A fast and precise DFT wavelet code

Splined Saddle method

A fast and precise DFT wavelet code
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Contents

Introduction

The purpose of this lesson is to get familiar with running the splsad executable which is based on the paper[1]

The Input-Output Files

INPUT FILES

  • Executable Media: splsad
  • standard input files + input.splsad
  • if hybrid approach is used, ll_input.dft is also required.
  • Two input configurations: posinp.xyz and posinp2.xyz
  • anchorposinp.xyz is required for a restart run. One can prepare it manually or copy one of the anchorpoints???.xyz files of the previous run.

OUTPUT FILES

  • saddle.xyz
  • anchorpoints???.xyz
  • path???.xyz
  • nogt.??? (depricated)
  • vogt.??? (depricated)
  • fort.???? (depricated)

Overview of input.splsad

  • All input parameters are set to default.
  • The parameters can be set in any order.
  • Lines starting with # are comment.
  • To set a parameter: first the keyword as the first word and in the same line the value as the second word.
  • In case of multiple occurance of a keyword, the last occurance is used.
  • runstat new or restart. Default value: new
  • approach BFGS or SD or FIRE. Default value: SD
  • alphax standard stepsize for minimization. Default value: $0.5$
  • fmaxtol convergence criterion for maximum component of force at the saddle point. Default value: $2.0\time 10^{-4}$
  • np number of anchor points plut one. Default value: $3$
  • npneb number of movable nodes in NEB plus one. Default value: same value as np (I do not mean $3$).
  • ns2 is used to increase number of points to estimate the starting point for maximization, i.e. np+ns2. Default value: $0$
  • maxforcecall Maximum number of iterations. Default value: $100$
  • vdtol Convergence tolerance for maximization step, values between $[0.1,0.01]$ are reasonable. Default value: $0.1$
  • htol tolerance for the minimum distance between two points during maximization. Default value: $2.0\times 10^{-2}$
  • hybrid yes or no. Default value: no
  • fmaxtolneb tolerance for maximum componenet of force for NEB. Use a loose value if you want to use NEB as apreliminary run for final splined saddle calculation. Default value: $2.0\times 10^{-2}$
  • pickbestanchorpoints
  • doneb yes or no. Default value: yes if runstat is new and no if it is restart
  • docineb yes or no. Then splined saddle method is not used. Default value: no

For an example look into: input.splsad file.

Useful keywords to grep from the standard output files

The output of BigDFT is divided into four parts:

  • SPINFO: All of the parameters, which can be set in input.splsad, will be listed by greping this keyword.
  • ENDs: Prints the energies and the norms of the forces on the two end points, namely posinp.xyz and posinp2.xyz. It is useful if you want to know whether the points are minima.
  • MIN: Lists information (target function, gradient norm and gradient maximum component,...) of the iterations both in NEB and splined saddle parts. In case of NEB the target function is the summation of force norms on the movable nodes and in case of splined saddle the energy of the maximum which is presumably the energy of the saddle points when it is converged.
  • fort51: Listed information of the iterations in the maximizations parts of the splined saddle part. Two important quantities are the norm of force at the current iteration of the maximation and the curvature at the current point. Latter must be negative because it must be a maximum. If it is positive, you should not tet the program continue for long since it cannot interpolate or even describe correctly the energy along the pathway.
  • fort52: Lists the force norm and force maximum componenet at the maximum point in each iteration of the splined saddle part. Greping for MIN in the splined saddle, provides information for the gradient norm and gradient maximum component of vmax. It is more useful to have information at the saddle point.

Example I: Mg5

visualisation of the real space mesh"

This is a very simple example in which the Nitrogen atom moves from one side of the H3 plane to another. We use the hybrid approach in order to reduce significantly the computational cost.

runstat new
approach SD
alphax 20.d0
fmaxtol 3.d-3
np 3
maxforcecall 350
vdtol 1.d-1
ns2 0
htol 2.d-2
hybrid yes
npneb 2
fmaxtolneb 3.d-2

Greping for SPINFO prints the splsad parameters:

SPINFO: runstat new
SPINFO: hybrid yes
SPINFO: fmaxtolneb   3.000000000000000E-002
SPINFO: approach SD        
SPINFO: alphax    20.0000000000000     
SPINFO: fmaxtol   3.000000000000000E-003
SPINFO: maxforcecall          350
SPINFO: dt   3.000000000000000E-002
SPINFO: np            3
SPINFO: npneb            2
SPINFO: ns2            0
SPINFO: vdtol   0.100000000000000     
SPINFO: htol   2.000000000000000E-002
SPINFO: typintpol cubic
SPINFO: doneb yes
SPINFO: docineb no
SPINFO: pickbestanchorpoints yes

