[CP2K-user] [CP2K:18711] modification of CELL_ parameters
Krack Matthias
matthias.krack at psi.ch
Tue Apr 25 12:16:41 UTC 2023
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<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 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/ZRAP278MB082756609080A0E18686BE9FF4649%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230425/9c8820f9/attachment-0001.htm>
More information about the CP2K-user
mailing list