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cluster 1.2 user manual Contents

1. When running the cluster program don t worry about the fact that in the PROGRAM SETTINGS section the default method for the program is echoed as opposed to template THEHHHEHHIHHIHIHHHIHHIHHIHHIHHHHHIHHHHHHE PROGRAM SETTINGS WHHHHHAARARH RARA ARA RH ARHAAHA System command g09 lt in s inp gt gt out s out 2 gt amp 1 30 processors 8 memory in MB 6000 method B3LYP 3 21G max opt 50 max scf 50 The input file did contain method template the default method is echoed here but the method s string echoed in the PROGRAM SETTINGS is not in the templates anymore so its value will not be used the run References 1 Anastassia N Alexandrova and Alexander I Boldyrev Search for the jg n 5 7 lowest energy 11 structures using the ab initio gradient embedded algorithm GEGA Elucidation of the chemical bonding in the lithium clusters J Chem Theory Comput 1 566 580 2005 Anastassia N Alexandrova Alexander I Boldyrev You Jun Fu Xin Yang Xue Bin Wang and Lai Sheng Wang Structure of the NaCl x 1 4 clusters via ab initio genetic algorithm and photo electron spectroscopy J Chem Phys 121 12 5709 5719 2004 Anastassia N Alexandrova H H20 clusters Microsolvation of the hydrogen atom via molecular ab initio gradient embedded genetic algorithm GEGA J Phys Chem A 114 12591 12599 2010 D M Deaven and K M Ho Molecular geometry optimization with a genetic algorithm Phys
2. In the output we see that the final population has the new structure optimized and indeed named H2S ADF 4 THHHHHHHHHHHHHHHHHHHH ALGORITHM END CONSIDERED 0 MATINGS JA4AHBHHHBHBHHHHPHPHHHHHHHHHHBE The run generated 1 candidate HHMAHMARARARAAARARARARAAARAARARARA FINAL POPULATION HAHAHAHA AR ARA AR ARA ARAARAA RA H2S_ADF_3 population E 1 280270003 R 183 440 v 124 91 H2S_ADF_4 population E 1 280059430 R 183 484 v 121 957 THEHHHHIHHIHHIHIHHHIHIHIHHIHIHIHIHIHHIHHIHHHHHHHHEI TIMINGS GARBHHHBHEIHHIHHIHIHHHHHIHIHHIHHIHIHHHIHHIHIEHHHIHHIHIEE From the csv file it is easy to see that the energy difference is only 0 135 kcal mol and the repulsion resolutions are only 0 044 hartree different while the comment for it suggests that it came from a reoptimization of the initial population name E Eh dE Eh dE eV dE kcal mol R Eh Freq cm 1 comment H2S8 ADF 3 1 280270003 0 000000000 0 000000000 0 000000 183 440 124 91 Population H28 r2 1 H2S_ ADF 4 1 280059430 0 000210573 0 005729991 0 132137 183 484 121 96 Initial 6 6 Nooptimization runs A somewhat peculiar use of the cluster program but considered a feature is to use it to only generate a library of structures that the cluster program would generate without automatically optimizing them This is achieved by setting the max_ freq to 0 since that flags the program that no frequency calculations are allowed Since there is no point in running a geometry optimization because any
3. Rev Let 75 2 288 291 1995 XYZ file format URL http en wikipedia org wiki XYZ file format Jmol an open source java viewer for chemical structures in 3d URL http jmol sourceforge net Frank Neese The orca program system WIREs Comput Mol Sci 2 72 78 2012 URL http cec mpg de forum M J Frisch G W Trucks H B Schlegel G E Scuseria M A Robb J R Cheeseman J A Mont gomery Jr T Vreven K N Kudin J C Burant J M Millam S S Iyengar J Tomasi V Barone B Mennucci M Cossi G Scalmani N Rega G A Petersson H Nakatsuji M Hada M Ehara K Toy ota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai M Klene X Li J E Knox H P Hratchian J B Cross V Bakken C Adamo J Jaramillo R Gomperts R E Stratmann O Yazyev A J Austin R Cammi C Pomelli J W Ochterski P Y Ayala K Morokuma G A Voth P Salvador J J Dannenberg V G Zakrzewski S Dapprich A D Daniels M C Strain O Farkas D K Malick A D Rabuck K Raghavachari J B Foresman J V Ortiz Q Cui A G Baboul S Clif ford J Cioslowski B B Stefanov G Liu A Liashenko P Piskorz I Komaromi R L Martin D J Fox T Keith M A Al Laham C Y Peng A Nanayakkara M Challacombe P M W Gill B Johnson W Chen M W Wong C Gonzalez and J A Pople Gaussian URL http ww gaussian com Gaussian Inc Wallingford
4. cluster program will determine the number of unpaired electrons from the multiplicity setting and uses spin_polarization d in the template file to do so For the frequency analysis calculation the default is to use analytical frequencies so a user has to use templates for functionals where analytical frequencies are not available The default frequency calculation template also contains ScanFreq 1000 0 for recalculating the imaginary frequencies The cluster program will replace the initially calculated frequency values as reported in the regular Vibrational and Normal Modes table with the new value from the scan frequencies output section for all vibrations whose old frequency is within 0 01 cm of the initial value so that all frequency values for degenerate modes are replaced The memory placeholder is not used in the templates The energy value is taken from the regular expression match of every line in the output file with r Total Bonding Energy 0 9 ADF Example 1 The example below is for an unrestricted calculation which requires a quite lengthy method line in the input to achieve this Only a small amount of the default values of the keywords may need to be reassigned In this case that has been kept to a minimum name Si4Li Note the method argument should be a single long string the split over two lines should not be in the real input file program ADF method XC nGGA BLYP nEND nBASI
5. the test jobs will be executed before the program exits test int 0 If Z 0 runs a single set of jobs on a 3D cluster and exits 3 3 Candidate definition The candidates to be considered are built by positioning fragments A fragment may consist of a single atom or a group of atoms The cluster program has a set of pre defined built in element and fragment libraries that are already ini tialized before the input file is parsed The element radii are taken from the WebElements web site The frag ments are ORCA optimized fragments using PBE TZVPP and VDW06 The somewhat arbitrary fragments H2 He2 N2 N OH CO H20 H20 NH3 NH3 CO MeOH CH30H EtOH CH3CH20H BeF BeF2 and BeCI2 BeCls are provided but the user can re define fragments and elements at will Whenever the parser encounters definitions for elements elements fragments fragments or the request to use a user defined element or fragment library eLementlib and fragmentlib respectively the directives are immediately processed so that the internal list of elements or fragments is immediately changed Thus these four keywords may occur multiple times in the input file Whenever a fragment is defined its atoms will have the properties of the elements as they are defined in the element library at that time of execution This way a redefinition of an element does not affect the existing fragments but will only affect fragments that are defined after the element was redefined Only aft
6. 0384564056 2 1715810038 1 1502910739 S 0 0607162347 2 0844603286 0 2061706737 9 ignored inf H 1 8611392375 1 1350155879 1 15 H 0 3947405456 1 3078773930 0 1021772479 S 1 7780389666 1 1034449824 0 0433127875 26 Qo m m umm 1 8784401317 1 3354105540 1 8510702418 0 9318295376 0 0384564056 0 0607162347 1 0099340188 0 3046479439 0 9959604779 0 9915431837 2 1715810038 2 0844603286 1 1544075407 0 2052837443 0 2046679226 0 1432715487 1 1502910739 0 2061706737 The input file should not request a reoptimization since H2S ADF 3 is still OK A regular restart will detect theinf for the energy ofthe second candidate which we called ignored and reoptimize only this candidate The input file looks the same as the earlier reoptimization one just without the reoptimization line itself name H2S ADF program ADF method XC nLDA SCF VWN nEND n nBASIS ntype TZP ncore Large nEND processors 8 memory 6000 multiplicity 1 charge 0 composition H2S 3 matings 0 energy resolution 1 repulsion resolution 1 energy window 1 fragmentlib home rkanters work cluster H2S fragments xyz Since we ran the input in a new folder where only a population library existed and not the all library and converged library the newly optimized structure numbers start with 1 above the largest one in the population library 1 e 4 The default duplicate checking will start with an empty list of converged structures to check against
7. 32 8 0 0514 0 0973 0 0505 0 0517 0 0882 0 0656 0 268 0 524 0 3122 51 8 0 1213 0 116 0 0834 0 1202 0 17 0 0366 0 0292 0 1557 0 0408 92 3 0 3474 0 4314 0 3077 0 3456 0 4123 0 4505 0 1408 0 0505 0 1607 9 test 3D 0 021712211 154 932 533 20 Build 3D scale 1 H 1 1518252540 2 1202304363 0 4178235809 H 0 1886989782 3 6200137545 0 4001815406 S 0 0961472187 2 3469205038 0 0118190440 H 1 2367631676 1 3648574145 0 1764851672 H 2 8606317737 2 0233658701 0 8145101256 S 2 5485261164 1 0962064923 0 0990490047 H 3 0582649197 1 9205378907 0 6013266369 H 2 4364364714 0 2065601384 0 2210352951 S 2 0181987237 1 4756368884 0 1130812179 THHHEHIHHIHEHHIHHHHIHIHIHHHHIHIHIHHHIHIHIHHHHHIHHHEHE DONE AREHEHIHIHIHIHEHIHIHIHIHHIHIHIHIHIHIHIHIHIHHIHIHIHIHHHIHIHHIHEIHE Thus we can use the cluster input file but with a larger number of geometry cycles for production runs and with the test 1 removed or commented out 6 2 Multiple runs It may be beneficial to run the same cluster search multiple times and refilter the viable or population can didates found from all runs combined This is most easily done by running each input in its own folder It may be useful to make sure that the name keyword contains something that allows one to retrace which run generated a particular candidate while keeping the rest of the input the same In the examples H2S folder this is done in the folders r1 r2 r3 r4 an
8. 5 5 4 MOPAC Requirements The MOPAC environment variable should be set to the full path of the MOPAC executable exe file since the cluster program executes MOPAC directly Defaults The default method is PM7 17 Specifics Since MOPAC does not write output to the standard output stream it can not be redirected to be ap pended to an earlier output in the program call itself Thus the final output file for a viable candidate only consists of the latest i e frequency calculation Since it wasn t clear how to restart an optimization using the Hessian from an earlier frequency calcula tions the reoptimization part is not implemented in the candidate optimization cycle so only multiple starts of optimizations will be performed up to max freq times The default max opt may be too small Since MOPAC is quite fast it doesn t hurt to make max opt a lot larger Consider using PRECISE after the method as well e g PM7 PRECISE This will tighten convergence criteria for the optimizations MOPAC reports the heat of formation energy in kcal mol which the cluster program converts to hartree units the memory and processors are not used in the templates Because the optimization and the frequency calculation report energies slightly differently two regular expression patterns are used when matching the lines from the output file The last match encountered will be the energy that the cluster program reports and uses for compari
