PBC-Guide Solid State Calculations Using Gaussian

March 26, 2018 | Author: Anas Yousef | Category: Condensed Matter Physics, Chemistry, Physics & Mathematics, Physics, Physical Sciences
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Solid State Calculations Using gaussian: The Definitive Guide to G09 PBC Calculations April 25, 2012 Contents 1 Conventions Used in this Document 1.1 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Additional Input Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Using the ICSD: Starting Structures 2.1 Performing A Search . . . . . . . . . . . 2.2 Saving the cif Files . . . . . . . . . . . . 2.3 A Sample cif File . . . . . . . . . . . . . 2.4 Opening the cif File in GaussView . . . 2.5 Saving a Job File Derived from a cif File 6 6 7 . . . . . 8 9 12 14 16 17 . . . . . . . . . 18 18 19 19 19 20 22 22 23 25 . . . . . 26 26 27 27 28 29 . . . . 30 30 30 31 32 6 Spin-Orbit Calculations 6.1 Example 1: Ge with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.2 Example 2: Hg with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 33 35 7 Dispersion Calculations 36 . . . . . 3 PBC Input Files 3.1 A Sample Input File . . . . . . . . . . . . 3.2 PBC Single Point Energy Calculations . . 3.2.1 Link 0 Commands . . . . . . . . . 3.2.2 The Route: Lines 1-3 . . . . . . . . 3.2.3 Title and Coordinate Specifications 3.3 Geometry Optimizations . . . . . . . . . . 3.3.1 Line-By-Line Description . . . . . . 3.4 Constrained Geometry Optimizations . . 3.5 Restarts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Antiferromagnetic Guess Calculations 4.1 Input . . . . . . . . . . . . . . . . . . . . . . 4.2 Example 1: H Triplet → Singlet . . . . . . . 4.3 Output File Info . . . . . . . . . . . . . . . 4.4 Example 2: Cr Triplet → Singlet . . . . . . 4.5 Example 3: LaTiO3 Ti Quintuplet → Singlet 5 Variable Magnetic Moment Calculations 5.1 Input . . . . . . . . . . . . . . . . . . . . 5.2 Output . . . . . . . . . . . . . . . . . . . 5.3 Example 1: Linear Monostrand of Pd . . 5.4 Example 2: Uranium Nitrides . . . . . . 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Running Band Structure and PDOS Jobs 8.1 The Usual Case: PDOS and BS Simultaneously 8.2 PDOS Only . . . . . . . . . . . . . . . . . . . . 8.2.1 Input Example . . . . . . . . . . . . . . 8.2.2 PDOS Output . . . . . . . . . . . . . . . 8.3 Band Structure Only . . . . . . . . . . . . . . . 8.3.1 Example Input File . . . . . . . . . . . . 8.3.2 Output Files . . . . . . . . . . . . . . . . 8.4 Obtaining BS/PDOS Later . . . . . . . . . . . . 8.5 Detailed Description of BS/PDOS IOps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 37 39 39 39 40 40 40 41 42 9 Symmetry 9.1 A Sample band.inp File . . . . . . . 9.2 Determining the SG for 3-D Systems 9.3 2-D Slabs/Films . . . . . . . . . . . . 9.4 1-D Monolayers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 44 45 47 47 10 Plotting BS and PDOS 10.1 A Basic PDOS Plot . . . . . . . . 10.2 A Sample PDOS *.gpt File . . . 10.3 Plotting Band Structure . . . . . 10.3.1 Using gpband to Plot BS 10.3.2 Default gpband Output . 10.3.3 Annotated Default gp File 10.3.4 Modified BS Output . . . 10.4 Locating k-Points . . . . . . . . . 10.4.1 Easy Indirect Gaps . . . . 10.4.2 Special Gaps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 48 49 50 50 50 51 52 53 53 53 . . . . . . 54 54 56 57 57 57 57 . . . . . 58 59 59 60 60 61 . . . . . . . . . . . . . . . . . . . . 11 Increasing the Accuracy and Efficiency of PBC 11.1 Practical Tips for G09 PBC Calculations . . . . 11.2 Diffuse Functions . . . . . . . . . . . . . . . . . 11.3 All PBC Keywords . . . . . . . . . . . . . . . . 11.3.1 Description . . . . . . . . . . . . . . . . 11.3.2 Options . . . . . . . . . . . . . . . . . . 11.3.3 Availability . . . . . . . . . . . . . . . . 12 Submitting Jobs at Rice 12.1 Modules: General Procedure 12.2 What You See: Logging In . 12.3 Module Commands . . . . . 12.3.1 Module Avail . . . . 12.3.2 Module Load . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 Basis Set Databases . . . . . . . . . . . . . .6. . . 13. . . . . .6. . . . 13. . . . . . . .6. . .3 Band Structure Plot–II . . . . . . . . . . . . . 13. . . . . . . . . 12. . . . . . . . . . . . . . . . . . . 15. . . . . .4 Global Hybrids . . . . . . . . . . . . . . .3 DaVinci Parallel (Linda) Job PBS Submission Script 13. 15. . . . . .3. . . . 13. . . 61 61 61 62 63 64 13 Scripts 13. .3 (Semi)Local Functionals . . . 80 80 80 81 81 81 15 Basis Sets for Extended Systems 15. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 STIC Serial Job PBS Submission Script . . . . . . . . . . . .2. . . . . 13. . . . . . . . . . . . . . . . . . . . . 15. . . . . . . . . . . .4 Example 3: Step-by-Step Modification for Cl . . . .5 Functional Bibliography . . . . . 14.2 Modifying Basis Sets for PBC Calculations . . . . . .2 Example 1: Modified PBC Basis Sets with No ECPs 15. . .5 Modules & Submission . . . . . . .2. . .3 Module List . . . . . . . . . . . . . . . .2. . . . . . . . . . . . . . .3. 14. . . . . . . .1 PBS Submission Scripts (Rice-Specific) . . . . . . . . . . 13. . 4 . . . .4 BioU Serial Job PBS Submission Script . . . . . . . . . . . . . . . . . 12. . . . .1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 Band Structure: gpband Default . . .1 Applications Modules on STIC . . . . . . .6 BS and PDOS Multiplot Example . . . . . . . . . . . . . . . .2 PDOS Vertical Template . . . . . . . . . . .3 PDOS Horizontal Template .4 The Rotated PDOS Plot-I . . . . . . . . . . . . . .1 Example: Ge . . . . .12. . . . . . . 13. . . . . . . . .2 Band Structure Plot . . . . . . . . . 13. . . . . . . . . . . .3.2.4 Module Unload . .1. 65 66 66 67 68 69 70 71 72 73 74 74 75 76 77 78 14 PBC Functionals 14. . . . . . . . . . . . . . . . . . . . . . . 13. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15. .1 Example: The 6-311G Basis Set for Fluorine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12. . . . . . . . . . . . . . . . .5 Modules Available on Group Workstations . . . . . . . . . . . . . . . . . . . . . . 13. . . . . . . . . 13. . . . . . . . . . . . . . . . . . . . . . 14. . . . . . . . . . . . . . . .5 Band Structure: Modified AlSb (HISS) gpt File . . . . . . . . . . . . . . . . 12. . . . . . . . . . . . . . . . . .2 Just-For-Solids Functionals 14. . . . . 15. . . . . . . . 13. . . . . . .6. . . . . . 15.1. .1 Header and Multiplot Set-Up . .2 STIC Parallel (Linda) Job PBS Submission Script . . . . . .4 G09 Modules Available on STIC . . . . . . .1 Scuseria Functionals . . . . . . . . . .1. . . . . .5 The Rotated PDOS Plot-II . . .3 Example 2: Modified Arsenic Basis Set + ECP . . .4. . . . . . .4 Converting cry to gbs Files: gbsutil . . . . . . . . . . . . . . . . . . 12. . . . . . . . 15.3 Using the EMSL . . . . . . . . . . . .3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13. . . . . . . 82 82 83 84 84 85 86 88 88 89 . . . . . . . .6. . . . . . . . . . .16 Backing Up Your Data 16. . .1 Using rsync: Examples . . . . . 5 90 90 . . . . . . . . . . . . . . . . . . . . . . . g.. INPUT and or the ROUTES 2. Note that the basis sets are generally not small since we are not limited to H. Like this and thus ready to use for a G09 job. 4. navy blue. there will always be some template. Links or paths to a database. If not. 1. etc. sgu1 appears in several examples. • sgu1 is an imaginary Scuseria Group User with an ID in the style that Rice uses. All of these files should be immediately useable via cut-N-paste from this document. will be in green. • Internal links to sections or files within this pdf file will be in a darker. if one exists. the EXAMPLES will be in monospace font and indented. which is typically 3 initials from your name followed by a number. Evince does not always work. e. will also be listed in this section. Li and Be in the 21st century. • External URL links will be in blue. somewhere.1 Conventions Used in this Document The following conventions will be used throughout: • KEYWORDS when discussed in the text will be in Bold face font • IOps when discussed in the text will be in red.. He. Types of examples to expect include: 1. Acrobat Reader should allow this. violet2.) if small enough. • Input and Output files for/from a G09 job.) 6 . Scripts (PBS. (But Acrobat works pretty much most of the time. will be included in Section 13 of this document or accessible locally by SCP from guscus:/projects/guscus/Manuals/scripts/. Small Basis Sets for illustrative purposes will be included in Section 15.1 Examples Generally. when discussed in the text. OUTPUT and or the cmd line commands to watch/work-up a job 3. • Directory paths on GUSCUS or any other machine will appear in. implementing the above HSE-for-PBC route and including all basis sets is located at: guscus:/projects/guscus/Manuals/examples/sc40 Last Modified March 26.2.5/33=1) SCF=(NoVarAcc. 2012 7 .chk #p HSEh1PBE/GenECP Int(Grid=UltraFine) Pop=Regular FMM=(print) IOp1=timestamp IOp(5/13=1.Sec. Simply replace the route line below in those *.NoIncFock. %chk= file. The unmodified (HSE03) input files and basis sets from this paper are located at online.3).Tight) A local version of the sc40 test set.2-3.2. Many of these may be taken from the Heyd 2005 paper on HSE. 1: Conventions Used in this Document 1. with the recommended route in Sections 3.2 Additional Input Examples Please note that there are numerous additional examples of PBC jobs that are small enough to run relatively quickly. (#265).com files. de.edu. This feature allows you to save your searches. or remotely.) • The orange arrow to the right indicates how you can log in. depending upon the chosen option.ezproxy.fiz-karlsruhe. If it does not show that you are logged in through Rice then you have access to the full database. since the license is via IP address. • NOTE: The contents of the center section change.fiz-karlsruhe. and personalize your account. You cannot access the full database at home.de.2 Using the ICSD: Starting Structures The ICSD Web database is located at icsd. 8 . which is very handy. For Rice users free access is available via IP address at icsd. • The red rectangle in the center shows you how you are logged in. Chemistry is the most frequently used option. while the choices to the far left and right remain the same.rice. • The yellow rectangle to the right shows you all of the options available for the different searches. green arrow. You can save your searches and recall them as necessary. Notice that the lower right of Figure 2 has saved searches. you should see a page similar to that depicted in Figure 1. Go to the left column and click “Chemistry.”as is delineated by the red arrow. Hit “Run Query” on the left. Once you have clicked on “Chemistry” you will be provided with an empty form. Figure 2: The ICSD page once you have logged in and are ready to begin a search.Sec. Type in the element/compound/alloy/system you are interested in the line marked by thered arrow This example is for bcc Cr. 1. Figure 1: The ICSD page once you have logged in and are ready to begin a search.) 3. 2: Using the ICSD: Starting Structures 2. as in Figure 2. 9 .orange arrow.1 Performing A Search Once you have logged in. (In this case “1”. indicated by the blue arrow in the lower left corner. Enter the number of elements in the system. 2. 10 . 4. since. 3. 2: Using the ICSD: Starting Structures The various crystal structures for your system available in the database then appear. the “High Quality Data only” option does not reduce the number of structures. So. as in the Cr example discussed and in Figure 3. The ICSD generally reports only the Hermann-Mauguin notation (HMN) to report the symmetry elements in the space groups. right. which is also listed in the band. we know we want bcc-Cr and it is a metal like W (Tungsten) select the Im¯3m structure. (The space group in HMN and as number(s) are in the *. See the orange arrow to the left. Click “Export Selected Data” at the top. • .BUT .) • The 4th column has the Structure Type.) 2. (See the red arrow to the far left.inp file names.Sec. 1. as indicated by the blue arrow. but in this example. It is better to use the most recent and/or highest quality structures. below. See the Green arrow.what if you do not know that much? Refer to Section ?? for more information on determining symmetry in various dimensions.cif files. Simply select the structure(s) with the space group(s) you need. as shown in Figure 4. The Warnings and Comments may be helpful in determining the quality of the structure 4.Sec. Once satisfied. click the Export CIF File button. 