Greping for MIN:

BFGSMIN      0  3.857402446444604E-01  0.000E+00 3.85740E-01 2.22111E-01  1.0000E+00
BFGSMIN      1  1.384956470119129E-01 -2.472E-01 1.38496E-01 8.11970E-02  1.0000E+00
BFGSMIN      2  1.310469909916346E-01 -7.449E-03 1.31047E-01 7.78390E-02  1.0000E+00
BFGSMIN      3  1.228428413736213E-01 -8.204E-03 1.22843E-01 7.43843E-02  1.0000E+00
BFGSMIN      4  1.087765815718121E-01 -1.407E-02 1.08777E-01 6.82878E-02  1.0000E+00
BFGSMIN      5  9.022088864933113E-02 -1.856E-02 9.02209E-02 5.83822E-02  1.0000E+00
BFGSMIN      6  7.621142124612373E-02 -1.401E-02 7.62114E-02 5.04867E-02  1.0000E+00
BFGSMIN      7  5.645190533935150E-02 -1.976E-02 5.64519E-02 3.91367E-02  1.0000E+00
BFGSMIN      8  3.912424367801893E-02 -1.733E-02 3.91242E-02 2.79393E-02  1.0000E+00
SDMIN        0 -0.422320882499190E+01  0.000E+00 0.36062E-01 0.18897E-01  0.0000E+00    0 T
SDMIN        1 -0.424197565216211E+01 -0.188E-01 0.14482E-01 0.86825E-02  0.1200E+01    0 T
SDMIN        2 -0.424631768381917E+01 -0.434E-02 0.12010E-01 0.56404E-02  0.1440E+01    1 T
SDMIN        3 -0.424988994410066E+01 -0.357E-02 0.77852E-02 0.37590E-02  0.1728E+01    0 T
SDMIN        4 -0.425189798254422E+01 -0.201E-02 0.47960E-02 0.25797E-02  0.2074E+01    1 T
SDMIN        5 -0.425272976476051E+01 -0.832E-03 0.25450E-02 0.11030E-02  0.2488E+01    2 T
SP-TIMINGS:     8   40   15    4.14138E+01    7.39875E+00    5.59740E+00

Greping for fort51:

fort51     0    0    4  -4.186037630120483E+00   3.662639E-05  4.35926E-02 -4.2579E-03  1.0000E+02  5.4714E+00  4.9751E-01
fort51     1    0    4  -4.205403669417376E+00   4.793565E-04  1.53984E-02 -1.3762E-03  1.0000E+02  6.1872E+00  5.3417E-01
fort51     2    0    4  -4.209619371536529E+00   9.257536E-05  1.35596E-02 -3.0485E-03  1.0000E+02  5.1688E+00  4.3711E-01
fort51     3    0    4  -4.214064267726933E+00  -2.343064E-04  1.19476E-02  2.7697E-04  1.0000E+02  6.1057E+00  5.0687E-01
fort51     3    1    4  -4.214124066312714E+00  -2.548101E-04  1.19451E-02  3.6230E-04  2.0000E+02  6.1291E+00  5.0882E-01
fort51     3    2    4  -4.214036060339280E+00  -2.498448E-04  1.19650E-02  2.5499E-04  2.0000E+02  6.1791E+00  5.1297E-01
fort51     3    3    4  -4.213877160160393E+00  -1.829750E-04  1.20055E-02  4.6183E-05  2.0000E+02  6.2290E+00  5.1712E-01
fort51     3    4    4  -4.213872028385962E+00  -1.596375E-04  1.20006E-02  4.5132E-05  2.0000E+02  6.2656E+00  5.2016E-01
fort51     3    5    4  -4.213776009036505E+00  -1.572581E-04  1.20162E-02 -8.7289E-05  2.0000E+02  6.2976E+00  5.2281E-01
fort51     4    0    4  -4.215091033633595E+00   1.898290E-04  9.56677E-03 -4.7131E-04  1.0000E+02  6.5595E+00  5.3552E-01
fort51     5    0    4  -4.215877232996801E+00   1.214433E-04  8.77141E-03 -6.6581E-04  1.0000E+02  6.1362E+00  4.9424E-01

