[QE-users] dipole moment
hi all, i am calculating dipole moment of water by pw.x. i do it correctly.but i don't understand "Elec. dipole" and " ion. dipole" in out put and relation them wit dipole. can i help me ? input : &CONTROL calculation = "scf" dipfield = .TRUE. disk_io = "default" iprint = 1 max_seconds = 8.64000e+04 nstep = 100 outdir = "./tmp1/" prefix = "H2Otest" pseudo_dir = "./" restart_mode = "from_scratch" tefield = .TRUE. title = "H2Otest" tprnfor = .TRUE. verbosity = "high" / &SYSTEM a = 10 degauss = 1.0e-02 ecutrho = 520 ecutwfc = 130 ibrav = 1 nat = 3 ntyp = 2 occupations = "smearing" smearing = "gaussian" edir = 1 emaxpos = 0.9 eopreg = 0.2 eamp = 0.0e+00 input_dft = "PBE" vdw_corr = "Grimme-D2" / &ELECTRONS conv_thr = 1.0e-06 electron_maxstep = 200 mixing_beta = 7.0e-01 startingpot = "atomic" startingwfc = "atomic+random" / K_POINTS {automatic} 3 3 3 0 0 0 ATOMIC_SPECIES O 15.99940 O.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} O 5 5 5 H 5 4.209 5.563 H 5 5.791 5.563 output: iteration # 6 ecut= 130.00 Ry beta=0.70 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged ethr = 7.81E-08, avg # of iterations = 6.6 negative rho (up, down): 0.438E-04 0.000E+00 Adding external electric field Computed dipole along edir(3) : Elec. dipole 0.0027 Ry au, 0.0068 Debye Ion. dipole 0.0040 Ry au, 0.0101 Debye Dipole 0.6902 Ry au, 1.7543 Debye Dipole field 0.0013 Ry au Potential amp. -0.0389 Ry Total length 15.1178 bohr total cpu time spent up to now is 152.0 secs End of self-consistent calculation best regards, sabike ghasemi phd student ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] dipole moment
Dear Sabike, [your affiliation please?] If I understand correctly your question, looking in the code in 'add_efield.f90': ... tot_dipole = -el_dipole + ion_dipole ... IF ( iverbosity > 0 ) THEN WRITE( stdout, '(8X,"Elec. dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & el_dipole, (el_dipole*au_debye) WRITE( stdout, '(8X,"Ion. dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & ion_dipole, (ion_dipole*au_debye) END IF WRITE( stdout, '(8X,"Dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & (tot_dipole* (omega/fpi)), ((tot_dipole* (omega/fpi))*au_debye) WRITE( stdout, '(8x,"Dipole field ", 1F15.4," Ry au, ")') tot_dipole Do those lines help? So something like "Dipole = (-el_dipole + ion_dipole) * volume / (4 pi)". Was this what you were looking for? Greetings from Lviv, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Sat, 17 Nov 2018, Sabike Ghasemi wrote: hi all, i am calculating dipole moment of water by pw.x. i do it correctly.but i don't understand "Elec. dipole" and " ion. dipole" in out put and relation them wit dipole. can i help me ? input : &CONTROL calculation = "scf" dipfield = .TRUE. disk_io = "default" iprint = 1 max_seconds = 8.64000e+04 nstep = 100 outdir = "./tmp1/" prefix = "H2Otest" pseudo_dir = "./" restart_mode = "from_scratch" tefield = .TRUE. title = "H2Otest" tprnfor = .TRUE. verbosity = "high" / &SYSTEM a = 10 degauss = 1.0e-02 ecutrho = 520 ecutwfc = 130 ibrav = 1 nat = 3 ntyp = 2 occupations = "smearing" smearing = "gaussian" edir = 1 emaxpos = 0.9 eopreg = 0.2 eamp = 0.0e+00 input_dft = "PBE" vdw_corr = "Grimme-D2" / &ELECTRONS conv_thr = 1.0e-06 electron_maxstep = 200 mixing_beta = 7.0e-01 startingpot = "atomic" startingwfc = "atomic+random" / K_POINTS {automatic} 3 3 3 0 0 0 ATOMIC_SPECIES O 15.99940 O.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} O 5 5 5 H 5 4.209 5.563 H 5 5.791 5.563 output: iteration # 6 ecut= 130.00 Ry beta=0.70 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged ethr = 7.81E-08, avg # of iterations = 6.6 negative rho (up, down): 0.438E-04 0.000E+00 Adding external electric field Computed dipole along edir(3) : Elec. dipole 0.0027 Ry au, 0.0068 Debye Ion. dipole 0.0040 Ry au, 0.0101 Debye Dipole 0.6902 Ry au, 1.7543 Debye Dipole field 0.0013 Ry au Potential amp. -0.0389 Ry Total length 15.1178 bohr total cpu time spent up to now is 152.0 secs End of self-consistent calculation best regards, sabike ghasemi phd student ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] dipole moment