1. that significantly more information about the structure appears. Note that if the “Show Detailed View” button is clicked once the structure has been selected (purple arrow of Figure 3). The Experimental section summarizes what can be found in the articles of the Bibliography section. (Circled in red. The structure is a Jmol animation with free rotation in and out of the ICSD window/tab. 2: Using the ICSD: Starting Structures Figure 3: Some of the many crystal structures available for Cr on the ICSD. 3. 2.) 11 . they are saved as a zip file.cif • If multiple files are selected. 2: Using the ICSD: Starting Structures Figure 4: The detailed view for Cr cif file ID #44731.) 2. 3. with the filenames Cr_bccX. once they are extracted. with the name Cr_bcc.. Click either “Single CIF FIle” or Multiple CIF Files to export. . (red arrows. Enter the name of the cif file(s) in the form (circled in red. with X= 1.) • In the Cr example. there will be only one file saved.. 2. 12 . 2. 1.Sec.2 Saving the cif Files The Export Selected Data page is depicted in Figure 5.cif . xls. if tabulated data is desired. 2: Using the ICSD: Starting Structures 3. 2012 13 .csv and *. so once they are downloaded. you are ready to go! Last Modified April 10.cif files as is. Figure 5: The Export Selected Data page for Cr cif file ID #44731.Sec. Notice that there are two other formats: *. NOTE: GaussView can read *. 88494 _cell_angle_alpha 90.’ _cell_length_a 2. (See guscus:/projects/guscus/Manuals/Cr_44731. _cell_volume 24.E.Sec.alpha’ _chemical_formula_structural Cr _chemical_formula_sum Cr1 _chemical_name_structure_type W _exptl_crystal_density_diffrn 7. C.-C.19 _cell_measurement_temperature 293. _cell_angle_beta 90. loop_ _citation_id _citation_journal_full _citation_year _citation_journal_volume _citation_page_first _citation_page_last _citation_journal_id_ASTM primary ’Zhurnal Eksperimental’noi i Teoreticheskoi Fiziki’ 1964 47 476 479 ZETFA7 loop_ _publ_author_name ’Straumanis. All rights reserved.88494(7) _cell_length_b 2.88494 _cell_length_c 2. The absorption and refraction corrections and the lattice constants of chromium . _publ_section_title . M.cif for the full file) #(C) 2012 by Fachinformationszentrum Karlsruhe.3 A Sample cif File This file has truncated symmetry equivalent positions. 2: Using the ICSD: Starting Structures 2. data_44731-ICSD _database_code_ICSD 44731 _audit_creation_date 2000-12-16 _audit_update_record 2006-04-01 _chemical_name_systematic ’Chromium . _cell_angle_gamma 90.01 _cell_formula_units_Z 2 _symmetry_space_group_name_H-M ’I m -3 m’ _symmetry_Int_Tables_number 229 14 .’ ’Weng. z. z’ 15 ’-x. z’ 13 ’-z. x. -x’ 2 ’y. -z’ 7 ’z. -x. z. . y. z’ 19 ’-z. y. -x. x. -z. x’ 8 ’y. 0 #End of data_44731-ICSD 15 . x’ 18 ’-x. y’ 10 ’z. -x’ 6 ’x. z. z. -x. 2: Using the ICSD: Starting Structures loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 ’z. 96 ’x+1/2. -y. -y. y’ 16 ’-z. -y’ 4 ’z. -z. x’ 12 ’x. -y’ 5 ’y. y’ 11 ’y. -z’ (TRUNCATED) . -y. x. y. x.Sec. y’ 17 ’-y. z’ 9 ’x. z+1/2’ loop_ _atom_type_symbol _atom_type_oxidation_number Cr0+ 0 loop_ _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_B_iso_or_equiv _atom_site_occupancy _atom_site_attached_hydrogens Cr1 Cr0+ 2 a 0 0 0 . . y. y+1/2. x’ 14 ’-y. -x’ 20 ’-y. -z’ 3 ’x. 1. 8. A window will appear as in the left of Figure 7 3. Figure 7: GaussView for cif files.cif” 6. Manipulate the file as you wish and then save.) 2. Right: The periodic system with cell axes and atoms constructed from the cif file by GaussView. The file name should appear in parentheses in the first box e. (See the right image of Figure 7. Left: The window to select and open a cif file in your directory. A new window will open with the crystal structure inside the box defined by the lattice parameters. and electrons as well as the charge and multiplicity. Click the blue Open button to the left and GaussView will open the structure 7. 16 . Select in the File type window “Crystallographic Information Files (*. “BaTiO3. 1.) • Note that the lower left corner contains information about the number of atoms. On the menu bar. 2: Using the ICSD: Starting Structures 2.cif)” 4..g.4 Opening the cif File in GaussView Figure 6: The GaussView main console. • The information to the right will change upon selection of atoms or bonds.Sec. Go to the directory you want and select the cif file you want 5. select FILE → OPEN (See Figure 6. Save it as a *. On the menu bar. 7. 17 . Paths to basis sets or ECPs can be added via the Add. 1.gjf file by going to the main window under FIle → Save. 2: Using the ICSD: Starting Structures 2.. All requisite keywords/IOps discussed in Section 3 are input via the Additional Keywords line. Figure 9: GaussView window for setting up a job. Store the file first by hitting the Retain button at the bottom (5th ) from the left. 3. A window will appear as in Figure 9 4. If you have already save a calculation scheme. you may do this. 5.5 Saving a Job File Derived from a cif File Figure 8: The Calculation Menu to set up and save a gjf file. Input tab to the far right. instead.Sec. select CALCULATE → Gaussian Calculation Setup.. (See Figure 8. 6.) 2. now. labeled by Tv 7.1 A Sample Input File %chk=CdS-wu_x.chk #p HSEh1pbe/GenECP Int(Grid=UltraFine) pop=regular fmm=(print) IOp1=timestamp IOp(5/13=1.38820939 2.00000000 3.35800000 5.5/33=1. 3. not a molecule) 6..38820939 1.06825000 2.5/181=10.gbs/N @/projects/guscus/basis/s-mHeyd2005.00000000 0.19410469 0.06825000 0. added in *.58231408 0. The basis set specification 18 .53193200 3.NoIncFock.13650000 -2.00000000 6. Three translation vectors.71600000 @/projects/guscus/basis/cd-heyd. Coordinates (for a unit cell.5/184=186) SCF=(NoVarAcc.gbs/N Quick File Description 1.00000000 0.00000000 0.Tight) CdS-Wurzite (hexagonal) using basis set from JJ Sowa xtal Solid State Sciences 2005 7 73 78 0 1 Cd S Cd S Tv Tv Tv 0. Charge and multiplicity specifications 5.00000000 2. The title line(s) 4. Link 0 commands: checkpoint file specification (%mem etc.00000000 2.pbs files) 2. Copying the route and using it should ensure that any small test PBC job will run reasonably smoothly. The route 3.00000000 2.88993200 0.3 PBC Input Files The example below contains the minimal input file you will need for running a PBC job.19410469 1.06825000 4. USE THIS FOR HSE.bib. Most requirements parallel what is normally used for molecular calculations. and HISS. %NProcShared. Gen. • All other functionals. Pop=Regular – molecular orbital printing and several types of population analysis. HSEh1PBE – Functional specification • HSEh1PBE is the HSE06h version of HSE – the most current and accurate “flavor” of HSE. 3. 4.) 5. use the keyword.1. the same grid must be used and the Ultrafine grid is generally better for PBC calculations.2. (G09 input is essentially free-format. #p – Requests more verbose print-out..1 Link 0 Commands 1. GenECP – Basis set specification: read in a basis set and and an ECP • GenECP is equivalent to the combination of Gen and Pseudo=Read.. • Note that there are numerous ways to specify this grid: consult the G09 Keyword page to see the other variations. • If no ECP is required. • References for the various functionals are also in Section 14 or may be found locally as bib file at guscus:/projects/guscus/Manuals/functionals.chk file is vital: PBC jobs run long. Section 14. A checkpoint. *. 19 . are prone to crash.1 is provided in the subsections that follow. PBE.2 PBC Single Point Energy Calculations A detailed description of each line and/or section of the input file in Section 3. PBEsol.Sec. period. • Frequently used functionals are SVWN5. 2. %mem. *ALWAY* use. and running in parallel becomes especially useful. (See the Gaussian09 Online Users Manual. the appropriate keywords and/or IOps are tabulated in the Functionals section. • Absolutely necessary for computing Band Structure and PDOS: leaving it out will result in much distress.2. Section 8. 2. 3.2 The Route: Lines 1-3 1. • To make valid energy comparisons among two or more jobs. TPSS. scratch file names/locations and other commands will be added via the various PBS scripts and are not necessarily PBC-related – other than that memory requirements will be much larger than those of molecules. Int(Grid=Ultrafine) – always use. so case usually DOES NOT matter. and are necessary for BS/PDOS calculations.) 3. 3: PBC Input Files 3. See the specific keyword pages for more details. • NoIncFock – Prevents the use of incremental Fock matrix formation. • NoVarAcc – Do not use the default of modest integral accuracy early in direct SCF. 186 = Wurtzite/hexagonal.Sec. • Do not use @ # ! . so explicitly stating this is a safety measure.. FMM=Print and IOp1=timestamp are useful for debugging and timings • Odds are. – There is a definite difference between HSE03 and HSE06. – If in doubt. Again. recording the name.1..2. 20 . Other important PBC IOps: (Check the G09 IOps Page for more details. check your output file. The SCF settings are key for both energy calculations and optimizations. ILSW flag ON • 5/33=1 – eigenvalues and MOs printed at end • 5/181=10 – run a PDOS calculation (See Section 8.. 3. 2. 227 = Diamond.inp file of space group ### and compute the band structure. overly large file.3 and 9.g.) • 5/184=### – look for a band. multiplicity the number to the right. – Note that "tight" varies by Gaussian version for PBC. etc. 3: PBC Input Files • Using the Pop=FULL option will result in an. symmetry._ \ or any control characters (especially Ctrl-G) • Use for “notes” e. These are all Overlay 5 → Direct link to Overlay 5) • 5/13=1 – continue running even in spite of non-convergence. .. 8.. switching to full accuracy later on.this is the minimal route for a PBC job. ICSD ID and lattice parameters of the compound. and it is the default for conventional SCF • Tight – SCF=Tight.. Line 4 starts the Title Section • Cannot exceed five (5) lines and must be preceded and followed by a blank line. 216 = Zincblende...2.g. 7. Charge and multiplicity specifications • Charge is the number to the left. – e. should be default: SCF details. 1.3 Title and Coordinate Specifications Notice that very little differs from a molecular file specification.. 6. you will use these at some point: put them in your template and be glad later. – See Sections 8. For examples. with the complete input file (including both basis sets) and the corresponding output file is provided locally at: guscus:/projects/guscus/Manuals/examples/CdS-wu/. Last modified March 26. 4. the basis set and/or ECP can be added to the end of the file. will usually see 0 1. The translation vectors always follow the cell coordinates • Labeled by Tv. • Always followed by a blank line. not the primitive cell. • Can be aprimitive. see Section 2. review the sample input files in Sections 4. or numerically as -2. y and z directions. simply deleting one (or two) of the rows from the bulk structure may not result in the desired lower dimensional structure. 5. NOTE: • Databases generally provide the unit cell. 3: PBC Input Files • For a neutral singlet. respectively. The basis set specification using a path • The/N prevents the basis set from being printed at the beginning if the output file • Alternatively. the full unit cell or a supercell. 5. but be aware of an older notation using commas: 0. • xyz Cartesian coordinates • Usually from a *. like the ICSD. as in molecular calculations 6. • Note that these directions/planes do not necessarily correlate with those for various Miller Indices of interest: when going from 3-D to a 2-D slab or 1-D monolayer. This example. The unit cell coordinates. • Correspond to the x. There are cases where additional specifications may be added to a file. and 6.Sec.cif file downloaded from a database. 2012 21 .1 3. 5/33=1.1 Line-By-Line Description 1. Add the keyword Opt 3. reading from the Fock matrix is better because: “Guess=Read uses the Fock matrix if NMtPBC in the chk file is the same as that of the current calculation. otherwise. very large (hundreds of MB or even a tens of GB) • If running a big job. back up the *chk file periodically. 2. 3: PBC Input Files 3. Keep the SCF=(NoVarAcc.NoIncFock.Tight) specification. Below is an example route for a PBC Optimization: %chk=CdS-wu_x.3. it uses the MO coefficients.Fock). The latter is good for weakly-interacting molecular solids. PBC optimizations benefit greatly from an initial guess. 