Re: [Pw_forum] Manual Kpoint Optimization for a Monoclinic lattice structured organic compound
Good day allI am very grateful for the response to this forum and every individual for contributing to help me with my challenges so far I have corrected the errors on my atomic position, now my kpoint grid has been sorted out all thanks to profs. Kim and Brendas and Prof. Giovani Now im considering doing vc-relax calculation or structural optimization of my structure, I need help with the most appropriate pseudopotential to use considering van der well on the organic compound pedot i have attached a copy of my crystal structure visualized with xcrysden to this mail Thank you all, im very grateful Agbaoye Ridwan OlamideM.Sc. Physics(in View)Federal University of Agriculture, abeokutaagbaoyerid...@yahoo.com On Friday, December 4, 2015 9:01 AM, Giovanni Cantele wrote: 1) what kind of convergence you haven’t reached yet? a) convergence of structural optimisation (atomic positions), or b) convergence of unit cell optimisation (e.g. if you use calculation=‘vc-relax’), or c) self-consistency cycle 2) if by improving the sampling of the Brillouin zone (2x2x2, 3x3x3, ….) nothing happens, maybe it can be that the parameter that prevents you system from reaching convergence is not the k-point grid!!! Which pseudo potentials do you use, and with which cutoff? For organic crystals, van der Waals interactions might be important as well, have you already tried to switch them on? Are you sure that the input positions are right, for example by visualising your input file with XCrysden (such a practice is advisable BEFORE any, maybe computationally expensive, run is started!) 3) the “acceptable" size of the k-point grid depends on the system under investigation and on the property you are interested in (for a given grid, there are properties that might be converged, and others that might be not!). 4) concerning grids that look like n x m x l instead of n x n x n , usually if for example axes a and b are in the ratio a/b = u, than n and m have the inverse ratio (n/m ~ 1/u). For example: a = b = c, use 4 x 4 x 4 ; a = b, c = 2a, use 4 x 4 x 2 (THIS ARE JUST EXAMPLES, THAT DO NOT PROVIDE CONVERGENCE CRITERIA!). GIOVANNI > On 04 Dec 2015, at 14:23, Ridwan Agbaoye wrote: > > > > On Thursday, December 3, 2015 11:41 AM, Ridwan Agbaoye > wrote: > > > I am doing structural optimization for a monoclinic latice structured organic > compound with 13 atoms, 4 types of atom (C,H,O and S) and , i need expertise > advice on how my automatic kpoint grid required for optimization will look > like, i tried 2 2 2 1 1 1, 3 3 3 1 1 1, 4 4 4 1 1 1... 9 9 9 1 1 1 but the > result havent reached convergence yet even with the very very high > computation time it require > > Recently i learnt i am not suppose to use the uniform kpoint grid but the > ones that looked like 6 4 6 1 1 1 , 6 1 1 1 1 1, 8 4 8 1 1 1 etc > > please help me with the best automatic kpoint grid required for my system and > how to determine the kind of kpoint grid to use for subsequent system > calculation > > Thank you very much > > > Agbaoye Ridwan Olamide > M.Sc. (in view) > Federal University of Agriculture, Abeokuta > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] HSE output for yambo TDDFT calculation
Dear QE users, I hope there is anybody who has experience with the output generation for yambo in case of hybrid functionals, especially for TDDFT. Usually one does a scf and a subsequent nscf calculation in pw.x. The nscf calculation, however, is not possible in the case of hse. So I’m using the output from the scf calculation with the input posted below. In principle, the developers from yambo don’t see a problem doing a TDDFT calculation on top of hybrid functional calculation but have either not yet really tried it. My problem is that the output does apparently not provide all input for yambo that is needed as information on the reciprocal lattice vectors is missing (RL vectors(WF):0) <---> :: Electrons : 68.0 <---> :: Temperature [ev]: 0.00 <---> :: Lattice factors [a.u.]: 8.757014 8.757014 8.757014 <---> :: K-points : 38 <---> :: Bands : 60 <---> :: Spinor components : 1 <---> :: Spin polarizations: 1 <---> :: Spin orbit