?BUG in test suite JDFTx 0.99.alpha (svn revision 1091)
Joint Density Functional Theory
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Possibly I have found a bug in test suite.
When running make test jdftx passes only one of two tests.
As I have found, jdftx complains for command pcm-variant SG14NL in file
/path-to-jdftx/testsuite/moleculeSolvation/CANDLE.in.
Jdftx says pcm-variant should be one of the following:
CANDLE GLSSA13 LA12 PRA05 SGA13
I have changed it to CANDLE (I'm not sure it is a good choise) and ran 'make test' again.
changed contents of CANDLE.in
include ${SRCDIR}/common.in
include common.ionpos
fluid LinearPCM
pcm-variant CANDLE
Some time later jdftx finished work at CANDLE.in with error
'FAILED: error running CANDLE' (file summary) and came to SaLSA.in.
I also post the contents of changed CANDLE.out. May be it will be helpful.
With best wishes, Igor.
** JDFTx 0.99.alpha (svn revision 1091) The playground for joint density functional theory ***
Start date and time: Thu Feb 5 15:29:16 2015
Running on hosts (process indices): localhost ( 0 )
Executable /src/jdftx/build/jdftx with command-line: -i /src/jdftx/testsuite/moleculeSolvation/CANDLE.in -d -o CANDLE.out
Maximum cpu threads by process: 2
Run totals: 1 processes, 2 threads, 0 GPUs
Input parsed successfully to the following command list (including defaults):
basis kpoint-dependent
coords-type cartesian
core-overlap-check vector
coulomb-interaction Isolated
coulomb-truncation-embed 0 0 0
davidson-band-ratio 1.1
dump End State
dump-name common.$VAR
elec-cutoff 20 100
elec-eigen-algo Davidson
elec-ex-corr gga-PBE
electronic-minimize \
dirUpdateScheme PolakRibiere \
linminMethod DirUpdateRecommended \
nIterations 100 \
history 15 \
knormThreshold 0 \
energyDiffThreshold 1e-08 \
nEnergyDiff 2 \
alphaTstart 1 \
alphaTmin 1e-10 \
updateTestStepSize yes \
alphaTreduceFactor 0.1 \
alphaTincreaseFactor 3 \
nAlphaAdjustMax 3 \
wolfeEnergy 0.0001 \
wolfeGradient 0.9 \
fdTest no
electronic-scf \
nIterations 50 \
nEigSteps 2 \
energyDiffThreshold 1e-08 \
eigDiffThreshold 1e-08 \
residualThreshold 1e-07 \
mixedVariable Potential \
mixFraction 0.5 \
mixFractionMag 1.5 \
qKerker 0.8 \
qMetric 0.8 \
history 10
exchange-regularization None
fluid LinearPCM 298.000000 1.013250
fluid-ex-corr (null) lda-PZ
fluid-gummel-loop 10 1.000000e-05
fluid-minimize \
dirUpdateScheme PolakRibiere \
linminMethod DirUpdateRecommended \
nIterations 400 \
history 15 \
knormThreshold 1e-11 \
energyDiffThreshold 0 \
nEnergyDiff 2 \
alphaTstart 1 \
alphaTmin 1e-10 \
updateTestStepSize yes \
alphaTreduceFactor 0.1 \
alphaTincreaseFactor 3 \
nAlphaAdjustMax 6 \
wolfeEnergy 0.0001 \