22 . • Why Guess=(Read. hence. Diaconu.Fock) 3.3 Geometry Optimizations Note that both the lattice parameters *and* the atomic positions are relaxed within a gaussian PBC optimization.Sec. Cristian V.” 4.Fock). The *chk files can become very. but becomes increasingly bad as the inter-cell interaction increases. A corrupted checkpoint file is an extremely sad thing • The STIC/DaVinci/BlueBioU file systems can and *will* corrupt checkpoint files – such is the price of cutting-edge computing. Guess=(Read.Tight) Opt Guess=(Read. folded in the unit cell. For nonmolecular solids I suggest always using Guess=(Read.5/184=186) SCF=(NoVarAcc.NoIncFock.5/181=10.Fock) and not just Guess=(Read)? • According to Dr.chk #p HSEh1pbe/GenEcp Int(Grid=UltraFine) Pop=Regular FMM=(Print) IOp1=timestamp IOpp(5/13=1. The best way to apply constraints in these geometry optimizations would be to use the keyword Opt=ModRedundant. not just freeze the length. and T1+T2+T3). and the same atom in cell T1+T2. for example. I see that you would like to constrain the lengths of T1 and T2 to be the same. the constraint would be to freeze the interatomic distance between an atom in the origin cell and the same atom in the contiguous cell along the direction of the translation vector of interest. in the input file you sent here. T2 and T3. if one wants to freeze the length of a translation vector. you could freeze the angle between an atom in cell T1. the same atom in cell O. Check Section 11. 3: PBC Input Files 3. T1+T2. Clemente of Gaussian Technical Support. Fernando R. T1+T3. If you were to freeze the length of the first translation vector (T1). plus the four contiguous cells along the diagonals. However. there are 8 cells to consider. you have 12 atoms plus the three translation vectors. In a 3-D periodic calculation. for instance. the redundant internal set does not allow to impose the identity condition between two coordinates. for this particular case. In your case. it would still be possible to do what you are trying here. In order to keep the lengths of T1 and T2 equal during the optimization. T1. For instance. Unfortunately.4 Constrained Geometry Optimizations This information originates from an email exchange between Rich Martin from LANL and Dr. The following shows how these cells are ordered for atom numbering purposes: Cell Start End O 1 T3 N+1 T2 2N+1 T2+T3 3N+1 T1 4N+1 T1+T3 5N+1 T1+T2 6N+1 T1+T2+T3 7N+1 N 2N 3N 4N 5N 6N 7N 8N where N is the number of entries in the input file. that makes N=15. you could freeze. The trick in applying constraints to PBC geometry optimizations is to get the correct numbering right. Note that the translation vectors count for the purpose of atom numbering even though they are obviously not atoms and thus their numbers cannot be used directly to apply a constraint. So.Sec. the interatomic distance between atom 1 (in cell O) and atom 61 (same atom but in cell T1). This angle 23 . T2+T3.3 for notes on additional PBC keyword usage. symbolic Z-matrices would not work well for PBC optimizations. the origin cell (O) and seven contiguous cells (one along each one of the three translation vector. that is the number of "real" atoms plus the three translation vectors. 46261950 0.maxcycles=64.59061950 3. -0.NoVarAcc) Guess=(Read.52341693 4.67382109 3.47678407 2.77512190 2.81959437 3.00000000 0. #p uTPSStpss/Gen PBC=(nkpoint=2000) pop=regular SCF=(convergence=7. exactly at the bisection (which implies that the two translation vectors will be equal in length).00000000 0.46062345 0. Below is an example of how to do this for your input file.0 F (high temperature).55460000 0.55460000 0.48764102 3.08147340 2.70280000 ! T1-O-T2 angle 90 deg.09075828 2.22374016 0.44482660 0.00000000 4.00000000 5. 2012 24 .73205066 0. ! T1-O-T1+T2 angle bisects above angle @v_towler.32683050 2.Fock) OPT=modredun V4O8 tetragonal rutile 0 5 V O O V V V O O O O O O Tv Tv Tv A 61 1 31 90.87756065 0.96076224 1.06368050 1.0 F A 61 1 91 45.35932265 0.19946950 3.bas @o_towler.bas Last Modified March 29.31262700 1.00000000 Towler V and O basis.27860530 1.00000000 4.Sec.94665196 2. 1.34462340 3. So.19126259 1.21367300 3.57577700 1. 3: PBC Input Files should bisect the angle between T1-O-T2.54382505 0.73225165 -0.00755669 2.18167660 0. given that your translation vectors form an angle of 90 degrees.0 degrees.27880629 0.19205909 3.48744003 2.95052300 3. the T1-O-T1+T2 angle should be frozen to be 45.06420500 4. adding Restart is sufficient. i.NoIncFock.Tight.Restart) • Optimization: SCF=(NoVarAcc. 3: PBC Input Files 3.Sec.4 for instructions on how to run constrained geometry optimizations Last modified March 27.NoIncFock.5 Restarts For both energy calculations and optimizations. • Energy Calculation: SCF=(NoVarAcc.Tight) OPT=Restart See also Section 3. 2012 25 ..e. Add the new spin multiplicity. a list of atoms whose spin densities are to be flipped should be specified after a blank line from the input file. 5. The NoSymm keyword prevents the reorientation and causes all computations to be performed in the input orientation.. IOp(5/150=1) and NoSymm. Input ONE (1) blank line after the last Tv 8. 4. NOTE: For version G09-b1-pbc-2.5. 5/150=0 turn off the AFM guess (default) 3. The first part of the input file should be the "unflipped" system 2. AGAIN: These IOps change by version.g. Add a blank space 3.3 the IOps are: 1.) 1.2 for more details. 5/150=1 turn on the AFM guess 2.) 26 . This is best accomplished by running a two-part calculation using Link 1. Add –Link1– 4. Add the list of atoms that will be spin flipped • Specify according to the atom numbers • Apparently vertically specified (See 4.1 Input If the AFM guess is turned on.Fock). The new route will include Guess=(Read. e. It is useful for generating AFM (antiferromagnetic) guesses from FM (ferromagnetic) calculations. so check before running. 0 3 → 0 1 6.4 Antiferromagnetic Guess Calculations The "Antiferromagnetic Guess" or "Spin-Flip" code for PBCS "flips" the spin density for a given set of atoms. Input the coordinates again (could Geom=Allchk be used) 7. (See Section 4. 0000 0. 4: Antiferromagnetic Guess Calculations 4.000 0.000 2.000 1. 27 .0000 0.0000 0. %chk=H.0000 0. the output file should contain the following message: "AfmFkG: AFM guess by flipping spin density" followed by the list of atoms and basis sets involved in the spin flipping.Sec.1000 0.000 2.0000 0.chk #p PBEPBE/cc-pvtz PBE H note this starts out as a triplet and will be flipped 0.chk #p PBEPBE/cc-pvtz Guess={Read.0000 0.2000 ! LIST OF ATOMS WHERE THE SPIN SHOULD BE FLIPPED ! Note only 1 linee between the Tv and the atom list 1 4.000 1.0000 0.000 0.0000 0. the comments are actually *in* the G09 input file.3 Output File Info At the beginning of the SCF.2 Example 1: H Triplet → Singlet In the following example.3 H H TV 0.Fock} IOp(5/150=1) NoSymm PBE H note that the total spin multiplicity is now 1 0.2000 --Link1-%chk=H. The input and output files – with comments – are located locally at: guscus:/projects/guscus/Manuals/AFMGuess/Example1-H.1000 0.1 H H TV 0. U. ! 0.3 Cr Cr TV 0.0000 0.571323846 A.000 4.chk #p PBEPBE/LANL2DZ PBE Cr 0.chk #p PBEPBE/LANL2DZ guess=read IOp(5/150=1) PBE Cr ! ! **** note that total spin multiplicity here is 1. 2nd line: Converged SCF energy corresponding to that of the singlet arising post spin-flip.513542291 SCF Done: E(UPBE-PBE) = -172.0000 0.0000 0.0000 0.0000 0.Sec.0000 Cr 0. 4: Antiferromagnetic Guess Calculations 4. after A.0000 0.000 4.log SCF Done: E(UPBE-PBE) = -172.4000 TV 0.1 Cr 0.000 0.U.4 Example 2: Cr Triplet → Singlet %chk=Cr.0000 0.8000 !LIST OF ATOMS WHERE THE SPIN SHOULD BE FLIPPED 1 Information from the output file: [sgu1@gw Example2-Cr]$ grep "SCF D" *.000 2.000 2.4000 0.8000 --Link1-%chk=Cr. 28 . after 55 cycles 30 cycles 1st line: Converged SCF energy corresponding to that of the triplet.000 0. A sample version of the input and output with comments is located locally at: guscus:/projects/guscus/Manuals/AFMGuess/Example2-Cr. 0.2.277038938.-1.edu %-------------------------------------------------%chk=LTO.5/33=1.3.0.7656449004..1. 2_SVP_La.0.2775004992.4.2743011984. Atoms 8 and 9 will have spin DOWN while 2 and 10 will keep spin UP.1.2.5812458804 Ti.-0.gbs @2_SVP_La.0.2.4.4982535617.3236264087.-0.0.8772833843.-3.2692554128.chk #p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine iop(5/13=1.0.-0.0649514287.0.0431335943.4446548897.4932384439.0.-0.2.27940315.3/18=1.-1.0.2692554128.-1.-0.1.1116294151 O.0.0.-2.-3.2052614311.0.0.0.0013274988.0.0.-1.0.0334301204.0334301204.el_mellouhi@qatar.1.-2.0.0.5559414972 O.4.9.0.5.1 La.0.3236264087.0.-3.0.3.0.4894430993.0.-1. 4: Antiferromagnetic Guess Calculations 4.2052614311.6296615465 O.-2.3/18=1.0.1.8.5812458804 Ti.-0.2766559378.112984379 O.0064109731.0.0.5568557237 Ti.0.5 Example 3: LaTiO3 Ti Quintuplet → Singlet In the following example.1604564175 O.3219594526.0554120936.3713792713 La.2942660209.-2.8895175017.-1.0.1.5.0.3952969214 O.0016897946.0.3/65=-25) GFInput pop=regular SCF=tight Ferro magnetic LaTiO3 Spin UP for all Ti atoms 2.-1.7656449004.1.0.2.1591920659 O.0.tamu.0001024768.0.5/150=1) GFInput pop=regular SCF=tight AntiFerromagnetic state will be obtained from the previous run by activating the IOP 5/150=1 indicating to flip spin for the Ti atoms.-2.8895175017.0.0.5.-1.0.4894430993.8756333904.3704292974 O.8229404289.0.-1.-1.1.0.-2.3.2743011984.3219594526.-3.-2.1.112984379 O.5802918116 O.2660765836.0. 0.-0.-0.3961952352 Ti.0.5815593191 O.0.0.Sec.5196374746.3713792713 La.0431335943.-0.-0.1.322861073 O.5815593191 O.0.0022507369 TV.5045921227.-2.0649514287.0.0.2660765836.3704292974 O.0.-0.890960693.-3.27940315.1.4825626149.gbs get from Fadwa El-Mellouhi ! fadwa.0.-0.0.-2.6309382415 TV.8791897066.4446548897.3188302628.-2.0.3961952352 Ti.-0.-2.chk #p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine Guess(Read.5997593459.0.5937990896.0.2766559378.-3.5802918116 O.0.0.gbs.0.-1.1.4815133703.9042794351 ! used basis sets @2_mod_SVP_Ti. %chk=LTO.8777073771.1591920659 O.7.580103775 Ti.-2.Fock) IOp(5/13=1.4815133703.2775004992.0.0. 2012 29 .gbs 9 8 Local versions of the input and output files (with comments) are located at: guscus:/projects/guscus/Manuals/AFMGuess/Example3-LTO.-0.-0.0.277038938.3188302628.0.0.322861073 O.0.3702238711 La.0.1116294151 O.5196374746.2793469199.2793469199.8791897066.5197041276.2. Last Modified March 28. SVP_O.0.1.490041081.0.8772833843.0554120936.3173586107.443200864.gbs.0.3173586107.0.-0.2. the comments are actually *in* the G09 input file.10 0.2942660209.3214858263 La.5997593459.0.5559414972 O.0.2.490041081.1.1.5197041276.-3.3716929806 O.-1.0.3716929806 O.9211487908..443200864.0.2.3.3/65=-25.6309382415 TV.6296615465 O.0.3702238711 La.0.0016897946.-1.922206137.-2.5337445538. Notice the free-format of the G09 input files.0.-0.4932384439.0.0004424492 TV.0013274988.8756333904.0.-3.0.0.922206137.-2.8777073771.4982535617.-1.5/33=1.1604564175 O.0001024768.5937990896.5.5045921227.0.2.4825626149.9211487908.-0.-2.9042794351 ! basis sets @2_mod_SVP_Ti.-1.0.580103775 Ti.0.0.2.5 La.0.3214858263 La.8229404289.0064109731.7.5568557237 Ti.0004424492 TV.gbs @Basis/SVP_O.5337445538.2.890960693.1.3952969214 O.-2.0022507369 TV.4.-1.0. 1 Input 1. Tue Mar 27 12:52:16 2012 0. For version G09-b1-pbc-2.Fock).588292 Bohr magneton per unit cell Eferm= -5.5 Variable Magnetic Moment Calculations The Variable Magnetic Moment (VMM) code is similar to that of the AFM Guess. 30 .03 cpu seconds.11D-15 ZInLT1: VMM Cor=Cln Er=-1..log which then provides the following information: VMM NIter= 20 Fermi level: -5.23345194178 Magnetic moment = 1. 5/150=-1 turn on the VMM code 2.3 the IOps are: 1. The new route will include Guess=(Read.00D+00 Er1=-7. after A. NOTE: These IOps change by version – please check before running. The first part of the input file should be the "unflipped" system 2.233452 NE= 36 Er0= 0.423823192 SCF Done: E(US-VWN5) = -254. 5/150=0 turn off the VMM guess (default) 3. 5.log SCF Done: E(US-VWN5) = -254. Add a blank space 4.884531549023800 End of ZIntLT.500741669 A.55D-13 Sum= -410. e.923914275660400 ZInLT1: VMM Cor=Yes Er=-4. 5D 7F in Example ?? 3. Input the coordinates again (could Geom=Allchk be used?) 5. IOp(5/150=-1) 6.U. after 37 cycles 16 cycles To watch job progress.g.60D+01 Sum= -209.2 Output For final energy information: [sgu1@gw VMM]$ grep "SCF D" test. type: [sgu1@gw VMM]$ grep -A5 "VMM N" test.U. Specify orbitals of interest. Add –Link1– 5. 000000 0.chk #p USVWN5/Gen Pseudo=read 5D 7F SCF=Tight Guess=Read IOp1=timestamp IOp(5/33=1.0000 ! basis set information provide in input file on ! guscus:/projects/guscus/Manuals/VMM/Example1-Pd ! Notice only one blank line between last Tv and --Link1-! --Link1-%mem=2500Mb %nproc=4 %chk=Pd.5.5 Pd Pd Tv multipl = 5 .5 Pd Pd Tv multipl = 5 old example from Juan Peralta . 