coupling : no <---> :: Symmetries [spatial]: 3 <---> ::[T-rev]: yes <---> :: Max WF components : 8469 <---> :: RL vectors(WF):0 <---> :: RL vectors(CHARGE): 67681 <---> :: XC potential : HSE06(XC) <---> :: Atomic species: 3 <---> :: Max atoms/species : 6 which is probably the reason for the tddft run to stop, though p2y works without complaining. Here’s the input I used in pw.x: &control calculation = 'scf' restart_mode='from_scratch', verbosity='high' prefix='LN', pseudo_dir = '/scratch/michaelf/work/input/qe/', outdir='.' wf_collect= .true. / &system ibrav= 0, nat= 10, ntyp= 3, ecutwfc =78.0, nbnd = 60, input_dft='hse', nqx1 = 1, nqx2 = 1, nqx3 = 1, force_symmorphic=.true. / &electrons !mixing_beta = 0.7 , conv_thr = 1.0d-10, electron_maxstep = 500 / ATOMIC_SPECIES Li 2.003_Li_ONCV.UPF Nb 2.041_Nb_ONCV.UPF O2.008_O_ONCV.UPF ATOMIC_POSITIONS crystal Li 0.283300360 0.283300360 0.283300360 Nb 0.0 0.0 0.0 O0.855421834 0.616149204 0.219876866 O0.219876866 0.855421834 0.616149204 O0.616149204 0.219876866 0.855421834 Li 0.783300360 0.783300360 0.783300360 Nb 0.5 0.5 0.5 O0.116149204 0.355421834 0.719876866 O0.719876866 0.116149204 0.355421834 O0.355421834 0.719876866 0.116149204 K_POINTS automatic 6 6 6 1 1 1 CELL_PARAMETERS bohr 5.647324820 -0.0 8.757014575 -2.823662411 4.890726758 8.757014575 -2.823662411 -4.890726758 8.757014575 Maybe there is someone who knows more about this? Is there a possibility to provide the same output to yambo from a hse run as from a scf—>nscf DFT run? As far as I know there shouldn’t be much of a difference in the format of the WF and in principle it should be possible?! Thank you Michael Friedrich Universität Paderborn Germany___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] HSE output for yambo TDDFT calculation
On Wed, Dec 9, 2015 at 10:34 AM, Michael Friedrich wrote: > > Maybe there is someone who knows more about this? > I know close to nothing about this, but I am quite sure that the format of the data file is the same irrespective of the type of calculation. Try to start Yambo from the same scf calculation, made with plain DFT, and see what happens Paolo Is there a possibility to provide the same output to yambo from a hse run > as from a scf—>nscf DFT run? As far as I know there shouldn’t be much of a > difference in the format of the WF and in principle it should be possible?! > > Thank you > Michael Friedrich > Universität Paderborn > Germany > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QHA applicatiom - F_QHA.x
On Tue, Dec 8, 2015 at 10:22 AM, Eleftheria Gkogkosi wrote: > > For test purposes, I run F_QHA.x for the cases of alpha- and beta- Tin. > I can see that "F_vibration vs T" graphs cross above 300 K (in > consistency with the phase transition). > This does not hold for the sum E_internal+F_vibration (which I assumed > to be the Heelmholtz free energy in the first place). > So, is it safe to conclude that F_vibration is actually the Helmholtz > free energy? from the source code, it looks like E_internal is the vibrational contribution to the energy, while F_vibration is the vibrational contribution to the free energy. In order to locate the phase transition, you should compare E_tot+F_vibration(T) for alpha and beta tin, where E_tot is what you get from the scf calculation. What does it mean when one gets negative frequencies in tjis file? > Is it a matter of poor k-point sampling or an indication of unstable > structure at a given Temperature? > short answer: it depends. Sometimes the latter, sometimes it is simply an unavoidable problem of violation of the Acoustic Sum Rule in approximate calculations. > Is it fair to erase the negative parts and proceed withy QHA for the > thermodynamical properties? > if the only negative values are those corresponding to zero-frequency acoustic modes at q=0, yes, it is Paolo > > Thank you very much, > -- > Eleftheria Gkogkosi > > Applied Mathematics & Physics Dept. > National Technical University of Athens > http://users.ntua.gr/elefthe > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Raman
