<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Paolo,<div>sorry for bothering you again.</div><div>Now I fixed the version of pw.x and ph.x (I'm using for both version 6.5) and checked the atomic positions in the input file.</div><div>I'm able to use dynmat.x only if I use cif2cell to generate the input, ibrav=0 and explicitly the cell vectors.</div><div>If I use spgroup and A, B, C, cos(beta) or celldm(1), celldm(2), etc, ph.x writes celldm(i) values different than those generated by pw.x.</div><div>Here is my new input file:</div><div><br></div><div><div>&CONTROL</div><div> title = 'Li2TiS3_monoclinic'</div><div> pseudo_dir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'</div><div> prefix = 'LTS_mono'</div><div> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono'</div><div> calculation = 'scf'</div><div> verbosity = 'high'</div><div> /</div><div> &SYSTEM</div><div> space_group = 15</div><div> uniqueb = .true.</div><div> A = 6.1839</div><div> B = 10.70446</div><div> C = 12.1280935</div><div> cosAC = -0.17166</div><div> nat = 8</div><div> ntyp = 3</div><div> ecutwfc = 52</div><div> ecutrho = 575</div><div> nbnd = 120</div><div> occupations = 'smearing'</div><div> degauss = 0.005</div><div> smearing = 'cold'</div><div> /</div><div> &ELECTRONS</div><div> electron_maxstep = 200</div><div> conv_thr = 1.0D-12</div><div> /</div><div><br></div><div>ATOMIC_SPECIES</div><div>Li 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF</div><div>Ti 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF</div><div> S 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF</div><div><br></div><div>ATOMIC_POSITIONS {crystal_sg}</div><div>Li 0.24488 0.08177 0.00019</div><div>Li 0.00000 0.08323 0.25000</div><div>Li 0.25000 0.25000 0.50000</div><div>Ti 0.00000 0.41656 0.25000</div><div>Ti 0.00000 0.74871 0.25000</div><div>S 0.39073 0.08366 0.36679</div><div>S 0.13716 0.25993 0.13331</div><div>S 0.13628 0.09205 0.63225</div><div><br></div><div>K_POINTS automatic</div><div>6 3 3 0 0 0</div></div><div><br></div><div>And for ph.x</div><div><div>Normal modes for LTS</div><div> &inputph</div><div> prefix='LTS_mono'</div><div> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono'</div><div> tr2_ph=1.0d-14</div><div> amass(1)=6.941</div><div> amass(2)=47.867</div><div> amass(3)=32.06</div><div> epsil=.false.</div><div> !lraman=.true.</div><div> trans=.true.</div><div> asr=.true.</div><div> fildyn='LTS.dmat'</div><div> /</div><div> 0.0 0.0 0.0</div></div><div><br></div><div>Part of the pw.x output file:</div><div><div>Title:</div><div> Li2TiS3_monoclinic</div><div><br></div><div><br></div><div> bravais-lattice index = -13</div><div> lattice parameter (alat) = 11.6859 a.u.</div><div> unit-cell volume = 2668.6492 (a.u.)^3</div><div> number of atoms/cell = 24</div><div> number of atomic types = 3</div><div> number of electrons = 144.00</div><div> number of Kohn-Sham states= 120</div><div> kinetic-energy cutoff = 52.0000 Ry</div><div> charge density cutoff = 575.0000 Ry</div><div> convergence threshold = 1.0E-12</div><div> mixing beta = 0.7000</div><div> number of iterations used = 8 plain mixing</div><div> Exchange-correlation= SLA PW PBX PBC</div><div> ( 1 4 3 4 0 0 0)</div><div><br></div><div> celldm(1)= 11.685877 celldm(2)= 1.731021 celldm(3)= 1.961237</div><div> celldm(4)= 0.000000 celldm(5)= -0.171660 celldm(6)= 0.000000</div><div><br></div><div> crystal axes: (cart. coord. in units of alat)</div><div> a(1) = ( 0.500000 0.865510 0.000000 )</div><div> a(2) = ( -0.500000 0.865510 0.000000 )</div><div> a(3) = ( -0.336666 0.000000 1.932125 )</div><div><br></div><div> reciprocal axes: (cart. coord. in units 2 pi/alat)</div><div> b(1) = ( 1.000000 0.577694 0.174246 )</div><div> b(2) = ( -1.000000 0.577694 -0.174246 )</div><div> b(3) = ( 0.000000 -0.000000 0.517565 )</div></div><div><br></div><div>Part of the ph.x output:</div><div><br></div><div><div>Normal modes for LTS</div><div><br></div><div> bravais-lattice index = 13</div><div> lattice parameter (alat) = 11.6859 a.u.