9. H20 L so that the libEFP program will use it s own H2O fragment name H20 4 program EFPMD multiplicity 1 charge 0 composition H20 L 4 nfreq cutoff 10 restart 0 2D 5 3D 30 matings 50 repulsion resolution 0 2 6 Cluster usage examples This section shows some examples on approaches of using the cluster program The input and output files are stored in the examples folder provided 6 1 Testing input To test an input file that will be used later with the computational method planned a test run calculation may be performed The input file shown below and available in the examples H2S test folder has already the planned build mating and acceptance keywords but since it contains the line test 1 only a single test of the program templates available will be executed Note that in this case the definition of H2S is stored externally in the H2S folder s fragments xyz file since it is not a fragment in the standard library and we will be using it a few times in these examples 20 name H2S test 1 program MOPAC method PM7 PRECISE charge 0 multiplicity 1 composition H2S 3 1D 2 2D 5 3D 20 matings 30 energy resolution 5e 4 repulsion resolution 2 fragmentlib fragments xyz After executing the cluster program with this input file the folder will contain the input and output files for each of the test runs using the name test 3D as the root name for the 3D build candidate that is generated The resultin
10. The use of templates can be a bit tricky so one may want to make use of utility runs to verify that the input files are created as you think the templates should as well as that the computational program does not have problems with it If the latter were to happen during a regular run of the cluster program it may quickly generate a lot of Failed candidates The easiest way to get started using templates is to use the cluster program to generate the template files that it needs based on the defaults for the program Here we will choose a Gaussian input and work with a system for which we have to define the basis set 1 e the Li4 system using the def2 TZVPP basis set and B3LYP calculations Since initially the folder examples tempate does not contain g09 template files the program will create them for us and exit We will use two input files Li4a in and Li4b in where the only difference is that the Li4b in does not have the test 1 line in it since that is the one that will actually do the cluster search The Li4a in will be used twice first to create the template files needed and second to run the tests on the template files after they have been modified The Li4a in looks as follows name Li4 test 1 program g09 method template processors 8 memory 6000 composition Li 4 29 multiplicity 1 charge 0 2D 2 3D 5 matings 10 The output generated tells us that indeed the three template files were written HHMAHMARAAARAAAARARARARA
11. always positioned before the ones following the a charge int 1 The charge of the candidate multiplicity int 1 The multiplicity of the candidate The cluster program will check and exit if the number of electrons in the candidate 1s incompatible with the provided multiplicity 3 4 Population initialization In order for a genetic algorithm to work an initial population of acceptable candidates needs to be available The population may be initialized by reading the population from a previous run and or by building and optimizing a set of new candidates Building candidates Based on the composition a prototype is created after the whole input file is parsed in which every fragment is centered at the origin i e all fragments are on top of each other The new candidate is a clone of this prototype in which the fragments are in a random sequence randomly rotated around their center and depending on the dimensionality of the build nD with n 1 2 3 translated along a random n dimensional vector The translation along that vector is such that the newly placed fragment atoms will at most touch one or more atoms in the already placed fragments so as to avoid inter atomic distances that are too small which could cause computational problems The atom size is the sum of the element radius and a possibly non zero extra radius associated with the definition of the fragment to whom the atom belongs see also Section 4 3 Finally the translati
12. converged geometry can not be checked 27 to see whether it is at a minimum or maximum in the PES the program will not even start the optimization cycles but abort the candidate and append its structure to the aborted library An example where this is done to create the library of structures that are built is provided in the exam ples noopt folder The input file also shows the use of in the composition for trying to build an NH3 surrounded by twenty water molecules The structural information for the two fragments were copied from the default fragment library which is stored in the 1ib folder of the cluster program In order to not have the molecules touch an extra radius of 0 3 for each fragment is introduced The value is half of the differ ence of an H bond in water 1 7 from which the sum of the H and O radii are subtracted 0 37 and 0 73 respectively name noopt composition NH3 1 8 H20 20 charge 0 multiplicity 1 3D 20 matings 0 max_freq 0 fragments 3 H20 0 3 ORCA PBE VDW06 TZVPP PModel TightSCF Opt UseSym 0 0 000000 0 000000 0 066734 H 0 000000 0 763595 0 529847 H 0 000000 0 763595 0 529847 4 NH3 0 3 ORCA PBE VDW06 TZVPP PModel TightSCF Opt UseSym N 0 000166 0 079017 0 000004 H 0 470994 0 317856 0 815661 H 0 470988 0 317858 0 815660 H 0 941816 0 317791 0 000005 The result of running this input is that only anoopt_aborted xyz file will be created that contains each structure built To generate o
13. hopes to be able to increase the population by executing more builds before starting the sequence of matings 3 5 Cluster optimization Since the goal is to build a population of candidates reflecting the geometry at minima in the PES any can didate that is generated either by a build or mating procedure needs to have its geometry optimized In order to optimize the candidates calculations are executed by a computational program defined with the program keyword The type of calculation performed may be a geometry optimization frequency calculation and 1f the program allows for it a restart of a geometry optimization using the Hessian from the previous frequency calculation The final geometry is always read from the computational program output and if the reorient flag is not zero the structure is reoriented in an attempt to make visual comparison with programs like Jmol easier If any calculation performed by the computational program encounters problems e g SCF convergence issues causing the generated output file not to contain the information needed to decide what to do with the result a status line with Failed x where x is the return code from the call to the computational program is printed before the candidate is added to the aborted library and the optimization is aborted For example in the output below the frequency calculation that followed the unconverged geometry optimzation caused the computational program to return the
14. opt 3 1821 max scf 3 memory 3 14 18 method 3 12 14 31 multiplicity 5 19 20 name 3 4 22 25 nfreq bifurcate 7 8 29 nfreq cutoff 4 7 8 15 20 nfreq displacement 7 8 OUT DIR 2 processors 3 18 program 3 4 6 reoptimize 6 reorient 4 7 9 repulsion resolution 4 9 10 restart 6 24 scale 5 6 10 33
15. radii in the library of predefined elements are taken from the WebElements web site They are read from a file in the cluster program s library folder lib elements dat In order to provide more flexibility it is also possible to read a new definitions from a user specified files or by defining elements directly in the input file The file format is a sequence of one liners defining an element or a comment comment line element line comment line string element line string key string element name int Z float radius The radius is in If the key string is omitted element name will be used as the key Ifthe key string is present as in the examples below any text after the radius will be ignored The key is the string that needs to be used in fragment element names and or in the composition string of candidates One can define atomic ions as if it were an element e g F and Hg with the lines F F 9 1 2 f larger than the 0 71 Angstrom in the built in library Hg2 Hg 80 0 7 f smaller than the 1 49 Angstrom in the built in library and use it in the composition or in fragment definition s 4 3 Fragment library and fragments format The predefined library of fragments located in in the library folder of the cluster program 1ib frag ments xyz consists of optimized geometries calculated with ORCA using PBE TZVPP and VDWO6 In order to provide more flexibility it is also possible to read fragments from user specified fi
16. AARARAAAARRAR TEMPLATES HHHHRARARAR AAA ARMAR AA ARA AA AR AA AA RA Written template for Freq to g09 Freq Written template for Opt to g09 Opt Written template for ReOpt to g09 ReOpt WARNING Consider editing the template s before run Exiting In this case we need to modify all of the template files Since the Freq and ReOpt calculations can use the checkpoint file for the basis set information only the method s needs to be changed to B3LYP ChkBasis e g for the g09 Freq file chk root s chk mem memory dMB nproc processors d B3LYP ChkBasis FREQ NORAMAN geom check guess read scfcyc max scf d root s Frequency Calculation charge d multiplicity d The Opt template needs to define the method B3LYP Gen as well as the basis set to be used and becomes quite lengthy chk root s chk mem memory dMB snproc processors d B3LYP GEN opt maxcycle max_opt d sym loose scfcyc max_scf d root s Optimization charge d multiplicity d xyz s Li 0 S 6 1 00 6269 2628010 0 20540968826E 03 940 31612431 0 15916554089E 02 214 22107528 0 82869829707E 02 60 759840184 0 33856374249E 01 19 915152032 0 11103225876 7 3171509797 0 27449383329 If you are concerned about whether this will all work you may rerun the Li4a in file and check the test 3D files generated This was done redirecting the cluster standard output to the Li4a_again out file which showed that things should work fine
17. CT 2004 G te Velde F M Bickelhaupt E J Baerends C Fonseca Guerra S J A van Gisbergen J G Snijders and T Ziegler Chemistry with adf J Comput Chem 22 931 967 2001 URL http www scm com Julio Daniel Carvalho Maia Gabriel Aires Urquiza Carvalho Jr Carlos Peixoto Mangueira Sid ney Ramos Santana Lucidio Anjos Formiga Cabral and Gerd B Rocha Gpu linear algebra libraries and gpgpu programming for accelerating mopac semiempirical quantum chemistry calculations J Chem Theory Comput 8 9 3072 3081 2012 URL http OpenMOPAC net Ilya A Kaliman and Lyudmila V Slipchenko Libefp A new parallel implementation of the effective fragment potential method as a portable software library J Comp Chem 34 26 2284 2292 2013 URL http www libefp org 31 12 Covalent radius URL http www webelements com periodicity covalent radius Accessed May 5 2012 13 Hartree URL http en wikipedia org wiki Hartree 32 Index 1D 5 template 3 12 14 2D 5 test 3 4 3D 5 unchanged 12 build 6 charge 5 19 20 composition 5 13 25 duplicate 6 8 elementlib 3 4 25 elements 3 4 13 energy resolution 4 8 10 energy window 4 9 10 filter 4 15 fragmentlib 3 5 25 fragments 3 5 13 inputs 3 4 keep fail 7 9 mating energy 10 11 mating max 11 mating probability 10 11 mating rebuild 10 11 matings 12 max freq 7 8 18 20 27 max mate try 10 max