wolfeGradient 0.9 \
fdTest no
fluid-site-params
fluid-solvent H2O 55.338 ScalarEOS \
epsBulk 78.4 \
pMol 0.92466 \
epsInf 1.77 \
Pvap 1.06736e-10 \
sigmaBulk 4.62e-05 \
Rvdw 2.61727 \
Res 1.42
forces-output-coords Positions
initial-state common.$VAR
inverseKohnSham-minimize \
dirUpdateScheme PolakRibiere \
linminMethod DirUpdateRecommended \
nIterations 100 \
history 15 \
knormThreshold 0 \
energyDiffThreshold 1e-08 \
nEnergyDiff 2 \
alphaTstart 1 \
alphaTmin 1e-10 \
updateTestStepSize yes \
alphaTreduceFactor 0.1 \
alphaTincreaseFactor 3 \
nAlphaAdjustMax 3 \
wolfeEnergy 0.0001 \
wolfeGradient 0.9 \
fdTest no
ion O 0.000000000000000 -0.011759668560055 0.000000000000000 1
ion H 0.000000000000000 1.126048517572887 1.451071073403969 1
ion H 0.000000000000000 1.126048517572887 -1.451071073403970 1
ion-species GBRV/$ID_pbe_v1.2.uspp
ion-species GBRV/$ID_pbe_v1.uspp
ion-width Ecut
ionic-minimize \
dirUpdateScheme L-BFGS \
linminMethod DirUpdateRecommended \
nIterations 0 \
history 15 \
knormThreshold 0.0001 \
energyDiffThreshold 1e-06 \
nEnergyDiff 2 \
alphaTstart 1 \
alphaTmin 1e-10 \
updateTestStepSize yes \
alphaTreduceFactor 0.1 \
alphaTincreaseFactor 3 \
nAlphaAdjustMax 3 \
wolfeEnergy 0.0001 \
wolfeGradient 0.9 \
fdTest no
kpoint 0.000000000000 0.000000000000 0.000000000000 1.00000000000000
kpoint-folding 1 1 1
latt-move-scale 1 1 1
latt-scale 1 1 1
lattice Cubic 15
lattice-minimize \
dirUpdateScheme L-BFGS \
linminMethod DirUpdateRecommended \
nIterations 0 \
history 15 \
knormThreshold 0 \
energyDiffThreshold 1e-06 \
nEnergyDiff 2 \
alphaTstart 1 \
alphaTmin 1e-10 \
updateTestStepSize yes \
alphaTreduceFactor 0.1 \
alphaTincreaseFactor 3 \
nAlphaAdjustMax 3 \
wolfeEnergy 0.0001 \
wolfeGradient 0.9 \
fdTest no
lcao-params -1 1e-06 0.001
pcm-variant CANDLE
reorthogonalize-orbitals 20 1.5
spintype no-spin
subspace-rotation-factor 30
symmetries automatic no
---------- Setting up symmetries ----------
Searching for point group symmetries:
48 symmetries of the bravais lattice
reduced to 4 symmetries with basis
---------- Initializing the Grid ----------
R =
[ 15 0 0 ]
[ 0 15 0 ]
[ 0 0 15 ]
unit cell volume = 3375
G =
[ 0.418879 0 0 ]
[ 0 0.418879 0 ]
[ 0 0 0.418879 ]
Minimum fftbox size, Smin = [ 64 64 64 ]
Chosen fftbox size, S = [ 64 64 64 ]
---------- Initializing tighter grid for wavefunction operations ----------
R =
[ 15 0 0 ]
[ 0 15 0 ]
[ 0 0 15 ]
unit cell volume = 3375
G =
[ 0.418879 0 0 ]
[ 0 0.418879 0 ]
[ 0 0 0.418879 ]
Minimum fftbox size, Smin = [ 60 60 60 ]
Chosen fftbox size, S = [ 60 60 60 ]
---------- Exchange Correlation functional ----------
Initalized PBE GGA exchange.
Initalized PBE GGA correlation.
