<div dir="ltr">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 class="gmail_quote"><div dir="ltr" class="gmail_attr">El mar, 25 abr 2023 a la(s) 14:16, Krack Matthias (<a href="mailto:matthias.krack@psi.ch">matthias.krack@psi.ch</a>) escribió: </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-1234508636108722512"> <div lang="en-CH" style="overflow-wrap: break-word;"> <div class="m_-1234508636108722512WordSection1"> 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-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"> From: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> on behalf of Andres Ortega <<a href="mailto:oandresg15@gmail.com" target="_blank">oandresg15@gmail.com</a>> Date: Tuesday, 25 April 2023 at 09:11 To: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@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="mailto:matthias.krack@psi.ch" target="_blank">matthias.krack@psi.ch</a>) escribió: </div> <blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm"> <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-top:1pt solid rgb(225,225,225);padding:3pt 0cm 0cm"> Von: <a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a> <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@googlegroups.com</a>> Im Auftrag von <a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a> Gesendet: Montag, 24. April 2023 19:16 An: cp2k <<a href="mailto:cp2k@googlegroups.com" target="_blank">cp2k@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">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-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-top:1pt solid rgb(225,225,225);padding:3pt 0cm 0cm"> Von: <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>> Im Auftrag von <a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a> Gesendet: Montag, 24. April 2023 17:30 An: cp2k <<a href="mailto:cp...@googlegroups.com" target="_blank">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-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-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"> From: <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>> on behalf of <a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a> <<a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a>> Date: Monday, 24 April 2023 at 16:56 To: cp2k <<a href="mailto:cp...@googlegroups.com" target="_blank">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-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-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm"> From: <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> <<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>> on behalf of <a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a> <<a href="mailto:oandr...@gmail.com" target="_blank">oandr...@gmail.com</a>> Date: Monday, 24 April 2023 at 16:33 To: cp2k <<a href="mailto:cp...@googlegroups.com" target="_blank">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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