18. IHHHHHIHHHHHHHHHHHHHHHHHEHE FILTERED POPULATION 3738 3 IHHHIHEHIHPIHIHHIHIHIHIHHHIHIHHIHEHIHE H2S r2 3 Filtered E 0 023558996 R 163 685 v 759 80 H2S r3 28 Filtered E 0 023558354 R 163 576 v 369 30 H2S r3 4 Filtered E 0 023558056 R 163 867 v 17 70 H2S8 r5 3 Filtered E 0 023557837 R 163 538 v 731 20 H2S r4 3 Filtered E 0 023557507 R 163 550 v 738 60 H2S rl 5 Filtered E 0 023556889 R 163 536 v 96 90 H2S rl 4 Filtered E 0 023556492 R 163 663 v 28 80 H2S rl 3 Filtered E 0 023555334 R 163 507 v 26 70 6 4 Reoptimizing a library A library like the one created in the examples H28S a11 folder may be used as the initial population for a reoptimization using another program e g ADF The files for the ADF cluster run are stored in the ex amples H2S ADF folder First we will copy the filtered library into the ADF folder Since we will use the name H2S ADF the population file that will be reoptimized is called H28 ADF population xyz Be cause the cluster program will overwrite the population library file we will keep a copy called initial xyz around in case we need to redo this part rkanters ADF rkanters cp p all all flt xyz initial xyz rkanters ADF rkanters cp initial xyz H28 ADF population xyz The input file for the cluster run itself should now specifically state that a reoptimization should be done It is important that the composition string is exactly the same as the one u
19. LYP re compile r CBS N 0 K 0 9 eED CBS re compile r s Energy 0 9 eED NIter SE from g03 g09 Example A similar example as the ADF Si4Li one but now for Si Lig using Gaussian s g09 the only modification to use g03 is to change g09 in the program line to g03 Note that since g03 and g09 automatically change a calculation to an unrestricted one when the multiplicity is not 1 we do not have to stipulate UB3LYP but we could For clarity the maximum number of optimization and SCF cycles have been explicitly defined name Si4Li3 program g09 method B3LYP SDD processors 8 memory 6000 max_opt 50 max scf 50 multiplicity 2 charge 0 composition Si 4 Li 3 1D 2 2D 5 3D 10 matings 40 16 energy resolution 5e 4 repulsion resolution 2 5 3 ORCA Requirements The ORCA environment variable should be defined as the folder containing the ORCA executable which should also be in the path because the cluster program calls SORCA orca directly Defaults The default method in the template for ORCA is RKS B3LYP G SV Specifics The energy value is taken from the regular expression match of every line in the output file with r FINAL SINGLE POINT ENERGY 0 9 ORCA Example A Li cluster using ORCA name Li4 program ORCA method RHF SV processors 1 memory 200 multiplicity 1 composition Li 4 charge 0 1D 1 2D 1 3D 1 restart 0 force to start from scratch matings
20. S ntype TZP ncore Large nEND nUNRESTRICTED processors 8 multiplicity 2 14 charge 0 composition Si 4 Li 1 1D 2 2D 5 3D 10 matings 40 energy resolution 5e 4 repulsion resolution 2 ADF Example 2 This example shows how the definition of a fragment can be done by using the ragments keyword With only three fragments in the cluster it is not really necessary to generate 3D candidates since the centers of three fragments are always in a 2D plane thus the default of not creating 3D candidates 1s kept in place In this particular case the n req cutoff is set to a negative value because earlier runs showed that it was hard to get structures without slightly negative frequencies after the initial build A filter run see ADF Example 3 can be performed later to get rid of these name 3xCal2 program ADF method XC nGGA BLYP nEND n nBASIS ntype TZP ncore Large nEND processors 8 multiplicity 1 charge 0 composition CaI2 3 1D 2 2D 10 matings 40 nfreq_cutoff 5 0 energy resolution 5e 4 repulsion_resolution 4 fragments 0 0 2 8316 2 8316 ADF Example 3 An example of a filter utility run where now the candidates with negative frequencies are removed from the viable population keeping the original file intact but generating the newly filtered population in the file 3xCaI2 flt xyz as well as the associated csv file The repulsion resolution has been set to a bit more lenient value as well name 3xCal2
21. Seeding the population library Due to the randomness in the build and mating procedures one is not guaranteed to get the same populations every time a cluster job is run If you executed the previous steps in finding a library of H2S 3 molecules it is likely that you would indeed get the same lowest energy structure s but when I executed the same set of runs before I did not encounter the trimer in which all three dangling H s are on the same side of the ring of S atoms To make sure that the program will consider this candidate we will seed the initial population with a duplicate of the lowest energy structure encountered but with the one H on the first H2S moved to the other side We will also remove the other candidates from the file This edited population library will be used in another ADF calculation this time stored in the examples H2S ADF2 folder We also need to flag that the second one needs optimization The initial population file to be used now looks like note the inf in the second structure as well as the change in the z coordinate of the first hydrogen is changed to 1 15 9 H2S ADF 3 1 280270003 183 440 124 91 Population H2S r2 1 H 1 8611392375 1 1350155879 1 3998146899 H 0 3947405456 1 3078773930 0 1021772479 S 1 7780389666 1 1034449824 0 0433127875 H 1 8784401317 1 0099340188 1 1544075407 H 1 3354105540 0 3046479439 0 2052837443 S 1 8510702418 0 9959604779 0 2046679226 H 0 9318295376 0 9915431837 0 1432715487 H 0
22. atings attempted unchanged int 0 The maximum number of consecutive times that the population is allowed not to be changed by the mating cycles If set to a value lt 0 this parameter will not affect termination 4 File Formats In order to provide flexibility in the workings of the program several types of files will be created or inter preted The notation for the file formats description uses for optional contents and for a repetition of 0 or more items between the If the is followed by a symbol that symbol refers to the number of times this item is expected The symbol separates different options of which one should be present 4 4 Computational program templates The cluster program uses hard coded python strings with placeholders to generate input files for the com putational programs it interfaces with To provide more flexibility in the complexity of the input files it is possible to have the cluster program read template strings from files in the working directory If method is set to template the template files with Opt for a geometry optimization Restart for a restart of a geometry optimization using force constants Freq for a frequency analysis Hessian calculation concatenated to the program may be needed The restart and frequency calculation runs can expect the cluster program to have kept the restart information needed If the required template files are not found in the current working directory the prog
23. atoms string name float E float R float freq string string elementname float x float y float z natoms 13 S Computational program interfaces and examples This sections provides some information regarding the implementation of the interface to specific computa tional packages It is strongly recommended to check out the example inputs for the ADF program even if one doesn t have that available because it shows some more advanced use of some of the available features in the cluster program 5 1 ADF Requirements The ADFBIN environment variable needs to be defined as well as the adfrc sh or adfrc csh should have been sourced because the cluster program calls the ADF program by using SADFBIN adf with the command line option n set to the number of processors requested in the cluster input file Defaults The default method for ADF calculations uses the LDA SCF VWN functional with a TZP basis set and a large core The default geometry optimization criterion for the energy is tightened to 1e 4 from the more permissive le 3 hartree Specifics The ADF program requires the method of calculation and basis set to be provided in blocks containing multiple lines As a result of that Xn is needed in the method keyword unless one decides to use the template value Note that the former can lead to a very long single line for this keyword ADF expects in the input the number of unpaired electrons as opposed to the spin multiplicity so the
24. cluster 1 2 user manual Ren P F Kanters February 2015 Contents 1 Introduction 2 Getting started 2 1 PrerequisiteS ok E 3o b Pee 3 A XR PA UR Sa a vec EO ee 409 NES 2 2 NInstallati n 45 5 v Ie okie tg S ds etes aee ol SRL RT ty Ca 2 3 Running the cluster program lll ss 2 4 Cluster program output less ss 3 Methodology and keywords 3 1 Computational program settings 4 ee 32 Utility TUNS 223A Rie xoxo IRA UY ee Xe A X edes 3 3 Candidate definition us rs pu erc eee RA AIRE EC Per AUR 3 4 Population initialization 2 ees 3 3 Cluster optimiza on e it Sy Ae ale Re appe Ra a 3 6 Duplicate and acceptance determination a 3 7 Genetic operations ee 3 8 Termination seges ot E EL A A e UE AT PIECE A TE Bee 4 File Formats 4 1 Computational program templates ee 4 2 Element library and elements format en 4 3 Fragment library and fragments format 2222s 4 4 Candidate library format ee 5 Computational program interfaces and examples Sl ADE a ite A A ey eee VEA RA A DA rant en 5X2 09 803 E Pee A O A Rb RA EXE eU EB 5 9 ORCA ee utetur os a bt eye ea e tr n Stat ely ena Se Rv etai 54 MOPAC gebe Kod Rh een GE en E hi AA xod e dep Kore oS Se 5 2 ADEUEE iodo Beg ug ached ai ead de Sots dee RP pun 5 6 EEPMD 74 ox XR EU poe Re Sea dere UR dU Goa A E NE SUR Boas 6 Cluster usage examples 6 1 Testing mpu ichs ns dE cs aee dente A do de d dtd cle de fo
25. clusterl 0 tgz This will result in a cluster1 0 folder with the cluster py main program a lib folder containing the modules for the program as well as the predefined elements and fragments this pdf file some example queue submission script generating python scripts as well as an examples folder with input and output files for the the usage examples in Section 6 2 3 Running the cluster program The program needs to be called from the command line Ifone wants the output to be immediately written to the standard output which may be redirected to a file one can invoke the program using the u option for the python interpreter python u clusterl 0 cluster py d h v v inputfilename The cluster1 0 part refers to the full path of where the cluster py file resides The items between square brackets are optional and have the following meaning d debug mode generates a lot more output for debugging purposes h provides this help text and exits v v verbosity level v an integer should be gt 0 Default value is 0 for minimum output The structure of the input file is provided in Section 3 All sample output in this manual are from running the cluster program with the default verbosity level 2 4 Cluster program output Output folder Unless changed by setting the OUT DIR environment variable the cluster program writes output files in the directory where the program was invoked Setting the OUT DIR environment variabl
