[CP2K-user] [CP2K:18701] modification of CELL_ parameters

oandr...@gmail.com oandresg15 at gmail.com
Mon Apr 24 17:15:48 UTC 2023
Previous message (by thread): [CP2K-user] [CP2K:18699] modification of CELL_ parameters
Next message (by thread): [CP2K-user] [CP2K:18701] modification of CELL_ parameters
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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
>
>  
>
> -- 
> 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.
> 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.
>
> 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.
>
> 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.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/dc90830c-f529-45f7-947e-63daab1dc3c7n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230424/979fb844/attachment-0001.htm>
Previous message (by thread): [CP2K-user] [CP2K:18699] modification of CELL_ parameters
Next message (by thread): [CP2K-user] [CP2K:18701] modification of CELL_ parameters
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the CP2K-user mailing list