In a nutshell: you have been told: "third-order derivatives are not implemented". Long answer: Raman intensities are proportional to the first derivatives of polarisabilities wrt nuclear displacements; polarizabilities, in turn, are the second derivatives of energy wrt to electric field components. In total, we end up with third, albeit mixed, derivatives. -- I. On Tue, Dec 8, 2015 at 6:25 PM, Mofrad, Amir Mehdi (MU-Student) wrote: > Dear Quantum Espresso users and developers, > > > Does anyone know that Quantum Espresso is capable of calculating Raman > intensities? When I want to do the phonon calculations I get the following > error: > > > error: task # 0 > from phq_setup : error # 1 > third order derivatives not implemented with GGA > > According to what is provided on the Quantum Espresso website, Raman > calculations work only with NC pseudo-potentials and I tried to use that > kind of PP in my scf calculations. Below is my scf and phonon calculations > input files. Any help would be thoroughly appreciated on how to get Raman > intensities. > > > SCF INPUT: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './scratch' , > wfcdir = './scratch' , > pseudo_dir = '/global/espresso/pseudo' , > prefix = 'SOD' , > verbosity = 'high' , > etot_conv_thr = 1e-5 , > forc_conv_thr = 1e-4 , > nstep = 50 , > tstress = .true. , > tprnfor = .true. , > > / > > &SYSTEM > ibrav = 0, > nat = 36, > ntyp = 2, > ecutwfc = 50 , > ecutrho = 200 , > > / > > &ELECTRONS > electron_maxstep = 100, > conv_thr = 3e-8 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > > / > CELL_PARAMETERS bohr > 16.7202967500.00.0 > 0.0 16.7202967500.0 > 0.00.0 16.720296750 > ATOMIC_SPECIES >Si 28.08600 Si.tpss-mt.UPF > O 15.99940 O.tpss-mt.UPF > ATOMIC_POSITIONS angstrom > Si 2.2114340870.04.42400 >Si 6.6365659130.04.42400 >Si 4.424002.2114340870.0 >Si 4.424006.6365659130.0 >Si 0.04.424002.211434087 >Si 0.04.424006.636565913 >Si 2.2114241384.42400 -0.0 >Si 6.6365758624.42400 -0.0 >Si 0.02.2114241384.42400 >Si 0.06.6365758624.42400 >Si 4.424000.02.211424138 >Si 4.424000.06.636575862 > O 1.2872841424.0775133401.287298380 > O 7.5607158584.7704866601.287298380 > O 7.5607158584.0775133407.560701620 > O 1.2872841424.7704866607.560701620 > O 1.2872983801.2872841424.077513340 > O 1.2872983807.5607158584.770486660 > O 7.5607016207.5607158584.077513340 > O 7.5607016201.2872841424.770486660 > O 4.0775133401.2872983801.287284142 > O 4.7704866601.2872983807.560715858 > O 4.0775133407.5607016207.560715858 > O 4.7704866607.5607016201.287284142 > O 8.5066504985.7138707755.713853509 > O 0.3413495023.1341292255.713853509 > O 8.5066504983.1341292253.134146491 > O 0.3413495025.7138707753.134146491 > O 5.7138707755.7138535098.506650498 > O 3.1341292255.7138535090.341349502 > O 3.1341292253.1341464918.506650498 > O 5.7138707753.1341464910.341349502 > O 5.7138535098.5066504985.713870775 > O 5.7138535090.3413495023.134129225 > O 3.1341464918.5066504983.134129225 > O 3.1341464910.3413495025.713870775 > K_POINTS automatic > 4 4 4 1 1 1 > > Phonon Input File > > > phonons of Sodalite at Gamma > &inputph > tr2_ph= 1e-14, > prefix= 'SOD', > amass(1) = 28.08600, > amass(2) = 15.9940, > outdir= './scratch/', > fildyn= 'SOD.dyn', > recover = .false., > epsil = .true., > lraman= .true., > trans = .true., > max_seconds = 35 > / > 0.0 0.0 0.0 > > Best regards, > > > Amir M. Mofrad > > University of Missouri > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- *** Ilya Ryabinkin Postdoctoral Scholar Physical and Environmental Sciences University of Toronto Scarborough http://www.utsc.utoronto.ca/~aizmaylov/Members.html
Re: [Pw_forum] Raman
On Wed, Dec 9, 2015 at 1:30 PM, Ilya Ryabinkin wrote: > In a nutshell: you have been told: "third-order derivatives are not > implemented". not exactly that. What is not implemented is "the third-order functional derivative of the exchange-correlation energy with respect to the charge density", which is an ingredient needed for computation of third-order energy derivatives. It is implemented for LDA only. Of course one can always comment out the check and keep the LDA part only. This will not however solve the problem, because in the scf calculation: >Si 28.08600 Si.tpss-mt.UPF > O 15.99940 O.tpss-mt.UPF TPSS meta-GGA is used, and phonons for meta-GGA are not implemented. Paolo -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Error in thermo_pw.x run