26. d r5 The input file in the r1 folder r1 in is as follows name H2S rl program MOPAC method PM7 PRECISE max opt 500 charge 0 multiplicity 1 composition H2S 3 1D 2 2D 5 3D 20 matings 30 energy resolution 5e 4 repulsion resolution 2 22 fragmentlib fragments xyz When the cluster runs are finished one may quickly see which runs generated which candidates in the popu lations by using grep on LINUX UNIX type systems only rkanters H2S rkanters grep _ r pop xyz rl H28 rl population xyz H28 rl 4 0 023556492 163 663 28 80 Build 2D scale 1 rl H28 rl population xyz H28 rl 18 0 021987541 144 368 3 40 Build 3D scale 1 r2 H28 r2 population xyz H28 r2 1 0 021989498 145 184 3 10 Build 1D scale 1 r2 H28 r2 population xyz H2S_r2 43 0 015519401 194 769 18 50 H2S r2 4 x H28 r2 4 r2 H28 r2 population xyz H2S_r2 4 0 012641140 180 537 13 10 Build 2D scale 1 r3 H28 r3 population xyz H2S8 r3 4 0 023558056 163 867 17 70 Build 2D scale 1 r3 H28 r3 population xyz H2S8 r3 13 0 022450474 159 517 22 30 Build 3D scale 1 r3 H28 r3 population xyz H28 r3 1 0 021960593 142 241 4 70 Build 1D scale 1 r4 H28 r4 population xyz H28 r4 6 0 022375850 160 280 31 90 Build 2D scale 1 r5 H28 r5 population xyz H2S r5 4 0 021980137 143 607 5 50 Build 2D scale 1 And it is immediately clear that in most runs the candidates were found during the build stage and not the mating cycles Since the population library is a subset of the viable librar
27. e is useful when running the program on a computational cluster where programs are executed on a compute node often from within in a folder located on a local file system By defining the OUT DIR environment variable the output can be directed to a more convenient folder e g the one from where the program was submitted to the queue Example scripts for an SGE and PBS queue system are provided in the distribution These are the actual scripts used to run the cluster program at the University of Richmond so they will require some modifications to make them work elsewhere Cluster standard output The text output generated is printed to the standard output stream Using the verbosity level of 0 it consists of the contents of the input file excluding any fragment definitions some information about the settings used in the program and the status of a candidate as the calculations for it progresses This status 1s a single line containing the name a message about the status the energy ofthe cluster in hartree or inf if not known yet the nuclear repulsion in hartree the lowest non zero vibrational frequency in cm or None if not known yet and a comment Cluster candidate libraries The cluster program will also generate several library files all ending with xxx xyz where xxx is the name of the library listed below These library files are multi step xyz files see Section 4 4 so they can be easily read by programs like Jmol The conten
28. e the input structure and the maximum are linear structures so the displacement in the opposite direction will result in the same solution and the nfreq bifurcate was set to 0 The output created does indeed show that a viable candidate was created from this THHHHHHHHHHHEHHHHHHHHHHHHEHHE CREATING 1D CANDIDATES 1 ZJHHEHRHHHHHHHHHHHHHEHHHHHEHEE Si4Li 1 1D Build E inf R 221 950 v None Si4Li 1 Opt 1 Converged E 0 575560063 R 228 936 v None Si4Li 1 Frequencies E 0 575560062 R 228 936 v 98 08557 Si4Li 1 Aborted E 0 575560062 R 228 936 v 98 08557 Si4Li 1p Opt 2 Not Converged E 0 640778775 R 268 970 v None Si4Li 1p Opt 3 Converged E 0 692719694 R 276 828 v None Si4Li lp Viable E 0 692719704 R 276 828 v 24 27 THHEHHHHEIHIPHHIHIHHHHEHHHHHHHHHEHHES INITIAL POPULATION 357 8 HEIHHIHEHIHIHIHHIEHHIHIEHIHHEHIHHIHIHE Si4Li lp population E 0 692719704 R 276 828 v 24 27 HHMAMARAAARAAARARARARAAARARAARA START ALGORITHM Z4 HB HHEIHHIHHIHIEHIHIHIEHIEHHIHEHIRBHIHHIERHIHIHE THHEHHIHHIHIHHHIHHHHHHHHHE ALGORITHM END CONSIDERED 0 MATINGS ZA HHEHHHHHHHEHBHHHEHPRHHIHE The run generated 1 candidate THHEHHHHEIHIPHHIHHHHHHIHIHHHHHIHHHHHEHE FINAL POPULATION H H HEHHIHAHHIHPEHHIHHHIHBHHIHIHHIEBHHIHIHRHIHIHE Si4Li lp population E 0 692719704 R 276 828 v 24 27 THHEHHHEHPHHIHIEHIHHEHIHHHIHHIHHIHHHIHHHHHEHE TIMINGS GEREHBRHEHHEIHHIHHIHHIHHIHHHIHHEHIEHHIHHHIRRHEHIERHIHIHE 6 8 Using templates
29. er program was changed in that it builds a set of candidates that may result in a quite small initial population The goal is then to update the population using genetic operators to create new acceptable candi dates that are different from the ones already present The population growth is implemented as a sequence in which the resulting candidates from only one mating may be added to the population if it is deemed ac ceptable Thus each new generation is the result from just one child This was deemed beneficial because the new acceptable candidate s may immediately be used in the creation of new candidates When using this approach it doesn t make sense to talk about generations anymore but focus on the number of matings performed 2 Getting started 2 1 Prerequisites Since the cluster program is written in python and tested with versions 2 4 3 up to 3 3 2 a python interpreter within that range 1s required The program has only been tested on Mac OS X and RedHat and makes use of OS calls so it can t be guaranteed to run on other operating systems The cluster program interfaces with a computational program in the background thus the program to be used has to be available and may also require certain environment variables as well as the path to be properly set More specifics of those requirements for each program interface are provided in Section 5 2 Installation The compressed tar file cluster1 0 tgz should be decompressed tar zxf
30. er the full input file is parsed will the prototype of a cluster be built so that it always uses the last defined fragments and elements The current defaults are for a H H20 2 cluster elementlib string The path to an element library file see Section 4 2 The elements in the file are interpreted immediately and may define new elements or redefine existing ones They are only used for fragments that are defined after the element library was read Thus existing fragments will not be affected elements element line This keyword forces the parser to interpret the following lines until an empty line is encountered as single line definitions of elements see Section 4 2 The internally defined elements are immediately updated but any fragments that were already defined are not affected similarly to reading an element library fragmentlib string The path to a fragment library file see Section 4 3 The fragments in the file are immediately interpreted and may define new fragments or redefine existing ones fragments fragment A sequence of fragment definitions see Section 4 3 The sequence of fragments needs to be terminated by an empty line composition name amount H 1 H20 2 A sequence of one or more fragment or element names followed by the amount of those in the candidate each separated by a space The symbol can be used to signify the start of a new layer in the build sequence i e the fragments before the are
31. er the optimization 1s considered to be a duplicate of the one just found The following keywords affect the optimization procedure max freq int 3 The maximum number of times that a frequency calculation may be performed in the optimization procedure If max freq 0 no optimization for any built candidate will be performed since the optimization cycle will be immediately aborted and the candidate is immediately added to the aborted library nfreq cutoff 10at 0 0 If the smallest non zero frequency reported by the frequency analysis is larger than this cut off value the candidate 1s assumed to represent a minimum in the PES and thus may be considered a viable candidate nfreq bifurcate int 1 If 0 only a positive step along the lowest non zero vibrational mode will be followed off a stationary point If 0 both directions will be followed nfreq displacement float 0 5 The multiplication factor for displacement along the lowest non zero vibrational mode Internally the dis placement vector for the vibration is scaled to a 1A sized vector so the multiplication vector may be con sidered the step size in along that vector Depending on the types of structures and the type of vibrational mode involved the 0 5 value may be too small duplicate int 2 A flag for determining which duplication check procedure should be used 0 do not check for duplicates This may result in lots of unnecessary frequency calculations and geometry reoptimizat
32. error code 256 Si4Li 7 2D Build E inf R 202 734 v None Si4Li 7 Opt 1 Not Converged E 1165 189208430 R 202 734 v None Si4Li 7 Failed 256 E 1165 189208430 R 202 734 v None Ifthe keep fail flag Z 0 the computational program s output file is retained so that the user can inspect more closely why the computational program had issues otherwise all files associated with the candidate are deleted The optimization of a candidate is performed by executing up to max freq times cycles that consist of a geometry optimization followed by a frequency calculation and a reoptimization of the geometry At the beginning of each cycle the candidate is added to the all library The implemented methodology tries to avoid time consuming calculations as much as possible One way in which that is done is by using libraries of converged structures 1 e the population library and converged library and comparing any newly converged structure against the candidates in one of those libraries Whether this comparison is done and which library may be used is determined by the duplicate keyword The method used to determine whether a candidate is considered a duplicate is explained in section 3 6 If the new candidate is a duplicate the status line with name where name is the name of the previously encountered candidate is printed before it is added to the duplicate library and the optimization aborted This way one may avoid unnecessary frequency calculat
33. esolutions of about 0 6 hartree name E Eh dE Eh dE eV dE kcal mol R Eh Freq cm 1 comment H28 ADF 3 1 280270003 0 000000000 0 000000000 0 000000 183 440 124 91 Population H28 r2 1 H28 ADF 1 1 280264632 0 000005371 0 000146155 0 003370 183 708 127 36 Population H28 r3 4 H28 ADF 2 1 280255768 0 000014235 0 000387342 0 008932 183 184 125 34 Population H2S r3 13 H28 ADF 4 1 280252325 0 000017677 0 000481028 0 011093 183 530 125 93 Population H2S r5 2 H28 ADF 5p 1 280045216 0 000224787 0 006116765 0 141056 183 402 119 34 Population H28 r2 43 H2S8 ADF 5n 1 274771463 0 005498540 0 149622877 3 450386 183 227 72 85 Population H28 r2 43 H2S ADF 6 1 267672306 0 012597697 0 342800768 7 905174 160 478 12 37 Population H2Smr2945 Thus we really wasted some time calculating the frequencies for candidates 2 and 4 1 would always be calculated and since 3 ends up with a slightly lower energy it would be calculated as well Inspection of the population library shows that within the four lowest energy structures contain non superimposable mirror images which even a slight filtering would have considered duplicates It is interesting to note that here we see a case where the bifurcation results in two different candidates in the population i e H2S ADF 5p and H28 ADF 5n both are the result from the optimization of the H2S r2 43 candidate from the initial population as can be gleaned from the comment for each candidate 6 5
