Re: [Pw_forum] Total forces not converging: relax calculation
Dear Josue, Thank you for your answer. If I may, Ill answer point by point. Concerning the representation of the system in XCrysden. I am using crystal_sg to specify the coordinates, indicating the appropriate space_group. When I open the output file of a converged scf with XCrysden, the cell contains the atoms as the original cif files. The only difference is that when I try to switch the Unit of Repetition from Unit Cell to translational asymmetric unit, nothing changes and the atoms outside the unit cell do not appear in the interior. I assumed this had to do with the fact that I'm reading the output; Is there something wrong in this? Concerning the type of calculation. I want to compute phonon dispersion at the gamma point. That is why I am using norm-conserving pseudopotentials. And in a first approach I do not want to change the cell parameters, only to relax the atomic coordinates in the unit cell. So yes, I would stick to 'relax' calculation. The system contains a lanthanide atom, which might be the cause for the behaviour different from the standard cases. Is there any particular keyword I could play with to affect the convergence of the total forces? Cheers ======== Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Josue Itsman Clavijo Penagos [jiclavi...@unal.edu.co] Sent: 24 April 2017 16:41 To: PWSCF Forum Subject: Re: [Pw_forum] Total forces not converging: relax calculation Dear Daniel, It would be more useful if you post the input file you're using, or at least the atomic coordinates. Also, check if the system is well represented by the coordinates you are intending to relax, since a well-defined system usually converges at E_cutoff values as low as 60 Ryd for simple SCF calculations. (Does he system look as you expect when viewed in XCrysden, for example?) , unless you include rather demanding features like spin polarization, electric fields, defects and so on. By the way, Are norm-conserving PP's the only choice?(how about Ultrasoft?) Moreover, what type of relax calculation do you want to study? judging by the info you sent, it is 'relax', but, Wouldn't be that your system need some cell parameters/angles relaxing (vc-relax), not just atomic coordinates one? Best regards, Prof. Josué Clavijo, PhD Cristiano, born again Assistant Professor Universidad Nacional de Colombia Sede Bogotá ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Total forces not converging: relax calculation
Dear all, I am running a calculation to optimize the atomic position within the cell. I am using a large ecutwfc value (110 Ry) because I am using nor-conserving pp. I will have to later check this value against the phonons, since it is this property the one I want to study. When I grep the Total force values I get this Total force = 2.649777 Total SCF correction = 0.000385 Total force = 1.693758 Total SCF correction = 0.000589 Total force = 0.484600 Total SCF correction = 0.000552 Total force = 0.280971 Total SCF correction = 0.000235 Total force = 0.118901 Total SCF correction = 0.000730 Total force = 0.105601 Total SCF correction = 0.000207 Total force = 0.087956 Total SCF correction = 0.000233 Total force = 0.067168 Total SCF correction = 0.000242 Total force = 0.051189 Total SCF correction = 0.000217 Total force = 0.040092 Total SCF correction = 0.000241 Total force = 0.033889 Total SCF correction = 0.000143 Total force = 0.030175 Total SCF correction = 0.000155 Total force = 0.026895 Total SCF correction = 0.98 Total force = 0.025422 Total SCF correction = 0.000163 Total force = 0.024484 Total SCF correction = 0.000153 Total force = 0.023613 Total SCF correction = 0.56 Total force = 0.020151 Total SCF correction = 0.000127 Total force = 0.017819 Total SCF correction = 0.000108 Total force = 0.018180 Total SCF correction = 0.56 Total force = 0.017125 Total SCF correction = 0.56 Total force = 0.015261 Total SCF correction = 0.000150 Total force = 0.014572 Total SCF correction = 0.000125 Total force = 0.015588 Total SCF correction = 0.000104 Total force = 0.015453 Total SCF correction = 0.67 Total force = 0.012640 Total SCF correction = 0.44 Total force = 0.011777 Total SCF correction = 0.000120 Total force = 0.011944 Total SCF correction = 0.98 Total force = 0.011262 Total SCF correction = 0.52 Total force = 0.010667 Total SCF correction = 0.69 Total force = 0.011162 Total SCF correction = 0.61 Total force = 0.012045 Total SCF correction = 0.91 It seems it got stuck and is unable to descent further, despite the SCF correction is almost zero. I am using the standard values for the &IONS specifications &IONS ion_dynamics='bfgs' ion_positions='default' / with &electrons conv_thr=1.D-7 / Could you please refer me to keywords or strategies that are sensible to the force convergence? Best regards ==== Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] from phq_readin : error # 19
