Add poisson-boltzmann to the SCRF #450
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #450 +/- ##
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+ Coverage 70.31% 70.54% +0.22%
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Files 190 195 +5
Lines 15308 15446 +138
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+ Hits 10764 10896 +132
- Misses 4544 4550 +6 ☔ View full report in Codecov by Sentry. |
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Add additional input for pb equation, all other tests passing, error with ion_radius variable add a harcoded to pass test for pb fix json error mid debug commit, the run_pb block produces different convergence despite being identical to the standard
Faster pb and lpb solver and proper test
Co-authored-by: Roberto Di Remigio Eikås <[email protected]>
…energy outputs of GPESolver was wrong
… 1.0e-3 prec after all
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| from .helpers import (parse_wf_method, write_rsp_calc, write_scf_fock, | ||
| write_scf_guess, write_scf_plot, write_scf_properties, | ||
| write_scf_solver) | ||
| from .periodictable import PeriodicTable as PT | ||
| from .periodictable import PeriodicTableByZ as PT_Z |
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did black and isort do this?
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I think, I did not edit this part of the file as far as I remember
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| DHScreening dhscreening(cavity_ion, kappa_o, kformulation); // this is now deciding the pb formulation, but it really shouldn't, the formulation here is for the DHScreening where we | ||
| // have 4 different parametrizations, not all implemented yet. | ||
| dhscreening.printParameters(); |
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these lines are repeated between PB and LPB. Can they be moved outside the if statements? Also, the comment doesn't seem to be relevant?
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* add poisson-boltzmann to the SCRF Add additional input for pb equation, all other tests passing, error with ion_radius variable add a harcoded to pass test for pb fix json error mid debug commit, the run_pb block produces different convergence despite being identical to the standard * PB working as intended (within a reasonable domain) Faster pb and lpb solver and proper test * add test for linearized pb * Rename SCRF to GPESolver in preparation for refactor. Use inheritance to implement PBESolver and LPBESolver Rename GPESolver::solveEquation to iterateEquation * Add new test references to pb and lpb solvent Update tests and Fix correct solvers running Add proper capitalisation to Debye-Huckel Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Remove unused setters in Cavity Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Pass parameters by const reference Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * fix tests for pb solver * Add documentation to the solvent classes * Add DHScreening to the StepFunction hierarchy * Reorder includes * Update python/template.yml Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * Update python/mrchem/api.py Co-authored-by: Roberto Di Remigio Eikås <[email protected]> * Post-rebase fixes * Formatting * debugging * more debugging * even more debugging * BUGFIX in PB_solver.cpp: rho_el was not zero and the ordering of the energy outputs of GPESolver was wrong * real BUGFIX: same as above but relax the thrs, we are running it with 1.0e-3 prec after all * attempt to fix test error * update python version for tests * update python version for singularity images * update python version for circleci config * Use newer base image with CircleCI * update minimum python requirements in installation.rst * create cavity even if we are running pb or lpb * use proper dividor * Be more consistent * Update input for PCM * rebase fix * rebase fix * all tests passing and PB_solver is correct --------- Co-authored-by: Roberto Di Remigio Eikås <[email protected]> Co-authored-by: Roberto Di Remigio Eikås <[email protected]>
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Here I have added the alternative to solve the 1:1 Poisson-Boltzmann equation as a part of the SCRF procedure. Right now the parameters are hardcoded but will soon make them user-determined.