</div><div> unit-cell volume = 2668.6492 (a.u.)^3</div><div> number of atoms/cell = 24</div><div> number of atomic types = 3</div><div> kinetic-energy cut-off = 52.0000 Ry</div><div> charge density cut-off = 575.0000 Ry</div><div> convergence threshold = 1.0E-14</div><div> beta = 0.7000</div><div> number of iterations used = 4</div><div> Exchange-correlation= PBE</div><div> ( 1 4 3 4 0 0 0)</div><div><br></div><div><br></div><div> celldm(1)= 11.68588 celldm(2)= 0.99955 celldm(3)= 0.00000</div><div> celldm(4)= -0.50022 celldm(5)= 0.00000 celldm(6)= 0.00000</div><div><br></div><div> crystal axes: (cart. coord. in units of alat)</div><div> a(1) = ( 0.5000 0.8655 0.0000 )</div><div> a(2) = ( -0.5000 0.8655 0.0000 )</div><div> a(3) = ( -0.3367 0.0000 1.9321 )</div><div><br></div><div> reciprocal axes: (cart. coord. in units 2 pi/alat)</div><div> b(1) = ( 1.0000 0.5777 0.1742 )</div><div> b(2) = ( -1.0000 0.5777 -0.1742 )</div><div> b(3) = ( 0.0000 -0.0000 0.5176 )</div></div><div><br></div><div>The celldm(i) values are different so when I run dynmat.x I get </div><div><br></div><div><div> Reading Dynamical Matrix from file LTS.dmat</div><div><br></div><div> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div><div> Error in routine latgen (13):</div><div> wrong celldm(3)</div></div><div><br></div><div>Could you please help me to solve the problem?</div><div><br></div><div>Thanks a lot in advance and best regards,</div><div>Mauro Sgroi.</div></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno ven 29 mag 2020 alle ore 15:41 Mauro Sgroi <<a href="mailto:maurofrancesco.sgroi@gmail.com">maurofrancesco.sgroi@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Dear Paolo,<div dir="auto">Thanks a lot for the clarification. </div><div dir="auto">Best regards, </div><div dir="auto">Mauro. </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il ven 29 mag 2020, 15:14 Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Fri, May 29, 2020 at 1:56 PM Mauro Sgroi <<a href="mailto:maurofrancesco.sgroi@gmail.com" rel="noreferrer" target="_blank">maurofrancesco.sgroi@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="auto"><br><div>My space group is 15. I've the coordinates of the not equivalent atoms from a cif experimental file.</div><div>Those Wyckoff positions are referred to the non-primitive conventional cell with 48 atoms.</div><div>[...] I imagine that pw.x automatically understands that those are referred to the conventional cell and transforms them in the equivalent positions in the primitive (24-atoms) cell.</div><div>Is this correct?</div></div></div></blockquote><div><br></div><div>I think that the code generates all atomic positions by applying all symmetry operations to the provided Wyckoff positions. Then, it throws away atoms that, modulo lattice translations, overlap. The code always assumes the smallest (primitive) unit cell.<br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="auto"><div>Or should I transform manually the coordinates referring them to the primitive monoclinic axes?</div></div></div></blockquote><div><br></div><div>I don't think you need to do anything (unless you don't get the correct number of atoms, of course): the code expects Wyckoff positions as they are defined in big crystallography books, produces atomic positions in the primitive unit cells as they are internally used.</div><div><br></div><div>Paolo<br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="auto"><div>Thanks a lot and best regards,</div><div>Mauro Sgroi.