dear Ari Thank you very much for your help. I never forget your tone. This was what I wanted. sabike ghasemi,phd student in Damghan university,IRAN - Original Message - From: "Ari P Seitsonen" To: "Quantum Espresso users Forum" Sent: Monday, November 19, 2018 8:02:01 PM Subject: Re: [QE-users] dipole moment Dear Sabike, [your affiliation please?] If I understand correctly your question, looking in the code in 'add_efield.f90': ... tot_dipole = -el_dipole + ion_dipole ... IF ( iverbosity > 0 ) THEN WRITE( stdout, '(8X,"Elec. dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & el_dipole, (el_dipole*au_debye) WRITE( stdout, '(8X,"Ion. dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & ion_dipole, (ion_dipole*au_debye) END IF WRITE( stdout, '(8X,"Dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) & (tot_dipole* (omega/fpi)), ((tot_dipole* (omega/fpi))*au_debye) WRITE( stdout, '(8x,"Dipole field ", 1F15.4," Ry au, ")') tot_dipole Do those lines help? So something like "Dipole = (-el_dipole + ion_dipole) * volume / (4 pi)". Was this what you were looking for? Greetings from Lviv, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ Ecole Normale Supérieure (ENS), Département de Chimie, Paris Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 On Sat, 17 Nov 2018, Sabike Ghasemi wrote: > hi all, > i am calculating dipole moment of water by pw.x. > i do it correctly.but i don't understand "Elec. dipole" and " ion. dipole" in > out put and relation them wit > dipole. can i help me ? > input : > &CONTROL > calculation = "scf" > dipfield = .TRUE. > disk_io = "default" > iprint = 1 > max_seconds = 8.64000e+04 > nstep = 100 > outdir = "./tmp1/" > prefix = "H2Otest" > pseudo_dir = "./" > restart_mode = "from_scratch" > tefield = .TRUE. > title = "H2Otest" > tprnfor = .TRUE. > verbosity = "high" > / > > &SYSTEM > a = 10 > degauss = 1.0e-02 > ecutrho = 520 > ecutwfc = 130 > ibrav = 1 > nat = 3 > ntyp = 2 > occupations = "smearing" > smearing = "gaussian" > edir = 1 > emaxpos = 0.9 > eopreg = 0.2 > eamp = 0.0e+00 > input_dft = "PBE" > vdw_corr = "Grimme-D2" > / > > &ELECTRONS > conv_thr = 1.0e-06 > electron_maxstep = 200 > mixing_beta = 7.0e-01 > startingpot = "atomic" > startingwfc = "atomic+random" > / > > K_POINTS {automatic} > 3 3 3 0 0 0 > > ATOMIC_SPECIES > O 15.99940 O.pbe-rrkjus.UPF > H 1.00794 H.pbe-rrkjus.UPF > > ATOMIC_POSITIONS {angstrom} > O 5 5 5 > H 5 4.209 5.563 > H 5 5.791 5.563 > > > > output: > > > iteration # 6 ecut= 130.00 Ry beta=0.70 > Davidson diagonalization with overlap > c_bands: 1 eigenvalues not converged > ethr = 7.81E-08, avg # of iterations = 6.6 > > negative rho (up, down): 0.438E-04 0.000E+00 > > Adding external electric field > > Computed dipole along edir(3) : > Elec. dipole 0.0027 Ry au, 0.0068 Debye > Ion. dipole 0.0040 Ry au, 0.0101 Debye > Dipole 0.6902 Ry au, 1.7543 Debye > Dipole field 0.0013 Ry au > > Potential amp. -0.0389 Ry > Total length 15.1178 bohr > > > total cpu time spent up to now is 152.0 secs > > End of self-consistent calculation > > > > best regards, > sabike ghasemi > phd student > > ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] dipole moment of isolated water molecule
