[CP2K-user] [CP2K:13314] SCCS Solvation Model Implementation - Molecule Radii Explodes
Dev Rana
dev.... at gmail.com
Sun May 17 16:02:21 UTC 2020
Hi Matthias,
Thank you so much! This worked. However, when I go beyond a dieletric
constant of 300 i.e. 300, 400, 500, 1000+, with no other changes to the
input file. The convergence starts to go beyond 1 again. Do you have a
reference that might help me understand what input parameters I should be
using to offset my changing conditions? I'm going to try and print a cube
file as you suggested and visualize it in VMD, I'm assuming with the newer
higher dieletric constants the surface might be too close to the molecule
and I will have to change my rho min/max to adjust for it. however I'm not
sure by how much and I hate to keep troubling you.
Best Regards,
Dev
On Friday, May 15, 2020 at 1:16:45 PM UTC-4, Matthias Krack wrote:
>
> 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:* c... at googlegroups.com <javascript:> <c... at googlegroups.com
> <javascript:>> *On Behalf Of *Dev Rana
> *Sent:* Freitag, 15. Mai 2020 17:47
> *To:* cp2k <c... at googlegroups.com <javascript:>>
> *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 <c... at googlegroups.com> *On Behalf Of *Dev
> Rana
> *Sent:* Donnerstag, 14. Mai 2020 00:29
> *To:* cp2k <c... at googlegroups.com>
> *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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