[CP2K-user] [CP2K:18753] modification of CELL_ parameters
Matthias Krack
matthias.krack at psi.ch
Tue May 2 12:44:23 UTC 2023
This PR
<https://github.com/cp2k/cp2k/commit/4aed5d1be1dbc943847ecc7c13c1b16a2985cc7a> fixes
hopefully the issue in the current CP2K development version.
Best regards
Matthias
On Tuesday, April 25, 2023 at 6:18:48 PM UTC+2 Krack Matthias wrote:
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.
Best
Matthias
*From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Andres
Ortega <oandr... at gmail.com>
*Date: *Tuesday, 25 April 2023 at 15:58
*To: *cp... at googlegroups.com <cp... at googlegroups.com>
*Subject: *Re: [CP2K:18718] modification of CELL_ parameters
Dear Matthias ,
Thank you again for the fast reply ,
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
best
Andres
El mar, 25 abr 2023 a la(s) 15:50, Krack Matthias (matthia... at psi.ch)
escribió:
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
*From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Andres
Ortega <oandr... at gmail.com>
*Date: *Tuesday, 25 April 2023 at 14:42
*To: *cp... at googlegroups.com <cp... at googlegroups.com>
*Subject: *Re: [CP2K:18716] modification of CELL_ parameters
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 (matthia... 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: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Andres
Ortega <oandr... at gmail.com>
*Date: *Tuesday, 25 April 2023 at 14:28
*To: *cp... at googlegroups.com <cp... 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 (matthia... 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: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Andres
Ortega <oandr... at gmail.com>
*Date: *Tuesday, 25 April 2023 at 09:11
*To: *cp... at googlegroups.com <cp... 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 (matthia... at psi.ch)
escribió:
You can try to drop the keyword FORMAT DCD_ALIGNED_CELL or use just FORMAT
DCD instead.
*Von:* cp... at googlegroups.com <cp... at googlegroups.com> *Im Auftrag von *
oandr... at gmail.com
*Gesendet:* Montag, 24. April 2023 19:16
*An:* cp2k <cp... 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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