hi all i calculated dipole moment of isolated water molecule with tefield keyword in qe.i gain it 1.7543 debye. it is approximately true.my input file and my output file is: &CONTROL calculation = "scf" dipfield = .TRUE. disk_io = "default" iprint = 1 max_seconds = 8.64000e+04 nstep = 100 outdir = "./tmp3/" prefix = "H2Otest" pseudo_dir = "./" restart_mode = "from_scratch" tefield = .TRUE. title = "H2Otest" tprnfor = .TRUE. verbosity = "high" / &SYSTEM a = 10 degauss = 1.0e-02 ecutrho = 520 ecutwfc = 130 ibrav = 1 nat = 3 ntyp = 2 occupations = "smearing" smearing = "gaussian" edir = 3 emaxpos = 0.9 eopreg = 0.2 eamp = 0.0e+00 / &ELECTRONS conv_thr = 1.0e-06 electron_maxstep = 200 mixing_beta = 7.0e-01 startingpot = "atomic" startingwfc = "atomic+random" / K_POINTS {automatic} 3 3 3 0 0 0 ATOMIC_SPECIES O 15.99940 O.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} O 5 5 5 H 5 4.209 5.563 H 5 5.791 5.563 scf correction = -0.00195330 Ry smearing contrib. (-TS) = -0. Ry iteration # 6 ecut= 130.00 Ry beta=0.70 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged ethr = 7.81E-08, avg # of iterations = 6.6 negative rho (up, down): 0.438E-04 0.000E+00 Adding external electric field Computed dipole along edir(3) : Elec. dipole 0.0027 Ry au, 0.0068 Debye Ion. dipole 0.0040 Ry au, 0.0101 Debye Dipole 0.6902 Ry au, 1.7543 Debye Dipole field 0.0013 Ry au Potential amp. -0.0389 Ry Total length 15.1178 bohr total cpu time spent up to now is 152.0 secs End of self-consistent calculation k = 0. 0. 0. (168933 PWs) bands (ev): -25.1105 -13.2479 -8.9087 -7.0939 -1.0094 0.4990 0.6919 1.0874 occupation numbers 1. 1. 1. 1. 0. 0. 0. 0. but i want to calculate it with lelfield keyword.i did it but i can not calculate dipole moment on output. my input file an my output file is: &CONTROL calculation = "scf" disk_io = "default" iprint = 1 max_seconds = 8.64000e+04 nstep = 100 outdir = "./tmp1/" prefix = "H2Otest" pseudo_dir = "./" restart_mode = "from_scratch" lelfield = .true. title = "H2Otest" tprnfor = .TRUE. verbosity = "high" / &SYSTEM a = 10 degauss = 1.0e-02 ecutrho = 520 ecutwfc = 130 ibrav = 1 nat = 3 ntyp = 2 occupations = "fixed" / &ELECTRONS conv_thr = 1.0e-06 electron_maxstep = 200 mixing_beta = 7.0e-01 startingpot = "atomic" startingwfc = "atomic+random" efield_cart(1)=0 efield_cart(2)=0 efield_cart(3)=0 / K_POINTS {automatic} 3 3 3 0 0 0 ATOMIC_SPECIES O 15.99940 O.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} O 5 5 5 H 5 4.209 5.563 H 5 5.791 5.563 iteration # 8 ecut= 130.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.72E-08, avg # of iterations = 2.0 negative rho (up, down): 0.440E-04 0.000E+00 Expectation value of exp(iGx): ( 0.96343770108935156 ,-4.95423895159652799E-010) 1. Electronic Dipole per cell (Ry a.u.) -4.37438805080789534E-009 Ionic Dipole per cell (Ry a.u.) 106.89905305190955 Expectation value of exp(iGx): ( 0.95658203681270559 ,-1.22862243921356336E-008) 1. Electronic Dipole per cell (Ry a.u.) -1.09259753344957216E-007 Ionic Dipole per cell (Ry a.u.) 106.89905305190956 Expectation value of exp(iGx): ( 0.93308524925395397 ,-0.22457706743625960 ) 1. Electronic Dipole per cell (Ry a.u.) -2.0092106448539888 Ionic Dipole per cell (Ry a.u.) 109.90826139532081 Electronic Dipole on Cartesian axes 1 -4.37438805080789534E-009 2 -1.09259753344957216E-007 3 -2.0092106448539888 Ionic Dipole on Cartesian axes 1 106.89905305190955 2 106.89905305190956 3 109.90826139532081 total cpu time spent up to now is 382.4 secs End of self-consistent calculation can every body help me? best regards, sabikeghasemi,phd student in damghan university,iran ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Dipole moment of the CO2 molecule
