1. The Nuts and Bolts of First-Principles Simulation Durham, 6th-13th December 2001 9: Is it running properly? CASTEP Developers’ Group with support from the ESF  k Network

2. Nuts and Bolts 2001 9: Is it running properly? 2 Outline  Why you have to read the output file  Sample output  The road to hell  Look after the pennies  Completely wrong  Right and wrong  Graphic detail  Summary

3. Nuts and Bolts 2001 9: Is it running properly? 3 What is the question?  We have to eliminate technical failures and separate artefacts from the proper predictions of DFT theory within an approximation (LDA, GGA)  Goes much further than just checking the basics, because testing is the bedrock of good simulation studies (see Lecture 10)  Here though we start with the basics

4. Nuts and Bolts 2001 9: Is it running properly? 4 Scrutinise the output file!  But I’ve got Materials Studio… CASTEP sets all the defaults….  But I have already set up the job properly…  But it finished ok without crashing…  But the results look ok, what else is there..?

5. Nuts and Bolts 2001 9: Is it running properly? 5 But I’ve got Materials Studio…  Defaults (interface or CASTEP) may not be appropriate  Choices made on your behalf: are they what you want?  The program tells you what it is doing and what’s going wrong

6. Nuts and Bolts 2001 9: Is it running properly? 6 But I have already set up the job properly… All of the previous, and  That doesn’t mean it has run properly  You have to verify that your intentions were realised: you might have asked the impossible  Are the results physically reasonable?

7. Nuts and Bolts 2001 9: Is it running properly? 7 But it finished ok without crashing… All of the previous, and  Finished because.. The task was finished and the tolerances met or it ran out of iterations?  Was it efficient? But the results look ok, what else is there..?

8. Nuts and Bolts 2001 9: Is it running properly? 8 The output file (.out.cst ) Input and defaults Initialisation Electronic minimisation (then MD, geometry optimisation) Calculate properties (Eigenvalues, forces and stress, band structure…) Finish

9. Nuts and Bolts 2001 9: Is it running properly? 9 Sample output: startup +-------------------------------------------------+ | | | It is no longer just Cambridge... | | it is no longer just serial... | | it is no longer just for total energies... | | | | but for marketing and legal reasons it is still | | | | CCC AA SSS TTTTT EEEEE PPPP | | C A A S T E P P | | C AAAA SS T EEE PPPP | | C A A S T E P | | CCC A A SSS T EEEEE P | | | +-------------------------------------------------+ | | | Welcome to Castep II.0, the DFT code for the | | professional user. | | | | Authors: | | M. Segall, P. Lindan, M. Probert, C. Pickard, | | P. Hasnip, S. Clark, M. Payne |

10. Nuts and Bolts 2001 9: Is it running properly? 10 Startup | | | Copyright 2000,2001 | | | | Please cite | | | | 2001--A Real and Reciprocal Space Odyssey | | (Comp. Phys. Comms 2001) | | | | in all publications arising from your use of | | this fine product. | | | +-------------------------------------------------+  Or perhaps M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias and J. D. Joannopoulos, Rev. Mod. Phys. 64 (1992) 1045  …but please acknowledge

11. Nuts and Bolts 2001 9: Is it running properly? 11 Inputs defaults Warning: parameters_read - missing parameters file, using defaults Strategy found: 1 g-vector groups containing 1 nodes. Initialising basis set. Standard grid dimensions: 27 27 27 Fine grid dimensions: 27 27 27 Plane wave load balancing: max 1899 min 1863 average 1881 Warning: parameters_output - missing parameters file, using defaults ************************************ Title ************************ ***************************** General Parameters ****************** output verbosity : normal (1) write checkpoint data to : si_8atoms.check type of calculation : single point energy unlimited duration calculation *********************** Exchange-Correlation Parameters *********** using functional : Local Density Approximation (LDA) initialisation

