Home

XtalOpt User Guide

1. ISMEAR 5 5 tetraedon 1 N Methfessel userl ENCUT user3 cutoff energy wares 0 PSTRESS user2 ISYM 0 user3 400 user4 a Save Session Resume stored session Optimized 0 Running 0 Failures 0 Begin Hide On the next tab load the optimization scheme by clicking the Load Opt Scheme button and selecting the samples vasp xtalopt scheme file that is distributed with the source code If you do not have a copy of the source code the scheme file can be obtained by clicking the Original Format link at the bottom of the page here For more details on optimization schemes see Optimization Schemes After loading the optimization scheme XtalOpt will prompt for the POTCAR files to use Select files appropriated for the prompted atom XtalOpt will construct the POTCAR files on the local computer and then copy them over to the cluster when the calculation is submitted It is necessary to have the VASP POTCAR files for each atomic species located somewhere on the local computer See the VASP manual for information on obtaining the POTCAR files Take a moment to look through each file for each optimization step Notice that the INCAR template includes two user specified values user2 and user3 for the external pressure and the energy cutoff respectively By entering appropriate values in the user2 and user3 fields on the left it is easy to update these values for all optimizati
2. GULP PWscf CASTEP Queue setup Using a remote PBS cluster Using a remote SGE cluster Using a remote SLURM cluster Running optimations locally What is written to the local directory Search Settings Begin Monitor progress View trends Further reading Optimization Schemes Saving and Resuming Sessions in XtalOpt 4 XtalOpt Tutorial 2 2 Launch XtalOpt Open avogadro go to the Extensions menu and select XtalOpt 2 3 Enter composition and restraints XK XtalOpt Vw x Structure Limits Optimization Settings Search Settings Progress Plot Log Composition Unit Cell Parameters Cell composition 012 Ti6 Minimum Maximum REA Length A A 1 00000 120 00000 22 Ti x 6 Length B A 1 00000 20 00000 ES Length C A 1 00000 20 00000 Es Angle a 60 00000 120 00000 0 Angle B 60 00000 120 00000 0 Angle y 60 00000 120 00000 Volume 42 1 00 500 00 0 _ Fixed volume v Limit interatomic distance A 0 50000 Save Session Resume stored session Optimized 0 Running O Failures 0 Begin Hide The interface opens to the Structure Limits tab shown above We will use a 6 for mula unit supercell of titanium dioxide for this tutorial so enter Ti6 O12 for the cell composition We will assume that we know nothing about the system and use very loose restraints Set all cell length minima to 1 angstrom and maxima to 20 angstro
3. button next to the optimizer selection menu For more details on optimization schemes see Optimization Schemes 2 6 What is written to the local directory A directory for each structure is created at Local working directory lt gen gt x lt id gt that will contain input output and data files specific to each structure Two additional files are also written to the local filesystem Local working directory xtalopt state which contains save resume information to continue a session that has been stopped and Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 7 Search Settings 15 Local working directory results txt which stores a list of all structures sorted by increasing enthalpy The latter file is handy for offline analysis since there is no need to open XtalOpt to find the most stable struc tures of a previous search 2 7 Search Settings Ku aos YUOY Structure Limits Optimization Settings Search Settings Progress Plot Log Initial Generation Search Parameters Duplicate matching tolerances Initial structures Pool size Enthalpy eV 0 002000 Volume A 1 000000 gt f oo Initial Seed Structures Continuous structures Limit running jobs Limit to 1 jobs Spacegroup A 0 050000 Ifa job fails 1 times replace with random vw lt gt In the Search Settings tab most of the default settings should suffice See CPC 2010 publication
4. N Sdescription S SgenSx id Soptsteps Include this for XtalOpt scripts export PBS_O WORKDIR rempath Change to structure s working directory copy input files to node s scratch dir s for node in cat PBS_NODEFILE sort uniq do rsh node cp SPBS_O_WORKDIR x PBSTMPDIR done Move to the scratch directory cd PBSTMPDIR echo running in directory PBSTMPDIR Set any environment variables needed for the optimizer MPI here Run optimizer be sure to use the filenames that XtalOpt expects See the template menu in XtalOpt and the example templates in the samples directory of the XtalOpt sources Don t forget to clean up after MPI if needed Print files from each node for node in cat SPBS_NODEFILE sort unig do echo Snode rsh node ls 1 SPBSTMPDIR done Copy back results from master node s scratch directory cp PBSTMPDIR x PBS_O_WORKDIR Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 5 Queue setup 11 For more details on optimization schemes see Optimization Schemes Be aware that every installation is different and it is almost certain that the job pbs file included with this scheme will not work on any cluster other than the Zurek group s par ity cluster at SUNY Buffalo s Center for Computational Resources lt may take some experimentation to get jobs to submit successfully and you may need to contact the mantainers of the cluster for assistance or