5: Variable Magnetic Moment Calculations 5. Files are accessible locally at: guscus:/projects/guscus/Manuals/VMM/Example1-Pd %chk=Pd.5/13=1) scf=(conver=8.0 .02.V06.3 Example 1: Linear Monostrand of Pd NOTE: The reference data is taken from Dr.V06.DAMP) PBC(NCellMin=120) Pd linear monostrand SVWN5 / 0. we used G09-B1.000 3.5/13=1) PBC(NCellMin=120) Pd linear monostrand SVWN5 / 0.CDIIS.5/150=-1.MaxCycle=300.000000 0.ccpvtzpp.000 0.000000 0.maxcycle=300.5.NoIncFock.CDIIS.0 6.SVWN5. At the time of this writing.000 0.000000 0.000 0.000 3.00000 .000 ! basis set information provide in input file on ! guscus:/projects/guscus/Manuals/VMM/Example1-Pd 31 .NoVarAcc) iop(5/33=1.00000 .0 6. Juan Peralta’s calculations run with GDV-F.000 0.Sec. Please exercise caution if using older or newer versions.ccpvtzpp.chk #p USVWN5/Gen Pseudo=read 5D 7F IOp1=timestamp SCF=(Conver=8.0 .SVWN5. Last Modified March 27. 2012 32 .Sec. Relevant files will be placed in: guscus:/projects/guscus/Manuals/VMM/Example2-UNx. M. Lucero and V. This example is being specially prepared in order to optimize all aspects of your learning experience.. Barone. the comments are actually *in* the G09 input file.. 5: Variable Magnetic Moment Calculations 5.4 Example 2: Uranium Nitrides In the following example. This is somewhere in the Refractories directory. This is the "molecular" calculation only to generate the intracell SO matrix elements in the cell 0... #p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp SCF(maxcycle=60.. Bulik for more information. As of April 1. @Ge. %subst l302 .cell.NKPoint=1000) IOp(5/193=1) IOp(5/155=3) ! ! ! ! Bulk Ge with ECP spin-orbit. 6. G09-B1 and gdv-H11 may be used with confidence. basis sets and ECP are all online @Ge.geom ! Coordinates. @Ge. This is the PBC part.6 Spin-Orbit Calculations The key is to use a gdv version that has Spin-Orbit Coupling implemented and to use IOp(3/117=1). 2012.ecp --Link1-%subst l502 .geom ! Coordinates. %KJob l302 #p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp gfprint iop(3/117=1) NosSmm Bulk Ge with ECP spin-orbit. IOps 5/193=1 and 5/155=3: Contact Irek W.cell.conver=5) PBC(cellrange=60. although gdv-H13 has been tested. After a regular PBC calculation GDV will read the SO matrices from the previous (molecular) calculation for the 0-0 cell.bas @Ge-SO. add it to the Fock matrix.bas @Ge-SO.. → This uses. basis sets and ECP are all online @Ge.ecp 33 .1 Example 1: Ge with ECP → The following job was run using gdv-H13. transform to k-space and diagonalize. after Conv=0.417271213 A.270861610394E-02 A.U.U.log = -588. 6: Spin-Orbit Calculations The output file provides the magnitude of the coupling via the cmd line: grep − A300 SCF D00 [sgu1@gw test-Ge-con]$ SCF Done: E(US-VWN5) NFock= 8 Spin-orb: E(2nd v) = TOTAL E(US-VWN5) grep -A3 "SCF D" Ge.414562597 A. 8 cycles Relevant job files may be accessed locally at: /projects/guscus/Manuals/Spin-Orbit/RECP-SO/test-pbc-3/testGe-con/ 34 .19D-05 -V/T= 2.4479 -0.SO. = -588.SVWN5.U.Sec. . 2012 35 .2 Example 2: Hg with ECP → The following job was run using gdv-H13 %subst l302 .log A. 6: Spin-Orbit Calculations 6. %KJob l302 #p NoSymm UHF/Gen Pseudo=read 5d 7F SCF=NoVarAcc test IOp(3/117=1) Hg with ECP spin-orbit.U. Relevant job files may be accessed locally at: /projects/guscus/Manuals/Spin-Orbit/RECP-SO/test-pbc-3/ttestHg-atom Last Modified March 29. This is the "molecular" calculation only to generate the intracell SO matrix elements in the cell 0.687956585 *.9834 A. after 23 cycles -V/T= 3. .U..532937892 NFock= 23 Conv=0. ! The basis set and ECP are online in the full input file.0000 0.Sec.155018692641 TOTAL E(UHF) = -152. The output file provides the magnitude of the coupling: [sgu1@gw test-Hg-atom]$ grep -A3 "SCF D" SCF Done: E(UHF) = -152.12D-07 Spin-orb: E(2nd v) = -0.U.0000 0. A. 0 1 Hg 0.0000 ! (12s12p9d3f2g)/[6s6p4d3f2g] basis set from Ref 37. . If you need immediate assistance.7 Dispersion Calculations How to run Irek’s 2. please contact Irek W. Bulik. Last Modified March 23.and 3-body code based This example is being specially prepared in order to optimize all aspects of your learning experience. 2012 36 . Examples will eventually be locally available in: guscus:/projects/guscus/Manuals/Dispersion/. 2.5/33=1) SCF=(NoVarAcc. 4.inp files are described in Section 9. The IOp 5/184=194 indicates that the k-path and labels for space group 194 (hexagonal) have been provided in the band.1 and located locally at guscus:/projects/guscus/Manuals/binps/. so a modified band. Both band structure and projected densities of states data will be produced at the end of this SPE calculation. it is easier to run PDOS and band structure calculations at the same time – if it becomes apparent that one part of the data is not needed.Tight) IOp(5/181=10.NoIncFock. 5. • The band.chk #p HSEh1PBE/GenECP Int(Grid=UltraFine) pop=regular FMM=print IOp1=timestamp iop(5/13=1.1 The Usual Case: PDOS and BS Simultaneously For the example route below. be aware that band structure and PDOS data tend to complement each other much of the time.[1] %chk=monohse. • Some PDOS data files appear during an energy calculation (see Section 8. The IOp 5/181=10 indicates that G09 should calculate the PDOS. 8. renamed and placed in the same directory as your job. the extraneous output can always be deleted.inp file with the correct symmetry (see Section 9 must be copied.log 37 . The monolayer is a 2-D system. • A band. 3. both PDOS and band data will be computed for the HSE single point energy calculation of a monolayer of MoS2 . Ensure that your pbs or other submission file has the following line at the very end: mkpdos -bias-from ‘‘$InpBase.inp file was used for this calculation. band structure data would appear at the end of each opt cycle.out’’ -f -v >& mkpdos.8 Running Band Structure and PDOS Jobs Generally.5/184=194) NOTE: 1. • If this had been an optimization. Nevertheless.inp file.2 but all files do not appear until the job completes. ) 2. The data is from the HSE SP calc of an MoS2 monolayer.33 eV. Lett. (See Section 13. The basis set file: mos_cvd.gjf and *.33 eV (D) −2 −2 −4 −4 −6 −6 −8 −8 Γ M K Γ K−Path 1 2 3 4 5 6 PDOS (states/eV/unit cell) Figure 10: An example of BS and PDOS as plotted using multiplot. (See #386. 99. Phys. 12 10 8 Energy (eV) 12 Ss Sp Sd Mos Mop Mod Total 10 8 6 6 4 4 2 2 MoS2 Monolayer SPE 0 EF HSE Gap 2.) 5.Sec. PDOS-relevant files: pdos.dat and pdos.txt (See Section 8. 2012 38 . Band-relevant files: band.legend.3.gpt that produces the plot.2. A multiplot gnuplot file both.gbs (See Section 15.out (See Section 3. 261908 (2011). Appl.dat and bandk. with a calculated direct band gap Eg of 2.dat (See Section 8. 8: Running Band Structure and PDOS Jobs Relevant files for data work-up include: 1.) Last updated: April 16.) 4. G09 input and output files: *.) All relevant files to reproduce the plot in Figure 10 may be copied from: guscus:/projects/guscus/Manuals/examples/MoS2mono See Section 10 for explicit details on using Gnuplot for BS/PDOS plots.) 3.6. .Sec.2.2 PDOS Only PDOS only jobs are fairly straightforward: 1.2. Place the following command at the end of your *.5/184=227) OPT Guess=(Read.log – describes what happened during the PDOS calculation.Fock) 8. • zpratl-pdos. • fort.NoIncFock.gjf or *pbs file: mkpdos − bias − from 0 $InpBase.5/33=1) SCF(NoVarAcc. 39 10 Figure 12: HSE opt of Si (dia) – vertical.Tight) IOp(5/181=10.121 – appears as the job runs and indicates that PDOS will be calculated.out0 − f − v > & mkpdos. 2. 2. • pdos. • mkpdos.2 PDOS Output Several PDOS-related files will appear once a job has finished. Add IOp 5/181=10 to the route.17 eV (I) 1.22 eV (I) Expt.legend. appears as jobs runs.dat – contains the data to plot Useful.txt – Legend for orbital populations on specific nuclei. Useful. = 1.log 8. 8: Running Band Structure and PDOS Jobs 8.5 PDOS (states/eV/unit cell) 2 Sis Sip Sid Total Fermi level Si (dia) HSE OPT Eg = 1.1 Input Example %chk=Si-dia_o. NOTE: A job will appear to be running until all PDOS-related files finish writing. • pdos.5 1 0.inp – a file necessary for the calculation. These files include: • pdos.5 0 -10 -8 -6 -4 -2 0 2 Energy (eV) 4 6 8 Figure 11: HSE opt of Si (dia) – horizontal.chk #p HSE1PBE/Gen Pop=Regular Int(Grid=UltraFine) FMM=Print IOp1=timestamp IOp(5/13=1.d – additional data that may be deleted at the end. Sec. the band structure code will choke.out and *. 2.inp. but require some knowledge of the symmetry of the system because of the necessary band. 8. 8: Running Band Structure and PDOS Jobs 8. 2.inp files. but it is not as large as band. The band. 8.g. at IOp(5/181=200) 3.dat) provide the number of electrons. See Section 9.3 Band Structure Only Band structure jobs are also easy to run and set up. 5. e.inp file that will have the coordinates and K-path for the specified space group.5/184=227) To properly use IOp 5/184 in your route: 1.3. Last updated: March 26. If the band.dat This contains everything you need to plot band structure.dat This is in the work-up.5/33=1) SCF=(NoVarAcc.1 Example Input File (This is for BS only.inp files will be discussed in detail in Subsection 9. no PDOS) %chk=AlSb_x. two (2) new files are produced: 1. bandk. containing the appropriate K-path and coordinates for the Brillouin zone for that space group must also be copied from the /binps directory (where ever it is) into the running directory of your job and re-namedband. The number of the space group for your system needs to be input as the 5/184 argument in the route of the input file. The band.1 for a detailed explanation/example of the band.1. IOp(5/184=227) indicates an FCC system with space group number 227.. NOTE: the name of the band. the HOCO and LUCO values. 4.dat and is not necessary once a gnuplot file has been set up.inp file is not present.Tight) IOp(5/181=200. 2012 40 . To ensure that PDOS is turned off. as the default is to look for a band.chk files that are necessary for processing the BS data.inp must be lower case. the indirect gap (after scaling) and mGap1/MGap1. band.2 Output Files In addition to the *.3.chk #p HSEh1PBE/GenECP Int(Grid=Ultrafine) fmm=(print) pop=regular IOp1=timestamp iop(5/13=1.inp files. The last 6 lines of the file (tail -6 band.inp file.NoIncFock. band structure and PDOS can be calculated “after the fact. charge. • To turn off PDOS. multiplicity and coordinates from the *chk file.5/184=227. IOp 5/14=20 uses the BS data from the already computed real-space Fock matrix. both PDOS and BS for a FCC system in space group 227.inp file in place for the restart from an good *chk file. but is generally not instant unless it is PDOS only.chk #p HSEh1PBE/ChkBas Geom=AllCheck Guess=(Read.” This requires a truly minimal input file assuming pop=regular was used in the job that generate the *chk file: %chk=AlN_x.Fock) IOp1=timestamp iop(5/13=1.5/14=20) ChkBas reads the basis set information from the *chk file Geom=AllCheck takes the title.5/33=1) IOp(5/181=10.Sec. (See Section 13) change the PDOS IOp to IOp(5/181=200). which should usually run automatically as it is in most *pbs scripts. • This “restart” is much faster than re-doing a full energy calculation. These 4 lines are sufficient to produce.4 Obtaining BS/PDOS Later If a *chk file is available for either an opt or energy calculation. 2012 41 . but if the *chk file was corrupted or there was not band. • This usually works. in this case. 8: Running Band Structure and PDOS Jobs 8. all sorts of weirdness will ensue. Last updated: March 26. inp4 Number of k-Points Sampled use KK*1000 k-points for sampling the path Special: 0 same as 2 (2000 k-points) [DEFAULT]4. 8: Running Band Structure and PDOS Jobs 8.5 Detailed Description of BS/PDOS IOps IOp IOp 5/181 Arguments 0 1 2 10 20 00 200 IOp 5/184 EE 00 00 99 00 00 FF 00 01 02 03 10 20 30 KK KK 00 0 SpG 1-228 IOp 5/183 0 -1 Table 1: IOps for BS and PDOS Explanation The PDOS IOp Should produce PDOS on every atom and orbital Read pdos. Last updated: March 24.5 Space group specification Space group #. same as 21 (???) k-path from band.inp4 labels from band. plot all possible bands k-Path Determination Default.. atom AOT atom type Produce files for the DOS (CVD says default ???) Turn off PDOS The BS IOp E window for band range1 print bands within EE eV of Fermi Level2 no window.inp appended to labels from library4 ignore labels from band.inp Run DOS/PDOS (Default) Perform projection group for ea.inp once file is produced Do NOT read pdos.inp appended to k-path from library4 ignore k-path from band. If you need immediate assistance.inp replaces k-path from library3 k-path from band.Sec. THIS SECTION IS A WORK IN PROGRESS. please contact Melissa Lucero..inp file in working directory The Auto BS IOp = EE KK FF Defaults No band structure NOTE: This is not final. band.inp replace labels from library4 labels from band. 2012 42 . then the symmetry changes must be noted.inp in the running directory 3.inp file with the appropriate SG to band. Recall that band.2 • 2-D Slabs/films/monolayers – Section 9. 