Dear Sir/Madam, I am a user of Quantum espresso. I am interested in elastic constant and install thermo_pw.0.3.0 in the quantum espresso (QE 5.2.1) root directory. I have followed the flowing steps- cd espresso-5.2.1 ./configure --enable-openmp cd thermo_pw make join_qe cd ../ make all Without showing any error thermo_pw.x has been built, but when I am trying to run example(example13) , I get the following error- running thermo_pw.x as: mpirun -np 4 /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x -ni 2 -nk 1 -nd 1 -nb 1 -nt 1 cleaning /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/tempdir... done running the thermo mur_lc_elastic_constants calculation to calculate the elastic constants of silicon at the equilibrium lattice constant. The results are in si.elastic.out... [cluster:05522] *** Process received signal *** [cluster:05522] Signal: Segmentation fault (11) [cluster:05522] Signal code: Address not mapped (1) [cluster:05522] Failing at address: 0x [cluster:05521] *** Process received signal *** [cluster:05521] Signal: Segmentation fault (11) [cluster:05521] Signal code: Address not mapped (1) [cluster:05521] Failing at address: 0x [cluster:05522] [ 0] /lib64/libpthread.so.0() [0x392240f500] [cluster:05522] [ 1] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24) [0x459fe4] [cluster:05522] [ 2] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a) [0x4aa88a] [cluster:05522] [ 3] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65) [0x44f145] [cluster:05522] [ 4] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a) [0xb742aa] [cluster:05522] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x392181ecdd] [cluster:05522] [ 6] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x() [0x44f019] [cluster:05522] *** End of error message *** [cluster:05521] [ 0] /lib64/libpthread.so.0() [0x392240f500] [cluster:05521] [ 1] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24) [0x459fe4] [cluster:05521] [ 2] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a) [0x4aa88a] [cluster:05521] [ 3] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65) [0x44f145] [cluster:05521] [ 4] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a) [0xb742aa] [cluster:05521] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x392181ecdd] [cluster:05521] [ 6] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x() [0x44f019] [cluster:05521] *** End of error message *** [cluster:05524] *** Process received signal *** [cluster:05524] Signal: Segmentation fault (11) [cluster:05524] Signal code: Address not mapped (1) [cluster:05524] Failing at address: 0x [cluster:05523] *** Process received signal *** [cluster:05523] Signal: Segmentation fault (11) [cluster:05523] Signal code: Address not mapped (1) [cluster:05523] Failing at address: 0x [cluster:05524] [ 0] /lib64/libpthread.so.0() [0x392240f500] [cluster:05524] [ 1] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24) [0x459fe4] [cluster:05524] [ 2] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a) [0x4aa88a] [cluster:05524] [ 3] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65) [0x44f145] [cluster:05524] [ 4] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a) [0xb742aa] [cluster:05524] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x392181ecdd] [cluster:05524] [ 6] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x() [0x44f019] [cluster:05524] *** End of error message *** [cluster:05523] [ 0] /lib64/libpthread.so.0() [0x392240f500] [cluster:05523] [ 1] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(clean_ngeo_+0x24) [0x459fe4] [cluster:05523] [ 2] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(thermo_readin_+0x296a) [0x4aa88a] [cluster:05523] [ 3] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(MAIN__+0x65) [0x44f145] [cluster:05523] [ 4] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x(main+0x2a) [0xb742aa] [cluster:05523] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x392181ecdd] [cluster:05523] [ 6] /home/Utpal/Quantum_espresso/espresso-5.2.1/espresso-5.2.1/bin/thermo_pw.x() [0x44f019] [cluster:05523] *** End of error message *** mpirun noticed that process rank 0 with PID 5521 on node cluster.hpc.org exited on signal 11 (Segmentation fault).
