<a href="https://github.com/cp2k/cp2k/commit/4aed5d1be1dbc943847ecc7c13c1b16a2985cc7a">This PR</a> fixes hopefully the issue in the current CP2K development version. <div>Best regards</div><div> </div><div>Matthias</div><div> </div><div><div dir="auto">On Tuesday, April 25, 2023 at 6:18:48 PM UTC+2 Krack Matthias wrote: </div><blockquote style="margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"> <div lang="en-CH" style="overflow-wrap: break-word;"> <div> Dear Andres You are right, the behavior of GEO_OPT and CELL_OPT is indeed different. Sorry, I missed that. Meanwhile, I checked the code. With CELL_OPT, the cell matrix is always transformed to a triangular form for non-orthorhombic cells and there is currently no way to change that by any input key. The triangular cell matrix setup/transformation makes sense for some cases (e.g. when ABC and ALBEGA are specified), but I am not sure if that is always needed. The fix would be easy, but it could have many unforeseen side effects. I have to perform further checks.</div></div><div lang="en-CH" style="overflow-wrap: break-word;"><div> Best Matthias <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of Andres Ortega <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Tuesday, 25 April 2023 at 15:58 To: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: Re: [CP2K:18718] modification of CELL_ parameters </div> <div> Dear Matthias , <div> </div> <div> Thank you again for the fast reply , </div> <div> so what I am observing is not like that , the GEO_OPT keep the cell parameters fixed , and the restart file that cp2k prints at the end of the GEO_OPT keeps the cell_parameters that were defined in the beginning </div> <div> </div> <div> best </div> <div> </div> <div> Andres </div> <div> </div> </div> <div> <div> El mar, 25 abr 2023 a la(s) 15:50, Krack Matthias (<a href="" rel="nofollow">matthia...@psi.ch</a>) escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> <div> Dear Andres As I said, the transformation is always carried out, even with a GEO_OPT run. The initial cell expression at the top of the CP2K output files reflects only what CP2K read from the input file. At the start of the GEO_OPT run, in contrast to the CELL_OPT run, there is no cell printout, but you can perform a GEO_OPT run and request the .cell file output. You will then see that the first row in the cell file is already the transformed cell. Best Matthias <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of Andres Ortega <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Tuesday, 25 April 2023 at 14:42 To: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: Re: [CP2K:18716] modification of CELL_ parameters </div> <div> Dear Matthias, <div> </div> <div> You are right, cp2k read cell parameters from the input, and then does the transformation when doing a CELL_OPT. </div> <div> The cell parameters do not suffer any transformation when the run is a GEO_OPT </div> <div> </div> <div> Is there a input choice to avoid this behaviour in the CELL_OPT? </div> <div> best </div> <div> </div> <div> Andres </div> </div> <div> <div> El mar, 25 abr 2023 a la(s) 14:37, Krack Matthias (<a href="" rel="nofollow">matthia...