---------- Setting up pseudopotentials ----------
Width of ionic core gaussian charges (only for fluid interactions / plotting) set to 0.397384
Reading pseudopotential file '/src/jdftx/build/pseudopotentials/GBRV/o_pbe_v1.2.uspp':
Title: O. Created by USPP 7.3.6 on 3-2-2014
Reference state energy: -15.894388. 6 valence electrons in orbitals:
|200> occupation: 2 eigenvalue: -0.878823
|210> occupation: 4 eigenvalue: -0.332131
lMax: 2 lLocal: 2 QijEcut: 6
5 projectors sampled on a log grid with 511 points:
l: 0 eig: -0.878823 rCut: 1.25
l: 0 eig: 0.000000 rCut: 1.25
l: 1 eig: -0.332132 rCut: 1.25
l: 1 eig: 0.000000 rCut: 1.25
l: 2 eig: 1.000000 rCut: 1.25
Partial core density with radius 0.7
Transforming core density to a uniform radial grid of dG=0.02 with 1166 points.
Transforming local potential to a uniform radial grid of dG=0.02 with 1166 points.
Transforming nonlocal projectors to a uniform radial grid of dG=0.02 with 432 points.
Transforming density augmentations to a uniform radial grid of dG=0.02 with 1166 points.
Transforming atomic orbitals to a uniform radial grid of dG=0.02 with 432 points.
Transforming overlap'd orbitals to a uniform radial grid of dG=0.02 with 432 points.
Core radius for overlap checks: 1.25 bohrs.
Reading pseudopotential file '/src/jdftx/build/pseudopotentials/GBRV/h_pbe_v1.uspp':
Title: H. Created by USPP 7.3.6 on 14-9-2013
Reference state energy: -0.458802. 1 valence electrons in orbitals:
|100> occupation: 1 eigenvalue: -0.238596
lMax: 0 lLocal: 1 QijEcut: 5
2 projectors sampled on a log grid with 395 points:
l: 0 eig: -0.238595 rCut: 0.9
l: 0 eig: 0.450000 rCut: 0.9
Transforming local potential to a uniform radial grid of dG=0.02 with 1166 points.
Transforming nonlocal projectors to a uniform radial grid of dG=0.02 with 432 points.
Transforming density augmentations to a uniform radial grid of dG=0.02 with 1166 points.
Transforming atomic orbitals to a uniform radial grid of dG=0.02 with 432 points.
Transforming overlap'd orbitals to a uniform radial grid of dG=0.02 with 432 points.
Core radius for overlap checks: 0.90 bohrs.
Folded 1 k-points by 1x1x1 to 1 k-points.
---------- Setting up k-points, bands, fillings ----------
No reducable k-points.
Computing the number of bands and number of electrons
Calculating initial fillings.
nElectrons: 8.000000 nBands: 4 nStates: 1
----- Setting up reduced wavefunction bases (one per k-point) -----
average nbasis = 14363.000 , ideal nbasis = 14418.257
---------- Setting up coulomb interaction ----------
Fluid mode embedding: using embedded box, but periodic Coulomb kernel.
(Fluid response is responsible for (approximate) separation between periodic images.)
Setting up double-sized grid for truncated Coulomb potentials:
R =
[ 30 0 0 ]
[ 0 30 0 ]
[ 0 0 30 ]
unit cell volume = 27000
G =
[ 0.20944 0 0 ]
[ 0 0.20944 0 ]
[ 0 0 0.20944 ]
Chosen fftbox size, S = [ 128 128 128 ]
Integer grid location selected as the embedding center:
Grid: [ 0 0 0 ]
Lattice: [ 0 0 0 ]
Cartesian: [ 0 0 0 ]
Constructing Wigner-Seitz cell: 6 faces (6 quadrilaterals, 0 hexagons)
Range-separation parameter for embedded mesh potentials due to point charges: 0.610753 bohrs.
Initializing van der Waals corrections
NOTE: vdW corrections apply only for interactions with fluid.
O: C6: 12.14 Eh-a0^6 R0: 2.536 a0
H: C6: 2.43 Eh-a0^6 R0: 1.892 a0
---------- Setting up ewald sum ----------
Optimum gaussian width for ewald sums = 9.965776 bohr.