4. NOTE: There are numerous systems to designate symmetry. When the conventional/crystallographic unit cells are large.inp file: 1. 2.g. refer Section 9.inp. • Not all space groups are represented by known compounds.. the argument of IOp (5/184=SG) is the space group number (SG) of the system. This enables gaussian to read the k-path and label the high symmetry points. Formally. then the prototype.) 2.g.. so familiarity with the more common systems will prove helpful when information other than SG is provided. If a supercell is created (e. Copy and rename the *.3 • 1-D Chains – Section 9.4 • Creating supercells and primitives – Section under construction • Other symmetry designations – Section under construction • List of additional resources – Section under construction 43 . To locate the appropriate *.1. (For more information. 186_MoS2-hex. the numbering is arbitrary. Note that the files are named first by the SG that would complete the argument of IOp (5/184=SG). Currently Available Information: • A sample band.inp file – Section 9. for doping).9 Symmetry To run band structure jobs. otherwise. as defined by the International Union of Crystallography. creating a smaller primitive is useful and requires knowledge of the SG before and after the cell size is reduced. the “space group number” refers to the unique numbers (1-230) assigned to all space group types.inp files are stored locally in guscus:/projects/guscus/Manuals/binps/ Other instances where knowing the SG is helpful: 1. • Groups within the same crystal system or point group have consecutive numbers.1 • 3-D (Bulk) systems – Section 9. followed finally by packing type e. especially for space groups lower than 200. in the case of optimizations where the symmetry has changed.inp File Below is an example of the band. G09 uses the SPACE GROUP as the argument to IOp(5/184). ! ! ! ! ! ! ! ! C Diamond A4 Fd bar3 FCC Pearson Symbol: cF8 Strukturbericht Designation: A4 Space Group: Fdbar3m Number: 227 Others: Si. Last updated: March 26. 2012 44 .inp file by default.inp. • Notice that fractions or decimal representations can be used.. nevertheless.g.inp in the /binps directory [needs a path] and renamed band.inp template files are in the /binps directory on guscusgw and are named (1) according to space group and lattice and/or (2) labeled to indicate any modifications or use in publications.inp copied from 227-Diamond-fcc.inp file is necessary because the internal library cannot always correctly identify the symmetry.inp files allow the path to be changed as necessary to match the literature or. (The band structure code looks for the band. 9: Symmetry 9.5 for the coordinates. Ge. p. 76 KLABELS: GM 0 K 3/8 L 1/2 U 5/8 W 1/2 X 1/2 0 3/8 1/2 1/4 1/4 0 0 3/4 1/2 5/8 3/4 1/2 KPATH: GM X W K GM L U W L K|U X IMPORTANT: • This external band. Sn Reference: Ashcroft and Mermin. re-run the job with the correct space group and path • Again. e.1 A Sample band. Notice that other symmetry designations in addition to space group are listed. 1/2 or 0.Sec. the band.) • More importantly. band. that will determine symmetry and convert to any of a number of primitive cell types. less frequently *.pdf ) file downloaded from a database. etc. the coordinates may be extracted from JMol. The space group of crystal structure is usually included in the *. another commonly used symmetry designation.cif (or. the Aflow Library is a searchable database of band structures and related properties. 2. containing: • The DFT+U band structure (fully-optimized) plotted alongside the PDOS. The Prototype list file in the guscus:/projects/gusucus/Manuals/ directory 6.g.2 Determining the SG for 3-D Systems NOTE: The following suggestions and/or instructions generally apply to undoped systems and any other of relatively high symmetry. Other means of acquiring SG information: 1.) • Effective masses. etc. The literature – the computational or experimental methods section(s) will include mention the SG. 4. 9: Symmetry 9. e. • CELLTRAN will transform unit cells • TRANSTRU transforms structures • Any of the other “Structure Utlities” 7. Vesta. 5.. Similarly. The Prototype list online at the The Navy Crystallographic site. Lower symmetry or esoteric systems may require more extensive effort. which contains also the “short symbols” to the far right. or at least the “short symbol” designations. The Energy Materials site maintained by Curtarolo’s group at Duke provides an online converter at ACONVASP Online. 45 . the ICSD or the AMS.) 8. e. The Bilbao Crystallographic Server has numerous utilities that are updated. Materials-specfic GUIs such as Materials Studio. electron mobilities. 3.. • A JMol animation of the primitive cell used for the calculation.. XcrysDen. lattice parameters before and after optimization.Sec. The space groups are numbers ranging from 1-230. Google (No joke. periodically.g. (Depending upon the browser and OS. as is seen to the far left column of Figure 13. and are thus not as widely used. as numbers 1-230.wikipedia. Other systems such as the Pearson for Struckturbericht designations are as not universally applicable. (From: en. 9: Symmetry Figure 13: Table of Space Groups in 3-D.Sec.org/wiki/Space_group) 46 . The other common system. The SGs used as the argument for IOp 5/184 are located in the far left column. the “International Short System” designations. are an abbreviated version of Hermman-Mauguin notation and form the column to the far right. Other means of acquiring this information include: 1. 2010. (b) Rectangular. Figure 14: 2D-Brillouin Zones. Vesta. The ACONVASP Online site (Curtarolo’s group at Duke) 3. Ref. and. α2 . the initial “space group” of your system in terms of how g09 identifies the point group is in the *. (c) Hexagonal with lattice constant a. (a) Square. (Taken from: Economou.g.3 2-D Slabs/Films Generally. The 2-D Space Groups Table (See Figure 14) 4. 9: Symmetry 9. Other means of acquiring this information: 1. The literature 2. Materials software like Materials Studio. [2]) 9. Non-Gaussview software Last updated: March 28. etc.cif file downloaded from a database. 2012 47 . the initial “space” group of your system is in the *.cif file downloaded from a database. The literature – the papers you start with 2. with lattice constant a. with lattice contants α1 .Sec. the ICSD or the AMS. e.4 1-D Monolayers Generally.. txt files generated by your job output and a *.0000 0.0000 0.0000 -0.0111 0.8800 -41.0000 -0.0000 0.0097 0.0335 0.0009 0.0000 0.0002 0.0000 0.0000 0.1437 4.0136 -0.0000 -0.0006 0.0000 -0.0000 0.0000 0.0000 -0.0000 0.0246 0.0000 -0.8400 -41.1274 -0.6400 -41.0004 -0.0000 0.0000 0.0009 -0.1489 0 In S a 0.0000 -0.0000 0.3139 0.7400 -41.0005 0. .0027 -0.0001 0.0066 0.0000 -0.0000 0.0000 0. The pdos.0000 0.0000 0.0000 0.6800 -41.1066 0.9556 189.0000 0.0097 0.0000 -0.0014 Total a 0.0488 -0.0000 -0.0000 0.7966 188.0014 0 In D a 0.1 A Basic PDOS Plot Density of states plots are generally *MUCH* easier to work-up than BS data: simply use the pdos.0000 -0.0000 0.9656 10.0000 0.0000 -0.0007 0.1885 64.0000 0.gpt Additional templates are located in Sections 13.0000 0. pdos.6600 -41.0000 0.0000 0.0000 -41.0000 0.0000 -0. This *gpt template file is provided at: guscus:/projects/guscus/Manuals/examples/pdos.0000 -0.1067 0.1827 -0.0000 0.0005 -0.8200 -41..3.0000 0.0000 0.0000 -0. 48 .2 and 13.3143 0.0003 -0.0000 0.1460 64.0000 0.0000 0.9200 -41.0000 0.1627 99.0000 0 Mg P a 0.9385 and the pdos.0000 0.0000 -0.0821 -0.0008 -0.9000 -41.9400 -41.0001 -0.0000 -0.0004 0.7200 -41.9583 38.0000 0.0003 -0.0001 0.1413 4.0001 -0.0000 -0.dat file for am MgInS2 LSDA OPT looks like this: # E/eV -42.0000 0.0000 -0.0000 0.0000 -0.0000 0.7600 -41.0000 0.0001 0.8543 2.0000 0.0000 0.0012 0 In P a 0.2417 0 S D a 0. .0000 0.0000 -0.8534 2.0000 0.0000 0.6200 .0000 -0.0000 0.0003 0.0018 0.0000 0.8000 -41.0000 0.0000 0.0172 0.0000 0.0000 0.0000 -0.gpt template file.0000 0.0334 0.8600 -41.0000 0.0000 0.0001 -0.10 Plotting BS and PDOS 10.6178 20.6060 20.7368 142.0000 -0.0011 -0.0002 -0.9800 -41.0011 -0.0007 -0.0000 0.0000 -0.0000 0.0001 -0.7800 -41.0000 0.0000 0.0006 0.legend.6258 142.0000 0.0000 -0.0000 0.0004 -0.0011 0.9350 38.0000 0.0000 0.0000 -0.0000 -0.0026 0.9601 10.dat.legend.0000 -0.0000 0.0326 0 S P a 0.7000 -41.0036 0.0000 0.0063 -0.0000 -0.0000 0.0026 0.9600 -41.0268 -0.0000 0.0000 -0.0000 0.0000 0.0000 0.2341 99. This helps you determine the color scheme of your gnuplot output.0000 0 S S a 0.0000 0. 0 Mg S a 0.0000 0.0000 -0.txt looks like this: 1 2 3 4 5 6 7 8 9 10 E(eV) 0 Mg S a 0 Mg P a 0 InS a 0 In P a 0 In D a 0 S S a 0 S P a 0 S D a Total a where the different orbitals for each atom are listed followed by the Total electron density. \ stub .5 1.5 1.5 set label 1 ’Fermi level’ at HOCO.5 1. ’dat’ using 1:(fa($6)) w l ls 7 title ’In_d’ .5 1. Adjust the color scheme according the the pdos.1252 set xrange [-5.txt file. 49 . graph 1 nohead lc rgbcolor "dark-red" lw 1. CVD S. graph 1 right rotate offset character 1.. \ stub . character -1 fa(x) = x fb(x) = 0 # The actual commands to plot your data plot 0 w l lt 0 notitle. ’dat’ using 1:(fa($3)) w l ls 3 title ’Mg_p’ . graph 0 to HOCO. ’dat’ using 1:(fa($7)) w l ls 8 title ’S_s’. \ stub . \ stub . 10: Plotting BS and PDOS 10.gpt File To use this template: 1. ’dat’ using 1:(fa($10)) w l ls 1 title ’Total’. bas .legend. ’dat’ using 1:(fa($8)) w l ls 9 title ’S_p’. Replace the argument for stub with the name of your PDOS *.5 1. ’/’ .5 1.’ # This is the name of your #. which will determine the legend/key. (This is illustrated in the last eight (8) lines in the example below.dat file: e.0] # range of x-axis will vary by system set yrange [-2:80] # range of y-axis will vary by system # Line styles and color set style line 1 lt 0 set style line 2 lt 1 set style line 3 lt 2 set style line 4 lt 1 set style line 5 lt 1 set style line 6 lt 1 set style line 7 lt 1 set style line 8 lt 1 set style line 9 lt 1 set style line 10 lt 3 scheme lc rgbcolor "black" lc rgbcolor "magenta" lc rgbcolor "magenta" lc rgbcolor "red" lc rgbcolor "blue" lc rgbcolor "cyan’ lc rgbcolor "green" lc rgbcolor "gray" lc rgbcolor "orange" lc rgbcolor "orange" pt pt pt pt pt pt pt pt pt pt 0 2 1 1 1 5 2 3 4 5 ps ps ps ps ps ps ps ps ps ps 1. ’dat’ using 1:(fa($9)) w l ls 10 title ’S_d’ This sample pdos *gpt file is provided at: guscus:/projects/guscus/Manuals/examples/pdos. ’ Fully-Relaxed XTAL Gap_I=Gap_D=2. ’dat’ using 1:(fa($5)) w l ls 6 title ’In_p’ . \ stub .3.5 set xlabel ’Energy (eV)’ set ylabel ’DOS (states/eV/unit cell)’ set xtics 0.dat file HOCO = 0 LUCO = 4.2 A Sample PDOS *.5 eV’ set title tit stub = ’MgInSlda.5 set ytics 5. \ stub . ’dat’ using 1:(fa($2)) w l ls 2 title ’Mg_s’ .g.2 and 13. \ stub .5 1.Sec. xc .0:8. stub = ’MgInSlda’ → stub = ’YourPDOS’ 2.0 #set mxtics 5 set arrow 1 from HOCO. \ stub . \ stub .5 1. ’dat’ using 1:(fa($4)) w l ls 5 title ’In_s’ . Crystal In ’ = ’DIRECT Mg_8In_{16}S_{32}: ’.) reset # Avoids ugliness in Gnuplot if something went wrong in the previous compilation # Below are optional short-cuts to help annotate your PDOS output bas tit = ’Towler Mg.gpt See also: Sections 13.5 1. the gpband script is stored at guscus:/projects/guscus/Manuals/scripts/gpband. • Labels.out. the easiest way to plot band structure data is to use the gpband Perl script written by Dr.3 Plotting Band Structure Currently.1 Using gpband to Plot BS 1. ran it and created band. • The default color scheme is most likely not what will be used in the final plot. • Of the many options. (There is no Gnuplot on most Rice clusters. Copy the gnuplot and *.3.dat • The files that are processed include band.2 Default gpband Output 20 10 Energy (eV) 0 −10 −20 −30 −40 Γ X W K Γ L U W K|U X k path 50 Figure 15: The band structure for AlSb optimized using HISS. gpband prepares a basic gp file that runs to produce eps output – see Figure 15.dat files to your desktop to plot the data.eps (to the left) automatically.dat seems to work the best.) 4. I-bars. 10. but may be adjusted for aesthetic reasons. Notice the default energy scale (taken from the gaussian PBC code defaults) is intentionally large and that the color scheme has each band coded in different linestyles and/or colors. Run gpband in the job’s working directory: gpband band. 10.Sec. hence the admonition to run gpband in the job’s working directory. As it is to large to include in Section 13. 