Greping for fort52:

SP    22    0   4.757115354252861E-02   3.406801760906211E-02 fort52         0.96630        0.96627
SP    26    1   1.842315395506353E-02   1.213072677909590E-02 fort52         0.45563        0.45560
SP    30    2   1.421250607161663E-02   7.621217945173115E-03 fort52         0.33748        0.33745
SP    39    3   9.885412123642032E-03   5.485024948392904E-03 fort52         0.24027        0.24024
SP    43    4   6.031625086261411E-03   3.526072680680818E-03 fort52         0.18563        0.18560
SP    47    5   3.374052409515318E-03   2.003757072556594E-03 fort52         0.16300        0.16297

Example II: Li6

visualisation of the real space mesh

This is a tricky system since in the linear synchronous transit two atoms collide which makes the ab initio calculations fail. Therefore, we provide the file anchorposinp.xyz manually and consider the run as restart. Greping for SPINFO:

runstat restart
approach BFGS
alphax 30.d0
fmaxtol 1.d-3
np 3
maxforcecall 350
vdtol 1.d-1
ns2 2
htol 2.d-2
hybrid yes
fmaxtolneb 3.d-2
doneb yes

Greping for SPINFO:

SPINFO: runstat restart
SPINFO: hybrid yes
SPINFO: fmaxtolneb   3.000000000000000E-002
SPINFO: approach BFGS      
SPINFO: alphax    30.0000000000000     
SPINFO: fmaxtol   1.000000000000000E-003
SPINFO: maxforcecall          350
SPINFO: dt   3.000000000000000E-002
SPINFO: np            3
SPINFO: npneb            3
SPINFO: ns2            2
SPINFO: vdtol   0.100000000000000     
SPINFO: htol   2.000000000000000E-002
SPINFO: typintpol cubic
SPINFO: doneb yes
SPINFO: docineb no
SPINFO: pickbestanchorpoints no

Greping for MIN:

BFGSMIN      0  2.658290296146267E-01  0.000E+00 1.88272E-01 7.68635E-02  1.0000E+00
BFGSMIN      1  1.901705069187815E-01 -7.566E-02 1.34782E-01 5.29611E-02  1.0000E+00
BFGSMIN      2  1.826133031000365E-01 -7.557E-03 1.29572E-01 5.23946E-02  1.0000E+00
BFGSMIN      3  1.752083968036609E-01 -7.405E-03 1.24503E-01 5.18801E-02  1.0000E+00
BFGSMIN      4  1.549930909226629E-01 -2.022E-02 1.10910E-01 5.14660E-02  1.0000E+00
BFGSMIN      5  1.351403380734329E-01 -1.985E-02 9.75939E-02 4.95805E-02  1.0000E+00
BFGSMIN      6  1.185494325538177E-01 -1.659E-02 8.60610E-02 4.62679E-02  1.0000E+00
BFGSMIN      7  6.985443361654739E-02 -4.869E-02 5.00733E-02 2.51274E-02  1.0000E+00
BFGSMIN      0 -1.354720673105489E+00  0.000E+00 3.63778E-02 1.69486E-02  1.0000E+00
BFGSMIN      1 -1.358829920354335E+00 -4.109E-03 3.25619E-02 1.43177E-02  1.0000E+00
BFGSMIN      2 -1.359571567471042E+00 -7.416E-04 3.19379E-02 1.38096E-02  1.0000E+00
BFGSMIN      3 -1.360362929149532E+00 -7.914E-04 3.12755E-02 1.35413E-02  1.0000E+00
BFGSMIN      4 -1.363625337585838E+00 -3.262E-03 2.87251E-02 1.20356E-02  1.0000E+00
BFGSMIN      5 -1.366804729734642E+00 -3.179E-03 2.63849E-02 1.10090E-02  1.0000E+00
BFGSMIN      6 -1.369789028155951E+00 -2.984E-03 2.41585E-02 9.94199E-03  1.0000E+00
BFGSMIN      7 -1.376378900374655E+00 -6.590E-03 1.94258E-02 7.98840E-03  1.0000E+00
BFGSMIN      8 -1.381902943657167E+00 -5.524E-03 1.52736E-02 5.95757E-03  1.0000E+00
BFGSMIN      9 -1.386447948555821E+00 -4.545E-03 1.16171E-02 4.72462E-03  1.0000E+00
BFGSMIN     10 -1.389898212818101E+00 -3.450E-03 8.47860E-03 3.70352E-03  1.0000E+00
BFGSMIN     11 -1.391872031076600E+00 -1.974E-03 9.02691E-03 3.97574E-03  1.0000E+00
BFGSMIN     12 -1.393213036819617E+00 -1.341E-03 7.60833E-03 3.91178E-03  1.0000E+00
BFGSMIN     13 -1.394478994028227E+00 -1.266E-03 5.78559E-03 3.54460E-03  1.0000E+00
BFGSMIN     14 -1.394604358192615E+00 -1.254E-04 3.66294E-03 1.65658E-03  1.0000E+00
BFGSMIN     15 -1.394955265367910E+00 -3.509E-04 3.00612E-03 1.43641E-03  1.0000E+00
BFGSMIN     16 -1.395203265832667E+00 -2.480E-04 2.94541E-03 1.50025E-03  1.0000E+00
BFGSMIN     17 -1.395260746653488E+00 -5.748E-05 2.76486E-03 1.41587E-03  1.0000E+00
BFGSMIN     18 -1.395178573447133E+00  8.217E-05 2.16733E-03 7.87022E-04  1.0000E+00
SP-TIMINGS:    21  126   42    5.09657E+01    8.69040E+00    5.86460E+00