</div><div dir="auto"><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il dom 17 mag 2020, 19:03 Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" rel="noreferrer" target="_blank">p.giannozzi@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Sat, May 16, 2020 at 10:23 PM Mauro Sgroi <<a href="mailto:maurofrancesco.sgroi@gmail.com" rel="noreferrer noreferrer" target="_blank">maurofrancesco.sgroi@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Checking the output of ph.x I found that the celldm parameters are changed with respect to the initial scf calculation (and also the number of atoms in the cell pass from 24 to 30).</div></div></div></div></div></div></blockquote><div><br></div><div class="gmail_quote">With your input and the latest development version, the self-consistent calculation also produces 30 atoms from your Wyckoff positions. I get exactly the same lattice parameters in the phonon and in the scf code. I also get this interesting message:</div></div><div class="gmail_quote"> BEWARE: axis for ibrav=-13 changed, see documentation!</div><div class="gmail_quote">related to this change I did some time ago upon suggestion by don't remember who:<br></div><div class="gmail_quote"><a href="https://gitlab.com/QEF/q-e/-/commit/962a723a9d1e79244c8a2d7468937ab9f29982f4" rel="noreferrer noreferrer" target="_blank">https://gitlab.com/QEF/q-e/-/commit/962a723a9d1e79244c8a2d7468937ab9f29982f4</a></div><div class="gmail_quote">Are you by any chance running different version of the scf and phonon code?<br></div><div class="gmail_quote"><br></div><div class="gmail_quote">Paolo</div><div class="gmail_quote"><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Could you please help me to solve this problem?</div><div>Below I'm attaching the input of pw.x, ph.x and the initial output of ph.x.</div><div>Thanks a lot in advance and best regards,</div><div>Mauro Sgroi.</div><div><br></div><div>SCF</div><div><div>&CONTROL</div><div> title = 'Li2TiS3_monoclinic'</div><div> pseudo_dir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'</div><div> prefix = 'LTS_mono'</div><div> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono_low_kpt_cell'</div><div> calculation = 'scf'</div><div> verbosity = 'high'</div><div> /</div><div> &SYSTEM</div><div> space_group = 15</div><div> uniqueb = .true.</div><div> celldm(1) = 11.552652</div><div> celldm(2) = 1.73103</div><div> celldm(3) = 1.952171</div><div> celldm(5) = -0.172475</div><div> nat = 8</div><div> ntyp = 8</div><div> ecutwfc = 52</div><div> ecutrho = 575</div><div> nbnd = 120</div><div> occupations = 'smearing'</div><div> degauss = 0.005</div><div> smearing = 'cold'</div><div> /</div><div> &ELECTRONS</div><div> electron_maxstep = 200</div><div> conv_thr = 1.0D-12</div><div> /</div><div><br></div><div><br></div><div>ATOMIC_SPECIES</div><div> Li1 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF</div><div> Li2 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF</div><div> Li3 6.941 Li.pbe-sl-kjpaw_psl.1.0.0.UPF</div><div> Ti1 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF</div><div> Ti2 47.867 Ti.pbe-spn-kjpaw_psl.1.0.0.UPF</div><div> S1 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF</div><div> S2 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF</div><div> S3 32.06 S.pbe-nl-kjpaw_psl.1.0.0.UPF</div><div><br></div><div>ATOMIC_POSITIONS {crystal_sg}</div><div>Li1 0.3368954 0.8267566 0.9998022</div><div>Li2 0.4164759 0.4164759 0.2500000</div><div>Li3 0.5000000 0.0000000 0.5000000</div><div>Ti1 0.0836168 0.0836168 0.2500000</div><div>Ti2 0.7514196 0.7514196 0.2500000</div><div>S1 0.1929125 0.9744265 0.6332331</div><div>S2 0.3771191 0.1029193 0.1331970</div><div>S3 0.4557540 0.7282681 0.3676504</div><div><br></div><div>K_POINTS automatic</div><div>6 3 3 0 0 0</div></div><div><br></div><div>PHonon</div><div><div>Normal modes for LTS</div><div> &inputph</div><div> prefix='LTS_mono'</div><div> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/LTS_mono_low_kpt_cell'</div><div> tr2_ph=1.0d-14</div><div> amass(1)=6.941</div><div> amass(2)=6.941</div><div> amass(3)=6.941</div><div> amass(4)=47.867</div><div> amass(5)=47.867</div><div> amass(6)=32.06</div><div> amass(7)=32.06</div><div> amass(8)=32.06</div><div> epsil=.false.