3. 10: Plotting BS and PDOS 10. • Note the numerous annotations within the script. . 2.dat bandk.dat and the *. additional lines and comments must be added by hand. The command gpband band.dat files are arranged. but feel free to explore. • The lowest gap is generally plotted. describing the program and how the band*.3.gp.dat produced a Gnuplot file. band-p. gpband nameoffile. Cristian Diaconu. Place a copy of gpbandon each machine where gaussian PBC code will be run. "K | U" x9_K. "X" x10_X ) E0 cHOCO HOCO cLUCO LUCO EF mGap MGap iGap = = = = = = = = = 10. graph 1 nohead lt -1 2 from x2_X. (Truncated list to save space) using using using using using using using using using using using using using using using using using using 1:(E($19)) t "27" with l ls 18. graph 1 nohead lt -1 10 from x10_X. \ 1:(E($12)) t "20" with l ls 11..inp file * They will be used in the next section of the gp file as x-tic labels * The values correspond to all x-coordinates. COLUMN where the HOCO is located.Sec. \ 1:(E($5)) t "13" with l ls 4. set xtics ( "{/Symbol G}" x1_GM.000000 x2_X = 0.. "{/Symbol G}" x5_GM. first E(HOCO) \ to graph 1. 51 . \ 1:(E($10)) t "18" with l ls 9.512322 x6_L = 3. Unscaled energy of the Lowest Unocc.] These are the values and labels of the high-symmetry k-points: * Their ordering was specified in the band. (The full script is in Section 13.701213 [Header and other non-band-related content deleted. first E(LUCO) nohead lt 20 Arrow for CBM set yrange [*:*] plot \ data data data data data data data data data data data data data data data data data data Horizontal k-path lines.371738 11 12. \ 1:(E($13)) t "21" with l ls 12.) x1_GM = 0.293143 x4_K = 1.420518 10. graph 0 to x1_GM. \ 1:(E($3)) t "11" with l ls 2. graph 1 nohead lt -1 3 from x3_W. set arrow arrow arrow . The VBM redefined as the Fermi Level Next highest gap after the indirect gap Next highest gap after the mgap The indirect gap # energy shifting function Scales the energies so that EF = 0 1 from x1_GM. "X" x2_X.786839 x8_W = 4. \ 1:(E($6)) t "14" with l ls 5. graph 0 to x10_X. \ 1:(E($4)) t "12" with l ls 3. \ 1:(E($18)) t "26" with l ls 17.. first E(HOCO) nohead lt 19 Arrow for Fermi Level/VBM set arrow 12 \ from graph 0. "L" x6_L. first E(LUCO) \ to graph 1. graph 0 to x3_W. \ 1:(E($17)) t "25" with l ls 16. \ 1:(E($8)) t "16" with l ls 7.091633 x9_K = 4. Crystal Orbital (HOCO.597934 x5_GM = 2. \ 1:(E($14)) t "22" with l ls 13.862114 x3_W = 1.3. Unscaled energy of the Highest Occ.371738 3. 10: Plotting BS and PDOS 10. "K" x4_K..258914 x7_U = 3.371738 10 10. Unscaled energy of the Valence Band Max (VBM).405779 2.3 Annotated Default gp File Annotated sections of the gp file that produced Figure 15.4.048780 E(y) = y . "W" x3_W. \ 1:(E($16)) t "24" with l ls 15. arrow These are the x-tic labels: easily modified. Crystal Orbital (LUCO. \ 1:(E($15)) t "23" with l ls 14. "U" x7_U. \ 1:(E($2)) t "10" with l ls 1 Default y-axis range Plotting the data. \ 1:(E($9)) t "17" with l ls 8.E0 set set set . graph 0 to x2_X. COLUMN where the LUCO is located. graph 1 nohead lt -1 set arrow 11 \ from graph 0.058369 8.396424 x10_X = 4. \ 1:(E($7)) t "15" with l ls 6. \ 1:(E($11)) t "19" with l ls 10. "W" x8_W. . dat files will be discussed in Section 10.33 eV (I) 2. • The conduction bands are all labeled in blue • The Fermi Level E = 0 is now labeled and the energy denoted as a horizontal black line • The conduction band maximum is depicted as a dashed orange line.[4] ï6 K X W K K L U W K|U X All files necessary to produce this plot and that of Figure 15 are locally available at guscus:/projects/guscus/Manuals/examples/AlSb-HISS. 10: Plotting BS and PDOS 10. The direct gap. Edir =2.84 experiment.3. e.3 has been modified in the following ways to produce Figure 16: • The scale of the y-axis is now from -7 to 10.05 eV (I) 0 ï2 ï4 Figure 16: The band structure for AlSb optimized using HISS. 52 .g.4 Modified BS Output The gp file in Section 10.Sec. The predicted indirect transition Eind occurs at 2. also compares favorably to 2.4..[3]).33 eV. • The valence band are all colored red.05 eV (compare to EF 1. indirect transition from Γ to somewhere near X is marked by both an arrow and a green I-bar. Mining the data in the band*.3. 10 8 6 Energy (eV) 4 2 2. The full gp files are also listed in Sections 10. so it is easier to see the “camel-back” structure of AlSb.5. locating points on the bands that are not along the high-symmetry k-lines for energy comparisons.4 and 13. • The slightly higher in energy direct gap is marked only with an I-bar. • Structure analysis.3. • The favored.69 eV for LT exp. dat file for energy via grep 2. Last updated: March 26. Search band. 10. please contact Melissa Lucero. so this becomes something of an art. If you need immediate assistance. locating the coordinates of various minima or maxima for comparison This example is being specially prepared in order to optimize all aspects of your learning experience. 2012 53 .4. direct gaps that are not on any high-symmetry points 3.2 Special Gaps This should be the more complex cases for 1.4 Locating k-Points This section is for locating points so that arrows can be drawn in Gnuplot to mark direct and indirect transitions.1 Easy Indirect Gaps This should be the easy case for an indirect gap from one k-point to another. Not all points of import are located on the lines corresponding to the symmetry points specified in the path of the band.4.Sec. Also need to do the reverse case. 1. 10: Plotting BS and PDOS 10. an indirect gap between one k-point and a point in between two others 2.inp file. 10. 1 Increasing the Accuracy and Efficiency of PBC Jobs Practical Tips for G09 PBC Calculations Contributed by Professor Gustavo E. Dimensionality: 3D calculations are more expensive than 2D. Aggressive thresholds 2. in turn. but we are working on it and even when it is. which does not have any density tail (well. yet. we recommend that you start playing in 1D and move your way up to 2D/3D slowly. Symmetry is not implemented..... which are. if you use a dense basis on a dense system and you end up with product bfs that are almost linearly dependent (overlap matrix eigenvalue at some k-point below a certain threshold). In these cases. diamond. e. The HFx (Hartree Fock exchange) portion with diffuse basis functions (bfs).11 11. 3. Diffuse bfs: They may be needed in some specific cases and for some specific properties but in general. or. A sloppy (or not accurate enough) xc quadrature grid. Scuseria for the 2009 Guide. it is a good idea to carefully analyze whether your chosen MOLECULAR basis set (i. anyway. The near-field portion of the FMM without symmetry included will be very costly. and default cutoffs will take forever.g.) What not to do: If you want to put your computer system on its knees. If you are not familiar with the PBC code and how to tune up its options. Linear dependencies: Our PBC code does not suffer from linear dependencies.e. 1. a full-range 1/r potential. i. 2. Hybrids: Any with full (global) or long-range 1/r potential are significantly more expensive (1020x or even more) than short-range hybrids like HSE that were designed with solids in mind. doping and disorder lower the symmetry. much more expensive than 1D. and it is almost guaranteed that a single iteration will exceed your patience. the code will remove the offending linear combination.e. the SCF will die with some error message (with the cause not trivially identifiable form the error message) being a combination of the above. but not in 3D). (The input file information in Section 3 has more information for PBC. Perhaps an FMM section would be useful... try B3LYP with a diffuse basis set on your favorite 3D system. there may be cases where the overall accuracy is affected because of 1. Be extremely careful if you want to do a PBC full or long-range hybrid. a basis set that was developed for atoms/molecules and usually contain fairly diffuse bfs to describe atomic tails) is really needed for your PERIODIC system. For Starters: Read the Gaussian 09 manual entries for Molecule Specifications and the keywords: PBC and FMM. 3. A sloppy (or not accurate enough) Brillouin zone (k-point) integration grid. 54 . However. it does if you are doing 1D or 2D.. Most PW calculations on metals are done at finite temperature. A radical solution is to start from a finite temperature calculation at ca. Your cpu time will go up because to achieve convergence you will need a larger basis than for semiconductors or insulators and lots of k-points. there is plenty of room of improvement by playing with many of the accuracy thresholds (explained in detail in Izmaylov’s piece). as in this example: #p BLYP/6-31G(d)/Auto Note that the slashes are required when a density fitting basis set is specified. Integration in k-point space is arduous. 3.01 eV) Density Fitting Gaussian provides the density fitting approximation for pure DFT calculations. otherwise convergence is rather difficult to achieve even with PW codes. See the Basis Sets entry in the Gaussian manual for more information.Sec. 11: Increasing the Accuracy and Efficiency of PBC Jobs bf Exponents: As a practical matter. bfs with exponents smaller than 0. See Section 3. 2. 2012 55 .¡ Semiconductors and Insulators: If you feel that your calculations are slow. which will increase cpu time printing and allow you to spot portions that are particularly expensive and amenable to improvement by fine-tuning thresholds. 1000 K and then try to cool off the system some or converge ILT (or similar) from there.e. Diffuse and polarization functions are generally important for metals.10-0. adapting a molecular basis for an efficient periodic calculation) is not required in our code (our numerics are usually robust enough to deal with them) but it will surely make your calculations much faster and your life much easier on thresholds. CPU Time Monitor your cpu time with flags like #p and IOp1=timestamp. The record for this type improvement may be the InAs case finely-tuned by Ed Brothers: he was able to achieve a 20x speed-up by tuning thresholds (from default values) with a minimal loss of accuracy for the band gap (less than 0. There are several options that can be tried here if one has convergence problems in the SCF.. The desired fitting basis set is specified as a third component of the model chemistry. Last Modified March 23. 1. Removing them (i. Metal calculations are tricky and costly.15 are problematic and usually not needed. Metals: Tread very carefully if your system is metallic. so use d in Bohr. This problem can be exacerbated for periodic calculations.2 Diffuse Functions Contributed by Dr. • The rule of thumb for diffuse functions: the smallest exponent for s-type functions should be larger than about αmin = 2/d2 . Izmaylov. so even if the near linear dependencies are eliminated at k = 0. See the PBC keyword page. Gaussian removes the culprits. the norms of the Bloch functions may still be too small at other values of k.Sec. The exponent input in Gaussian is in Bohr −2 . • NMtPBC is determined for k = 0.ATTENTION-------------------There is a problem with the total charge. and Ionut D. thus having an extra s-type function that can be nearly linear dependent with the existing s-type functions. especially when using a 5d basis set as a 6done. The norms are also k-dependent. Unfortunately. 56 . (see Section ?? but when this happens the basis functions are too diffuse and is usually associated with the previous problem (not enough cells included in PBC) or Gaussian dies with an error of the following type: -------------------. The number of cells may increase toward k = ±π.