.00124
0.1599980.4199980.00125
0.150.4166650.00126
0.1733320.4133320.00127
0.1799980.4099980.00128
0.1866650.4066650.00129
0.1933310.4033310.00130
0.180.380.00131
0.2066650.3966650.00132
0.2133310.3933310.00133
0.2199980.3899980.00134
0.2266640.3866640.00135
0.210.3833310.00136
0.2399980.3799980.00137
0.2466640.3766640.00138
0.2533310.3733310.00139
0.2599970.3699970.00140
0.240.340.00141
0.2733310.3633310.00142
0.2799970.3599970.00143
0.2866640.3566640.00144
0.2933300.3533300.00145
0.270.3499970.00146
0.3066640.3466640.00147
0.3133300.3433300.00148
0.3199970.3399970.00149
0.3266630.3366630.00150
0.300.300.00151
scf input:
calculation = "scf",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
prefix='bulk'
/
ibrav = 4,
a = 2.457917036,
b = 2.457917036,
c = 6.302440996,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.01,
london=.true.,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C0.0 0.0 0.0
C0.0 1.419079061 0.0
C0.0 0.0 3.151220498
C1.228958518 0.709539531 3.151220498
K_POINTS {automatic}
10 10 5 1 1 1
Many Thanks
Masoud Nahali
SUT
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20100819/92edd179/attachment-0001.htm
[Pw_forum] Additional informations about XSpectra - Peaks at negative energies?
Thanks to Matteo Calandra for his answers. Regarding the Fermi level, I have now an additional question based on an example we are dealing with. With a preliminar run of XSpectra I see a Fermi energy of -0.259, so I use this value for ef_r in following calculations. If I include negative energies (say -30 eV, with respect to this one) in the input file then in the resulting spectrum I see a *sharp* peak at about -5 eV. Now, if levels at negative energy should be all occupied, how can it result such an evident absorption peak? Is it related to the "cut_occ_states" option? By default it is .false. What does this mean exactly? Thanks again for your help. Cristian > (1) is the energy range (xemin,xemax) referred to the Fermi energy > > of the preliminar scf calculation? > > No, it is referred to the Fermi level given in input in the xspectra > file (input variable ef_r in the input_xspectra namelist. This means > that if you do not specify the Fermi level then ef_r=0.0 and > they are referred to the energy zero of the preliminary scf run. -- ___ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web:http://www.df.unibo.it/fismat/theory ___
[Pw_forum] epitaxial thin file, dofree, and target pressure
Dear PWscf developers and users, I am currently studying an epitaxial thin-film system. I would like to find the optimized the structure with the lattice parameters a and b being constrained, namely, finding the optimized lattice parameter c (and the internal structure). I am aware that this procedure can be done manually. But that would cost lots of CPU hours. I am considering using cell_dofree, and I am wondering how this option works. Suppose I put cell_dofree= 'z' under the namelist How should I specify the target pressure? For a thin film with constrained a, b and optimized c, the stress tensor should look like sigma_xx = sigma_yy = a non-vanishing value. sigma_xy = sigma_yx = also a non-vanishing value sigma_zz = sigma_xz = sigma_yz = 0 But when specifying press= 0, I think (maybe I am wrong) the program is searching for a structure with sigma_ij=0, i,j=x,y,z. How should I specify the target pressure (stress tensor) if I perform vc-relax with dofree= 'z'? Thank you in advance for your response and hint. Han -- * Han Hsu, Ph.D. Postdoctoral Associate Department of Chemical Engineering & Materials Science University of Minnesota http://www.cems.umn.edu/~hsuhan <http://www.cems.umn.edu/%7Ehsuhan> * -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100819/129d3562/attachment-0001.htm
[Pw_forum] OpenMPI / QE INSTALLATION ISSUES
Hi, I am in the process of installing Quantum espresso but, am experiencing issues compiling my OpenMPI. I get the error "configure: error: could not run a simple Fortran 77 program. Aborting." Am using gcc-4.2.2 and OpenMPI-1.4.2 on CentOS-5.4. The configure instruction isssued appears as below: ./configure --prefix=/opt/openmpi/1.4.2 --with-tm=/opt/torque/2.5.1 CC=gcc CXX=g++ F77=gfortran FC=gfortran -- Regards, EDMUND OCHIENG'.