12. Nuts and Bolts 2001 9: Is it running properly? 12 ************************* Pseudopotential Parameters ************** pseudopotential representation : reciprocal space representation : reciprocal space **************************** Basis Set Parameters ***************** basis set accuracy : FINE finite basis set correction : automatic **************************** Electronic Parameters **************** number of electrons = 32 number of up spins = 16 number of down spins = 16 number of spin components = 1 number of bands = 19 ********************* Electronic Minimisation Parameters ********** Method: Treating system as metallic with ensemble DFT treatment of electrons, and number of SD steps = 1 and number of CG steps = 9 total energy convergence tolerance = 0.1000E-04 Electron Volt eigen-energy convergence tolerance = 0.1000E-05 Electron Volt periodically dump wavefunctions to : si_8atoms.wvfn *******************************************************************

13. Nuts and Bolts 2001 9: Is it running properly? 13 ------------------------------- Unit Cell ------------------------------- Real Lattice(Angstrom) Reciprocal Lattice(Angstrom-1) 5.4306811 0.0000000 0.0000000 1.1569792 0.0000000 0.0000000 0.0000000 5.4306811 0.0000000 0.0000000 1.1569792 0.0000000 0.0000000 0.0000000 5.4306811 0.0000000 0.0000000 1.1569792 Lattice parameters(Angstrom) Cell Angles a = 5.430681 alpha = 90.000000 b = 5.430681 beta = 90.000000 c = 5.430681 gamma = 90.000000 Current cell volume = 160.163261 Angstrom^3 ------------------------------- Cell Contents ------------------------------- Total number of ions in cell = 8 Total number of species in cell = 1 Max number of any one species = 8

14. Nuts and Bolts 2001 9: Is it running properly? 14 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Element Atom Fractional coordinates of atoms x x Number u v w x x----------------------------------------------------------x x Si 1 0.000000 0.000000 0.000000 x x Si 2 0.000000 0.500000 0.500000 x x Si 3 0.500000 0.500000 0.000000 x x Si 4 0.500000 0.000000 0.500000 x x Si 5 0.750000 0.250000 0.750000 x x Si 6 0.250000 0.250000 0.250000 x x Si 7 0.250000 0.750000 0.750000 x x Si 8 0.750000 0.750000 0.250000 x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx No user defined ionic velocities ------------------------------- Details of Species ------------------------------- Mass of species in amu Si 28.0855000 Files used for pseudopotentials: Si Si_00.recpot

15. Nuts and Bolts 2001 9: Is it running properly? 15 ------------------------------- k-Points For BZ Sampling ------------------------------- MP grid size for SCF calculation is 0 0 0 Number of kpoints used = 2 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Number Fractional coordinates Weight + +-----------------------------------------------------+ + 1 0.000000 0.000000 0.000000 0.5000000 + + 2 0.250000 0.250000 0.250000 0.5000000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++ ------------------------------- Symmetry and Constraints ------------------------------- There are no symmetry operations specified or generated for this cell Centre of mass is constrained Number of ionic constraints = 3 Set iprint > 1 for details of ionic constrains Number of cell constraints= 0 Cell constraints are: 1 2 3 4 5 6 External pressure/stress (Gigapascal) 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000

16. Nuts and Bolts 2001 9: Is it running properly? 16 ----------------------------------------------------------------------- <-- SCF SCF loop Energy Energy gain Timer <-- SCF Initial Final per atom (sec) <-- SCF ----------------------------------------------------------------------- <-- SCF 1 6.90786323E+002 -8.25830112E+002 1.89577054E+002 28.05 <-- SCF 2 -8.27390859E+002 -8.27487108E+002 1.20311299E-002 65.96 <-- SCF 3 -8.27512262E+002 -8.27514161E+002 2.37421982E-004 122.35 <-- SCF 4 -8.27514161E+002 -8.27514980E+002 1.02415786E-004 141.14 <-- SCF 5 -8.27515398E+002 -8.27515628E+002 2.87334596E-005 178.73 <-- SCF 6 -8.27515764E+002 -8.27515847E+002 1.04204861E-005 216.27 <-- SCF 7 -8.27515900E+002 -8.27515935E+002 4.32558230E-006 253.84 <-- SCF 8 -8.27515958E+002 -8.27515974E+002 1.95561376E-006 291.48 <-- SCF 9 -8.27515985E+002 -8.27515992E+002 9.44235482E-007 329.08 <-- SCF 10 -8.27515992E+002 -8.27515998E+002 6.72174059E-007 347.90 <-- SCF 11 -8.27515998E+002 -8.27516001E+002 4.85180904E-007 367.72 <-- SCF ----------------------------------------------------------------------- <-- SCF Electronic minimisation  NB: “very-beta” test run and timings! Try this one yourself