5. extension of scheme Generated on Thu Jun 2 2011 12 22 36 by Doxygen 28 Optimization Schemes 4 6 Howto load an optimization scheme Loading an optimization is quite simple just click the Load Opt Scheme button and select the scheme file you wish to load This will also update the current queuing system and optimizer to those specified by the scheme 4 7 Whatis saved The optimization scheme files contain more than just the templates for each optstep They also store queue and optimizer specific settings This is useful for storing config uration options for different clusters along with the scheme Note that although XtalOpt will prompt for an SSH password if needed it is NOT stored in the scheme file 4 8 Suggestions for optimization schemes 4 8 1 Crystals XtalOpt The following list describes the optimization steps used in the samples vasp xtalopt scheme file distributed with the XtalOpt source code 1 Fix unit cell only optimize atomic coordinates A very loose convergence criterion is used and the number of KPOINTs is kept small 2 The cell volume is fixed but atomic positions and cell parameters are allowed to vary The convergence criteria is the same as before as is the KPOINT grid 3 All degrees of freedom are considered using the same convergence criteria as before but with a finer KPOINT grid 4 Same as before but with a stricter convergence criteria 5 Same as before but with a stricter
6. Creating a working scheme from scratch may take some time We recommend checking the samples directory of the source code to obtain sample scheme for each optimizer see How to load an optimization scheme and verifying that they are appropriate for the system under consideration before starting a search If there is not an appropriate sample the following prescription may be used to generate your own 1 Generate a random structure of the system under consideration This may be done by hand or by running a search just long enough to create the first random generation and saving one of the structures Generated on Thu Jun 2 2011 12 22 36 by Doxygen 4 5 How to save an optimization scheme for later 27 2 Create a starting optstep with the desired convergence criteria 3 Manually submit the optimization 4 If the optimization fails a First determine why if the maximum iterations were exceeded or the op timization was aborted due to a badly performing minimizer try one of the ideas below Other optimization problems are beyond the scope of this doc ument b Reduce the convergence criteria of the current trial optstep c Remove degrees of freedom e g by fixing cell parameters atomic posi tions etc d Reduce the accuracy of the calculation in other ways use a courser inte gration grid etc e Change the minimizer e g tell the optimizer to use conjugate gradients rather than BFGS etc 5 Once the op
7. We arbitrarily set the initial structures to 20 and the continuous structures to 5 although these may need to be adjusted based on available resources We will not specify initial seeds but the option to do so exists on this screen It is not neccessary to limit the number of running jobs unless running locally as the PBS queue on the cluster will manage job control for us If running locally set the job limit no higher than number of available processor cores 1 e g for a quadcore processor allow three jobs to run simultaneously This allows one core to remain free for the system to run Generated on Thu Jun 2 2011 12 22 36 by Doxygen 16 XtalOpt Tutorial 2 8 Begin Ke XtalOpt quickjob E thewho ccr buffalo edu D YoY Structure Limits Optimization Settings Search Settings Progress plot Log Gen Mol Job ID Time Elapsed Enthalpy eV Volume Space Group Ancestry 0 00 00 N A 75 04 1 P1 Randomly generated 0 00 00 N A 328 24 1 P1 Randomly generated 0 00 00 N A 178 63 1 P1 Randomly generated 0 00 00 N A 97 52 KPT Randomly generated 0 00 00 N A 482 32 P1 Randomly generated N A PL Randomly generated N A y PL Randomly generated N A PE Randomly generated N A A Pi Randomly generated N A E AB Randomly generated N A i RPL Randomly generated N A i ea bh Randomly generated N A y SP
8. and XtalOpt will automatically save the session every time a structure is updated XtalOpt will also write a file structure state in each candidate structure s directory This file stores XtalOpt specific information about the structure 3 3 How to resume your session To resume a session simply click Resume stored session highlighted above and select the xtalopt state file in the working directory of the session you would like to resume XtalOpt will then begin to load the structures and search parameters You can monitor the progress with the progress bar that appears at the bottom of the window While the structures are loading you may encounter errors that say Error no or not appropriate for OPTIMIZER xtal data in DIRECTORY This could be a result of resuming a structure that has not yet done any local optimizations If so safely ignore this message As mentioned in the message these can typically be ignored if it only happens for a handful of structures This occurs when a structure has been generated in XtalOpt but it has not completed any geometry optimization so there are no output files from which to load the geometry If it happens for a significant number of structures or structures that are known to have completed at least one geometry optimization step the output files from the optimizer may be missing or corrupt After resuming a session XtalOpt will ask if you would like to continue the search or enter