34. ext output it generates shows that indeed no duplicates are taken from the new filtered set of struc tures THHHHHHHHHHHEHHHHHHHHHHHHHHHH E DUPLICATES IN VIABLES JJ HHETHHHEHEHHHIHHIHIHHHIHHIHIHHHHHHEE THHHHHHHHHHHHHHHHHHHHHHHHHHHHE FILTERED POPULATION ZH HHHETHHHHHHHIHIHIHIHIHHIHHHIHHHHHHEE H2S r3 4 Filtered E 0 023558056 R 163 867 v 17 70 H2S rl 4 Filtered E 0 023556492 R 163 663 v 28 80 H2S rl 3 Filtered E 0 023555334 R 163 507 v 26 70 H2S r3 13 Filtered E 0 022450474 R 159 517 v 22 30 H2S r4 6 Filtered E 0 022375850 R 160 280 v 31 90 H2S r2 1 Filtered E 0 021989498 R 145 184 v 3 10 H2S rl 18 Filtered E 0 021987541 R 144 368 v 3 40 23 H2S8 r5 4 Filtered E 0 021980137 R 143 607 v 5 50 H2S r5 2 Filtered E 0 021979759 R 143 056 v 3 70 H2S rl 1 Filtered E 0 021974507 R 142 948 v 6 20 H2S r3 1 Filtered E 0 021960593 R 142 241 v 4 70 H2S r2 43 Filtered E 0 015519401 R 194 769 v 18 50 H2S r2 4 Filtered E 0 012641140 R 180 537 v 13 10 One may double check by visualizing the structures in the all_sorted xyz file using Jmol or any other visualization program that can deal with multi step xyz files to see which candidates do indeed look similar enough to be considered duplicates An energy resolution of 0 0001 and a very generous repulsion resolution of 2 will filter several duplicates out as shown in the 1t out which is the result of using
35. filter flt energy resolution 5e 4 repulsion resolution 10 15 5 2 909 g03 Requirements The gaussian interfaces for g09 and g03 require that the gaussian root environment variables g09root or g03root are defined as well as that their respective login files have been sourced i e the normal gaussian setup has been performed because the cluster programs executes either g03 or g09 directly Defaults The default method for gaussian calculations is B3LYP 3 21G Specifics The g09 and g03 program interfaces are the same with respect to input file create and output file parsing The only differences are in how the program is called and that the g03 program limits the number of processors to 8 Because the text used to report the energy 1s not the same for the different methods that Gaussian supports several regular expression patterns are used when matching the lines from the output file The last match encountered will be the energy that the cluster program reports and uses for comparison The list of patterns and the type of calculation it matches are as follows EpatSearch re compile r SCF Done 0 9 eED f SE g09 HF DFT re compile r E CORR 0 9 eED CCx and QCI re compile r E UR MP 0 9 eED MP2 3 and CIS re compile r UR MP4 0 9 eED MP4 re compile r E CI 0 9 eED CISD re compile r E 2PLYP 0 9 eED 2P
36. g output from the cluster program itself which was redirected to the test out file shows that the prototype of the trimer indeed uses 3 H2S fragments from the fragment library which have an extra radius of 0 3 A THHHHHHHHHHHHHHHHHHHHH LIBRARIES READ WHILE PARSING INPUT A44 5385HHHHHIPIHHHHIHHIHHIHIHIHE fragmentlib fragments xyz HHMAMARAARARAAARARARARAA RARA RAS BUILDING PROTOTYPE Z4 HEHHBIHHIHEHIHIHHIHIERHHIHEHIHBHHIHIERHIHIHE 3 x H2S extra radius 0 300 Angstrom H 0 2863440033 0 0647336800 0 9761714367 H 0 4595735367 0 6015626800 0 6826481633 S 0 1732295333 0 5368290000 0 2935232733 For an overall composition of H2S 3 Having 9 atoms and 54 electrons THHEHHHEIHIPHHIHHHHIHHIHIHHHHIHHHHHHEHHE PROGRAM SETTINGS ZAHHHHHHIHHIHEHIHIHHIHIEBHHIHHHIRBHEIHIHRHIHIHE Below that a one liner result of the optimization and frequency runs are given each followed with the cluster library entry for the candidate after the computational program finished No ReOpt run is performed since the MOPAC interface does not support this Inspection of the Opt and Freq output lines shows that no error codes are returned the None values More importantly the geometry optimization was not able to converge in the default 50 optimization cycles allowed Since the MOPAC interface only supports running several direct optimizations in a row without a frequency analysis and reoptimization in between we should increase the max opt The frequency calculation does
37. gainst a candidate in the converged library that has negative frequencies the absolute difference of the energies of the two is compared against the energy resolution Only if all criteria that are to be checked suggest that the candidates are duplicates will the candidate be considered a duplicate Acceptance determination method In order to determine whether a viable candidate can be accepted in the population it is added to a list of the candidates in the population which is then sorted and filtered sequentially for duplicates starting with the lowest energy candidate A duplicate 1s removed from the list before the next higher energy candidate is considered If the energy of the candidate is more than energy window higher than the lowest energy candidate it is also removed Since the progression through the population is from low to high E more candidates may remain than if the list was traversed the other way An example illustrates this Let the energies for three candidates be 0 0 0 9 and 1 8 With an energy resolution of 1 0 the duplicates filtered population will retain the candidates with E of 0 0 and 1 8 If one were to traverse the from high to low energy only the candidate with the E of 0 0 energy would remain The more accepting methodology was chosen so as to reduce the chance that the population may be filtered too heavily The energy units used for E and R are in hartree Eh 1 Eh 627 509469 kcal mol 27 21138386 eV energ
38. ier run or help in testing the input files that the program generates filler string If the argument is not the default empty string a filtering procedure on the viable library will be performed before the program exits This is useful if the initially used acceptance criteria were too small and duplicate candidates still ended up in the population library The program appends the filter argument to the name keyword for the names of the new xyz and csv files generated so the user has to be careful not to use a string value that would overwrite the regular libraries created by the cluster run i e do not use aborted all converged duplicate population or viable Since the filtering is purely based on inter preting the comment line in the viable library structures see Section 4 4 a run in which filter is used does not require the definition of the candidate composition or anything else except for non default values for du plicate and acceptance settings see Section 3 6 i e energy resolution repulsion resolution energy window as well as nfreq cutoff and possibly reorient inputs int 0 If Z 0 creates an input file based on each template associated with the program for a 3D cluster The user can use these to determine whether or not the input files created by the cluster program may work The names of the input files will be test 3D JOB inp where JOB is the name of the template used to create the file If the test keyword Z 0 as well
39. il to produce any transfers if no fragments of the same type are below the two planes If that is the case the random rotation and transfer is attempted again up to max mate try times Thus a mating may fail to produce offspring If that happens the mating rebuild keyword determines whether or not a 3D build will be used as the child as opposed to aborting the mating If it was possible to transfer fragments the set of fragments transferred as a whole is positioned along the translation vector of the center of the atoms transferred such that atoms will at most touch similar to the method used in the build procedure see Section 3 4 but without using a scale factor for the translation vector A status text line will be printed that conveys how many fragments were transferred between which parents e g the following line shows that candidate number 7 was created from a candidate 1 into which two fragments were transferred from candidate 5 Si4Li 7 1 lt 2 5 E inf R 220 656 v None Two examples of successful matings are shown in Figure 1 Only four keywords affect the mating algorithm mating probability int 1 The probability method used in the selection process of the parents from the population The probability p for each parent 7 which has energy E is proportional to the following expressions where Emin is the lowest energy in the population and Emax the highest Ej Emin E 1 Boltzmann p e Em with Em determined b
40. in the separate runs When seeding the population with user built candidates in this fashion care has to be taken that the atoms are in the sequence that the program expects which is based on how the composition was defined This approach allows one to force the program to consider a candidate that it may not otherwise consider Any optimization done at this stage will also be checked for duplicates thus if one edits a candidate in the population so that it is taken out of the existing population as opposed to adding new ones that need to be optimized it may not be added again depending on how the duplicate check Is performed see the duplicate keyword in Section 3 6 If 0 all library files as well as output files associated with the candidates from possible earlier runs are deleted and an empty population library will be the starting point thus triggering the build procedures reoptimize int 0 If Z 0 the population library is read and all of the candidates are reoptimized This is useful if the calculation program or method is changed and one wants to use the population from an earlier run All library files and candidate output files from the earlier run are deleted as if restart 0 since their contents are not valid due to possible program or method changes build int 0 If Z 0 will force the cluster program to build and optimize candidates to be added to a possibly already existing population This is useful for a restart run where one
41. in which the optimization of a candidate progresses Here the default values for the optimization keywords were used Si4Li 6 2D Build E inf R 250 604 v None Si4Li 6 Opt 1 Not Converged E 0 533228167 R 263 045 v None Si4Li 6 ReOpt 1 Converged E 0 549502938 R 256 877 v None Si4Li 6 Opt 2 Converged E 0 549446191 R 256 875 v None Si4Li 6 Frequencies E 0 549446206 R 256 875 v 79 511 Si4Li 6 Aborted E 0 549446206 R 256 875 v 79 511 Si4Li 6n Opt 3 Converged E 0 570403659 R 273 269 v None Si4Li 6n Viable E 0 570428117 R 273 269 v 14 538 Si4Li 6p Si4Li 6n E 0 570403472 R 273 284 v None In this example one sees that after the initial 2D build of the candidate the first optimization didn t converge A frequency calculation whose results are not reported since it doesn t have any meaning is executed and using the Hessian a reoptimization is performed which did converge The second cycle results in a converged optimization so the frequencies are calculated Since the lowest non zero frequency is considered a negative frequency this candidate aborted but with bifurcation default turned on two new candidates with their atoms displaced in opposite directions along this vibrational mode are generated for use in the next and last cycle 3 The first of the two converged and since the frequency calculation shows that is a minimum it is flagged asa viable candidate The other one aft