No... I submitted it with 6 processors instead of 12. I did not know I had to mantain the same number. Thank you very much Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Paolo Giannozzi [p.gianno...@gmail.com] Sent: 21 April 2017 09:58 To: PWSCF Forum Subject: Re: [Pw_forum] from phq_readin : error # 19 Is the mentioned file there, and not empty? if so: are you running with the same number of processors and same parallelization as the scf calculation? On Thu, Apr 20, 2017 at 2:01 PM, Daniel Reta wrote: > Oh wow, that was embarrassing! sorry for the silly question. > > However, now I get another error, which I hope is not as silly > > Error in routine diropn (10): > error opening /scratch/mbdssdr5/QE/Dy_III-Cl_O/Dy_III.wfc5 > > Cheers > > > ==== > > Dr. Daniel Reta, > Post-doctoral Research Associate, > Computational Chemistry, School of Chemistry > University of Manchester > > Email: daniel.r...@manchester.ac.uk > > > > > From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of > Paolo Giannozzi [p.gianno...@gmail.com] > Sent: 20 April 2017 12:08 > To: PWSCF Forum > Subject: Re: [Pw_forum] from phq_readin : error # 19 > > pseudo_dir is not an input variable of the phonon code, IIRC. Paolo > > Il 20/apr/2017 11:36 AM, "Daniel Reta" > mailto:daniel.r...@manchester.ac.uk>> ha > scritto: > Dear all, > > I am trying to run a phonon calculation at the gamma point. This is my input > > &inputph > prefix='Dy_III', > pseudo_dir='CurDir', > outdir='Scratch', > epsil=.true., > fildyn='dyn.G', > tr2_ph=1.0d-14 > / > 0.0 0.0 0.0 > > where CurDir and Scratch are defined in the same manner as in the previous > scf calculation which converged properly. Dy_III is the prefix for the wfc of > the previous calculation. > > I get the following error printed in the CRASH file > > > task # 1 > from phq_readin : error #19 > reading inputph namelist > > task # 5 > from phq_readin : error #19 > reading inputph namelist > > > and this > > Error in routine phq_readin (19): > reading inputph namelist > > in the output file. > > Could anyone please indicate me what I am doing wrong? > > Best regards > > > > Dr. Daniel Reta, > Post-doctoral Research Associate, > Computational Chemistry, School of Chemistry > University of Manchester > > Email: daniel.r...@manchester.ac.uk<mailto:daniel.r...@manchester.ac.uk> > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org<mailto: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 -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, 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
Re: [Pw_forum] from phq_readin : error # 19
Oh wow, that was embarrassing! sorry for the silly question. However, now I get another error, which I hope is not as silly Error in routine diropn (10): error opening /scratch/mbdssdr5/QE/Dy_III-Cl_O/Dy_III.wfc5 Cheers Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Paolo Giannozzi [p.gianno...@gmail.com] Sent: 20 April 2017 12:08 To: PWSCF Forum Subject: Re: [Pw_forum] from phq_readin : error # 19 pseudo_dir is not an input variable of the phonon code, IIRC. Paolo Il 20/apr/2017 11:36 AM, "Daniel Reta" mailto:daniel.r...@manchester.ac.uk>> ha scritto: Dear all, I am trying to run a phonon calculation at the gamma point. This is my input &inputph prefix='Dy_III', pseudo_dir='CurDir', outdir='Scratch', epsil=.true., fildyn='dyn.G', tr2_ph=1.0d-14 / 0.0 0.0 0.0 where CurDir and Scratch are defined in the same manner as in the previous scf calculation which converged properly. Dy_III is the prefix for the wfc of the previous calculation. I get the following error printed in the CRASH file task # 1 from phq_readin : error #19 reading inputph namelist task # 5 from phq_readin : error #19 reading inputph namelist and this Error in routine phq_readin (19): reading inputph namelist in the output file. Could anyone please indicate me what I am doing wrong? Best regards Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk<mailto:daniel.r...@manchester.ac.uk> ___ Pw_forum mailing list Pw_forum@pwscf.org<mailto: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] from phq_readin : error # 19
Dear all, I am trying to run a phonon calculation at the gamma point. This is my input &inputph prefix='Dy_III', pseudo_dir='CurDir', outdir='Scratch', epsil=.true., fildyn='dyn.G', tr2_ph=1.0d-14 / 0.0 0.0 0.0 where CurDir and Scratch are defined in the same manner as in the previous scf calculation which converged properly. Dy_III is the prefix for the wfc of the previous calculation. I get the following error printed in the CRASH file task # 1 from phq_readin : error #19 reading inputph namelist task # 5 from phq_readin : error #19 reading inputph namelist and this Error in routine phq_readin (19): reading inputph namelist in the output file. Could anyone please indicate me what I am doing wrong? Best regards Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Absolute energy dependent on ATOMIC_POSITION specification
