SCF, MD run-time verses atomic species.
Simiam Ghan
simia... at gmail.com
Fri Jul 1 11:38:47 UTC 2016
Dear all,
I am running NVT MD with Quickstep on a box of water with 64 molecules.
If I replace a water molecule with a KCl ion pair, i observe that the MD
and SCF step times more than double on my setup. (MD from ~20 sec to ~46
sec). SCF iterations are converging (except the very first MD step) in
around 30 steps in both cases but each SCF now takes over twice as long as
before. Is there an explanation of why such a 'small' change in system
could double the run time? Is KCl really so heavy to calculate compared to
H2O? The number of electrons in the system increases by 8, from 512 to
520. Below my KCl input file.
Greetings,
Simiam
&GLOBAL
PROJECT H2O_KCl
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep ! GPW method.
&SUBSYS ! A subsystem: coordinates,
topology, molecules and cell.
&CELL ! Supercell setup.
ABC [angstrom] 12.414 12.414 12.414 ! Using 64 H2O molecules, we thus
get a density of 1g/cm^3.
PERIODIC XYZ ! Use PBC in all dimensions.
&END CELL
&COORD
UNIT angstrom
H -0.567712 -0.469646 -0.645913
H 0.626116 -0.687796 0.308193
O 0 0 0
(...)
K 2.1035 2.1035 4.2735
Cl 4.1035 4.1035 2.6035 ###
H 3.73881 3.10388 5.46104
H 3.65742 2.89924 6.989
O 3.1035 3.1035 6.207
(...)
&END COORD
&KIND O
BASIS_SET DZVP-MOLOPT-GTH-q6
POTENTIAL GTH-PBE-q6
&END KIND
&KIND H
BASIS_SET DZVP-MOLOPT-GTH-q1
POTENTIAL GTH-PBE-q1
&END KIND
&KIND K
BASIS_SET DZVP-MOLOPT-SR-GTH-q9
POTENTIAL GTH-PBE-q9
&END KIND
&KIND Cl
BASIS_SET DZVP-MOLOPT-GTH-q7
POTENTIAL GTH-PBE-q7
&END KIND
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
! SPIN_POLARIZED ! Do spin-polarized calculation
&POISSON
PERIODIC XYZ
&END POISSON
&QS
METHOD GPW
EPS_DEFAULT 1.0E-10 ! Set various epsilons for QS to values that
will lead
! to energy correct up to 1e-10.
&END QS
&MGRID
CUTOFF 400 ! This is Ecut of eq. 39 in VandeVondele (2005), i.e.,
plane-wave cutoff
! that determines size of finest grid (see caption of Fig. 1).
Cutoffs for
! the subsequent, coarser grid levels are given by eq. 39.
NGRIDS 4 ! This is N of eq. 39 in VandeVondele (2005), i.e.,
number of grids used.
REL_CUTOFF 40 ! This controls the grid level onto which Gaussians
will be mapped.
&END MGRID
&XC
&XC_FUNCTIONAL
&PBE
PARAMETRIZATION ORIG
&END PBE
&END XC_FUNCTIONAL
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
CALCULATE_C9_TERM .TRUE.
PARAMETER_FILE_NAME dftd3.dat
R_CUTOFF 15.0
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&END XC
&SCF
SCF_GUESS RESTART ! Use data from previous run as initial guess for
wavefunction.
EPS_SCF 1.0E-6 ! Threshold for converged total energy.
MAX_SCF 300 ! Maximum number of SCF iterations performed.
&OT
PRECONDITIONER NONE ! This should be stable with respect to the
"Cholesky errors"
&END OT
&PRINT
&RESTART ON
BACKUP_COPIES 1
&EACH
MD 1
&END EACH
ADD_LAST NUMERIC
&END RESTART
&END PRINT
&END SCF
&PRINT
&E_DENSITY_CUBE
STRIDE 1 1 1
&EACH
MD 99999999
&END EACH
ADD_LAST NUMERIC
&END E_DENSITY_CUBE
&PDOS
COMPONENTS .FALSE.
NLUMO = -1
FILENAME dosfile
LOG_PRINT_KEY TRUE
&EACH
MD 99999999
&END EACH
ADD_LAST NUMERIC
&END PDOS
&END PRINT
&END DFT
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NVT
STEPS 10000
TEMPERATURE 300.0 ! K
TIMESTEP 0.5 ! fs
&THERMOSTAT
REGION GLOBAL
TYPE NOSE
&NOSE
LENGTH 3 ! Length of Nose-Hoover chain
TIMECON 20.0 ! Period of typical vibrational motion in system in fs
&END NOSE
&END THERMOSTAT
&END MD
&PRINT
&RESTART
&EACH
MD 1
&END EACH
ADD_LAST NUMERIC
&END RESTART
&TRAJECTORY ON
ADD_LAST NUMERIC
FILENAME trajectory
&END TRAJECTORY
&END PRINT
&END MOTION
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