9. each structure s ancestory i e parent s and parameters for the genetic operator that generated it A status bar on the bottom of the window shows the number of structures that are optimized running and failing at any given time This information is visible regardless of which tab is currently being viewed An additional feature of the progress table is the ability to immediately visualize any of the individuals in the Avogadro main window simply clicking on a row in this table will display the three dimensional structure in Avogadro where it can be visualized modified or exported If the user would like to add a bit of intelligent design to the evolutionary process a structure can be modified and then resubmitted using a context right click menu from the progress table The context menu provides tools to un kill a structure resubmit for local optimization at an arbitrary optimization step or replace a problematic structure with a new random individual Generated on Thu Jun 2 2011 12 22 36 by Doxygen 18 XtalOpt Tutorial 2 9 1 View trends K XtalOpt quickjob thewho ccr buffalo edu 2 D Structure Limits Optimization Settings Search Settings Progress Plot Log Options Plot Type Trends v Trend Plot Options Y axis label Enthalpy ev v X axis label Structure v _ Show duplicate structures __ Show incomplete structures v Label points SG Symbol v Structure Refresh Toggle options Save
10. scoordsFrac percent ENDBLOCK POSITIONS_FRAC Add Remove Help Save Opt Scheme Load Opt Scheme userl user2 user3 user4 Save Session Resume stored session Optimized 0 Running 0 Failures 0 Begin Hide On the next tab load the optimization scheme that is distributed with the source code un der the samples directory The scheme that we want is named castep xtalopt scheme If the source code is not available the scheme file can be obtained by clicking the Orig inal Format link at the bottom of the page here For more details on optimization schemes see Optimization Schemes It is important to note that CASTEP input files require the character to define blocks The percent character is special in the XtalOpt input template parser to define keywords see below To insert a literal into the input use percent E g Specification of the fractional coordinate block in the cell template should look like Spercent SBLOCK POSITIONS_FRAC ScoordsFracs SpercentSENDBLOCK POSITIONS_FRAC Take a moment to look through each file for each optimization step Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 5 Queue setup 9 Notice the keyword values in the job pbs templates These are used to enter in formation that is specific to a search or structure when the actual input files are written prior to job submission Click the Help button for a full listing of the av
11. waves 1 1 Stripple 2x7 stdev 0 50000 amp 0 34073 waves 1 1 Permustrain 2x7 stdev 0 06139 exch 4 Stripple 2x2 stdev 0 38608 amp 0 67483 waves 1 1 Permustrain 3x5 N A 0 00 02 233 302 231 60 N A 0 00 02 238 802 182 20 N A i 0 00 01 235 177 174 27 N A 0 00 02 234 15 190 93 N A 0 00 03 236 265 169 17 N A 0 00 02 232 906 213 36 N A 0 00 02 235 342 198 59 N A 0 00 03 238 802 182 20 136 P4_2 mnm N A 0 00 02 238 59 180 75 14 P2_1 c N A 0 00 03 238 802 182 20 136 P4_2 mnm Stdev 0 14267 exch 4 N A 0 00 02 236 131 170 65 11 P2_1 m a Ad aoai Nia a la Crossover 1 13 43 1x13 wooo m peas sis ee Refresh Refresh period 1 seconds Refresh all Save Session Resume stored session Optimized 42 Running 4 Failures 0 Begins _Hide_ Figure 2 2 The Progress tab mid run As XtalOpt performs the search the progress table continuously updates providing in formation about each structure We see individuals in various stages of completion most are optimized in yellow structure 2x7 has been automatically marked as a dupli cate dark green of structure 3x3 and removed from the breeding pool structure 4x4 is currently undergoing a local optimization light green while structure 4x5 is waiting to be optimized blue Other useful information is displayed about each structure such as the time spent in optimization the optimized enthalpy the cell volume spacegroup and
12. 0 5 cell Sas SbS Sc SalphaDegs SbetaDegs SgammaDeg frac ScoordsFracs species Tu 2 196 O 1 098 buck Ti Ti 31120 1 0 1540 5 25 15 O O 11782 7 0 2340 30 22 15 Ti 16957 5 0 1940 12 59 15 lennard 12 6 Ti Ti 1015 o 6 1015 Tio 1015 Alternatively one can load the scheme file distributed with the source code under samples gulp TiO xtalopt scheme If the source code is not available the scheme file can be obtained by clicking the Original Format link at the bottom of the page here For more details on optimization schemes see Optimization Schemes Note the surrounding various keywords These will be replaced by the structure specific data when the optimizer is invoked for each structure Click Help to view all of the keywords available The number of optimization steps can be modified with the Add Resume buttons The user fields in the lower left corner allow users to specify their own keyword value pairs which is useful for making changes to multiple Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 4 Optimizer setup 7 optimization steps at once We will only be using one optimization step in this tutorial XtalOpt expects GULP to use the following filenames gulp lt xtal gin gt xtal got Skip to next section 2 4 3 PWscf E XtalO pt Y V OG Structure Limits Optimization Settings Search Settings Progress Plot Log Queue PBS v Configure amp CONTROL A Optimizer PWscf w Conf