Dear Paolo, Thank you very much for your prompt answer. Best regards Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Paolo Giannozzi [p.gianno...@gmail.com] Sent: 13 April 2017 09:31 To: PWSCF Forum Subject: Re: [Pw_forum] Absolute energy dependent on ATOMIC_POSITION specification On Thu, Apr 13, 2017 at 10:20 AM, Daniel Reta wrote: > I have run the same calculation specifying the atomic position with "crystal" > and with "angstrom", and I got two different absolute energies. Is this > correct? make a "diff" of the two outputs and you will find that they are not "the same calculation" > Also, the system is a molecular crystal with some ligands coordinated to > Ytrium. I find that I have to go to very high values of ecutwfc to converge > the absolute energy. I'm talking about 100 or 110 Ry approximately. Is this a > known feature? the convergence of absolute energies may be very slow, depending upon the pseudopotentials used. Energy differences between different structures of the same material typically converge much better. This is a known feature, yes. > Does working with such high values of ecutwfc introduce some biases in the > calculations? no, it just requires a big computer and a lot of time Paolo > Best regards > > > > > Dr. Daniel Reta, > Post-doctoral Research Associate, > Computational Chemistry, School of Chemistry > University of Manchester > > Email: daniel.r...@manchester.ac.uk > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, 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] Absolute energy dependent on ATOMIC_POSITION specification
Dear all, I have run the same calculation specifying the atomic position with "crystal" and with "angstrom", and I got two different absolute energies. Is this correct? Also, the system is a molecular crystal with some ligands coordinated to Ytrium. I find that I have to go to very high values of ecutwfc to converge the absolute energy. I'm talking about 100 or 110 Ry approximately. Is this a known feature? Does working with such high values of ecutwfc introduce some biases in the calculations? Best regards ==== Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION
Dear Tone, Thank you very much for this. Best Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Tone Kokalj [tone.kok...@ijs.si] Sent: 11 April 2017 09:59 To: pw_forum@pwscf.org Subject: Re: [Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION On Tue, 2017-04-11 at 08:37 +, Daniel Reta wrote: > Hi, > > I have a crystal with two molecular units in the unit cell, but they > are related by an inversion centre (triclinic). I am indicating the > inequivalent atomic positions only, using the appropriate space_group > and crystal_sg. xcrysden currently does not understand "crystal_sg" specs of coordinates from pw.x input (there are plans to implement this feature). Hence, the way to proceed is to visualize the structure from the output as you did. Best regards, Tone -- J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax: +386-1-251-9385) ___ 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] Xcrysden and crystal_sg ATOMIC_POSITION
Hi, I have a crystal with two molecular units in the unit cell, but they are related by an inversion centre (triclinic). I am indicating the inequivalent atomic positions only, using the appropriate space_group and crystal_sg. When I submit the job, the output contains the correct number of atoms in the translational cell (double the ones indicated in the input) The problem is that when I open the input file with xcrysden, only one of the molecule appears. Am I doing something wrong or it is a Xcrysden issue? The input looks like &control prefix='adpm416', pseudo_dir='CurDir', outdir='Scratch', calculation='scf' / &system ibrav=14, celldm(1)=22.12623628, celldm(2)=1.067214977, celldm(3)=1.711616149, celldm(4)=-0.120708606, celldm(5)=-0.00120427689, celldm(6)=-0.180913961, nat=138, ntyp=5, ecutwfc=40.0, vdw_corr='Grimme-D2', space_group=2 / &electrons conv_thr=1.D-7 / ATOMIC_SPECIES Y 88.90585 Y.pbe-sp-hgh.UPF F 18.9984 F.pbe-hgh.UPF C 12.011 C.pbe-hgh.UPF B 10.81 B.pbe-hgh.UPF H 1.008 H.pbe-hgh.UPF ATOMIC_POSITIONS crystal_sg Y 0.878770.31670 0.71532 C 0.6920 0.39090.7461 ** K_POINTS automatic 4 4 2 1 1 1 Thank you very much in advance. Best Dr. Daniel Reta, Post-doctoral Research Associate, Computational Chemistry, School of Chemistry University of Manchester Email: daniel.r...@manchester.ac.uk ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