Greping for fort51:

fort51     0    0    7  -1.349325224899804E+00   1.059722E-03  4.49622E-02 -1.3382E-02  3.7365E+01  5.9589E+00  5.5193E-01
fort51     1    0    6  -1.353430604720599E+00   7.429175E-04  4.03056E-02 -1.3106E-02  3.8150E+01  5.9308E+00  5.4438E-01
fort51     2    0    5  -1.354172421357464E+00   5.568802E-04  3.94531E-02 -1.2663E-02  3.9486E+01  5.9212E+00  5.4251E-01
fort51     3    0    6  -1.354954537759627E+00   6.754601E-04  3.87121E-02 -1.2479E-02  4.0066E+01  5.9329E+00  5.4247E-01
fort51     4    0    6  -1.358211401894834E+00   5.459173E-04  3.55530E-02 -1.1324E-02  4.4154E+01  5.9322E+00  5.3796E-01
fort51     5    0    6  -1.361369220519085E+00   5.720272E-04  3.26756E-02 -1.0190E-02  4.9065E+01  5.9806E+00  5.3705E-01
fort51     6    0    6  -1.364334459279385E+00   5.487001E-04  2.98985E-02 -8.8790E-03  5.6313E+01  6.0230E+00  5.3535E-01
fort51     7    0    6  -1.370783574853893E+00   5.506419E-04  2.40312E-02 -6.8429E-03  7.3069E+01  6.1770E+00  5.3453E-01
fort51     8    0    6  -1.376310137892820E+00   3.807269E-04  1.87057E-02 -4.6373E-03  1.0000E+02  6.3064E+00  5.3014E-01
fort51     9    0    6  -1.380851509027939E+00   1.379105E-04  1.38639E-02 -2.3133E-03  1.0000E+02  6.4178E+00  5.2292E-01
fort51    10    0    6  -1.384378946396093E+00   2.846158E-05  9.80852E-03 -3.9474E-04  1.0000E+02  6.5099E+00  5.1385E-01
fort51    11    0    6  -1.386027480367171E+00  -2.562233E-04  9.76806E-03 -7.5386E-04  1.0000E+02  4.2155E+00  3.2342E-01
fort51    12    0    6  -1.387427812537331E+00  -2.736263E-04  8.54286E-03 -6.3564E-04  1.0000E+02  4.2829E+00  3.2353E-01
fort51    13    0    6  -1.388727699392891E+00  -3.168835E-04  6.91781E-03 -5.6796E-04  1.0000E+02  4.4136E+00  3.2760E-01
fort51    14    0    5  -1.389114105745670E+00   1.168217E-04  3.97928E-03 -4.2634E-04  1.0000E+02  7.6629E+00  5.6206E-01
fort51    15    0    6  -1.389446738027391E+00   3.067774E-04  3.27604E-03 -7.0741E-04  1.0000E+02  8.0194E+00  5.7939E-01
fort51    16    0    6  -1.389482429249552E+00  -3.613402E-04  4.41419E-03 -6.1808E-04  1.0000E+02  4.8586E+00  3.4781E-01
fort51    17    0    6  -1.389542886892510E+00  -3.767532E-04  4.24607E-03 -5.9897E-04  1.0000E+02  4.8298E+00  3.4600E-01
fort51    18    0    6  -1.389772886701583E+00   5.236147E-04  2.67091E-03 -2.9684E-04  1.0000E+02  8.1815E+00  5.8836E-01
fort51    18    1    6  -1.389742557477353E+00   5.119415E-04  2.61011E-03 -3.7299E-04  2.0000E+02  8.1315E+00  5.8476E-01
fort51    18    2    6  -1.389788596645344E+00   4.952957E-04  2.55558E-03 -1.2983E-04  2.0000E+02  8.0815E+00  5.8117E-01
fort51    18    3    6  -1.389761492823693E+00   4.698196E-04  2.51302E-03 -1.9222E-04  2.0000E+02  8.0315E+00  5.7757E-01
fort51    18    4    6  -1.389743831012979E+00   4.426949E-04  2.47638E-03 -2.2599E-04  2.0000E+02  7.9815E+00  5.7398E-01
fort51    18    5    6  -1.389731164777037E+00   4.151490E-04  2.44509E-03 -2.4345E-04  2.0000E+02  7.9315E+00  5.7038E-01
fort51    18    6    6  -1.389696857462997E+00   3.874437E-04  2.42063E-03 -7.2383E-04  2.0000E+02  7.8815E+00  5.6679E-01
fort51    18    7    6  -1.389713364562108E+00   3.549326E-04  2.39789E-03  2.2539E-04  2.0000E+02  7.8315E+00  5.6319E-01
fort51    18    8    6  -1.389726365143919E+00   3.220476E-04  2.38637E-03  1.9382E-04  2.0000E+02  7.7815E+00  5.5960E-01
fort51    18    9    6  -1.389746278122353E+00   2.898396E-04  2.37622E-03  2.3707E-04  2.0000E+02  7.7315E+00  5.5600E-01
fort51    18   10    6  -1.389708378826690E+00   2.558396E-04  2.37223E-03 -6.4340E-05  2.0000E+02  7.6815E+00  5.5240E-01
fort51    18   11    6  -1.389670484314958E+00   2.227677E-04  2.36285E-03 -2.5646E-04  2.0000E+02  7.6315E+00  5.4881E-01