13. L Randomly generated Randomly generated Figure 2 1 The Progress tab immediately after starting a search XtalOpt has everything it needs to start its search at this point click the Begin button in the lower right corner of the application to tell it to start the search algorithm A progress bar appears as the random first generation is created Switch to the Progress tab and 20 entries will appear all with a status of Waiting for Optimization Click Refresh on this tab to begin the local optimizations From here XtalOpt will continue to run without user input starting new optimizations and generating new structures until it is stopped by the user Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 9 Monitor progress 17 2 9 Monitor progress Ae XtalOpt quickjob themho ccr buffalo edu Y Ye Structure Limits Optimization Settings Search Settings Progress Plot Log Gen Mol Job ID Status Time Elapsed Enthalpy eV Volume Space Group Ancestry Stripple 1x6 stdev 0 50000 amp 0 13173 waves 1 1 Permustrain 2x7 stdev 0 39208 exch 4 N A 0 00 02 238 802 182 20 136 P4_2 mnm N A 0 00 03 233 584 197 17 Randomly generated excessive failures Permustrain 1x6 stdev 0 14819 exch 4 Stripple 2x1 stdev 0 25098 amp 0 65678 waves 1 1 Stripple 2x11 stdev 0 33402 amp 0 72635 waves 1 1 Permustrain 2x12 stdev 0 07879 exch 4 Stripple 2x1 stdev 0 31247 amp 0 61055
14. Session Optimized 112 Running 4 Failures O Hide Figure 2 3 The Plot tab mid run displaying enthalpy vs volume Each structure is labeled with its Hermann Mauguin spacegroup symbol Another visualization and analysis tool available during the search is the interactive plot The plot is capable of investigating trends in the search by plotting a point for each in dividual using structure number generation number enthalpy energy PV enthalpy term lattice parameters or cell volume on either axis This powerful feature allows the user to visualize complex relationships present in the generated structures E g a plot of enthalpy vs structure number provides an overview of the search s progress Or recalling that H U PV plotting enthalpy vs PV enthalpy term or energy lends insight into whether the enthalpy H is dominated by atomic interactions U or cell pa rameters PV Further information is available by labeling the points with the individual s spacegroup number Hermann Mauguin spacegroup symbol enthalpy energy PV term volume generation or index number A particularly useful plot is that of enthalpy vs cell volume as shown above From this view we see a general trend that enthalpy increases with volume the effect is much more pronounced for systems at higher pressures and also that below a certain volume enthalpy rises sharply From this data set we see that there is a cluster of very low e
15. XtalOpt User Guide Release r7 0 Generated by Doxygen 1 7 4 Thu Jun 2 2011 12 22 36 See http xtalopt openmolecules net for the latest versions of these guides Contents 1 User documentation 2 XtalOpt Tutorial EM GOMERA ee Re ea ede a ded 2 a 2 i we ee ee beech ee Le be bebe 2 3 Enter composition and restraints 24 II AN 242 GULP ecas ee SS hha pad a aed ZAS PM ok cee a da Ree A de a ee ae aa 2244 CASIEP sy kote ee Sd EG ade REG a a eM 25 QUEUIESCOUA o i he ee be Hed be ed eee A oe i 2 5 1 Using a remote PBS cluster 0 2 5 2 Using a remote SGE cluster 0 5 2 5 3 Using a remote SLURM cluster 2 5 4 Running optimations locally 2 6 Whatis written to the local directory 27 SCAN GEIMGS ceso ciar aa a a e a 20 BOQ ook hand eae deb hbt bee hi e the a e a 29 Monit r progress ci abba ek a a e RRS eS A 294 WiOWWONUS 3 5 sae hw eee dy Soe a eS 2 10 Farther reading 2 0 0 6 4 5 be ee wee ee REREAD ee es 3 Saving and Resuming Sessions in XtalOpt Qt GOMAS fon bee eR VER ESR ESO Eo eS 3 2 Howto save yoursession 2 2002200022 R 11 12 14 14 15 16 17 18 19 ii CONTENTS 3 3 How to resume your session o e 22 4 Optimization Schemes 23 41 DOMEM ced ea a A A Sl eee a i i 23 4 2 Overview What are optimimization schemes and why use them 24 421 I
16. ailable keywords Be aware that every PWscf CASTEP installation is different and it is almost certain that the job pbs file included with this scheme will not work on any cluster other than the Zurek group s parity cluster at SUNY Buffalo s Center for Computational Resources It may take some experimentation to get jobs to submit successfully and you may need to contact the mantainers of the cluster for assistance for information about MPI ex ecutable locations etc Perhaps the easiest method to find the correct PBS script is to run some trial submissions by hand and then replace the structure search specific information with the appropriate keywords once a working script has been generated XtalOpt expects CASTEP to use the following filenames XtalOpt will write xtal cell xtal param castep xtal CASTEP will create xtal castep 2 5 Queue setup XtalOpt currently supports using the PBS SGE and SLURM queuing systems on re mote SSH accessible clusters as well as an internal local queue that manages calcu lations on the user s workstation Each queueing interface is detailed in its own section below 2 5 1 Using a remote PBS cluster K PBS Queue Configuration y Y O OS Host parity ccr buffalo edu SSH Port 22 User davidlon Working directory Server user davidlon proj Ti204 Working directory Local home dl xtaloptCalcs Ti204 Description Ti204x6 Path to qsub qsub Path to qdel qdel Path to qst
17. at qstat BY OK Cancel Select PBS from the list of Queues and then click the Configure button A new window will prompt for host The hostname of the PBS cluster s head node Generated on Thu Jun 2 2011 12 22 36 by Doxygen 10 XtalOpt Tutorial e user The username used to log into the cluster e Working directory Server A directory that is readable writable by user on the cluster used when performing optimizations e Working directory Local A directory that is readable writable by the current user on the local computer This is where the final structures and resume files are written Description Used for the description keyword in input templates Path to qsub Where to find the qsub executable on the remote cluster Note that if qsub is in the clusters PATH setting this to just qsub will work Path to qdel Where to find the qdel executable on the remote cluster Note that if qdel is in the cluster s PATH setting this to just gdel will work e Path to qstat Where to find the qstat executable on the remote cluster Note that if qstat is in the clusters PATH setting this to just qstat will work A new template job pbs is added to the list of available templates This is the job submission script for PBS This script should roughly follow this design bin bash PBS 1 nodes 1 ppn 8 PBS o gen x id optstep out PBS e gen x id optstep err PBS
