[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
>
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/d1809a50-7ad4-41a3-abe9-d10c4e3e8d2dn%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/d1809a50-7ad4-41a3-abe9-d10c4e3e8d2dn%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
>
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/dee9e13a-1c47-4128-bff2-17ea252ac5d9n%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/dee9e13a-1c47-4128-bff2-17ea252ac5d9n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
>
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/31e61f34-1b3c-4ac6-b3f6-282c1f6fca3an%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/31e61f34-1b3c-4ac6-b3f6-282c1f6fca3an%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/dc90830c-f529-45f7-947e-63daab1dc3c7n%40googlegroups.com
> <https://groups.google.com/d/msgid/cp2k/dc90830c-f529-45f7-947e-63daab1dc3c7n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/ZRAP278MB082714CDE688C852BA276A30F4679%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM
> <https://groups.google.com/d/msgid/cp2k/ZRAP278MB082714CDE688C852BA276A30F4679%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/CAME5veCsApUjw3gjN75F7WDqeR4oOd4sb4Oq897-Vo0ee0F%2Bzw%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAME5veCsApUjw3gjN75F7WDqeR4oOd4sb4Oq897-Vo0ee0F%2Bzw%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/cp2k/8C0g5vialvA/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/ZRAP278MB082756609080A0E18686BE9FF4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM
> <https://groups.google.com/d/msgid/cp2k/ZRAP278MB082756609080A0E18686BE9FF4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/CAME5veBM-eoQVYkq64VcjQH_A%3DOJH6R4MAjFmau6RQmgokyiFw%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAME5veBM-eoQVYkq64VcjQH_A%3DOJH6R4MAjFmau6RQmgokyiFw%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+unsubscribe at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/ZRAP278MB08271C48903F4193CC827841F4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM
> <https://groups.google.com/d/msgid/cp2k/ZRAP278MB08271C48903F4193CC827841F4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer>
> .
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/CAME5veBt_V%2BzD-63LGTQ2kx0HN%2BK-AGNZHS-ZNstmRYy%2BZ%2BaGw%40mail.gmail.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230425/c1c28cf7/attachment-0001.htm>


More information about the CP2K-user mailing list