[CP2K-user] [CP2K:18716] modification of CELL_ parameters
Andres Ortega
oandresg15 at gmail.com
Tue Apr 25 12:42:15 UTC 2023
Dear Matthias,
You are right, cp2k read cell parameters from the input, and then does the
transformation when doing a CELL_OPT.
The cell parameters do not suffer any transformation when the run is a
GEO_OPT
Is there a input choice to avoid this behaviour in the CELL_OPT?
best
Andres
El mar, 25 abr 2023 a la(s) 14:37, Krack Matthias (matthias.krack at psi.ch)
escribió:
> 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
>
>
>
> *From: *cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Andres
> Ortega <oandresg15 at gmail.com>
> *Date: *Tuesday, 25 April 2023 at 14:28
> *To: *cp2k at googlegroups.com <cp2k at googlegroups.com>
> *Subject: *Re: [CP2K:18714] modification of CELL_ parameters
>
> Dear Matthias,
>
>
>
> Thank you for your email,
>
> So what i notice , is that the user can define the A, B , C in a different
> way that the conventional .
>
> Actually, the first scf, cp2k do not modify the cell parameters , is when
> the CELL_OPT starts.
>
> This transformation could modify results that are related to the symmetry
> of a system, like computing a property like a tensor.
>
>
>
> 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.
>
> Is there a choice to avoid this change in the CELL_OPT ?
>
>
>
> best,
>
>
>
> Andres
>
>
>
> El mar, 25 abr 2023 a la(s) 14:16, Krack Matthias (matthias.krack at psi.ch)
> escribió:
>
> 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.
>
>
>
> *From: *cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Andres
> Ortega <oandresg15 at gmail.com>
> *Date: *Tuesday, 25 April 2023 at 09:11
> *To: *cp2k at googlegroups.com <cp2k at googlegroups.com>
> *Subject: *Re: [CP2K:18703] modification of CELL_ parameters
>
> Dear Matthias,
>
>
>
> I tried your suggestion,
>
> the transformation still occurs in the first step of the optimization , I
> also try just keeping using the default of FORMAT, it doesnt work
>
>
>
> best,
>
>
>
> Andres
>
>
>
> El lun, 24 abr 2023 a la(s) 21:21, Krack Matthias (matthias.krack at psi.ch)
> escribió:
>
> You can try to drop the keyword FORMAT DCD_ALIGNED_CELL or use just FORMAT
> DCD instead.
>
>
>
> *Von:* cp2k at googlegroups.com <cp2k at googlegroups.com> *Im Auftrag von *
> oandr... at gmail.com
> *Gesendet:* Montag, 24. April 2023 19:16
> *An:* cp2k <cp2k at googlegroups.com>
> *Betreff:* Re: [CP2K:18701] modification of CELL_ parameters
>
>
>
> Dear Matthias,
>
> this could be an example
>
>
>
>
> &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
>
> 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
>
> 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 aiida.coords.xyz
> MULTIPLE_UNIT_CELL 4 4 1
> &END TOPOLOGY
> &END SUBSYS
> &END FORCE_EVAL
>
> &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
>
> &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
>
> El lunes, 24 de abril de 2023 a la(s) 18:08:49 UTC+2, Krack Matthias
> escribió:
>
> Without the full input, it is difficult to give further hints.
>
>
>
> *Von:* cp... at googlegroups.com <cp... at googlegroups.com> *Im Auftrag von *
> oandr... at gmail.com
> *Gesendet:* Montag, 24. April 2023 17:30
> *An:* cp2k <cp... at googlegroups.com>
> *Betreff:* Re: [CP2K:18699] modification of CELL_ parameters
>
>
>
> Dear Mathias,
>
>
>
> I tried the KEEP_ANGLES, and indeed it keeps the cell vectors, but only
> the first step, after that it applies the same transformation .
>
>
>
> 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
>
>
>
> I wonder if is possible to stop this behaviour ,
>
>
>
> best,
>
>
>
> Andres Ortega
>
>
>
> El lunes, 24 de abril de 2023 a la(s) 17:09:45 UTC+2, Krack Matthias
> escribió:
>
> Yes, you can try KEEP_ANGLES, but this is not exactly the same constraint,
> because a and b are allowed to differ in length.
>
>
>
> Matthias
>
>
>
> *From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of
> oandr... at gmail.com <oandr... at gmail.com>
> *Date: *Monday, 24 April 2023 at 16:56
> *To: *cp2k <cp... at googlegroups.com>
> *Subject: *Re: [CP2K:18697] modification of CELL_ parameters
>
> Dear Mathias ,
>
> thank you for your email
>
>
>
> However how can I make a cell opt, where I keep the symmetry,
>
> then I should just use KEEP_ANGLES , will it be enough?
>
>
>
> best
>
>
>
> Andres
>
>
>
> El lunes, 24 de abril de 2023 a la(s) 16:40:52 UTC+2, Krack Matthias
> escribió:
>
> 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
>
>
>
> *From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of
> oandr... at gmail.com <oandr... at gmail.com>
> *Date: *Monday, 24 April 2023 at 16:33
> *To: *cp2k <cp... at googlegroups.com>
> *Subject: *[CP2K:18695] modification of CELL_ parameters
>
> Dear Cp2k users and developers,
>
>
>
> I was wondering if you could help me with a doubt i have ,
>
> does cp2k modifies the cell vectors (applies an operation to them) once
> you set up a cell opt calculations
>
>
>
> for example
>
> say you have a systems with these cell parameters in the input file
>
> &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
>
>
>
>
>
> but once the simulations starts it becomes
>
>
>
> 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
>
>
>
> So if you notices the magnitudes are the same but vector a, and b are in a
> different basis.
>
> Is there a way to avoid this ?
>
>
>
> best
>
>
>
> Andres Ortega
>
>
>
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