18. convergence criteria and more KPOINTs 6 Same as before but with more KPOINTs This is only one of many possible optimization schemes that may work for crystals It may need to be modified to work for your particular system Generated on Thu Jun 2 2011 12 22 36 by Doxygen
19. ies of optimization steps optsteps that are to be performed in sequence on a structure Each optimization step consists of a set of input file templates for the queuing system and optimizer to be used and the structure is updated after each completes So if an optimization scheme contains three optimization steps a stucture s lifecycle is 1 Generation of initial structure Perform optstep 1 on initial structure Update structure from the results of optstep 1 Perform optstep 2 on current structure result of optstep 1 Update structure from the results of optstep 2 Perform optstep 3 on current structure result of optstep 2 Update structure from the results of optstep 3 OO oN oT OP om NM Current structure result of optstep 3 is either accepted into the breeding pool or discarded depending on its enthalpy relative to the other optimized structures 4 2 2 More details The efficiency of searching a potential energy surface for a global minimum can be sig nificantly improved by moving each candidate structure to the nearest local minimum i e performing a geometry optimization The differences between searching with and without carrying out these local optimizations are explored in detail in Woodley SM Cat low CRA Comp Mat Sci 2009 45 1 84 95 Available at http linkinghub elsevier com retri Why not just perform a single geometry optimization on each structure Stochastic search techniques such as XtalOpt will of
20. igure nstep 100 Template Tacna at forc_conv_thr 1 0D 2 Optimization 1 calculation relax pruna pseudo_dir san projects3 ezurek software src espresso 4 1 2 pseudo Optimization 4 outdir tmp Optimization 5 Optimization 6 ESYSTEM ibrav 0 celldm 1 1 0 nat hnumAtoms ntyp numSpecies ecutwfc 20 D0 SELECTRONS electron_maxstep 1000 conv_thr 1 D 6 Add Remove Help J mixing_beta 0 3D0 Save Opt Scheme Load Opt Scheme amp IONS userl user2 CELL a cell_dynamics bfgs user3 cell_factor 2 0D0 nserk press 1 03 S Save Session Resume stored session Optimized 0 Running 0 Failures 0 Begin Hide On the next tab load the optimization scheme that is distributed with the source code un der the samples directory The scheme that we want is named pwscf xtalopt scheme If the source code is not available the scheme file can be obtained by clicking the Orig inal Format link at the bottom of the page here For more details on optimization schemes see Optimization Schemes Each PWscf input file will need to be edited to specify 1 The pseudo_dir containing the pseudopotential files on the remote cluster and 2 The pseudopotentials for each atom under ATOMIC_SPECIES Take a moment to look through each file for each optimization step Notice the keyword values in the job pbs templates These are used to enter in formation that
21. information about MPI executable locations etc Perhaps the easiest method to find the correct PBS script is to run some trial sub missions by hand and then replace the structure search specific information with the appropriate keywords once a working script has been generated A handy trick for monitoring jobs outside of XtalOpt is to include the following line in job pbs PBS N description gen x id toptstep This will name each job for example xtalSearch 3x4 2 where xtalSearch is a user specified description of the search and 3x4 2 means that it is the fourth structure in the third generation running its second optimization step Skip to next section 2 5 2 Using a remote SGE cluster K n PBS Queue Configuration v Host parity ccr buffalo edu SSH Port 22 User davidlon Working directory Server user davidlon proj Ti204 Working directory Local home dl xtaloptCalcs Ti204 Description Ti204x6 Path to qsub qsub Path to qdel qdel Path to qstat qstat VY OK Cancel Todo Get screenshots of SGE config dialog Select SGE from the list of Queues and then click the Configure button A new window will prompt for e host The hostname of the SGE cluster s head node user The username used to log into the cluster Generated on Thu Jun 2 2011 12 22 36 by Doxygen 12 XtalOpt Tutorial e Working directory Server A directory that is readable writable by user
22. is specific to a search or structure when the actual input files are written prior to job submission Click the Help button for a full listing of the available keywords Be aware that every PWscf CASTEP installation is different and it is almost certain that the job pbs file included with this scheme will not work on any cluster other than the Zurek group s parity cluster at SUNY Buffalo s Center for Computational Resources Generated on Thu Jun 2 2011 12 22 36 by Doxygen 8 XtalOpt Tutorial lt may take some experimentation to get jobs to submit successfully and you may need to contact the mantainers of the cluster for assistance for information about MPI ex ecutable locations etc Perhaps the easiest method to find the correct PBS script is to run some trial submissions by hand and then replace the structure search specific information with the appropriate keywords once a working script has been generated XtalOpt expects PWscf to use the following filenames pw x lt xtal in gt xtal out Skip to next section 2 4 4 CASTEP ETA XtalOpt Y y YY Structure Limits Optimization Settings Search Settings Progress Plot Log Queue PBS___v Configure percent BLOCK LATTICE _CART Optimizer CASTEP w Configure cellVectorlAngstronts Toe AAA cell Vector2Angstroms s tarce my scellVector3Angstroms Optimization 1 spercent ENDBLOCK LATTICE_CART percent BLOCK POSITIONS_FRAC
