[CP2K-user] [CP2K:13314] SCCS Solvation Model Implementation - Molecule Radii Explodes

Krack Matthias (PSI) matthi... at psi.ch
Fri May 15 17:16:40 UTC 2020
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Hi Dev

The attached revised input converged after a few steps using SCCS with a dielectric constant of 80. I changed the method and adapted the rho_min and rho_max values which define the surface of the cavity and thus they are system dependent to some extent. If rho_max is chosen too large for instance, the surface might be too close to the molecule. It is often helpful to plot the cavity, e.g. with VMD, using a cube file dump of the dielectric function<https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/DFT/PRINT/SCCS/DIELECTRIC_FUNCTION.html>.
HTH

Matthias

From: cp... at googlegroups.com <cp... at googlegroups.com> On Behalf Of Dev Rana
Sent: Freitag, 15. Mai 2020 17:47
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:13314] SCCS Solvation Model Implementation - Molecule Radii Explodes

Hi Matthias,

Thank you again for all your help. I went a bit beyond your suggestion and changed EPS_SCF to 1E-12 and changed cell size to 10 x 10 x 10 A3. To answer your questions:

1.) I was able to run GEO_OPT without SCCS and the simulation completed.
2.) I was able to converge and complete a SCCS GEO_OPT simulation with a dielectric constant of 1.

I then took the dieletric constant back up to 80 (with no other changes), and the convergence fails - in fact the convergence Hartree's are trending greater than 1.

I'm going to do a small ramp up in dielectric constant: 2, 5, 10, etc. To see what happens. But I should be able to use 80+ as the dielectric constant without issues.

What do you think? Am I missing something?

Again input, output, and XYZ attached.

&GLOBAL
 PROJECT SCCS
 RUN_TYPE geo_opt
 PRINT_LEVEL medium
 SAVE_MEM TRUE
&END GLOBAL


&FORCE_EVAL
 METHOD Quickstep
 # STRESS_TENSOR analytical
 &DFT
    BASIS_SET_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/BASIS_MOLOPT
    POTENTIAL_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/POTENTIAL

  &QS
    METHOD GPW
    EPS_DEFAULT 1.0E-12
    EXTRAPOLATION ASPC
  &END QS

  &MGRID
    NGRIDS 5
    CUTOFF [Ry] 600
  &END MGRID

  &SCCS
   ALPHA [N*m^-1] 0.0
   BETA [GPa] 0.0
   DELTA_RHO 2.0E-5
   DERIVATIVE_METHOD fft
   DIELECTRIC_CONSTANT 80
   GAMMA 0.0
   EPS_SCCS 1.0E-12
!   EPS_SCF 1.0E-10
   MAX_ITER 100
!   METHOD Andreussi
   METHOD Fattebert-Gygi
   MIXING 0.6
!   &ANDREUSSI
!    RHO_MAX 0.008
!    RHO_MIN 0.00015
!   &END ANDREUSSI
   &FATTEBERT-GYGI
    BETA 1.3
    RHO_ZERO 0.00078
   &END FATTEBERT-GYGI
  &END SCCS

  &SCF
    SCF_GUESS ATOMIC
    MAX_SCF 300
    EPS_SCF 1.0E-12
    &DIAGONALIZATION ON
      ALGORITHM STANDARD
    &END DIAGONALIZATION
!    &OT on
!     MINIMIZER DIIS
!     PRECONDITIONER FULL_ALL
!     ENERGY_GAP 0.002
!    &END OT
    &OUTER_SCF
     EPS_SCF 1e-12
     MAX_SCF 30
    &END OUTER_SCF
  &END SCF

  &XC
   &XC_FUNCTIONAL PBE
   &END XC_FUNCTIONAL
  &END XC

  &PRINT
    &PDOS
      &EACH
        GEO_OPT 1
      &END EACH
      APPEND TRUE
    &END PDOS
    &SCCS ON
      &EACH
       GEO_OPT 10
      &END EACH
     &DENSITY_GRADIENT off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END DENSITY_GRADIENT
     &DIELECTRIC_FUNCTION off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END DIELECTRIC_FUNCTION
     &POLARISATION_POTENTIAL off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END POLARISATION_POTENTIAL
    &END SCCS
  &END PRINT