</div><div> !lraman=.true.</div><div> trans=.true.</div><div> asr=.true.</div><div> fildyn='dmat.lts'</div><div> /</div><div> 0.0 0.0 0.0</div></div><div><br></div><div>Part of Phonon output</div><div><div>bravais-lattice index = 13</div><div> lattice parameter (alat) = 11.5527 a.u.</div><div> unit-cell volume = 2566.1373 (a.u.)^3</div><div> number of atoms/cell = 30</div><div> number of atomic types = 8</div><div> kinetic-energy cut-off = 52.0000 Ry</div><div> charge density cut-off = 575.0000 Ry</div><div> convergence threshold = 1.0E-14</div><div> beta = 0.7000</div><div> number of iterations used = 4</div><div> Exchange-correlation = PBE ( 1 4 3 4 0 0)</div><div><br></div><div><br></div><div> celldm(1)= 11.55265 celldm(2)= 0.99956 celldm(3)= 0.00000</div><div> celldm(4)= -0.50022 celldm(5)= 0.00000 celldm(6)= 0.00000</div><div><br></div><div> crystal axes: (cart. coord. in units of alat)</div><div> a(1) = ( 0.5000 0.8655 0.0000 )</div><div> a(2) = ( -0.5000 0.8655 0.0000 )</div><div> a(3) = ( -0.3367 0.0000 1.9229 )</div><div><br></div><div> reciprocal axes: (cart. coord. in units 2 pi/alat)</div><div> b(1) = ( 1.0000 0.5777 0.1751 )</div><div> b(2) = ( -1.0000 0.5777 -0.1751 )</div><div> b(3) = ( 0.0000 -0.0000 0.5200 )</div><div><br></div><div><br></div><div> Atoms inside the unit cell:</div><div><br></div><div> Cartesian axes</div><div><br></div><div> site n. atom mass positions (alat units)</div><div> 1 Li1 6.9410 tau( 1) = ( -0.49974 0.56563 1.92254 )</div><div> 2 Li1 6.9410 tau( 2) = ( -0.00531 0.56563 0.96184 )</div><div> 3 Li1 6.9410 tau( 3) = ( 0.16304 1.16540 0.00038 )</div><div> 4 Li1 6.9410 tau( 4) = ( -0.33139 1.16540 0.96108 )</div><div> 5 Li2 6.9410 tau( 5) = ( 0.33230 0.72093 0.48073 )</div><div> 6 Li2 6.9410 tau( 6) = ( -0.50065 0.72093 0.48073 )</div><div> 7 Li2 6.9410 tau( 7) = ( -0.16900 0.14458 1.44219 )</div><div> 8 Li2 6.9410 tau( 8) = ( -0.33605 0.14458 1.44219 )</div><div> 9 Li3 6.9410 tau( 9) = ( -0.16835 0.86552 0.96146 )</div><div> 10 Li3 6.9410 tau( 10) = ( 0.00000 0.86552 0.00000 )</div><div> 11 Ti1 47.8670 tau( 11) = ( -0.00056 0.14474 0.48073 )</div><div> 12 Ti1 47.8670 tau( 12) = ( -0.16779 0.14474 0.48073 )</div><div> 13 Ti1 47.8670 tau( 13) = ( 0.16386 0.72077 1.44219 )</div><div> 14 Ti1 47.8670 tau( 14) = ( -0.66891 0.72077 1.44219 )</div><div> 15 Ti2 47.8670 tau( 15) = ( 0.16724 0.43521 0.48073 )</div><div> 16 Ti2 47.8670 tau( 16) = ( -0.33559 0.43521 0.48073 )</div><div> 17 Ti2 47.8670 tau( 17) = ( -0.00395 0.43030 1.44219 )</div><div> 18 Ti2 47.8670 tau( 18) = ( -0.50111 0.43030 1.44219 )</div><div> 19 S1 32.0600 tau( 19) = ( -0.52030 0.82125 1.21765 )</div><div> 20 S1 32.0600 tau( 20) = ( 0.01525 0.82125 1.66672 )</div><div> 21 S1 32.0600 tau( 21) = ( 0.18360 0.90978 0.70526 )</div><div> 22 S1 32.0600 tau( 22) = ( -0.35195 0.90978 0.25620 )</div><div> 23 S2 32.0600 tau( 23) = ( -0.16773 1.04367 0.25613 )</div><div> 24 S2 32.0600 tau( 24) = ( -0.00062 1.04367 0.70533 )</div><div> 25 S2 32.0600 tau( 25) = ( -0.16897 0.68736 1.66679 )</div><div> 26 S2 32.0600 tau( 26) = ( -0.33608 0.68736 1.21758 )</div><div> 27 S3 32.0600 tau( 27) = ( -0.16803 0.39514 0.70696 )</div><div> 28 S3 32.0600 tau( 28) = ( -0.00032 0.39514 0.25450 )</div><div> 29 S3 32.0600 tau( 29) = ( -0.16867 1.33589 1.21595 )</div><div> 30 S3 32.0600 tau( 30) = ( -0.33638 1.33589 1.66842 )</div></div><div><br></div><div><br></div></div></div></div></div></div>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer noreferrer noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
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_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer noreferrer noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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