Re: [Pw_forum] Raman
Dear Amir AFAIK Raman intensities can be calculated at the LDA level of theory only. You are using meta-GGA HTH Giuseppe On Tuesday, December 08, 2015 11:25:05 PM Mofrad, Amir Mehdi wrote: > Dear Quantum Espresso users and developers, > > Does anyone know that Quantum Espresso is capable of calculating Raman > intensities? When I want to do the phonon calculations I get the following > error: > > > error: task # 0 > from phq_setup : error # 1 > third order derivatives not implemented with GGA > > > According to what is provided on the Quantum Espresso website, Raman > calculations work only with NC pseudo-potentials and I tried to use that kind > of PP in my scf calculations. Below is my scf and phonon calculations input > files. Any help would be thoroughly appreciated on how to get Raman > intensities. > > > SCF INPUT: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './scratch' , > wfcdir = './scratch' , > pseudo_dir = '/global/espresso/pseudo' , > prefix = 'SOD' , > verbosity = 'high' , > etot_conv_thr = 1e-5 , > forc_conv_thr = 1e-4 , > nstep = 50 , > tstress = .true. , > tprnfor = .true. , > > / > > &SYSTEM > ibrav = 0, > nat = 36, > ntyp = 2, > ecutwfc = 50 , > ecutrho = 200 , > > / > > &ELECTRONS > electron_maxstep = 100, > conv_thr = 3e-8 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > > / > CELL_PARAMETERS bohr > 16.7202967500.00.0 > 0.0 16.7202967500.0 > 0.00.0 16.720296750 > ATOMIC_SPECIES >Si 28.08600 Si.tpss-mt.UPF > O 15.99940 O.tpss-mt.UPF > ATOMIC_POSITIONS angstrom > Si 2.2114340870.04.42400 >Si 6.6365659130.04.42400 >Si 4.424002.2114340870.0 >Si 4.424006.6365659130.0 >Si 0.04.424002.211434087 >Si 0.04.424006.636565913 >Si 2.2114241384.42400 -0.0 >Si 6.6365758624.42400 -0.0 >Si 0.02.2114241384.42400 >Si 0.06.6365758624.42400 >Si 4.424000.02.211424138 >Si 4.424000.06.636575862 > O 1.2872841424.0775133401.287298380 > O 7.5607158584.7704866601.287298380 > O 7.5607158584.0775133407.560701620 > O 1.2872841424.7704866607.560701620 > O 1.2872983801.2872841424.077513340 > O 1.2872983807.5607158584.770486660 > O 7.5607016207.5607158584.077513340 > O 7.5607016201.2872841424.770486660 > O 4.0775133401.2872983801.287284142 > O 4.7704866601.2872983807.560715858 > O 4.0775133407.5607016207.560715858 > O 4.7704866607.5607016201.287284142 > O 8.5066504985.7138707755.713853509 > O 0.3413495023.1341292255.713853509 > O 8.5066504983.1341292253.134146491 > O 0.3413495025.7138707753.134146491 > O 5.7138707755.7138535098.506650498 > O 3.1341292255.7138535090.341349502 > O 3.1341292253.1341464918.506650498 > O 5.7138707753.1341464910.341349502 > O 5.7138535098.5066504985.713870775 > O 5.7138535090.3413495023.134129225 > O 3.1341464918.5066504983.134129225 > O 3.1341464910.3413495025.713870775 > K_POINTS automatic > 4 4 4 1 1 1 > > > Phonon Input File > > > phonons of Sodalite at Gamma > &inputph > tr2_ph= 1e-14, > prefix= 'SOD', > amass(1) = 28.08600, > amass(2) = 15.9940, > outdir= './scratch/', > fildyn= 'SOD.dyn', > recover = .false., > epsil = .true., > lraman= .true., > trans = .true., > max_seconds = 35 > / > 0.0 0.0 0.0 > > > Best regards, > > > Amir M. Mofrad > > University of Missouri - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM)
Re: [Pw_forum] Raman
Thank you all everyone for your responses. Amir M. Mofrad University of Missouri From: pw_forum-boun...@pwscf.org on behalf of Giuseppe Mattioli Sent: Wednesday, December 9, 2015 7:10 AM To: pw_forum@pwscf.org Subject: Re: [Pw_forum] Raman Dear Amir AFAIK Raman intensities can be calculated at the LDA level of theory only. You are using meta-GGA HTH Giuseppe On Tuesday, December 08, 2015 11:25:05 PM Mofrad, Amir Mehdi wrote: > Dear Quantum Espresso users and developers, > > Does anyone know that Quantum Espresso is capable of calculating Raman > intensities? When I want to do the phonon calculations I get the following > error: > > > error: task # 0 > from phq_setup : error # 1 > third order derivatives not implemented with GGA > > > According to what is provided on the Quantum Espresso website, Raman > calculations work only with NC pseudo-potentials and I tried to use that kind > of PP in my scf calculations. Below is my scf and phonon calculations input > files. Any help would be thoroughly appreciated on how to get Raman > intensities. > > > SCF INPUT: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './scratch' , > wfcdir = './scratch' , > pseudo_dir = '/global/espresso/pseudo' , > prefix = 'SOD' , > verbosity = 'high' , > etot_conv_thr = 1e-5 , > forc_conv_thr = 1e-4 , > nstep = 50 , > tstress = .true. , > tprnfor = .true. , > > / > > &SYSTEM > ibrav = 0, > nat = 36, > ntyp = 2, > ecutwfc = 50 , > ecutrho = 200 , > > / > > &ELECTRONS > electron_maxstep = 100, > conv_thr = 3e-8 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > > / > CELL_PARAMETERS bohr > 16.7202967500.00.0 > 0.0 16.7202967500.0 > 0.00.0 16.720296750 > ATOMIC_SPECIES >Si 28.08600 Si.tpss-mt.UPF > O 15.99940 O.tpss-mt.UPF > ATOMIC_POSITIONS angstrom > Si 2.2114340870.04.42400 >Si 6.6365659130.04.42400 >Si 4.424002.2114340870.0 >Si 4.424006.6365659130.0 >Si 0.04.424002.211434087 >Si 0.04.424006.636565913 >Si 2.2114241384.42400 -0.0 >Si 6.6365758624.42400 -0.0 >Si 0.02.2114241384.42400 >Si 0.06.6365758624.42400 >Si 4.424000.02.211424138 >Si 4.424000.06.636575862 > O 1.2872841424.0775133401.287298380 > O 7.5607158584.7704866601.287298380 > O 7.5607158584.0775133407.560701620 > O 1.2872841424.7704866607.560701620 > O 1.2872983801.2872841424.077513340 > O 1.2872983807.5607158584.770486660 > O 7.5607016207.5607158584.077513340 > O 7.5607016201.2872841424.770486660 > O 4.0775133401.2872983801.287284142 > O 4.7704866601.2872983807.560715858 > O 4.0775133407.5607016207.560715858 > O 4.7704866607.5607016201.287284142 > O 8.5066504985.7138707755.713853509 > O 0.3413495023.1341292255.713853509 > O 8.5066504983.1341292253.134146491 > O 0.3413495025.7138707753.134146491 > O 5.7138707755.7138535098.506650498 > O 3.1341292255.7138535090.341349502 > O 3.1341292253.1341464918.506650498 > O 5.7138707753.1341464910.341349502 > O 5.7138535098.5066504985.713870775 > O 5.7138535090.3413495023.134129225 > O 3.1341464918.5066504983.134129225 > O 3.1341464910.3413495025.713870775 > K_POINTS automatic > 4 4 4 1 1 1 > > > Phonon Input File > > > phonons of Sodalite at Gamma > &inputph > tr2_ph= 1e-14, > prefix= 'SOD', > amass(1) = 28.08600, > amass(2) = 15.9940, > outdir= './scratch/', > fildyn= 'SOD.dyn', > recover = .false., > epsil = .true., > lraman= .true., > trans = .true., > max_seconds = 35 > / > 0.0 0.0 0.0 > > > Best regards, > > > Amir M. Mofrad > > University of Missouri - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistan
Re: [Pw_forum] HSE output for yambo TDDFT calculation
Dear Michael, some time ago, yambo was not able to perform a calculation from an hybrid or +U. Check if this is possible in the new yambo release. cheers Layla 2015-12-09 11:51 GMT+01:00 Paolo Giannozzi : > > > On Wed, Dec 9, 2015 at 10:34 AM, Michael Friedrich < > michael.friedr...@upb.de> wrote: > >> >> Maybe there is someone who knows more about this? >> > > I know close to nothing about this, but I am quite sure that the format of > the data file is the same irrespective of the type of calculation. Try to > start Yambo from the same scf calculation, made with plain DFT, and see > what happens > > Paolo > > Is there a possibility to provide the same output to yambo from a hse run >> as from a scf—>nscf DFT run? As far as I know there shouldn’t be much of a >> difference in the format of the WF and in principle it should be possible?! >> >> Thank you >> Michael Friedrich >> Universität Paderborn >> Germany >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Thin Film
Hello All, I am trying to simulate a material of a certain thickness onto which a thin film is applied. Please explain how to 1) modify the supercell. I am trying to use the Modify option in XCrysDen, but the option is not working. QE requires the coordinates for all the atoms in the supercell, but I don't know how to determine them. Any advice? 2) How do I determine the coordinates for the atoms of the thin film if I do not know where they attach to the first material? Thanks, Stephen ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