 &END DFT

 &SUBSYS
    &CELL
      ABC [angstrom] 10 10 10
!      PERIODIC XYZ
!      MULTIPLE_UNIT_CELL 1 1 1
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME Al4C.xyz
      COORD_FILE_FORMAT XYZ
!      MULTIPLE_UNIT_CELL 1 1 1
    &END
    &KIND C
      ELEMENT C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND Al
      ELEMENT Al
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q3
    &END KIND
 &END SUBSYS

&END FORCE_EVAL

&MOTION
 &GEO_OPT
  TYPE MINIMIZATION
  OPTIMIZER BFGS
  MAX_ITER  100
 &END GEO_OPT
 &CONSTRAINT
   &FIXED_ATOMS
     COMPONENTS_TO_FIX XYZ
     LIST 1
   &END FIXED_ATOMS
 &END CONSTRAINT
 &PRINT
  &STRUCTURE_DATA
    DISTANCE 1 2
    DISTANCE 1 3
    DISTANCE 1 4
    DISTANCE 1 5
    DISTANCE 2 3
    DISTANCE 2 4
    DISTANCE 2 5
    DISTANCE 3 4
    DISTANCE 3 5
    DISTANCE 4 5
    ANGLE 1 2 3
    ANGLE 1 2 4
    ANGLE 1 2 5
    ANGLE 1 3 2
    ANGLE 1 3 4
    ANGLE 1 3 5
    ANGLE 1 4 2
    ANGLE 1 4 3
    ANGLE 1 4 5
    ANGLE 1 5 2
    ANGLE 1 5 3
    ANGLE 1 5 4
    &EACH
      GEO_OPT 1
    &END EACH
  &END STRUCTURE_DATA
  &TRAJECTORY
    &EACH
      GEO_OPT 1
    &END EACH
  &END TRAJECTORY
  &VELOCITIES
    &EACH
      GEO_OPT 1
    &END EACH
  &END VELOCITIES
  &FORCES
    &EACH
      GEO_OPT 1
    &END EACH
  &END FORCES
  &CELL
    &EACH
      GEO_OPT 1
    &END EACH
  &END CELL
  &RESTART
    &EACH
      GEO_OPT 1
    &END EACH
  &END RESTART
 &END PRINT
&END MOTION


On Wednesday, May 13, 2020 at 8:08:47 PM UTC-4, Matthias Krack wrote:
Hi Dev

The settings in the regression tests are often physically not meaningful, since these test runs have to be completed after a few seconds.
SCCS%EPS_SCF delays the start of the inner SCCS convergence loop only for values greater zero. Otherwise that value is not considered and the inner SCCS cycle is activated immediately.
SCCS%EPS_SCCS, the convergence threshold of the inner SCCS loop for the polarization charge should be smaller (tighter) than 1.0E-6, at least 1.0E-8. As soon as the inner SCCS loop is activated, the timings for each SCF iteration step will increase significantly. Also the implicit solvent comes not for free. You can reduce the box size to save computer resources, because your system is small. Does the setup for your system CAl4 work/converge properly for a geo_opt run in gas phase, i.e. without SCCS? If that is the case then I would start with a smaller dielectric constant than 80 for the SCCS and see how the system evolves. The print level medium provides a detailed SCCS output.

HTH

Matthias

From: c... at googlegroups.com<javascript:> <c... at googlegroups.com<javascript:>> On Behalf Of Dev Rana
Sent: Donnerstag, 14. Mai 2020 00:29
To: cp2k <c... at googlegroups.com<javascript:>>
Subject: Re: [CP2K:13298] SCCS Solvation Model Implementation - Molecule Radii Explodes

I take back what I previously said. The 0th geo opt step finishes quickly with SCF steps taking 20-25s each. The 2st geo opt step does not finish and each SCF step takes 5+ minutes. Here's my input file and output for that.  I'm also running this on GPU.

What do you advise? I've attached the input output files and paste input below. The convergence values keep increases, rather than decreases. And Total Energy keep lowering.