Real space sum over 1331 unit cells with max indices [ 5 5 5 ]
Reciprocal space sum over 2197 terms with max indices [ 6 6 6 ]
---------- Allocating electronic variables ----------
Initializing wave functions: reading from 'common.wfns'
----- createFluidSolver() ----- (Fluid-side solver setup)
Initializing fluid molecule 'H2O'
Initializing site 'O'
Electron density: proportional to exp(-r/0.36935)erfc((r-0.51523)/0.36823) with norm 6.826
Charge density: gaussian nuclear width 0.478731 with net site charge 0.826
Polarizability: cuspless exponential with width 0.32 and norm 3.73
Hard sphere radius: 2.57003 bohrs
Positions in reference frame:
[ +0.000000 +0.000000 +0.000000 ]
Initializing site 'H'
Electron density: proportional to exp(-r/0.34641)erfc((r-0)/0.390882) with norm 0.587
Charge density: gaussian nuclear width 0.377945 with net site charge -0.413
Polarizability: cuspless exponential with width 0.39 and norm 3.3
Positions in reference frame:
[ +0.000000 -1.441945 +1.122523 ]
[ +0.000000 +1.441945 +1.122523 ]
Net charge: 0 dipole magnitude: 0.927204
Initializing spherical shell mfKernel with radius 2.61727 Bohr
deltaS corrections:
site 'O': -7.54299
site 'H': -6.83917
Correction to mu due to finite nuclear width = -0.000293985
Cavity determined by nc: 0.00142 and sigma: 0.707107
Nonlocal vdW cavity from gaussian model electron density with norm = 8 and sigma = 0.993594 bohr
Charge asymmetry in cavity with sensitivity pCavity = 36.5 e-bohr/Eh
Electrostatic cavity expanded by eta = 1.46 bohrs
Weighted density cavitation model constrained by Nbulk: 0.0049383 bohr^-3, Pvap: 3.14029 kPa, Rvdw: 2.61727 bohr and sigmaBulk: 4.62e-05 Eh/bohr^2 at T: 298 K.
Weighted density dispersion model using vdW pair potentials with single solvent site with sqrtC6eff: 0.77 SI.
Reading fluid state from 'common.fluidState'
---- Citations for features of the code used in this run ----
Software package:
R. Sundararaman, K. Letchworth-Weaver and T.A. Arias, JDFTx, available from http://jdftx.sourceforge.net (2012)
Algebraic framework:
S. Ismail-Beigi and T.A. Arias, Computer Physics Communications 128, 1 (2000)
gga-PBE exchange-correlation functional:
J.P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996)
Wigner-Seitz truncated coulomb interaction:
R. Sundararaman and T.A. Arias, Phys. Rev. B 87, 165122 (2013)
Van der Waals correction pair-potentials:
S. Grimme, J. Comput. Chem. 27, 1787 (2006)
Framework of Joint Density Functional Theory:
S.A. Petrosyan SA, A.A. Rigos and T.A. Arias, J Phys Chem B. 109, 15436 (2005)
Charge-asymmetric nonlocally-determined local-electric (CANDLE) solvation model:
R. Sundararaman and W.A. Goddard III, J. Chem. Phys. 142, accepted (2015)
Total energy minimization:
T.A. Arias, M.C. Payne and J.D. Joannopoulos, Phys. Rev. Lett. 69, 1077 (1992)
This list may not be complete. Please suggest additional citations and report
any other bugs by creating a ticket at https://sourceforge.net/p/jdftx/tickets
-------- Electronic minimization -----------
Will mix electronic potential at each iteration.
Linear fluid (dielectric constant: 78.4) occupying 0.977453 of unit cell: Completed after 0 iterations.
Linear fluid (dielectric constant: 78.4) occupying 0.977737 of unit cell: Completed after 9 iterations.
SCF: Cycle: 0 Etot: -17.281211411427435 dE: -2.909e-04 |deigs|: 4.550e-05 |Residual|: 1.426e-03
Linear fluid (dielectric constant: 78.4) occupying 0.977711 of unit cell: Completed after 7 iterations.