Dear Experts, users and all I found the dipoles of CO2 calculated by Quantum ESPRESSO as : Computed dipole along edir(3) : Elec. dipole 0.3112 Ry au, 0.7909 Debye Ion. dipole 0.8137 Ry au, 2.0683 Debye Dipole 41.9812 Ry au, 106.7055 Debye Dipole field 0.5025 Ry au, I assumed the third value is the sum of the electronic and ionic contributions. The input and output files are attached herewith. Since CO2 is non-polar molecule (with polar bonds), shouldn't the total dipole moment be zero? -- Endale Abebe Program coordinator and Lecturer Faculty of Materials Science and Engineering Jimma Institute of Technology Jimma University P.O.Box 378, Jimma, Ethiopia Mobile: +251921381598 CO2_nscf.out Description: Binary data CO2_nscf.in Description: Binary data ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Dipole moment of the CO2 molecule
An issue with your input is that you place the point where the external saw-tooth potential has a discontinuity in its derivative at emaxpos = 0.5 (it is in crystal units, so because edir = 3, it means that the potential depends on z and the discontinuity is at (0,0,a/2)). However, the CO2 molecule is placed along the x axis at fixed y = a/2 and z = a/2. As such, the discontinuity, which is unphysical since in serves to compensate the spurious dipole field that would arise as a consequence of the periodic boundary conditions, is located in a region where the charge density is not zero. emaxpos should be set in such a way that the discontinuity il located in the vacuum, in the region where the charge density is zero or in any case very small. In your setup it seems that a good choice would be emaxpos=0. Giovanni PS since you’re studying an isolated molecule, provided the size of your supercell is sufficiently large, the eigenvalues should exhibit no dependence on k. As a consequence, in this case, a 4x4x4 sampling of the Brillouin zone, should provide results equivalent to a gamma only sampling. So, you can switch to KPOINTS automatic 1 1 10 0 0 or, even better, KPOINTS gamma to make your calculation faster while keeping the same accuracy. > On 27 May 2020, at 03:42, ENDALE ABEBE wrote: > > Dear Experts, users and all > > I found the dipoles of CO2 calculated by Quantum ESPRESSO as : > > Computed dipole along edir(3) : > Elec. dipole 0.3112 Ry au, 0.7909 Debye > Ion. dipole 0.8137 Ry au, 2.0683 Debye > Dipole 41.9812 Ry au, 106.7055 Debye > Dipole field 0.5025 Ry au, > > I assumed the third value is the sum of the electronic and ionic > contributions. > The input and output files are attached herewith. > Since CO2 is non-polar molecule (with polar bonds), shouldn't the total > dipole moment be zero? > > -- > Endale Abebe > Program coordinator and Lecturer > Faculty of Materials Science and Engineering > Jimma Institute of Technology > Jimma University > P.O.Box 378, Jimma, Ethiopia > Mobile: +251921381598 > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Giovanni Cantele, PhD CNR-SPIN c/o Dipartimento di Fisica Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy e-mail: giovanni.cant...@spin.cnr.it gcant...@gmail.com Phone: +39 081 676910 Skype contact: giocan74 Web page: https://sites.google.com/view/giovanni-cantele ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Dipole moment of the CO2 molecule
Dear Dr. Giovanni Cantele Thank you very much for this helpful information. After modifying the input, I found that the choice of *eopreg *also affects the result. I found the dipole value close to zero using the attached input, but I still don't know how to chose the value of the *eopreg. Would you mind to give me some more explanation on the eopreg?* With Regards On Tue, May 26, 2020 at 6:15 AM Giovanni Cantele < giovanni.cant...