[CP2K-user] [CP2K:18701] modification of CELL_ parameters
Krack Matthias
matthias.krack at psi.ch
Mon Apr 24 19:21:40 UTC 2023
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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