[Pw_forum] Band Structure of Graphite
0.000.230.0074
> 0.000.240.0075
> 0.000.250.0076
> 0.000.260.0077
> 0.000.270.0078
> 0.000.280.0079
> 0.000.290.0080
> 0.000.300.0081
> 0.000.310.0082
> 0.000.320.0083
> 0.000.330.0084
> 0.000.340.0085
> 0.000.350.0086
> 0.000.360.0087
> 0.000.370.0088
> 0.000.380.0089
> 0.000.390.0090
> 0.000.400.0091
> 0.000.410.0092
> 0.000.420.0093
> 0.000.430.0094
> 0.000.440.0095
> 0.000.450.0096
> 0.000.460.0097
> 0.000.470.0098
> 0.000.480.0099
> 0.000.490.00100
> 0.000.500.00101
> 0.0066670.4966670.00102
> 0.010.490.00103
> 0.020.490.00104
> 0.020.480.00105
> 0.030.480.00106
> 0.040.480.00107
> 0.040.470.00108
> 0.050.470.00109
> 0.050.460.00110
> 0.060.460.00111
> 0.070.460.00112
> 0.070.450.00113
> 0.080.450.00114
> 0.0933320.4533320.00115
> 0.090.440.00116
> 0.100.440.00117
> 0.1133320.4433320.00118
> 0.110.430.00119
> 0.1266650.4366650.00120
> 0.120.420.00121
> 0.130.420.00122
> 0.1466650.4266650.00123
> 0.1533320.4233320.00124
> 0.1599980.4199980.00125
> 0.150.4166650.00126
> 0.1733320.4133320.00127
> 0.1799980.4099980.00128
> 0.1866650.4066650.00129
> 0.1933310.4033310.00130
> 0.180.380.00131
> 0.2066650.3966650.00132
> 0.2133310.3933310.00133
> 0.2199980.3899980.00134
> 0.2266640.3866640.00135
> 0.210.3833310.00136
> 0.2399980.3799980.00137
> 0.2466640.3766640.00138
> 0.2533310.3733310.00139
> 0.2599970.3699970.00140
> 0.240.340.00141
> 0.2733310.3633310.00142
> 0.2799970.3599970.00143
> 0.2866640.3566640.00144
> 0.2933300.3533300.00145
> 0.270.3499970.00146
> 0.3066640.3466640.00147
> 0.3133300.3433300.00148
> 0.3199970.3399970.00149
> 0.3266630.3366630.00150
> 0.300.300.00151
>
> scf input:
>
>
> calculation = "scf",
> pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
> outdir = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
> prefix='bulk'
> /
>
> ibrav = 4,
> a = 2.457917036,
> b = 2.457917036,
> c = 6.302440996,
> cosab = -0.5,
> cosac = 1.0,
> cosbc = 1.0,
> nat = 4,
> ntyp = 1,
> ecutwfc = 40.D0,
> ecutrho = 480.D0,
> occupations = 'smearing'
> smearing ='mp',
> degauss = 0.03,
> nspin = 2,
> starting_magnetization(1)= 0.01,
> london=.true.,
> /
>
> conv_thr= 1.D-6,
> mixing_beta = 0.7D0,
> diagonalization = "david",
> /
> ATOMIC_SPECIES
> C 12.0107 C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C0.0 0.0 0.0
> C0.0 1.419079061 0.0
> C0.0 0.0 3.151220498
> C1.228958518 0.709539531 3.151220498
> K_POINTS {automatic}
> 10 10 5 1 1 1
>
> Many Thanks
> Masoud Nahali
> SUT
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Phillip W. Otieno Nyawere,
International Center for Theoretical Physics, ICTP,
Strada Costriera, 11 - 34014,
Galileo Guest House,
Trieste,
Italy.
Tel +393382213805
pnyawere at gmail.com, potieno at kabarak.ac.ke
The battle belongs to the Lord.
-- next part --
An HTML attachment was scrubbed...