23. m Constrain the angles to be between 60 and 120 degrees and the volume from between 1 and 500 cubic angstrom Specify a minimum interatomic distance of 0 5 angstrom Note that due to the angle adjustment described in the CPC 2010 publication 60 120 degrees is the largest range of cell angles that XtalOpt will generate 2 4 Optimizer setup XtalOpt currently supports the VASP GULP PWscf and CASTEP codes for performing geometry optimizations Each is detailed in its own section below Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 4 Optimizer setup 5 2 4 1 VASP Ke XtalO pt MATO Structure Limits Optimization Settings Search Settings Progress Plot Log Queue PBS v Configure filename Optimizer VASP v Configure Template INCAR ay cutput options z LWAVE FALSE write or don t write WAVECAR Optimization 1 LCHARG FALSE write or don t write CHG and CHGCAR Opemiestioni2 LELF FALSE write ELF Optimization 3 Optimization 4 Piet ionic relaxation ee NSW 20 number of ionic steps IBRION 2 2 conjucate gradient 1 Newton like ISIF 2 3 relax everything 2 relax ions only 4 keep volume fixed precision parameters EDIFF 1E 3 1E 3 very low precision for pre relaxation use 1E 5 next EDIFFG 1E 2 usually 10 EDIFF PREC med precision low med high accurate Add Remove Help Save Opt Scheme Load Opt Scheme electronic relaxation
24. nenuisnell cosacos BERS Babee we a Ee 24 422 MOPS OBS one baw a RR A A a i 24 4 3 Optimization scheme user interface 0 25 4 3 1 Optimization step list 25 4 3 2 Add new optimization Step 26 4 3 3 Remove current optimization Step 26 4 3 4 Selecttemplate 26 4 3 5 Template editor e ooo be ee sra 26 430 Gavescheme rs vas oeras raara a A 26 4 3 7 Resume scheme ao s ag saie aese ee eee 26 4 4 Howto build an optimization scheme 26 4 5 Howto save an optimization scheme for later 27 4 6 Howto load an optimization scheme 28 47 Wall saved co ea 6464 44 G4 soe Gon ere e A 28 4 8 Suggestions for optimization schemes 2 2 28 48 1 Crystals XtalOp s 2 coi ee ee d a a ee 28 Generated on Thu Jun 2 2011 12 22 36 by Doxygen Chapter 1 User documentation e XtalOpt Tutorial Demonstrates how to use XtalOpt with the various supported optimizers and queuing systems Optimization Schemes What are Optimization Schemes and how are they used e Saving and Resuming Sessions in XtalOpt How to continue a session that has stopped User documentation Generated on Thu Jun 2 2011 12 22 36 by Doxygen Chapter 2 XtalOpt Tutorial 2 1 Contents Launch XtalOpt Enter composition and restraints Optimizer setup VASP
25. nterface rae xtalopt TTE Structure Limits Optimization Settings Search Settings Progress Plot Log Queue PBS y _Configure _ F i ename Optimizer VASP v Configure 4 output options v Template LINCAR LWAVE FALSE write or don t write WAVECAR Optimization 1 _ LCHARG FALSE write or don t write CHG and CHGCAR as LELF FALSE write ELF Optimization 4 Optimization 5 ionic relaxation Optimizadon 6 NSW 20 number of ionic steps IBRION 2 2 conjucate gradient 1 Newton like ISIF 2 3 relax everything 2 relax ions only 4 keep volume fixed precision parameters EDIFF 1E 3 1E 3 very low precision for pre relaxation use 1E 5 next EDIFFG 1E 2 usually 10 EDIFF PREC med precision low med high accurate Add Remove 3 Help Save Opt scheme Load Opt scheme J electronic relaxation ISMEAR 5 5 tetraedon 1 N Methfessel userl ENCUT user3 cutoff energy ukara 0 PSTRESS userZ A ISYM 0 user3 400 user4 5 Save Session Resume stored session Optimized 0 Running 0 Failures 0 Begin Hide We will use the above screenshot as we describe the process of creating saving and loading optimization schemes The numbers indicate 1 List of optimization steps Button to add new optimization step Button to remove current optimization step Template selection menu Template editor Butt
26. nthalpy structures with cell volumes around 180 cubic angstroms Armed with this data we can update the starting volume on the Cell Initialization tab mid run to reflect this new piece of information that the search has provided us Many of the other parameters governing structure generation and algorithm specifics can be similarly modified during a search without the need to restart the algorithm The plot is also interactive zooming and panning are possible using simple mouse controls Clicking on a structure s point on the plot will load it in the main Avogadro Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 10 Further reading 19 window allow all the same functionality as described above in Monitor progress 2 10 Further reading From here you may be interested in Optimization Schemes Saving and Resuming Sessions in XtalOpt Generated on Thu Jun 2 2011 12 22 36 by Doxygen 20 XtalOpt Tutorial Generated on Thu Jun 2 2011 12 22 36 by Doxygen Chapter 3 Saving and Resuming Sessions in XtalOpt 3 1 Contents e How to save your session How to resume your session 22 Saving and Resuming Sessions in XtalOpt 3 2 How to save your session XtalOpt will write a small file named xtalopt state to its working directory that contains the information necessary to resume the session at a later time The file can be rewrit ten manually by clicking the Save Session button highlighted above