42. indeed give us frequencies which suggests that that calculation works as it should Note that even though it has converged True in the information about the Freq calculation one does not have to worry about this because the cluster program will retain the information about the geometry convergence from the earlier geometry re optimization s HAHEHHHHHHHHHHHHHHHHH TEST INPUT FILES FOR A 3D CANDIDATE 34H53 HH I HIHETHIHHIHHEHIHHIHHIHE Opt None code None E 2 169030E 02 converged False failed False Freq 9 test 3D 0 021690302 154 932 inf Build 3D scale 1 H 1 1518252540 2 1202304363 0 4178235809 H 0 1886989782 3 6200137545 0 4001815406 S 0 0961472187 2 3469205038 0 0118190440 H 1 2367631676 1 3648574145 0 1764851672 21 H 2 8606317737 2 0233658701 0 8145101256 S 2 5485261164 1 0962064923 0 0990490047 H 3 0582649197 1 9205378907 0 6013266369 H 2 4364364714 0 2065601384 0 2210352951 S 2 0181987237 1 4756368884 0 1130812179 Freq None code None E 2 171221E 02 converged True failed False Freq 533 2 0 0076 0 0021 0 0222 0 0066 0 0142 0 0031 0 0084 0 0502 0 0221 89 8 0 0059 0 0083 0 0471 0 0056 0 0 0 0153 0 0119 0 0222 0 0304 81 5 0 1259 0 0057 0 1394 0 1259 0 0188 0 0139 0 6485 0 0363 0 0101 46 7 0 0273 0 0498 0 5469 0 0263 0 0737 0 0733 0 1545 0 0711 0 1189 38 3 0 1771 0 2375 0 6545 0 1718 0 1934 0 0836 0 0885 0 1109 0 1303
43. ion followed by the list of the keywords that are separated by some vertical space Each keyword in the list 1s in boldface text and is followed by the type of the argument s followed by a colon and the default value of the keyword which are in a monospaced font Ifthe parser encounters a keyword that does not exist it will report the error and exit the program Note the keywords are case sensitive The order in which the keywords are encountered in the input file is not important except for the e1 ementlib fragmentlib elements and fragments More details on this are provided in the Sec tion 3 3 3 1 Computational program settings This set of keywords may affect the contents ofthe input files for the computational program which are created from text templates that are either built in or read from the user defined template files see also Section 4 1 Note that not all programs allow one to set all corresponding parameters listed here In that case the parameter is not used in the template so it does not end up in the input file for the program If in doubt either run with method template to see what the actual template is that is created or perform a inputs or test utility run to have the program generate input files and optionally execute each type of calculation that the computational program is expected to be able to perform see also Section 3 2 program string ORCA The string is the key for the program to be used At the moment
44. ions 1 use the population library 2 use the converged library i e all unique mimima and maxima encountered For a previously encoun tered maximum only the absolute energy difference between the two candidates 1s compared against theenergy resolution value The assumption is that 1f the candidate encountered before didn t yield a new candidate in the population earlier it will not do so again This may not necessarily be the case for option 2 since the number of times the optimization cycle has been executed may be less than before and the additional allowed optimizations may yield an acceptable candidate See also Section 3 6 keep fail int 0 If 0 the computational output files will not be deleted when a calculation failed This allows inspection of the computational program s output file if candidates keep failing to get optimized reorient int 1 If 0 the candidates in the libraries will be centered on the center of the fragments If Z 0 the coordinates will be such that the structure is centered on the atoms and rotated so that the largest eigenvalue of the charge weighted not mass weighted inertia matrix is along x and the smallest one along z This may aid in comparing similar structures since they will be oriented in a similar fashion For either case the coordinates in the cluster libraries are very likely to be different from the ones shown in the computational program s output file 3 6 Duplicate and acceptance determi
45. ions During the optimization frequency calculation and reoptimization cycle the following decisions are made If the geometry optimization did not converge a status line with Opt x Not Converged with x the optimization cycle number is printed If the computational program can do a geometry reoptimization using the Hessian information from a previous frequency calculation and at least two more frequency calculations may be performed a frequency calculation will be performed followed by a geometry reoptimization calculation If this results in a converged geometry and the candidate is not a duplicate the next cycle in the optimization procedure is started This means that some unnecessary optimization steps may be performed but one would expect that to be a very small number This is preferred since this way any candidate in the viable library and thus population library as well will have been calculated based on the same two last calculations an optimization followed by a frequency calculation If the geometry optimization resulted in a converged geometry that is not a duplicate a status line with Opt x Converged with x the optimization cycle number is printed before a frequency calculation is performed after which the candidate is added to the converged library The stationary point is considered a minimum if the lowest non zero vibrational mode s wavenumber is larger than the cut off value defined by the n req cutoff keyword In
46. les The file for mats consists of a concatenation single fragment descriptions each of which is xyz file formatted with the modification that in that the comment line has specific information encoded 1 e the fragment library format is as follows int natoms string name float radius string string elementkey float x float y float z natoms The name is the string needed in the composition string of candidates while radius is an additional radius in A used in building candidates and genetic operations see Sections 3 4 and 3 7 The elementkey in an xyz file is the element name The cluster program allows a bit more flexibility because the key is the key for the element in the element library which may differ from the actual element name thus it is possible to use the following fragment definition as long as the Hg2 and F elements are defined see Section 4 2 3 HgF2 1 0 just a silly example Hg2 0 0 0 F 2 0 0 F 200 4 4 Candidate library format The file format for a library of candidates is also a slightly modified version of the standard multistep xyz file format in that the comment line has specific information encoded for the name energy nuclear repulsion energy R and lowest vibrational frequency freq followed by an optional comment If the energy and or frequency are not computed the float strings inf and inf are used respectively The file format for a cluster library is as follows int n
47. lida a 6 2 Multiple Tuns sc once EA SUR gU ee Eu ess OIM EM EUR MO bns 6 3 Sorting and refiltering libraries ee 6 4 Reoptimizingalibrary lees 6 5 Seeding the population library ee 6 6 No optimization TUNS o E Hh ed A a A Aia 6 7 Single fragmentTUNS o oa 25 24 desde a a rU REOR XO 6 3 Usine templates bu ras a a a FE ES A NRP sj he NOVOA hu W 1 Introduction The cluster program implements a gradient enhanced genetic algorithm to generate a set of structures 1 e a population of candidates associated with verified minima in a multi dimensional potential energy surface PES Candidates consists of one or more fragments where a fragment can be either a single atom or a set of atoms The implementation is loosely based on ideas presented in papers by Anastassia Alexandrova and Deaven and Ho Generally implementations of a genetic algorithms start with a possibly large initial population and use one or more genetic operators to breed new candidates from that population A subset of those new candidates may then replace candidates in the population thus maintaining a fixed sized population In the implementation presented here this approach is slightly modified Due to the goal of only retaining candidates associated with verified minima in the PES it is computa tionally and time wise costly to seed the population with large number of candidates Thus the approach in the clust
48. mber of candidates in the resulting population library Thus if one thinks that the initial input file that created the viable library contained too generous duplicate determination criteria one should inspect the duplicate library for the runs to see whether a restart could be in order Ofcourse one may want to consider sorting without any filtering i e also allowing negative frequencies in the candidates but doing that with the converged library as opposed to the viable library This allows one to see whether there are low energy maxima that had problems optimizing to a lower energy structure suggesting that an actual minimun that should be present was not found For instance in the examples H2S converged folder one may execute cat r conv xyz conv viable xyz And use the following input file to only sort the candidates leaving candidates with negative frequencies in the mix by using inf for the frequency cutoff as shown in conv sorted in name conv filter sorted energy resolution 1 repulsion resolution 1 energy window 1 nfreq cutoff inf The start ofthe filtered population that this gives shows that the frequency calculation may be problematic for the lowest energy candidates listed here even though they really are practically the same structures based on inspection of the generated population library 24 THHHHHHHHHHIHHHHHHHHHHHHHHHHHE DUPLICATES IN VIABLES JJ 383 I HBHIHHIHIHIHIHHIHIHIHIHHHIHIHIHIHEHIHRE THHHHEH
49. nation Since it is important to determine whether two candidates may be identical and thus not unique it is important to find good metrics that allow us to make these decisions The energy E of the candidate is a good metric since that 1s the property of the candidate that is minimized and provided by the computational programs But different structures may accidentally have very similar energies so the nuclear repulsion energy R i e the sum of all pair wise Coulomb repulsion energies of the nuclei may be used as a metric as well The nuclear repulsion is calculated by the cluster program itself so it is known at any time R is quite sensitive to differences in relative nuclear positions Using both criteria allows the cluster program to consider two geometrically different structures that happen to have very similar E values to still be unique and keep them both in the population library Note that these comparisons are not able to distinguish between non super imposable mirror images of candidates Duplicate determination method Candidate 1 having an energy E Ej and nuclear repulsion energy R F4 is considered a duplicate of candidate 2 which has E E and R Rg if e its energy is less than the value ofenergy_resolution E above that of candidate 2 i e Ej gt E and E E2 lt OE as well as when the repulsions differ by less than repulsion_resolution R i e R Ra lt R Ifa candidate is checked a