URL:
http://www.democritos.it/pipermail/pw_forum/attachments/20100819/013846dc/attachment.htm
[Pw_forum] Graphene Structural Relaxation
In my opinion your input structure is wrong. It's very curious that it still looks good when visualized with xcrysden. If you run pw.x with verbosity='high', you will get the atomic positions in crystal coordinates, as follows Crystallographic axes site n. atom positions (cryst. coord.) 1 C tau( 1) = ( -0.5001249 -0.3326688 0.000 ) 2 C tau( 2) = ( -0.7501874 -0.2499829 0.000 ) 3 C tau( 3) = ( -0.7501874 -0.0826851 0.000 ) 4 C tau( 4) = ( 0.000 -0.3326688 0.000 ) 5 C tau( 5) = ( -0.2500625 -0.2499829 0.000 ) 6 C tau( 6) = ( -0.2500625 -0.0826851 0.000 ) 7 C tau( 7) = ( -0.5001249 0.000 0.000 ) 8 C tau( 8) = ( -0.5001249 0.1672981 0.000 ) 9 C tau( 9) = ( -0.7501874 0.2499829 0.000 ) 10 C tau( 10) = ( -0.7501874 0.4172810 0.000 ) 11 C tau( 11) = ( 0.5001249 -0.3326688 0.000 ) 12 C tau( 12) = ( 0.2500625 -0.2499829 0.000 ) 13 C tau( 13) = ( 0.2500625 -0.0826851 0.000 ) 14 C tau( 14) = ( 0.000 0.000 0.000 ) 15 C tau( 15) = ( 0.000 0.1672981 0.000 ) 16 C tau( 16) = ( -0.2500625 0.2499829 0.000 ) 17 C tau( 17) = ( -0.2500625 0.4172810 0.000 ) 18 C tau( 18) = ( -0.5001249 0.4999669 0.000 ) 19 C tau( 19) = ( 0.5001249 0.000 0.000 ) 20 C tau( 20) = ( 0.5001249 0.1672981 0.000 ) 21 C tau( 21) = ( 0.2500625 0.2499829 0.000 ) 22 C tau( 22) = ( 0.2500625 0.4172810 0.000 ) 23 C tau( 23) = ( 0.000 0.4999669 0.000 ) 24 C tau( 24) = ( 0.5001249 0.4999669 0.000 ) To me it seems that some atoms are almost overlapping. For instance, the positions of atom 1 and atom 11 differ by a vector nearly equal to the first lattice vector. I think that you have included also some atoms not belonging to the cell centered in the orgin when building your cell. Try to remove the extra atoms. HTH GS On 08/19/2010 11:10 AM, meysam pazoki wrote: > > > > Dear pwscf users > Thanks for the answers.As I said,I See the honeycomb structure in > xcrysden. > I dont know what is wrong, I have attached the .in file. > Thanks for considering my question > Regards > meysam Pazoki > PhD. student of physics > sharif university of technology > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100819/1b54ba53/attachment.htm
[Pw_forum] Graphene Structural Relaxation
I would not use mp smearing with a zero dos(Ef) metal like graphene... m-v or even gaussian should give more reliable results. the reason is that m-p smearing is not positive definite leading to spurious negative densities if the k-point sampling is not good enough ... whichi, I guess, will never be with graphene. stefano meysam pazoki wrote: > Dear pwscf users > > Thanks for the answers.As I said,I See the honeycomb structure in xcrysden. > I dont know what is wrong, I have attached the .in file. > > Thanks for considering my question > Regards > meysam Pazoki > PhD. student of physics > sharif university of technology > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] 回复： Intel MPI
Paolo, I have been using Intel MPI these years, from its 2.x, 3.1 to 3.2 now. I use it with two job schedulers, torque and lsf, on two clusters of course. At least, there are no big problems. I had ever tried to switch to openmpi, but found it was slower than Intel MPI at that time (about 3 years ago when openmpi was in 1.2.x). huiqun zhou @earth sciences, nanjing university, china - - ???: Paolo Giannozzi ???: PWSCF Forum ?: Wed, 18 Aug 2010 21:16:49 +0800 (CST) ??: [Pw_forum] Intel MPI Can anybody report any experience linking with Intel version of MPI? P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Intel MPI
Hello, On Wed, Aug 18, 2010 at 12:28 PM, Paolo Giannozzi wrote: > > On Aug 18, 2010, at 19:03 , joaquin peralta wrote: > > > We use a surface of Al with 81 atoms in 128 cpus using intelMPI and > > openMPI 1.4 > > but not in the same way! the first job uses 8 pools of 16 processors, > the second > Yes it's true, not the same way. > 1 pool of 128 processors. The first choice seems to be reasonable, > the second > After i recheck my times again, and compare a more realistic run. > isn't, since an enormous amount of time is spent in communications > (look at the > time spent in fft_scatter). > > Is possible know previously how is the best parameter to use with -np, I mean if somebody recommend me a thread about the uses (i don't understand very well the manual yet) of the optimization flags (pool, image, ntg, diag). Thanks in advance Joaquin Peralta > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Group of NanoMaterials http://www.gnm.cl Joaqu?n Andr?s Peralta Camposano http://zeth.ciencias.uchile.cl/~jperalta In a world without frontiers, who needs Gates and Win. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100819/742ae77c/attachment-0001.htm