27. on steps Notice the other keyword values in the job pbs templates These are used to enter information that is specific to a search or structure when the actual input files are written prior to job submission Click the Help button for a full listing of the available keywords XtalOpt expects VASP to use the default filenames mainly POSCAR CONTCAR and OUTCAR Skip to next section Generated on Thu Jun 2 2011 12 22 36 by Doxygen 6 XtalOpt Tutorial 2 4 2 GULP Re XtalO pt 2 O Structure Limits Optimization Settings Search Settings Progress Plot Log Queue Local y Configure opti conj conp Optimizer GULP v Configure Switch_minimiser bfgs gnorm 0 5 cel Template xtal ain as b C alphaDeg sbetaDeg gammaDeg Optimization 1 frac coordsFrac species Ti 2 196 O 1 098 buck Ti Ti 31120 1 0 1540 5 25 15 O O 11782 7 0 2340 30 22 15 Ti O 16957 5 0 1940 12 59 15 lennard 12 6 Ti Ti 1015 001015 TiO 1015 Add Remove Help Save Opt Scheme Load Opt Scheme userl user2 user3 user4 Save Session Resume stored session Optimized 0 Running O Failures 0 Begin Hide On the next tab we choose GULP for the local optimizer and enter a template for GULP to use Select GULP as the Optimizer and xtal gin as Template Next fill out the text field on the right with the following template opti conj conp switch_minimiser bfgs gnorm
28. on the cluster used when performing optimizations e Working directory Local A directory that is readable writable by the current user on the local computer This is where the final structures and resume files are written Description Used for the description keyword in input templates Path to qsub Where to find the qsub executable on the remote cluster Note that if qsub is in the clusters PATH setting this to just qsub will work Path to qdel Where to find the qdel executable on the remote cluster Note that if qdel is in the cluster s PATH setting this to just gdel will work Path to qstat Where to find the qstat executable on the remote cluster Note that if qstat is in the clusters PATH setting this to just qstat will work Todo Get template for job sge scripts A new template job sge is added to the list of available templates This is the job submission script for SGE lt may take some experimentation to get jobs to submit successfully and you may need to contact the mantainers of the cluster for assistance or information about MPI executable locations etc Perhaps the easiest method to find the correct SGE script is to run some trial submissions by hand and then replace the structure search specific information with the appropriate keywords once a working script has been generated For more details on optimization schemes see Optimization Schemes Skip to next section 2 5 3 U
29. on to save current optimization scheme to file N 2 np wo YN Button to load optimization scheme from file 4 3 1 Optimization step list This list shows the currently available optimization steps in the order that they will be performed The optstep that is currently selected for editing is highlighted and the editable optstep can be selected by clicking the appropriate entry Generated on Thu Jun 2 2011 12 22 36 by Doxygen 26 Optimization Schemes 4 3 2 Add new optimization step Clicking this button will append a new optimization step to the optstep list The new optstep s templates will be copies of the currently selected optstep s templates 4 3 3 Remove current optimization step Click this button to delete the currently selected optimization step 4 3 4 Select template This menu contains the filenames of the templates that are required by the currently selected queuing system e g PBS SGE local and optimizer The currently selected template is displayed in the template editor and selecting a different template will update the editor 4 3 5 Template editor This text editor is used to view and edit the currently selected template for the current optstep 4 3 6 Save scheme This button will prompt for a location to save a scheme file containing the current opti mization step 4 3 7 Resume scheme This button will prompt for an existing scheme file to load 4 4 How to build an optimization scheme
30. read only mode Read only mode will not generate new structures or submit ge ometry optimizations Note If you are considering resuming a read only session take a look at the results txt file in the working directory It contains a list of all structures sorted by enthalpy with additional useful information This can save some time when trying to locate the most stable structure of a old search The working directories for XtalOpt are relocatable meaning that the directory contain ing xtalopt state and the gen x id structure folders may be moved tarred zipped etc and still be resumed at a later time from a different location on the filesystem or even a different computer Generated on Thu Jun 2 2011 12 22 36 by Doxygen Chapter 4 Optimization Schemes 4 1 Contents e Overview What are optimimization schemes and why use them Ina nutshell More details Optimization scheme user interface Optimization step list Add new optimization step Remove current optimization step Select template Template editor Save scheme Resume scheme e How to build an optimization scheme How to save an optimization scheme for later e How to load an optimization scheme e What is saved e Suggestions for optimization schemes Crystals XtalOpt 24 Optimization Schemes 4 2 Overview What are optimimization schemes and why use them 4 2 1 In a nutshell An optimization scheme is a ser