&GLOBAL
 PROJECT SCCS
 RUN_TYPE geo_opt
 PRINT_LEVEL low
 SAVE_MEM TRUE
&END GLOBAL


&FORCE_EVAL
 METHOD Quickstep
 # STRESS_TENSOR analytical
 &DFT
    BASIS_SET_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/BASIS_MOLOPT
    POTENTIAL_FILE_NAME /shared/centos7/cp2k/cp2k-6.1.0/data/POTENTIAL

  &QS
    METHOD GPW
    EPS_DEFAULT 1.0E-12
    EXTRAPOLATION ASPC
  &END QS

  &MGRID
    NGRIDS 5
    CUTOFF [Ry] 600
  &END MGRID

  &SCCS
   ALPHA [N*m^-1] 0.0
   BETA [GPa] 0.0
   DELTA_RHO 2.0E-5
   DERIVATIVE_METHOD cd5
   DIELECTRIC_CONSTANT 80
   GAMMA [mN/m] 0.0
   EPS_SCCS 1.0E-6
   EPS_SCF 1.0E-7
   MAX_ITER 100
!   METHOD Andreussi
   METHOD Fattebert-Gygi
   MIXING 0.6
!   &ANDREUSSI
!    RHO_MAX 0.001
!    RHO_MIN 0.0001
!   &END ANDREUSSI
   &FATTEBERT-GYGI
    BETA 1.3
    RHO_ZERO 0.00078
   &END FATTEBERT-GYGI
  &END SCCS

  &SCF
    SCF_GUESS ATOMIC
    MAX_SCF 300
    EPS_SCF 1.0E-7
    &DIAGONALIZATION ON
      ALGORITHM STANDARD
    &END DIAGONALIZATION
!    &OT on
!     MINIMIZER DIIS
!     PRECONDITIONER FULL_ALL
!     ENERGY_GAP 0.002
!    &END OT
    &OUTER_SCF
     EPS_SCF 1e-7
     MAX_SCF 30
    &END OUTER_SCF
  &END SCF

  &XC
   &XC_FUNCTIONAL PBE
   &END XC_FUNCTIONAL
  &END XC

  &PRINT
    &PDOS
      &EACH
        GEO_OPT 1
      &END EACH
      APPEND TRUE
    &END PDOS
    &SCCS ON
      &EACH
       GEO_OPT 10
      &END EACH
     &DENSITY_GRADIENT off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END DENSITY_GRADIENT
     &DIELECTRIC_FUNCTION off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END DIELECTRIC_FUNCTION
     &POLARISATION_POTENTIAL off
      &EACH
       GEO_OPT 10
      &END EACH
      APPEND
     &END POLARISATION_POTENTIAL
    &END SCCS
  &END PRINT

 &END DFT

 &SUBSYS
    &CELL
      ABC [angstrom] 30 30 30
!      PERIODIC XYZ
!      MULTIPLE_UNIT_CELL 1 1 1
    &END CELL
    &TOPOLOGY
      COORD_FILE_NAME Al4C.xyz
      COORD_FILE_FORMAT XYZ
!      MULTIPLE_UNIT_CELL 1 1 1
    &END
    &KIND C
      ELEMENT C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND Al
      ELEMENT Al
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q3
    &END KIND
 &END SUBSYS

&END FORCE_EVAL

&MOTION
 &GEO_OPT
  TYPE MINIMIZATION
  OPTIMIZER BFGS
  MAX_ITER  100
 &END GEO_OPT
 &CONSTRAINT
   &FIXED_ATOMS
     COMPONENTS_TO_FIX XYZ
     LIST 1
   &END FIXED_ATOMS
 &END CONSTRAINT
 &PRINT
  &STRUCTURE_DATA
    DISTANCE 1 2
    DISTANCE 1 3
    DISTANCE 1 4
    DISTANCE 1 5
    DISTANCE 2 3
    DISTANCE 2 4
    DISTANCE 2 5
    DISTANCE 3 4
    DISTANCE 3 5
    DISTANCE 4 5
    ANGLE 1 2 3
    ANGLE 1 2 4
    ANGLE 1 2 5
    ANGLE 1 3 2
    ANGLE 1 3 4
    ANGLE 1 3 5
    ANGLE 1 4 2
    ANGLE 1 4 3
    ANGLE 1 4 5
    ANGLE 1 5 2
    ANGLE 1 5 3
    ANGLE 1 5 4
    &EACH
      GEO_OPT 1
    &END EACH
  &END STRUCTURE_DATA
  &TRAJECTORY
    &EACH
      GEO_OPT 1
    &END EACH
  &END TRAJECTORY
  &VELOCITIES
    &EACH
      GEO_OPT 1
    &END EACH
  &END VELOCITIES
  &FORCES
    &EACH
      GEO_OPT 1
    &END EACH
  &END FORCES
  &CELL
    &EACH
      GEO_OPT 1
    &END EACH
  &END CELL
  &RESTART
    &EACH
      GEO_OPT 1
    &END EACH
  &END RESTART
 &END PRINT
&END MOTION



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