[CP2K-user] [CP2K:13327] SCCS Solvation Model Implementation - Molecule Radii Explodes
Dev Rana
dev.... at gmail.com
Wed Jun 3 14:15:12 UTC 2020
Hi Matthias,
Thank you for your help!
I was able to go to 200 without it crashing. My rationale for going above
100+ is that in the COSMO model the dielectric constant has a range that
goes towards infinity because of metals. A dielectric constant of 80, is
good for water but does not accurately represent an infinity model which
COSMO does for metals. But I'm pushing forward with the capabilities that
we have with CP2K, as I do not have access to the COSMO model.
Best Regards,
Dev
On Monday, May 18, 2020 at 2:52:54 AM UTC-4, Matthias Krack wrote:
>
> Hi Dev
>
>
>
> Never tried such large dielectric constants of 100-1000. Values much
> larger than 80 for a solvent seem to me unusual.
>
>
>
> Matthias
>
>
>
> *From:* c... at googlegroups.com <javascript:> <c... at googlegroups.com
> <javascript:>> *On Behalf Of *Dev Rana
> *Sent:* Sonntag, 17. Mai 2020 18:02
> *To:* cp2k <c... at googlegroups.com <javascript:>>
> *Subject:* Re: [CP2K:13327] SCCS Solvation Model Implementation -
> Molecule Radii Explodes
>
>
>
> 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 <c... at googlegroups.com> *On Behalf Of *Dev
> Rana
> *Sent:* Freitag, 15. Mai 2020 17:47
> *To:* cp2k <c... 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 <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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