[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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