-0. The only solution to this problem is to prune the diffuse basis functions (especially the p-type). the norms of the Bloch functions become exponentially small when the exponents become small (norm ca. and Gaussian will die with the error: Possibly not enough cells included in PBC. where d is the smallest distance between two atoms. Numerical problems in PBC.use less-diffuse basis functions.002902253251 -------------------. • There is also a problem with 5d/6d basis sets. While the number of cells is enough at k = 0. the convergence of the Bloch sums with the numberof cells depends on k for the Bloch sum form currently used in Gaussian. exp(−k 2 /a). This is usually not a problem. -OR. too: a 6d basis set may assume to have an extra s-type functions from the d-type shells. This is true the other way.ATTENTION-------------------Total charge is not ZERO --. Diaconu with comments from Drs. 11: Increasing the Accuracy and Efficiency of PBC Jobs 11. Cristian V. this may become a huge problem. however. This condition leads to warnings from subroutine ZFrmV2 of the form: ZFrmV2: there are 14 very small orbitals for k= 617 kxyz= 7 15 3. it may not be enough as k = ±π. If this happens the only way around it is to increase the number of cells by forcing a larger range: PBC=(CellRange=N). since the calculations become prohibitively expensive with diffuse functions anyway. Prodan for the October 2009 version of this guide. for diffuse functions. Artur F. • Due to the same problem of the form of the Bloch functions. See the Basis Sets entry in the Gaussian Õ09 manual. if exact exchange is included. 11.3.Sec. NKPoint=N Do approximately N k-points. then this is twice the number of cells used for overlap-related quantities and XC quadrature. Not valid with SCRF or Charge.3 All PBC Keywords This page contains the entirety of the PBC keyword page at Gaussian.1 Description The PBC keyword allows you to specify options for Periodic Boundary Conditions jobs.3.3. NCellDFT=N Include at least N cells in DFT XC quadrature. 2012. NCellMin=N Include at least N cells. 2012 57 . NCellXC is synonymous. Last modified March 27.2 Options GammaOnly Do just the Γ point (k = 0) rather than full k-integration. 11: Increasing the Accuracy and Efficiency of PBC Jobs 11.com as of March 28. • By default. NCellMax=N Include at most N cells in any part of the calculation. and this keyword is used only to control how PBC calculations are performed. acceptable performance may only be feasible by using a pure DFT functional in combination with density fitting. CellRange=N Go out N Bohr in each direction in setting up image cells. For periodic systems of any reasonable size. 11. If you do not need any of these options. Note: PBC is turned on simply by including translation vectors in the input structure. NCellK=N Include at least N cells in exact exchange.3 Availability HF and DFT energy and optimizations. you do not have to include the keyword PBC to perform a PBC calculation. 11. press release SUG@R . BlueBioU . Figure 17: STIC. (An older machine. SUG@R is also available. x86-64 hybrid. and SUG@R. DaVinci and STIC.” for access to the public nodes. but change the queue name to “common. it is more efficient to use the guscus condo (see Section 13). see the Getting Started documentation. BlueBioU. For general information. DAVinCI. STIC .12 Submitting Jobs at Rice The module system is employed on Scuseria Group workstations as well as on the shared computational resources at Rice: BlueBioU.Data Analysis and Visualization Cyber-Infrastructure. but is is non-ideal for PBC jobs. An Intel Nahalem computing cluster. 58 . An IBM Power 7 System.) A “condo” of Scuseria-Group-Only nodes exists on each of the Rice clusters.Shared University Grid @ Rice An older Intel Xeon compute cluster.Shared Tightly Integrated Cluster.Primarily for biocomputing. press release DAVinCI . Normally. Type ’qsub *.) -OR5.rice. 1. 12: Submitting Jobs at Rice 12.. 2012 59 .Sec.pbs file (See Section 13 for the necessary scripts. Run the script to create the *.EDU Questions and Problem Reports -> http://helpdesk.2.rice.rcsg. Rice University ============================================== Unauthorized access is prohibited.3.2.) 7. EVER run jobs on a login node ******************************************** -bash-3.g.3) 8.rice.2 What You See: Logging In # THIS IS STEP 1a [mylaptop:~] scucserian% ssh [email protected]) 6. STIC. Login via ssh 2.2$ source .scratch/sgu1 # THIS IS STEP 2 # THIS IS STEP 3 Last Modified March 27.edu ----------------------------------------------------------------------Ken Kennedy Institute for Information Technology. cd to shared.edu’s password: # Below is what will appear once you log into STIC: Last login: Tue Mar 13 12:23:58 2012 from worf. # SERIOUSLY. sgu1 is an imaginary Scuseria Group user with a login ID of the type that Rice usually sets up: typically 2-3 initials from your name and a number. Type “module avail” to see what modules are available (See Section 12.3” to load the module for PBC calculations (See Section 12.2$ cd /shared. e.edu/stic ----------------------------------------------------------------------****************IMPORTANT******************* NOTICE TO COMP422 and COMP322 USERS!! DO NOT RUN JOBS ON THE LOGIN NODES.3. (See Section 12.3. Type “module load gdv-h11-hiss-and-pbc.pbs’ to submit your job 10.edu # THIS STEP 1b [email protected]. Type “module list” to confirm which modules are already loaded.. The following is the procedure for STIC.3. never.edu Documentation and User News -> http://rcsg. /projects/guscus/. but the procedure works the same on all Rice computers.1 Modules: General Procedure For the examples in this section..bashrc file containing the Gaussian paths in it: source /projects/guscus/. Source the .bashrc 3.) 9.bashrc -bash-3. 12. Type ’qstat’ to see that your job was submitted and is in the queue you want it to be in. cd /shared.scratch. Check to see that the module loaded successfully by typing “module list” (See Section 12.scratch/sgu1 4.1) for the output.RICE. • The g09. which includes G09. 12: Submitting Jobs at Rice 12. PDOS. AFM. as in the example. • The gdv. not development versions of the gaussian code. 60 .3. the module you should load is gdv-h11-hiss-and-pbc. SO or Dispersion.3. • The most stable for PBC. with the most features and options is gdv-h11-hiss-and-pbc.2. USE THIS unless otherwise instructed.Sec. For PBC jobs.2. The bottom section lists various applications that may be of use. but no PBC features like BS.3 12. like matlab.3.series are actual g09 versions. below: [sgu1@login1 sgu1]$ module avail The gaussian-related codes are listed in the top section. VMM. all usable gdv versions and the Portland Group compilers. • gdv-h11-sol has PBEsol incorporated in it.series are developement versions of gaussian.1 Module Commands Module Avail Typing “module avail” will allow you to see which modules are currently available on the machine you have logged into. confirm with “module list” [sgu1@login1 sgu1]$ module unload gdv-h11-hiss-and-pbc. 12: Submitting Jobs at Rice 12.sticman 349056.pbs [mjl3@login1 mjl3]$ qstat | grep guscus 346944. type: “module list” [sgu1@login1 sgu1]$ module list Currently Loaded Modulefiles: 1) pgi-10 2) gdv-h11 3) gdv-h11-hiss-and-pbc.2.2.2.gjf 10 [mjl3@login1 mjl3]$ qsub PCBInputFile.3.sticman 348858.3 Module List To CONFIRM the module was loaded.1.Sec.2. [mjl3@login1 mjl3]$ module load gdv-h11-hiss-and-pbc. 12.2 Module Load To LOAD a module.3.3 [sgu1@login1 sgu1]$ module list No Module Files Currently Loaded 12.” [sgu1@login1 sgu1]$ module load gdv-h11-hiss-and-pbc.3.3 12.4 Module Unload To UNLOAD a module.3.sticman 346954.3 Notice that at least 3 files are loaded. or LIST modules already loaded. type “module unload ModuleName”. submit job and check the queue as in Section 12. 2012 61 .3 [mjl3@login1 mjl3]$ pbcscript PBCjobFile. The module you want usually has the highest number.5 Modules & Submission Put it all together: Load/confirm modules.sticman LiMoS2-hse11_o LiMoS2-pbe_o 20 n2-ksghf PCBInputFile mjl3 mjl3 ks19 rmi1 sgu1 190:28:0 187:12:3 235:00:3 04:32:08 00:02:08 R R R R R guscus guscus guscus guscus guscus Last Modified March 27.3 [mjl3@login1 mjl3]$ module list Currently Loaded Modulefiles: 1) pgi-10 2) gdv-h11 3) gdv-h11-hiss-and-pbc. simply type “module load module name.sticman 349052.2. 3..2. 2012) on STIC Module G09 Versions g09-b1 g09-b1-linda g09-b1-pbc-2. but PBEsol works Ask Irek Ask Irek Ask Irek Oldest Old Latest Check which version loads w/code Check which version loads w/code Check which version loads w/code [1] This version will eventually also include PBEsol.t g09-c1 g09-c1-linda G09 Development gdv-g1 gdv-h1 gdv-h1-D gdv-h1-extra-HISS gdv-h10 gdv-h11 gdv-h11-hiss-and-pbc. Irek’s dispersion code..9 pgi-11 Description Notes This is previous G09 When in doubt use this Runs in parallel STIC. 12: Submitting Jobs at Rice 12. Source /projects/guscus/.3 gdv-h11-ib3 gdv-h11-sol gdv-h12p gdv-h12p-D gdv-h13 PGI Compilers pgi-10 pgi-10. use 4 nodes A version of the PBC code not sure This PBC code works Used for publications Latest G09 Use at own risk Latest G09 in parallel Timings are weird Ancient Very Old Very Old Old for HISS Old Old RECENT Irek’s working version PBEsol New New Latest Needed for some calcs. This will be the version that will be kept current.4 G09 Modules Available on STIC The availability on the other machines will vary. any new Bulik functionals and any other code that is to be used by many. PBC or not. Table 2: Gaussian Modules Currently Available (as of March 27. Last Modified March 27.bashrc and then type ’module avail’ to see the list below.Sec. don’t use Don’t use Daniel’s? Don’t use unless checking data Probably not used by anyone *NO* PBC so not useful Use this. 2012 62 . Has HISS and PBC1 Don’t use No BS/PDOS. but will tend to have the same versions of the more recent codes.3 g09-b1-pbc-2. Sec. 12: Submitting Jobs at Rice 12.4.1 Applications Modules on STIC Source /projects/guscus/.bashrc and then type ’module avail’ to see the list below... Table 3: Applications Modules Currently Available on STIC (As of March 27, 2012), sorted according to potential interest to the Scuseria Group. Module gaussian/g09-c1-linda intel/2011.0.13(default) intel/3.2.1.015 jdk/1.6.0_12 matlab/2008b(default) matlab/2009b matlab/2011a pgi/9.0.4 pgi/10.9 python3/3.2.1 R/2.11.1-gcc siesta/3.0-rc2 Description Parallel G09 compiler compiler Jason’s PQT code Check w/Irek Check w/Irek Check w/Irek Check w/Irek Can we use this? openmpi/1.3.3-gcc openmpi/1.3.3-intel openmpi/1.3.3-pgi openmpi/1.4.4-gcc openmpi/1.4.4-intel(default) openmpi/1.4.4-pgi 63 Module Notes amber/11 Bio FF code cilk++/8503 cmake/2.8.5 comsol/3.5a comsol/4.0a comsol/4.1 fftw/3.2.2-intel globus/5.0.4-xsede gmt/4.5.3 gromacs/4.5.5 Bio visualizer hdf5/1.8.4p1 hdf5/1.8.8(default) hpctoolkit/2011-05-16 hypre/2.0.0-intel lammps/20Aug11 lumerical/6.5.5(default) lumerical/7.5.1 lumerical/7.5.3 mvapich/1.2rc1-intel namd/2.7 namd/2.8 netcdf/4.1.1 papi/3.7.0 opencl/2.5rc2 slog2sdk/1.2.6 totalview/8.7.0 totalview/8.9.2 turnin/2.0 turnin/2.1 turnin/3.0(default) Sec. 12: Submitting Jobs at Rice 12.5 Modules Available on Group Workstations You need to source /projects/guscus/.bashrc and then type ’module avail’ to see the list below. To run gnuplot and others APPS, type ’module load Apps’ Table 4: Modules Currently Available on Workstations (as of March 27, 2012) Module Description Notes Applications Apps numerous apps like gnuplot type ’module load Apps’ GaussView/5.0.9 load a G09 module, then type ’module load GaussView’ G09 Versions g09-b1 This is previous G09 When in doubt use this g09-c1 Latest G09 Use at own risk g09-c1-linda Latest G09 in parallel Timings are weird G09 Development ’module load gdv-x’ x=gdv ver. gdv-f2 Before time Remote chance will need gdv-g1 Ancient Needed for some calcs; don’t use gdv-h1 Very Old Don’t use gdv-h10 Old Probably not used by anyone gdv-h11 Old *NO* PBC so not useful gdv-h11-ib3 Irek’s Local development gdv-h12p New Ask Irek gdv-h13 Latest Ask Irek G09 PBC Code Any of these ∼ STIC? ’module load g09-y’ y=g09 ver. g09-b1-extra-dosj Very Old experimental PBC? g09-b1-extra3 -pbc-2.devel Old experimental PBC g09-b1-pbc-2.3t This PBC code works Used for publications g09-b1-pbc-2.3 An older version not sure g09-b1-pbc-2.3.5 Old experimental PBC ? PGI Compilers ’module load pgi-z’ z=pgi ver. pgi-7.2 Older Check which version loads w/code pgi-10 Older Check which version loads w/code pgi-10.8 Older Check which version loads w/code pgi-10.9 Old Check which version loads w/code pgi-11 Latest on STIC Check which version loads w/code pgi-11.9 Latest Newer than that on STIC Last Modified March 27, 2012 64 13 Scripts The scripts provided herein are optimized for quick cut-N-paste. Alternatively, local users may copy them from: guscus:/projects/guscus/Manuals/scripts Questions, comments or better implementations are welcome. Please feel free to contact Melissa Lucero. The scripts are broken into three groups: 1. PBS submission scripts → Section 13.1. (a) STIC see Sections 13.1.1 (serial) and 13.1.2 (parallel) (b) DaVinci see Section 13.1.3 (parallel) (c) BlueBioU aka BioU see Section 13.1.4 (serial) (d) All of the above scripts are locally available at guscus:/projects/guscus/Manuals/scripts. 