50. nly the mated structures based on an available population library from a run which therefor should be present in the folder one would only have to change the matings to the number of children to be created and rely on the default restart settings for the program Note that since the mated structures would be appended to the aborted library one may want to delete that file first 6 7 Single fragment runs Since the cluster program is able to follow the PES off a stationary point that is not a minimum the program may also be useful to do just optimizations of a structure that consist of a single fragment An example of the optimization of an Si4Li uncharged doublet system stored in examples Si4Li uses the Si4Li in input file name Si4Li program ADF method XC nLDA SCF VWN nEND nBASIS ntype TZP ncore Large nEND nUNRESTRICTED processors 8 fragmentlib Si4Li xyz composition Si4Li 1 charge 0 multiplicity 2 28 restart 0 1D 1 nfreq bifurcate 0 matings 0 to only request a single 1D build of the fragment which really is the whole structure to be optimized The input structure stored as an external fragment is a linear structure known to have imaginary frequencies If the symmetry of a converged maximum is low it may be possible that the opposite directions of following the lowest frequency can give rise to different structures in which case one may benefit from the default nfreq bifurcate value as was seen in Section 6 4 In this cas
51. not create inter atomic distances that are too small which is not a trivial requirement for three dimensional structures with possibly a large amount of atoms Thus the first reason is to keep complexity down Secondly the computational program optimizes all atomic positions which effectively are already muta tions of atomic positions but admittedly not random ones Thirdly a form of mutation is inherent in the mating methodology by virtue of the random rotation of the parents in the procedure Even when mating the same parents multiple times different children will result thus a set of children from the two same parents will be different just as if a mutation was applied Finally it also bears pointing out that in a system with molecular fragments due to the geometry optimiza tion of the candidates not only the relative positions of the fragment centers themselves changes but also the relative atomic positions within the fragment This can be considered a mutation of the fragments themselves which may be used in future mating procedures 11 3 8 Termination As described above the cluster program will build or rebuild an initial population that will be used as a source of parents for the creation of a single child which will be optimized in each mating cycle Two keywords are available that can be used to terminate the main cycle of matings Whenever one of them is met the program will exit matings int 1 The maximum number of m
52. on 4 3 to have better control over the positioning of fragments since this extra radius is respected in both the building and mating procedures of the program and thus is used more consistently Restart and reoptimization using the population library Since it is hard to predict how many candidates should be built and how many matings may be required to get a good sampling of the PES it is useful to be able to restart the cluster program in such a way as to use results from earlier runs and or build new candidates If after the initialization stage based on the restart and reoptimization options the size of the population is still zero or if build Z 0 the build methodology is used for the requested nD canidates The default settings are such that a restart will be performed restart int 1 If Z 0 the population library is used as the starting population The converged library is also read so duplicates can be checked against results from the previous run The all library file is read to determine the candidate number needed to avoid overwriting old candidate output files By using inf for the energy in the comment line for a candidate in the population library see Section 4 4 or only have the name in the comment line without anything else the program will ignore the given name and optimize the candidate before adding any resulting acceptable candidates to the population It is up to the user to maintain consistency in the computational method used
53. on vectors are multiplied by the value of scale a scale factor that allows for a more closed or open topology of the candidate After the build is performed a status line for the candidate is printed showing only a numerical value for the nuclear repulsion in the structure since no other calculations have been performed on it yet e g Si4Li 6 2D Build E inf R 250 604 v None A very small number of keywords are needed to direct the program about how and how many initial candidates are built The default settings are such that no candidate will be built 1D int 0 The number of candidates to be built with displaced fragment centers along x only 2D int 0 The number of candidates to be built with displaced fragment centers along x and y only 3D int 0 The number of candidates to be built with displaced fragment centers along z y and z scale float 1 0 The value used as a multiplication factor for the translation vectors of each fragment thus allowing with a value lt 1 0 to create a closed and with values gt 1 0 a more open topology for the candidates Since this keyword is a multiplication factor in the fragment translation fragments farther from the center will be affected more than those close to the center This keyword is only used when building candidates not during matings The mating procedure always treats the clusters as a closed cluster One may want to use the extra radius field in the fragment definitions see Secti
54. quency calculations the reoptimization part is not implemented in the candidate optimization cycle Only multiple starts of optimizations will be performed up to max freq times Since EFPMD treats fragments as a whole the hessian is not calculated on a per atom basis This means that calculated displacement vectors from the frequency calculation can not be used to displace atomic coordinates and the cluster program will not be able to move away from a maximum so local maxima are immediately aborted EPFMD often shows small negative frequencies in its minima so set nfreq cutoff to a negative value Only themax opt keyword is used in the templates But the charge and multiplicity must be set appropriately since the multiplicity value is tested against what is possible based on the number of electrons in the system If one wants to use libEFP library fragments the fragment name with _L should also be defined in the library files that the cluster program parses The sequence of the atom types in the two fragments should be the same Currently the libEPF fragments distributed with 1 2 1 are part of the cluster known fragments EFPMD Example A water tetramer cluster H20 4 Because of issues with the normal mode analysis not being atom but fragment based see above and often having small negative frequencies the nf req cutoff is set to a largish negative value one could even use inf to accept all stationary points The fragment name is
55. ram will create them and exit If one needs the extra flexibility that the use of templates provides it is advised to first have the cluster program generate the template files that the implemented interface in the cluster program requires This can be done by not having any template files in the folder as the cluster program is executed with the method keyword set to template The template files created may then be modified as needed and will be used in future runs of the cluster program in that folder see also Section 6 8 A template file should be a properly formatted input file and may have the following placeholders for the parameters see also Sections 3 1 and 3 3 xyz s the cartesian coordinate block for optimization charge d the charge of the candidate multiplicity d the multiplicity of the candidate 2S 1 spin polarization d the number of unpaired electrons 2S method s the computational method and basis set etc to be used processors d the number of processors memory d the amount of memory in MB max scf d the maximum number of SCF cycles max opt d the maximum number of geometry optimization steps root s will be the name of the candidate rootpath s will be the OUT DIR path with the name of the candidate appended If one keeps the method s placeholder in the template file the default method for the particular program will be used 12 4 2 Element library and elements format The element
56. s UFF program by using SADFBIN uff with the command line option n set to the number of processors requested in the cluster input file Defaults Since this is an MD type program no method needs to be specified Specifics Since one can not restart an optimization using the Hessian from an earlier frequency calculations the reoptimization part is not implemented in the candidate optimization cycle Only multiple starts of optimizations will be performed up to max freq times Only themax opt keyword is used in the templates But the charge and multiplicity must be set appropriately since the multiplicity value is tested against what is possible based on the number of electrons in the system ADFUFF Example A water tetramer cluster H20 4 Since the default mechanism for associating atom types in the structure is completely based on the automatically determined bond connectivity this run generates some strange struc tures name H20 4 program ADFUFF multiplicity 1 charge 0 composition H20 L 4 nfreq cutoff 10 restart 0 2D 5 3D 30 matings 50 repulsion resolution 0 2 5 6 EFPMD Requirements The EFPMD environment variable should be set to the full path of the efpmd executable file since the cluster program executes EFPMD directly Defaults Since this is an MD type program no method needs to be specified 19 Specifics Since one can not restart an optimization using the Hessian from an earlier fre
57. sed to generate the libraries since it affects the sequence in which atoms are expected to be found in the xyz file formats The input file listed below is to be run on a computational cluster where the programs are executed in a temporary folder and not within the current working directory This means that one has to use the full path for ragment1lib or elementlib which should be on a file system that all compute nodes have access to Thus H28 ADF in looks like name H2S ADF program ADF method XC nLDA SCF VWN nEND n nBASIS ntype TZP ncore Large nEND processors 8 memory 6000 multiplicity 1 charge 0 composition H2S 3 reoptimize 1 matings 0 energy resolution 1 repulsion resolution 1 energy window 1 fragmentlib home rkanters work cluster H2S fragments xyz Just for illustrative reasons the cluster program is to not filter out any optimized geometries based on the energies by turning off all energy related acceptance criteria Normally one would have a reasonable idea about the criteria to use and avoid unnecessary frequency calculations Also no matings are requested since we only want to reoptimize the population library 25 At the end of the cluster output we see that four of the six candidates are reoptimized to basically the same structure From the inspection of the H28 ADF population csv file it is clear just how close the first four structures are in energy 1 e within 0 011 kcal mol and a range of the repulsion r