31. sing a remote SLURM cluster E SLURM Queue Configuration 2 Y es Host parity cer buffalo edu SSH Port 22 User davidlon Working directory Server user davidlon proj Ti204 Working directory Local home dl xtaloptCalcs Ti204 Description Ti204x6 Path to sbatch sbatch Path to scancel scancel Path to squeue squeue O cance Generated on Thu Jun 2 2011 12 22 36 by Doxygen 2 5 Queue setup 13 Select SLURM from the list of Queues and then click the Configure button A new window will prompt for host The hostname of the SGE cluster s head node user The username used to log into the cluster e Working directory Server A directory that is readable writable by user on the cluster used when performing optimizations e Working directory Local A directory that is readable writable by the current user on the local computer This is where the final structures and resume files are written Description Used for the description keyword in input templates e Path to sbatch Where to find the sbatch executable on the remote cluster Note that if sbatch is in the clusters PATH setting this to just sbatch will work Path to scancel Where to find the scancel executable on the remote cluster Note that if scancel is in the cluster s PATH setting this to just scancel will work Path to squeue Where to find the squeue executable on the remote cluster No
32. te that if squeue is in the cluster s PATH setting this to just squeue will work Todo Get template for job slurm scripts A new template job slurm is added to the list of available templates This is the job submission script for SLURM It may take some experimentation to get jobs to submit successfully and you may need to contact the mantainers of the cluster for assistance or information about MPI executable locations etc Perhaps the easiest method to find the correct SLURM script is to run some trial submissions by hand and then replace the structure search specific information with the appropriate keywords once a working script has been generated For more details on optimization schemes see Optimization Schemes Skip to next section Generated on Thu Jun 2 2011 12 22 36 by Doxygen 14 XtalOpt Tutorial 2 5 4 Running optimations locally DE es avogadro 2 sl e 00 Local working directory home dlodtaloptCalcs Ti204 OK SH Cancel Select Local from the list of Queues and then click the configure button A new window will prompt for e Local working directory A directory that is readable writable by the current user on the local computer This is where the final structures and resume files are written If the optimizer s executable vasp gulp pw x castep etc is not in your system path you will need to specify the location of the executable by clicking the Configure
33. ten need to perform geometry optimizations on structures that are far from a stationary point on the potential energy surface For example the randomly generated structures in the first generation of an evolutionary search are often highly disordered with unrealistic atomic separations If these struc tures were to be optimized in a single step with accurately small convergence criteria it would be quite expensive Also it is more than likely that most of the optimizations would not finish successfully before reaching the maximum number of geometry steps allowed by the optimizer or specified in the input A second issue is that complex structures periodic crystals for example often have so many degrees of freedom that conver gence in a single step is difficult from a poor starting point consider the effect on atomic coordinates when a unit cell s translation vector is modified The first problem effectively optimizing to small convergence can be solved by imple menting an optimization scheme that optimizes to successively smaller convergence cutoffs Generated on Thu Jun 2 2011 12 22 36 by Doxygen 4 3 Optimization scheme user interface 25 The second problem can be addressed by reducing the degrees of freedom in the early optsteps and only optimizing everything once each component has individually con verged to a reasonable parameterization See Suggestions for optimization schemes for examples 4 3 Optimization scheme user i
34. timization succeeds create another set of input files with the desired convergence criteria for all degrees of freedom 6 Manually submit the new optimization step If it fails try the ideas above until it converges 7 Once the structure has converged to the desired level of accuracy try to opti mize another randomly generated structure using the optsteps that succeeded previously Refine them if needed 8 Once you have successfully optimized enough random structures that you are confident in your method gather all of the inputs used and write your scheme from them The scheme may be written by copying each input file into the template editor with the appropriate optstep and template selected of course and replacing the structure specific information with the appropriate keywords Click the Help button for the com plete list of Keywords We have found that the optimization schemes are surprisingly transferable within an optimizer so once you have a working optimization scheme for a given optimization code only minor tweaks usually to the energy cutoffs etc are necessary to use itona different chemical system 4 5 How to save an optimization scheme for later Once you have written your optimization scheme you will want to save it for fast retrieval later otherwise you will need to copy paste and edit all of the templates again To save simply click the Save Opt Scheme button and enter an appropriate filename with an

XtalOpt User Guide

Contents

Download Pdf Manuals

Related Search

Related Contents