17. Nuts and Bolts 2001 9: Is it running properly? 17 The road to hell I thought I had Used the rPBE functional... Run it as a metal... Used the gamma point... Continued a run… Altered the lattice parameters… Used that other pseudopotential… Run without symmetry… Fed the dog my homework...  Or anything you care to mention. The truth is in the output file!

18. Nuts and Bolts 2001 9: Is it running properly? 18 Look after the pennies If CASTEP ran what you wanted it to:  Are there any warning messages? Do you know if they are important or irrelevant?  Has it converged or just stopped?  Are all the obvious quantities reasonable? Total energy: negative? Expected value? Forces and stress: zero if they should be? Too large? Electronic energies: related to known values?

19. Nuts and Bolts 2001 9: Is it running properly? 19 Completely wrong  Apart from the obvious: The job never started The job crashed  There are many ways a calculation can be rendered useless, but usually are avoided via systematic testing (Lecture 10) Inadequate plane-wave cutoff, k-point sampling Pseudopotential ghost states, poor transferability System size  However, within a single calculation things can still go wrong, a few examples follow

20. Nuts and Bolts 2001 9: Is it running properly? 20 Right and wrong I  Although density mixing never does produce a smooth E vs. n curve (e.g. Cu unit cell)...

21. Nuts and Bolts 2001 9: Is it running properly? 21 …right and wrong I  Sometimes it just doesn’t work (e.g isolated Carbon atom,  -point)

22. Nuts and Bolts 2001 9: Is it running properly? 22 Right and wrong II  Symmetry Use of (point group) symmetry imposes constraints The supercell imposes the translational symmetry constraints Both can lead to the wrong answer

23. Nuts and Bolts 2001 9: Is it running properly? 23 Right and wrong III  Load balancing On a parallel computer the node with the most work dictates overall performance Example (artificial!) 4 k-point calculation on three nodes, k-parallel Max. speedup is only 2X, not 3X

24. Nuts and Bolts 2001 9: Is it running properly? 24 Graphic detail  Use graphics to see what you are calculating ------------------------------------------------------------------------------ xo yo zo dx dy dz ------------------------------------------------------------------------------ 1 1 1.495000 2.345000 4.690000 0.002742 0.340039 -1.159912 2 2 1.495000 7.035000 4.690000 0.008477 0.208466 0.197382 3 3 1.495000 -2.345000 4.690000 -0.031550 -0.157330 -0.072624 4 4 0.000000 0.000000 2.345000 -0.003381 -0.117283 -0.012302 5 5 0.000000 4.690000 2.345000 -0.006252 0.345081 0.220537 6 6 0.000000 -4.690000 2.345000 -0.007750 -0.034518 -0.030432 7 7 1.495000 2.345000 0.000000 -0.004739 0.031681 0.003218 8 8 1.495000 7.035000 0.000000 -0.002625 -0.044991 0.003218 9 9 1.495000 -2.345000 -4.690000 0.039800 -0.330420 1.176514 10 10 1.495000 7.035000 -4.690000 0.033740 -0.188561 -0.190576 11 11 1.495000 2.345000 -4.690000 -0.017993 0.145789 0.038332 12 12 0.000000 0.000000 -2.345000 -0.003354 0.140803 0.013367 13 13 0.000000 -4.690000 -2.345000 0.032009 -0.349785 -0.179074 14 14 0.000000 4.690000 -2.345000 -0.002460 0.011580 0.000154 15 15 1.495000 -2.345000 0.000000 -0.009564 -0.008779 0.003218

25. Nuts and Bolts 2001 9: Is it running properly? 25 Summary  The output file contains the basic information on the identity, health and sanity of your calculation  Here we have looked at a tiny fraction of the potential pitfalls  Always use/check the most basic data first  Plot graphs, use graphic images  If it can go wrong it will - but only when you are not looking!