@spin.cnr.it> wrote: > An issue with your input is that you place the point where the external > saw-tooth potential > has a discontinuity in its derivative at emaxpos = 0.5 (it is in crystal > units, so because edir = 3, > it means that the potential depends on z and the discontinuity is at > (0,0,a/2)). > However, the CO2 molecule is placed along the x axis at fixed y = a/2 and > z = a/2. As such, > the discontinuity, which is unphysical since in serves to compensate the > spurious dipole field that > would arise as a consequence of the periodic boundary conditions, is > located in a region where the > charge density is not zero. emaxpos should be set in such a way that the > discontinuity il located > in the vacuum, in the region where the charge density is zero or in any > case very small. In your setup > it seems that a good choice would be emaxpos=0. > > Giovanni > > PS since you’re studying an isolated molecule, provided the size of your > supercell is sufficiently large, > the eigenvalues should exhibit no dependence on k. As a consequence, in > this case, a 4x4x4 sampling > of the Brillouin zone, should provide results equivalent to a gamma only > sampling. So, you can switch to > KPOINTS automatic > 1 1 10 0 0 > or, even better, > KPOINTS gamma > to make your calculation faster while keeping the same accuracy. > > On 27 May 2020, at 03:42, ENDALE ABEBE wrote: > > Dear Experts, users and all > > I found the dipoles of CO2 calculated by Quantum ESPRESSO as : > > Computed dipole along edir(3) : > Elec. dipole 0.3112 Ry au, 0.7909 Debye > Ion. dipole 0.8137 Ry au, 2.0683 Debye > Dipole 41.9812 Ry au, 106.7055 Debye > Dipole field 0.5025 Ry au, > > I assumed the third value is the sum of the electronic and ionic > contributions. > The input and output files are attached herewith. > Since CO2 is non-polar molecule (with polar bonds), shouldn't the total > dipole moment be zero? > > -- > Endale Abebe > Program coordinator and Lecturer > Faculty of Materials Science and Engineering > Jimma Institute of Technology > Jimma University > P.O.Box 378, Jimma, Ethiopia > Mobile: +251921381598 > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > > -- > > Giovanni Cantele, PhD > > CNR-SPIN > c/o Dipartimento di Fisica > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > > e-mail: giovanni.cant...@spin.cnr.it > gcant...@gmail.com > Phone: +39 081 676910 > Skype contact: giocan74 > Web page: https://sites.google.com/view/giovanni-cantele > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Endale Abebe Program coordinator and Lecturer Faculty of Materials Science and Engineering Jimma Institute of Technology Jimma University P.O.Box 378, Jimma, Ethiopia Mobile: +251921381598 CO2_scf.in Description: Binary data ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Dipole moment correction on adsorcion energy calculations
Dear Quantum Espresso community: My system consists of an interface of a perovskite and an organic molecule. This system has 20 Angstrom of vacuum space and the slab is ubicated at the middle of the supercell. I read the tutorial provided from Christoph Wolf ( https://christoph-wolf.at/2018/05/02/dipole-correction-in-quantum-espresso/) and I understand the emax, eopreg and eamp parameters. However, I don 't know how to check if these parameters have the correct values. In this issue, what is the protocol to do this?. The input file is attached and the detail is shown below: &control calculation='relax', restart_mode='from_scratch', pseudo_dir = '.', outdir='./tmp' prefix='SystemTest' forc_conv_thr = 1d-5, tstress = .true., tprnfor = .true., tefield = .true., dipfield = .true., disk_io = 'none' / &system ibrav = 0, nat= 128, ntyp= 5, ecutwfc = 50.0, ecutrho = 400.0 vdw_corr = 'grimme-d3' eamp = 0.002, edir = 3, emaxpos = 0.95, eopreg = 0.05, / &electrons diagonalization='cg' conv_thr = 1.0e-8 mixing_beta = 0.7 / &ions ion_dynamics = 'bfgs', / ! &CELL ! cell_dynamics = 'bfgs', ! press = 0.0, ! press_conv_thr = 0.5, / Regards Ignacio Lizana PhD Student University of Concepción DipoleCorrection.in Description: Binary data ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users