58. son The two patterns are r HEAT OF FORMATION 0 9 eE r HEAT 0 9 eE MOPAC Example A water pentamer cluster H2O calculation using the PM3 method with the PRECISE keyword Note that the maximum number of optimization cycles allowed is increased by quite a bit from the standard 50 This example also forces the calculation to start from scratch 1 e any previously calculated results found in the work folder will be deleted name w5 program MOPAC method PM3 PRECISE max_opt 500 composition H20 5 charge 0 multiplicity 1 restart 0 2D 3D 20 40 matings 50 repulsion_resolution 1 5 5 ADFUFF The default implementation of the UFF program by ADF may not work too well because the cluster program only generates the coordinates of the input structures and not the atom types nor bonds The interface was written because a user can by using input templates have UFF use the user s atom type database for automatic atom type assignment and force field parameters for those atom types One can also consider using the ADFUFF program to generate an initial population that in a subsequent run with a different program can be made to be optimized using a better methodology see reoptimize 18 Requirements Just like for the ADF interface the ADFBIN environment variable needs to be defined as well as the ad frc sh or adfrc csh should have been sourced because the cluster program calls ADF
59. that case a status line with Viable f is printed before the candidate is added to the viable library Based on the acceptance criteria the candidate may then also be promoted into the population library The method used to decide the promotion into the population library is explained in section 3 6 Independent of whether or not the candidate ends up in the population library the optimization is finished at this stage If the stationary point was a maximum a status line with Frequencies is printed followed by one with Aborted before the candidate is added to the aborted library If no more frequency calculations are allowed the optimization is terminated otherwise the whole cycle is recursively re entered with a candidate whose geometry moves away from the local maximum along the lowest non zero vibrational mode The size of that step is determined by n req displacement and may be done in one or two directions If n req bifurcate Z 0 both directions are followed otherwise only one direction is followed Thus a single candidate may generate multiple candidates The names of these candidates have an n or p appended to them When re entering the cycle the number of frequency calculations performed is not reset to zero so that each candidate will have in its history a maximum of max freq frequency calculations and the recursion will never go into an infinite loop A little excerpt of status lines printed may help to understand the sequence
60. the flt in input file THHHEHHIHHHHHIHHHHHHHHHHHHHHHHHE DUPLICATES IN VIABLES HH ARA AAA RARA RARA H28 rl 4 H2S r3 4 E 0 023556492 R 163 663 v 28 80 H28 rl 3 H2S r3 4 E 0 023555334 R 163 507 v 26 70 H28 r4 6 H2S r3 13 E 0 022375850 R 160 280 v 31 90 H2S_r1_18 H2S_r2 1 E 0 021987541 R 144 368 v 3 40 H28 r5 4 H2S r2 1 E 0 021980137 R 143 607 v 5 50 H28 rl 1 H2S r5 2 E 0 021974507 R 142 948 v 6 20 H28 r3 1 H2S r5 2 E 0 021960593 R 142 241 v 4 70 THHHHEHIHHHHIHHIHHHIHIHHIHHHHHHHHHHEHIE FILTERED POPULATION Z4 4H HHHHHIHIHIHIHHIHIHIHIHIHHIHIHHIHIHHIHHIEE H28 r3 4 Filtered E 0 023558056 R 163 867 v 17 70 H28 r3 13 Filtered E 0 022450474 R 159 517 v 22 30 H2S_r2_1 Filtered E 0 021989498 R 145 184 v 3 10 H2S_r5_2 Filtered E 0 021979759 R 143 056 v 3 70 H2S_r2_43 Filtered E 0 015519401 R 194 769 v 18 50 H2S_r2_4 Filtered E 0 012641140 R 180 537 v 13 10 Note that H2S_r2_1 and H2S_r5_2 have very similar energies but their nuclear repulsion resolutions are quite different suggesting that they may be different structures Keep in mind that since no new optimizations are performed none ofthis will find any candidates that were considered duplicates during the initial runs but not according to the new criteria i e setting the duplicate detection criterion settings tighter than what was used in the initial runs will not increase the nu
61. the cluster program has interfaces for ORCA 203 g09 ADF the ADF UFF implementation using the key ADFUFF MOPAC and EFPMD As sociated with each program is a default method the specifics of which are provided for each program in Section 5 method strings RKS B3LYP G SV The remainder of the line after the keyword itself will be used in the input templates If the method definition needs more than one line in the computational input file one should use Nn in the one liner If a more complicated form of input files for the system 1s needed use the word template see Section 4 1 In that case if the program does not encounter the template files needed in the current working directory it will create them and exit This allows the user to adjust the template file s as needed and rerun the cluster application processors int 1 The number of processors to use in the run The value may be used to create the input file and or to call the program memory int 2000 The amount of memory to be used in MB max scf int 50 The maximum number of SCF cycles allowed max opt int 50 The maximum number of geometry optimization cycles allowed name string c The root name of the files and candidate names to be created Only the first word in the string will be used 3 2 Utility runs A few keywords exist that will not start the population optimization process itself These are useful to either do a post processing of the results of an earl
62. ts of these libraries are updated as the program progresses aborted candidates for which no acceptable minimum was found all every candidate for which an cluster optimization cycle was started converged candidates at local extremes on the PES duplicate candidates that are a duplicate of a candidate in the population and or converged libraries population candidates at local minima on the PES that are considered unique viable candidates at local minima on the PES The cluster optimization algorithm see Section 3 5 explains in more detail how the decisions are made as when where and why a candidate is added to which library In addition to these library files a comma separated value csv file is maintained which contains some information about the candidates in the population library in a format that most spreadsheet programs can easily interpret Computational program output If possible the program only retains the last geometry optimization and frequency calculation outputs con catenated for candidates that are in the viable library These files will have the extension out This feature is not possible for MOPAC calculations since the output it creates can not be redirected appended 3 Methodology and keywords This section provides the keywords allowed in the input file It is organized by conceptual groups in associa tion with how they are used in a cluster program s methodology Most sections start with small introduct
63. y resolution float 1 6e 4 The value in hartree that a new candidate has to differ from an existing one in order to be considered a different candidate If a negative value is used the energy criterion will be ignored The default is about 0 1 kcal mol repulsion resolution 10at 0 05 The value in hartree within which the nuclear repulsion R of two candidates needs to be the same to be considered duplicates If a negative value is used the nuclear repulsion energy criterion will be ignored energy window float 0 16 The amount of energy in hartree above the lowest E in the population within which new candidates are accepted If a negative value is used the window will be ignored The default value is about 100 kcal mol 3 7 Genetic operations Most genetic algorithms implement several genetic operators usually at least a crossover a k a recombina tion or mating operator as well as a mutation operator Mating procedure To create a child two parents are randomly chosen from the population where the probability of choosing each parent is determined by the mating probability keyword Each parent is cloned and randomly rotated around the center of the fragment centers The child is initially set equal to the clone of the first parent The recombination itself then consists of transferring as many of the same type of fragments based on their names whose centers lie below the xy plane from the second parent s clone to the child This may fa
64. y the mating energy keyword Ei Emin 2 Linear ranges p 1 0 PERSEO ETT With n number of candidates in the population 3 Equalranges p 1 0 10 parent 1 parent 2 parent 1 parent 2 9 rotated 9 rotated rotated rotated te A om o A dq 7 e we ud transfer O transfer Figure 1 Two examples of matings On the left for Si4Li where two Si atomic fragments from parent 2 are transferred to parent 1 and positioned in the final child so as to avoid interatomic distances that are too small On the right hand side three water molecules are transferred in a H20 s cluster All images are viewed along y with the z axis pointing up mating energy float 1 0 A parameter used in the Boltzmann distribution based mate selection i e mating probability 1 If lt 0 the E used will be Em Emaz Emin otherwise it will be used as is mating max int 3 The amount of times that mating 1s attempted before it is considered to have failed mating rebuild int 1 If 4 0 performs a 3D build if a mating fails Mutation procedure Mutation of a single candidate is not implemented for several reasons In our type of candidates i e unique geometries representing minima on a multidimensional potential energy surface a mutation is a geometry modification of fragments and or atoms in such a way that the mutation is still a candidate that a computational program can work with This means that care needs to be taken to
65. y we will combine the viable libraries of all runs intoaanall viable xyz library file in the examples H2S al11 folder wherein is executed with the idea that any filter utility run using name a11 will be working with the library cat r via xyz all viable xyz Theall viable xyz viable library can now be used for sorting and or refiltering as described next 6 3 Sorting and refiltering libraries Since the viable library does not store the candidates sorted by energy it may be useful to perform a filter utility run that will only sort not actually filter it to create a new population library that contains all the viable candidates sorted by energy Inspecting the resulting library or inspecting the text output may help in determining the repulsion and energy resolution values one should use to filter out only the unique structures in a subsequent run To sort the viable library all one needs is a simple filter input file which is in the examples H28S a11 folder called sort via in By turning all energy acceptance criteria off every structureintheall viable xyz will be considered unique Since the original viable libraries contained candidates with positive frequencies we can keep the frequency based filter to its default settings name all filter sorted energy resolution 1 repulsion resolution 1 energy window 1 Since the filter procedure only parses the comment lines in the xyz files no composition information is needed The t

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