@psi.ch</a>) escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> <div> Dear Andres If I am not mistaken, the transformation is directly performed after the cell information has been read from the input. Thus all calculations in CP2K are done with that transformed cell including the first SCF. Best Matthias <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of Andres Ortega <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Tuesday, 25 April 2023 at 14:28 To: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: Re: [CP2K:18714] modification of CELL_ parameters </div> <div> Dear Matthias, <div> </div> <div> Thank you for your email, </div> <div> So what i notice , is that the user can define the A, B , C in a different way that the conventional . </div> <div> Actually, the first scf, cp2k do not modify the cell parameters , is when the CELL_OPT starts. </div> <div> This transformation could modify results that are related to the symmetry of a system, like computing a property like a tensor. </div> <div> </div> <div> In principle, if i use this input and just do a GEO_OPT , the cell parameters do not suffer a transformation to the conventional from cp2k. </div> <div> Is there a choice to avoid this change in the CELL_OPT ? </div> <div> </div> <div> best, </div> <div> </div> <div> Andres </div> </div> <div> <div> El mar, 25 abr 2023 a la(s) 14:16, Krack Matthias (<a href="" rel="nofollow">matthia...@psi.ch</a>) escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> <div> CP2K always initializes the cell by aligning the lattice vector a with the x axis and then the vector b is placed in the xy plane, even if A, B, and C are explicitly specified in the input. That transformation should not matter as the atomic coordinates are transformed accordingly. Sorry, could have noted that earlier. <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of Andres Ortega <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Tuesday, 25 April 2023 at 09:11 To: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: Re: [CP2K:18703] modification of CELL_ parameters </div> <div> Dear Matthias, <div> </div> <div> I tried your suggestion, </div> <div> the transformation still occurs in the first step of the optimization , I also try just keeping using the default of FORMAT, it doesnt work </div> <div> </div> <div> best, </div> <div> </div> <div> Andres </div> </div> <div> <div> El lun, 24 abr 2023 a la(s) 21:21, Krack Matthias (<a href="" rel="nofollow">matthia...@psi.ch</a>) escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> <div> You can try to drop the keyword FORMAT DCD_ALIGNED_CELL or use just FORMAT DCD instead. <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(225, 225, 225); padding: 3pt 0cm 0cm;"> Von: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Im Auftrag von <a href="" rel="nofollow">oandr...@gmail.com</a> Gesendet: Montag, 24. April 2023 19:16 An: cp2k <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Betreff: Re: [CP2K:18701] modification of CELL_ parameters </div> Dear Matthias, <div> this could be an example </div> <div> </div> <div> &FORCE_EVAL &DFT BASIS_SET_FILE_NAME BASIS_MOLOPT BASIS_SET_FILE_NAME BASIS_MOLOPT_UCL CHARGE 0 &MGRID CUTOFF 700 NGRIDS 5 REL_CUTOFF 70 &END MGRID MULTIPLICITY 0 &POISSON PERIODIC XYZ &END POISSON POTENTIAL_FILE_NAME GTH_POTENTIALS &PRINT &MO_CUBES ADD_LAST SYMBOLIC &EACH CELL_OPT 0 GEO_OPT 0 &END EACH NHOMO 1 NLUMO 1 WRITE_CUBE .FALSE. &END MO_CUBES &MULLIKEN ON ADD_LAST SYMBOLIC &EACH CELL_OPT 0 GEO_OPT 0 &END EACH &END MULLIKEN &END PRINT &QS EPS_DEFAULT 1e-12 METHOD GPW &END QS &SCF </div> <div> EPS_SCF 5e-08 MAX_ITER_LUMO 5000 MAX_SCF 80 &MIXING ALPHA 0.4 BETA 0.5 METHOD DIRECT_P_MIXING &END MIXING &OT MINIMIZER CG PRECONDITIONER FULL_ALL &END OT &OUTER_SCF EPS_SCF 5e-08 MAX_SCF 60 &END OUTER_SCF &PRINT &RESTART BACKUP_COPIES 0 &END RESTART &END PRINT &END SCF UKS .FALSE. &XC DENSITY_CUTOFF 1e-10 GRADIENT_CUTOFF 1e-10 TAU_CUTOFF 1e-10 &VDW_POTENTIAL &PAIR_POTENTIAL PARAMETER_FILE_NAME dftd3.dat REFERENCE_FUNCTIONAL PBE R_CUTOFF 10.0 TYPE DFTD3(BJ) &END PAIR_POTENTIAL POTENTIAL_TYPE PAIR_POTENTIAL &END VDW_POTENTIAL &XC_FUNCTIONAL &PBE </div> <div> PARAMETRIZATION ORIG &END PBE &END XC_FUNCTIONAL &END XC &END DFT METHOD QUICKSTEP STRESS_TENSOR ANALYTICAL &SUBSYS &CELL A -1.59515785 -2.7628944422923 -3.9070099102745e-16 B -1.59515785 2.7628944422923 1.9535049551373e-16 C 0.0 0.0 -14.879004 MULTIPLE_UNIT_CELL 4 4 1 &END CELL &KIND Mo BASIS_SET TZVP-MOLOPT-SR-GTH-q14 POTENTIAL GTH-PBE-q14 &END KIND &KIND S BASIS_SET DZVP-MOLOPT-SR-GTH-q6 POTENTIAL GTH-PBE-q6 &END KIND &TOPOLOGY COORD_FILE_FORMAT XYZ COORD_FILE_NAME <a href="http://aiida.coords.xyz" target="_blank" rel="nofollow">aiida.coords.xyz</a> MULTIPLE_UNIT_CELL 4 4 1 &END TOPOLOGY &END SUBSYS &END FORCE_EVAL </div> <div> &GLOBAL ELPA_KERNEL GENERIC PRINT_LEVEL MEDIUM PROJECT aiida RUN_TYPE CELL_OPT &END GLOBAL &MOTION &CELL_OPT &BFGS TRUST_RADIUS [angstrom] 0.2 &END BFGS EXTERNAL_PRESSURE [bar] 0.0 KEEP_ANGLES .TRUE. KEEP_SYMMETRY .FALSE. MAX_DR [bohr] 0.0005 MAX_FORCE [bohr^-1*hartree] 0.00010 MAX_ITER 1000 OPTIMIZER BFGS PRESSURE_TOLERANCE [bar] 100 RMS_DR [bohr] 0.0005 RMS_FORCE [bohr^-1*hartree] 0.00010 TYPE DIRECT_CELL_OPT &END CELL_OPT &GEO_OPT &BFGS TRUST_RADIUS [angstrom] 0.20 &END BFGS MAX_DR [bohr] 0.0005 MAX_FORCE [bohr^-1*hartree] 0.00010 MAX_ITER 1000 OPTIMIZER BFGS RMS_DR [bohr] 0.0005 RMS_FORCE [bohr^-1*hartree] 0.00010 TYPE MINIMIZATION &END GEO_OPT </div> <div> &PRINT &RESTART BACKUP_COPIES 0 &EACH CELL_OPT 1 GEO_OPT 1 MD 1 &END EACH &END RESTART &TRAJECTORY &EACH CELL_OPT 1 GEO_OPT 1 MD 1 &END EACH FORMAT DCD_ALIGNED_CELL &END TRAJECTORY &END PRINT &END MOTION 161,1 Bot </div> <div> <div> El lunes, 24 de abril de 2023 a la(s) 18:08:49 UTC+2, Krack Matthias escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> Without the full input, it is difficult to give further hints. </div> </div> <div> <div> <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(225, 225, 225); padding: 3pt 0cm 0cm;"> Von: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Im Auftrag von <a href="" rel="nofollow">oandr...@gmail.com</a> Gesendet: Montag, 24. April 2023 17:30 An: cp2k <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Betreff: Re: [CP2K:18699] modification of CELL_ parameters </div> Dear Mathias, <div> </div> <div> I tried the KEEP_ANGLES, and indeed it keeps the cell vectors, but only the first step, after that it applies the same transformation . </div> <div> </div> <div> CELL_REF| Volume [angstrom^3]: 2098.417005 CELL_REF| Vector a [angstrom -6.381 -11.052 -0.000 |a| = 12.761263 CELL_REF| Vector b [angstrom -6.381 11.052 0.000 |b| = 12.761263 CELL_REF| Vector c [angstrom 0.000 0.000 -14.879 |c| = 14.879004 CELL_REF| Angle (b,c), alpha [degree]: 90.000000 CELL_REF| Angle (a,c), beta [degree]: 90.000000 CELL_REF| Angle (a,b), gamma [degree]: 120.000000 CELL_REF| Numerically orthorhombic: NO CELL_OPT| Pressure tolerance [bar]: 100.0 CELL_OPT| Keep angles between the cell vectors: YES CELL_OPT| Keep cell symmetry: NO CELL_OPT| Constraint: NONE *** STARTING CELL OPTIMIZATION *** CELL| Volume [angstrom^3]: 2098.417005 CELL| Vector a [angstrom]: 12.761 0.000 0.000 |a| = 12.761263 CELL| Vector b [angstrom]: -6.381 11.052 0.000 |b| = 12.761263 CELL| Vector c [angstrom]: 0.000 0.000 14.879 |c| = 14.879004 CELL| Angle (b,c), alpha [degree]: 90.000000 CELL| Angle (a,c), beta [degree]: 90.000000 CELL| Angle (a,b), gamma [degree]: 120.000000 CELL| Numerically orthorhombic: NO CELL| Volume [angstrom^3]: 2083.849671 CELL| Vector a [angstrom]: 12.727 0.000 0.000 |a| = 12.726904 CELL| Vector b [angstrom]: -6.363 11.022 0.000 |b| = 12.726904 CELL| Vector c [angstrom]: 0.000 0.000 14.856 |c| = 14.855602 CELL| Angle (b,c), alpha [degree]: 90.000000 CELL| Angle (a,c), beta [degree]: 90.000000 CELL| Angle (a,b), gamma [degree]: 120.000000 CELL| Numerically orthorhombic: NO </div> <div> </div> <div> I wonder if is possible to stop this behaviour , </div> <div> </div> <div> best, </div> <div> </div> <div> Andres Ortega </div> <div> </div> <div> <div> El lunes, 24 de abril de 2023 a la(s) 17:09:45 UTC+2, Krack Matthias escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> Yes, you can try KEEP_ANGLES, but this is not exactly the same constraint, because a and b are allowed to differ in length. </div> </div> <div> <div> Matthias <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of <a href="" rel="nofollow">oandr...@gmail.com</a> <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Monday, 24 April 2023 at 16:56 To: cp2k <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: Re: [CP2K:18697] modification of CELL_ parameters </div> Dear Mathias , <div> thank you for your email </div> <div> </div> <div> However how can I make a cell opt, where I keep the symmetry, </div> <div> then I should just use KEEP_ANGLES , will it be enough? </div> <div> </div> <div> best </div> <div> </div> <div> Andres </div> <div> </div> <div> <div> El lunes, 24 de abril de 2023 a la(s) 16:40:52 UTC+2, Krack Matthias escribió: </div> <blockquote style="border-top: none; border-right: none; border-bottom: none; border-image: initial; border-left: 1pt solid rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin: 5pt 0cm 5pt 4.8pt;"> <div> <div> Hi Andres The keyword SYMMETRY MONOCLINIC_GAMMA_AB changes the cell as requested. Drop that keyword, if you want to keep the cell vectors from your input. HTH Matthias </div> </div> <div> <div> <div style="border-right: none; border-bottom: none; border-left: none; border-image: initial; border-top: 1pt solid rgb(181, 196, 223); padding: 3pt 0cm 0cm;"> From: <a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of <a href="" rel="nofollow">oandr...@gmail.com</a> <<a href="" rel="nofollow">oandr...@gmail.com</a>> Date: Monday, 24 April 2023 at 16:33 To: cp2k <<a href="" rel="nofollow">cp...@googlegroups.com</a>> Subject: [CP2K:18695] modification of CELL_ parameters </div> Dear Cp2k users and developers, <div> </div> <div> I was wondering if you could help me with a doubt i have , </div> <div> does cp2k modifies the cell vectors (applies an operation to them) once you set up a cell opt calculations </div> <div> </div> <div> for example </div> <div> say you have a systems with these cell parameters in the input file </div> <div> &CELL A -1.59515785 -2.7628944422923 -3.9070099102745e-16 B -1.59515785 2.7628944422923 1.9535049551373e-16 C 0.0 0.0 -14.879004 MULTIPLE_UNIT_CELL 4 4 1 SYMMETRY MONOCLINIC_GAMMA_AB </div> <div> </div> <div> </div> <div> but once the simulations starts it becomes </div> <div> </div> <div> CELL_TOP| Volume [angstrom^3]: 2098.417005 CELL_TOP| Vector a [angstrom 12.761 0.000 0.000 |a| = 12.761263 CELL_TOP| Vector b [angstrom -6.381 11.052 0.000 |b| = 12.761263 CELL_TOP| Vector c [angstrom 0.000 0.000 14.879 |c| = 14.879004 CELL_TOP| Angle (b,c), alpha [degree]: 90.000000 CELL_TOP| Angle (a,c), beta [degree]: 90.000000 CELL_TOP| Angle (a,b), gamma [degree]: 120.000000 CELL_TOP| Requested initial symmetry: MONOCLINIC_GAMMA_AB CELL_TOP| Numerically orthorhombic: NO </div> <div> </div> <div> So if you notices the magnitudes are the same but vector a, and b are in a different basis. </div> <div> Is there a way to avoid this ? </div> <div> </div> <div> best </div> <div> </div> <div> Andres Ortega </div> <div> </div> </div> </div> <div> <div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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