[CP2K-user] [CP2K:18717] modification of CELL_ parameters
Krack Matthias
matthias.krack at psi.ch
Tue Apr 25 13:50:43 UTC 2023
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: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Andres Ortega <oandresg15 at gmail.com>
Date: Tuesday, 25 April 2023 at 14:42
To: cp2k at googlegroups.com <cp2k 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 (matthias.krack at psi.ch<mailto: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<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Andres Ortega <oandresg15 at gmail.com<mailto:oandresg15 at gmail.com>>
Date: Tuesday, 25 April 2023 at 14:28
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto: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<mailto: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<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> on behalf of Andres Ortega <oandresg15 at gmail.com<mailto:oandresg15 at gmail.com>>
Date: Tuesday, 25 April 2023 at 09:11
To: cp2k at googlegroups.com<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto: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<mailto: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<mailto:cp2k at googlegroups.com> <cp2k at googlegroups.com<mailto:cp2k at googlegroups.com>> Im Auftrag von oandr... at gmail.com<mailto:oandr... at gmail.com>
Gesendet: Montag, 24. April 2023 19:16
An: cp2k <cp2k at googlegroups.com<mailto: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<http://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<mailto:cp... at googlegroups.com> <cp... at googlegroups.com<mailto:cp... at googlegroups.com>> Im Auftrag von oandr... at gmail.com<mailto:oandr... at gmail.com>
Gesendet: Montag, 24. April 2023 17:30
An: cp2k <cp... at googlegroups.com<mailto: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<mailto:cp... at googlegroups.com> <cp... at googlegroups.com<mailto:cp... at googlegroups.com>> on behalf of oandr... at gmail.com<mailto:oandr... at gmail.com> <oandr... at gmail.com<mailto:oandr... at gmail.com>>
Date: Monday, 24 April 2023 at 16:56
To: cp2k <cp... at googlegroups.com<mailto: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<mailto:cp... at googlegroups.com> <cp... at googlegroups.com<mailto:cp... at googlegroups.com>> on behalf of oandr... at gmail.com<mailto:oandr... at gmail.com> <oandr... at gmail.com<mailto:oandr... at gmail.com>>
Date: Monday, 24 April 2023 at 16:33
To: cp2k <cp... at googlegroups.com<mailto: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<mailto:cp2k%2Buns... 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<mailto:cp2k%2Buns... 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<mailto:cp2k%2Buns... 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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<https://groups.google.com/d/msgid/cp2k/CAME5veBt_V%2BzD-63LGTQ2kx0HN%2BK-AGNZHS-ZNstmRYy%2BZ%2BaGw%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/ZRAP278MB0827789413C8E807A11FD046F4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230425/03a1bbc7/attachment-0001.htm>
More information about the CP2K-user
mailing list