SCF: Cycle: 1 Etot: -17.281236920402669 dE: -2.551e-05 |deigs|: 1.973e-03 |Residual|: 7.669e-04
Linear fluid (dielectric constant: 78.4) occupying 0.977712 of unit cell: Completed after 2 iterations.
SCF: Cycle: 2 Etot: -17.281237596195869 dE: -6.758e-07 |deigs|: 3.769e-04 |Residual|: 1.792e-04
Linear fluid (dielectric constant: 78.4) occupying 0.977714 of unit cell: Completed after 0 iterations.
SCF: Cycle: 3 Etot: -17.281237739601522 dE: -1.434e-07 |deigs|: 1.255e-04 |Residual|: 6.386e-05
Linear fluid (dielectric constant: 78.4) occupying 0.977715 of unit cell: Completed after 2 iterations.
SCF: Cycle: 4 Etot: -17.281237729339150 dE: 1.026e-08 |deigs|: 1.792e-05 |Residual|: 3.524e-05
Linear fluid (dielectric constant: 78.4) occupying 0.977715 of unit cell: Completed after 0 iterations.
SCF: Cycle: 5 Etot: -17.281237736443032 dE: -7.104e-09 |deigs|: 3.550e-05 |Residual|: 1.335e-05
Linear fluid (dielectric constant: 78.4) occupying 0.977715 of unit cell: Completed after 0 iterations.
SCF: Cycle: 6 Etot: -17.281237737434800 dE: -9.918e-10 |deigs|: 1.077e-05 |Residual|: 5.404e-06
SCF: Converged (|Delta E|<1.000000e-08 for 2 iters).
Ionic positions in cartesian coordinates:
ion O 0.000000000000000 -0.011759668560055 0.000000000000000 1
ion H 0.000000000000000 1.126048517572887 1.451071073403969 1
ion H 0.000000000000000 1.126048517572887 -1.451071073403970 1
Forces in Cartesian coordinates:
force O 0.000000000000000 -0.002788566884640 0.000000000000000 1
force H 0.000000000000000 0.001477189114913 0.002391887388614 1
force H 0.000000000000000 0.001477189114913 -0.002391887388614 1
Energy components:
A_diel = -0.0166669582223318
Eewald = 3.8296549448260815
EH = 18.4010010476681316
Eloc = -45.8373577903111808
Enl = 2.2518749204359190
Exc = -4.3558292218590262
Exc_core = 0.0650395011027160
KE = 8.3810458189248855
IonicMinimize: Iter: 0 Etot: -17.281237737434800 |grad|_K: 1.619e-03
IonicMinimize: None of the convergence criteria satisfied after 0 iterations.
--- Lowdin population analysis ---
oxidation-state O -0.802
oxidation-state H +0.460 +0.460
Dumping 'common.wfns' ... done
Dumping 'common.fluidState' ... done
End date and time: Thu Feb 5 15:33:17 2015 (Duration: 0-0:04:00.47)
Done!
Hi Igor,
Thanks for catching this bug. I recently updated the SG14NL internal code name for a solvation model to its published name, CANDLE, but I forgot to change the testsuite to reflect that.
Your change was exactly what needed to be done, thanks for catching that!
Fixed in latest svn ...
Cheers,
Shankar
PS: Next time, if you find bugs, please report them using the ticketing interface on this site. The bug report / ticket emails sound a little bit more urgent, so they will likely get addressed even quicker!
Dear Shankar.
Thanks for such fast bug correction.
Today I have updated my jdftx files and after about 3 hours of computation it have successfully passed both tests. So the bug solved.
[user@localhost testsuite]$ make test
Running tests...
Test project /src/jdftx/build/testsuite
Start 1: vibrations
1/2 Test #1: vibrations ....................... Passed 133.02 sec
Start 2: moleculeSolvation
2/2 Test #2: moleculeSolvation ................ Passed 8902.91 sec
100% tests passed, 0 tests failed out of 2
Total Test time (real) = 9036.08 sec