Greping for fort52:

SP    27    0   4.582739728652108E-02   2.211695178525666E-02 fort52         1.42937        1.42937
SP    33    1   4.118141822842685E-02   1.906098140079709E-02 fort52         1.31755        1.31755
SP    39    2   4.032768960411765E-02   1.842921252071412E-02 fort52         1.29737        1.29737
SP    45    3   3.958755501807201E-02   1.813047464298359E-02 fort52         1.27584        1.27584
SP    51    4   3.642295876055287E-02   1.631228556027465E-02 fort52         1.18706        1.18706
SP    57    5   3.353889980745835E-02   1.501096407908051E-02 fort52         1.10055        1.10055
SP    63    6   3.075331976323187E-02   1.366601352132298E-02 fort52         1.01934        1.01934
SP    69    7   2.485565784166293E-02   1.111230727845575E-02 fort52         0.84002        0.84002
SP    75    8   1.948102525467053E-02   8.470133890077683E-03 fort52         0.68970        0.68970
SP    81    9   1.456443524534309E-02   6.100816835265441E-03 fort52         0.56603        0.56603
SP    87   10   1.034883225884659E-02   4.496290482181775E-03 fort52         0.47214        0.47214
SP    93   11   8.899636348450568E-03   3.948363360681770E-03 fort52         0.41843        0.41843
SP    99   12   7.517797390829734E-03   3.908929257556252E-03 fort52         0.38194        0.38194
SP   105   13   5.735201330212355E-03   3.545492527160656E-03 fort52         0.34749        0.34749
SP   111   14   4.626062469243877E-03   2.151723427328924E-03 fort52         0.34408        0.34408
SP   117   15   3.829185491328242E-03   1.876452919022026E-03 fort52         0.33453        0.33453
SP   123   16   3.046040944581332E-03   1.528556333746436E-03 fort52         0.32778        0.32778
SP   129   17   2.870283127641142E-03   1.449471721290002E-03 fort52         0.32622        0.32622
SP   146   18   2.871620541945113E-03   1.399718124331447E-03 fort52         0.32845        0.32845
  1. S.A. Ghasemi and S. Goedecker, J. Chem. Phys. 135, 014108 (2011).
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