2. BS and PDOS Gnuplot Scripts (a) The gpband perl script is too large to include, copy from in guscus:/projects/guscus/Manuals/scripts. A “How-To” explaining how to use it may be in order... (b) PDOS A straightforward example → from Section 10.2 • Cut-N-Paste templates from Sections 13.2 and 13.3 • -OR- at guscus:/projects/guscus/Manuals/examples/Si-pdos/. (c) BS The example used in Section ?? • Pared down here, in Section ?? • -OR- at guscus:/projects/guscus/Manuals/examples/band.gpt (d) A Multiplot script with both BS and PDOS aligned vertically. → Section 13.6 • • • • Produces the example in Section 8.1 Heavily annotated Broken into smaller pieces for Cut-N-Pase The original is located at: guscus:/projects/guscus/Manuals/examples/MoS2mono/ 3. Other Gnuplot Scripts → a work in progress • Other gnuplot data representations • Stacks, histograms, bars Note: The script content may vary slightly as the OS for each cluster is updated and or with new gdv/G09 versions. If in doubt, please feel free to contact Irek W. Bulik or Melissa J. Lucero. Last Modified March 29, 2012 65 . comment out if no PBC code EOF This script may also be found at guscus:/projects/guscus/Manuals/scripts/stic-serial.gjf 10 #!/bin/bash set -o errexit set -o pipefail # exit on errors # or failure in a pipe if [ $# -eq 0 ].gjf walltime (in days) e. then echo "No Input File Specified" exit 1 fi if [ -z "$2" ].sh 66 . 13: Scripts 13.out" %mem=23500mb EOFPBS cat $Inp >> $SubFile echo "EOGJF" >> $SubFile cat << EOF >> $SubFile echo \$? mkpdos -bias-from "\$InpBase.1 PBS Submission Scripts (Rice-Specific) 13.1 STIC Serial Job PBS Submission Script cmd line input: ./sticpbs-serial InputFile.pbs #Prepare submission script cat <<EOFPBS >$SubFile #!/bin/bash #PBS -N $InpBase #PBS -V #PBS -m n #PBS -r n #PBS -o $InpBase. then echo "Wall Time Not Specified" exit 1 fi WALLTIME=$(( 24 * $2 )):00:00 InpBase=${Inp%. [sgu1@login2]$ . then cat <<EOF USAGE: ${0##*/} Input NNodes WallTime_in_days EOF exit 1 fi Inp=$1 # test if we got needed data if [ -z "$Inp" ].scratch/\$USER/tmp/\$PBS_JOBID export GAUSS_SCRDIR \${GAUSS_MEMDEF:=2415919104} cd \$PBS_O_WORKDIR exec &>$InpBase./stic-serial.*} SubFile=$InpBase.sh SiC.log # Required to run PDOS.pbserr #PBS -j oe #PBS -l nodes=1:ppn=12.err set -x trap "rm -rf \$GAUSS_SCRDIR" EXIT mkdir -p \$GAUSS_SCRDIR # print commands before executing # clean up at exit df -h uname -a printenv time \$GAU <<EOGJF >"\$InpBase.g.Sec.out" -f -v >& mkpdos.1.walltime=$WALLTIME #PBS -l mem=24000mb #PBS -q guscus InpBase=$InpBase TIMEFORMAT="TIMING: %3R %3U %3S" # Format for bash time builtin GAUSS_SCRDIR=/shared. gjf # nodes (4 is best) walltime (in days) e.scratch/\$USER/tmp/\$PBS_JOBID export GAUSS_SCRDIR \${GAUSS_MEMDEF:=2415919104} cd \$PBS_O_WORKDIR exec &>$InpBase. [sgu1@login1]$ ./script InputFile./stic-linda..’ |sed ’s/. 13: Scripts 13.pbserr #PBS -j oe #PBS -l nodes=$NNodes:ppn=12.1.Sec.sh 67 .2 STIC Parallel (Linda) Job PBS Submission Script cmd line input: .walltime=$WALLTIME #PBS -l mem=24000mb #PBS -q guscus InpBase=$InpBase TIMEFORMAT="TIMING: %3R %3U %3S" # Format for bash time builtin GAUSS_SCRDIR=/shared. then # test if we got needed data echo "No Input File Specified" exit 1 fi if [ -z "$2" ].err set -x trap "rm -rf \$GAUSS_SCRDIR" EXIT mkdir -p \$GAUSS_SCRDIR # print commands before executing # clean up at exit df -h uname -a printenv LINDA_WORKERS=\$(cat \$PBS_NODEFILE |sort -u |tr ’\n’ ’.pbs #Prepare submission script cat <<EOFPBS >$SubFile #!/bin/bash #PBS -N $InpBase #PBS -V #PBS -m n #PBS -r n #PBS -o $InpBase.*} SubFile=$InpBase.sh InP. then echo "Wall Time Not Specified" exit 1 fi if [ -z "$NNodes" ].out" %nprocsh=6 %mem=23500mb %LindaWorkers=\$LINDA_WORKERS EOFPBS cat $Inp >> $SubFile echo "EOGJF" >> $SubFile cat << EOF >> $SubFile echo \$? EOF This script may also be found at guscus:/projects/guscus/Manuals/scripts/stic-linda.g.$//’) time \$GAU <<EOGJF >"\$InpBase. then cat <<EOF USAGE: ${0##*/} Input NNodes WallTime_in_days EOF exit 1 fi Inp=$1 NNodes=$3 if [ -z "$Inp" ].gjf 4 10 #!/bin/bash set -o errexit set -o pipefail # exit on errors # or failure in a pipe if [ $# -eq 0 ]. then echo "Number Of Nodes Not Specified" exit 1 fi WALLTIME=$(( 24 * $2 )):00:00 InpBase=${Inp%. then echo "No Input File Specified" exit 1 fi if [ -z "$NNODES" ].gjf 10 #!/bin/bash set -o errexit set -o pipefail # exit on errors # or failure in a pipe if [ $# -eq 0 ].err set -x trap "rm -rf \$GAUSS_SCRDIR" EXIT mkdir -p \$GAUSS_SCRDIR # print commands before executing # clean up at exit df -h uname -a printenv LINDA_WORKERS=\$(cat \$PBS_NODEFILE |sort -u |tr ’\n’ ’.sh AlN. 13: Scripts 13.1..gjf walltime (in days) e.pmem=4000mb #PBS -q parallel INPBASE=$INPBASE TIMEFORMAT="TIMING: %3R %3U %3S" # Format for bash time builtin GAUSS_SCRDIR=/scratch/\$USER/tmp/\$PBS_JOBID export GAUSS_SCRDIR : \${GAUSS_MEMDEF:=2415919104} cd \$PBS_O_WORKDIR exec &>$INPBASE.3 DaVinci Parallel (Linda) Job PBS Submission Script cmd line input: .sh 68 .’ |sed ’s/.out" %nprocsh=12 %mem=42GB %LindaWorkers=\$LINDA_WORKERS EOFPBS cat $INP >> $SUBFILE echo "EOGJF" >> $SUBFILE cat << EOF >> $SUBFILE echo \$? EOF This script may be obtained at: guscus:/projects/guscus/Manuals/davinci-linda.pbserr #PBS -j oe #PBS -l nodes=$NNODES:ppn=12.Sec.$//’) time \$GAU <<EOGJF >"\$INPBASE. then echo "Number Of Nodes Not Specified" exit 1 fi INPBASE=${INP%. [sgu1@login1]$ .pbs cat <<EOFPBS >$SUBFILE #!/bin/bash #PBS -N $INPBASE #PBS -V #PBS -m n #PBS -r n #PBS -o $INPBASE./davy-linda. then cat <<EOF USAGE: ${0##*/} INPut NNODES EOF exit 1 fi INP=$1 NNODES=$2 # test if we got needed data if [ -z "$INP" ]./script InputFile.g.*} #Prapare submission script SUBFILE=$INPBASE. gjf walltime (in days) e. then # cat <<EOF #USAGE: # ${0##*/} Input NNodes WallTime_in_days #EOF # exit 1 #fi Inp=$1 # test if we got needed data if [ -z "$Inp" ].walltime=24:00:00 #PBS -l mem=24000mb #PBS -q serial InpBase=$InpBase TIMEFORMAT="TIMING: %3R %3U %3S" # Format for bash time builtin GAUSS_SCRDIR=/shared.out" %mem=23500mb EOFPBS cat $Inp >> $SubFile echo "EOGJF" >> $SubFile cat << EOF >> $SubFile echo \$? mkpdos -bias-from "\$InpBase.pbs #Prepare submission script cat <<EOFPBS >$SubFile #!/bin/bash #PBS -N $InpBase #PBS -V #PBS -m n #PBS -r n #PBS -o $InpBase. then echo "No Input File Specified" exit 1 fi #if [ -z "$2" ].out" -F -v >& mkpdos. 13: Scripts 13.sh 69 ./biou-serial.log EOF Download this script locally from: guscus:/projects/guscus/Manuals/biou-serial.4 BioU Serial Job PBS Submission Script cmd line input: .err set -x trap "rm -rf \$GAUSS_SCRDIR" EXIT mkdir -p \$GAUSS_SCRDIR # print commands before executing # clean up at exit df -h uname -a printenv time \$GAU <<EOGJF >"\$InpBase..gjf 10 #!/bin/bash set -o errexit set -o pipefail # exit on errors # or failure in a pipe #if [ $# -eq 0 ].sh ZnS.scratch/\$USER/tmp/\$PBS_JOBID export GAUSS_SCRDIR \${GAUSS_MEMDEF:=17179869184} cd \$PBS_O_WORKDIR exec &>$InpBase.g.1.*} SubFile=$InpBase. then # echo "Number Of Nodes Not Specified" # exit 1 #fi #WALLTIME=$(( 24 * $2 )):00:00 InpBase=${Inp%.pbserr #PBS -j oe #PBS -l nodes=1:ppn=128. then # echo "Wall Time Not Specified" # exit 1 #fi #if [ -z "$NNodes" ]./script InputFile.Sec. [sgu1@login2]$ . 0.Sec.0 lc rgb ’black’ not.0 set xlabel ’PDOS (states/eV/unit cell)’ set ytics 2.5 set yrange [-10.0 lc rgbcolor ’gold’ line 7 lt 1 lw 1.4 ’{/Helvetica=16 Exp.5.Depending upon OS and Gnuplot version.40.\ data using 5:1 w l ls 1 t ’Total’ 70 .2.0 # THIS IS BASED ON A SMALL UNIT CELL.0 tc rgb ’dark-red’ set label 2 at 1.\ data using 3:1 w l ls 3 t ’Q_{/Helvetica-oblique p}’. reset set term postscript portrait enhanced dashed lw 2.0] # THESE WILL CHANGE BASED ON YOUR SYSTEM set xrange [-0.1.9.0 color ’Times-Roman’ 20 # DEFINE INPUT AND OUTPUT set output ’output.17 eV (I)}’ tc rgb ’dark-red’ set key at 2. as in the figure below. graph 0 to 0.6 ’{/Helvetica=16 HSE OPT}’ tc rgb ’navy’ set label 4 at 1.5.22 eV (I)}’ tc rgb ’navy’ set label 5 at 1.0 lc rgbcolor ’royalblue’ line 6 lt 1 lw 1.5 lc rgbcolor ’red’ line 3 lt 1 lw 1. with the valence band at the bottom and the conduction band populations at the top.1.2 PDOS Vertical Template This minimal example produces a vertical PDOS plot.\ data using 2:1 w l ls 2 t ’Q_{/Helvetica-oblique s}’.50.0 lc rgbcolor ’sea-green’ line 9 lt 1 lw 1.0 lc rgbcolor ’plum’ line 8 lt 2 lw 1. may be Helvetica-Italic set label 1 ’{/Helvetica-oblique=18 E_{F}}’ at 2.50 right # X-coord of Upper Left Corner and Y-coord of Upper Right Corner # LINE STYLES -set style set style set style set style set style set style set style set style set style set style use as many as necessary line 1 lt 1 lw 2.5 set rmargin 0. graph 1 nohead lc rgb ’dark-gray’ lw 1.FIRST LINE IS DASHED BLACK LINE FOR FERMI LEVEL plot 0 w l lt 2 lw 2.5 lc rgbcolor ’blue’’ line 5 lt 1 lw 1.5 # ARROWS # The gray baseline along the y-axis set arrow 1 from 0.0 lc rgbcolor ’gray50’ line 10 lt 0 lc rgbcolor ’white’ # PLOT THE DATA -.2 ’{/Helvetica=22 Si (dia) }’ tc rgb ’royalblue’ set label 3 at 1. = 1.5 lc rgbcolor ’forest-green’ line 4 lt 1 lw 1. ADJUST AS NECESSARY set xtics 0.0:10.5. Copy the gpt file and relevant data for Si from guscus:/projects/guscus/Manuals/examples/Si-pdos.5] # LEAVES A LITTLE SPACE TO SEE IF BASIS SET IS OKAY set ylabel ’Energy (eV)’ offset 1. 13: Scripts 13.03:2.\ data using 4:1 w l ls 4 t ’Q_{/Helvetica-oblique d}’.dat’ # dat file # DEFINE PLOT RANGES set lmargin 5.0 # LABELS -.55.0 lc rgbcolor ’black’ line 2 lt 3 lw 1.ps’ # name of output file data = ’pdos.0 ’{/Helvetica-oblique=16 E_{g} }{/Helvetica=16 = 1.3. 5 # ARROWS and LABELS set arrow 1 from 0. plot 0 w l lt 1 lw 3.Sec.1:2. the Fermi level in the center.0] set yrange [-0.0 lc rgbcolor ’royalblue’ line 6 lt 4 lw 1.3 ’{/Helvetica=20 Si (dia) }’ tc rgb ’dark-red’ set label 3 at -9. reset set term postscript eps enhanced dashed dl 2.0 set ytics 0.eps’ # name of output file data = ’pdos.5 set xrange [-10.22 eV (I)}’ tc rgb ’navy’ set label 5 at -9.22 eV (I) Expt.3.0 lc rgbcolor ’gold’ line 8 lt 2 lw 0.0 color ’Times-Roman’ 20 # INPUT AND OUTPUT set output ’pdos.\ ls 1 t ’Total’ 71 2.45 right # Plot the data.0:10.\ ls 3 t ’Q_{/Helvetica-Italic s}’.\ ls 2 t ’Q_{/Helvetica-Italic p}’. graph 0 to 0. = 1. 13: Scripts 13.dat’ # dat file # PLOT RANGES set lmargin 5.7 ’{/Helvetica=16 Expt.17 eV (I)}’ tc rgb ’red’ set key at 9.0 lc rgbcolor ’khaki’ line 10 lt 0 lc rgbcolor ’white’ PDOS (states/eV/unit cell) # LINE STYLES -set style set style set style set style set style set style set style set style set style set style HSE OPT Eg = 1.17 eV (I) 1.0 set xtics 2.2. graph 1 right rotate offset character 1..0 lc rgbcolor ’black’ line 2 lt 1 lw 1.5 Si (dia) 2 Sis Sip Sid Total Fermi level Add more colors or styles as required line 1 lt 1 lw 2.3 PDOS Horizontal Template This minimal example produces a horizontal PDOS plot.0 set label 1 ’Fermi level’ at 0..2. and the conduction band populations to the right. as in the figure below. with the valence band to the left.1 ’{/Helvetica=16 HSE OPT}’ tc rgb ’navy’ set label 4 at -9. = 1.5 0 -10 -8 -6 -4 -2 0 2 Energy (eV) 4 6 8 10 .1.0 lc data using 1:2 w l data using 1:3 w l data using 1:4 w l data using 1:5 w l rgb ’gray’ not.2.0 lc rgbcolor ’forest-green’ line 7 lt 1 lw 1.8 lc rgbcolor ’forest-green’ line 9 lt 1 lw 1. Copy the gpt file and relevant data for Si from guscus:/projects/guscus/Manuals/examples/Si-pdos. character -1 tc rgb ’navy’ set label 2 at -9.1.5 lc rgbcolor ’blue’ line 3 lt 2 lw 1.5 1 0.0 lc rgbcolor ’red’ line 5 lt 1 lw 1. graph 1 nohead lc rgb ’dark-gray’ lw 1.0 lc rgbcolor ’green’ line 4 lt 4 lw 2.5] # Allows view of baseline set xlabel ’Energy (eV)’ set ylabel ’PDOS (states/eV/unit cell)’ offset 1.\ ls 4 t ’Q_{/Helvetica-Italic d}’.9 ’{/Helvetica-Italic=16 E_{g} = }{/Helvetica=16 1.7. graph 0 to x8_W. 13: Scripts 13. graph 0 to x3_W. graph 0 to x9_K.000000 x2_X = 0. \ 1:(E($16)) t "24" with l ls 15.3. "X" x10_X ) E0 cHOCO HOCO cLUCO LUCO EF mGap MGap iGap = = = = = = = = = 10. "X" x2_X. first E(HOCO) to graph 1. graph 0 to x5_GM. \ 1:(E($12)) t "20" with l ls 11. first E(HOCO) nohead lt 19 set arrow 12 \ from graph 0.5. graph 1 nohead lt -1 6 from x6_L. graph 1 nohead lt -1 9 from x9_K.0 data = ’band. graph 0 to x4_K. \ 1:(E($10)) t "18" with l ls 9.420518 10. graph 0 to x10_X. "K" x4_K.3. \ 1:(E($4)) t "12" with l ls 3. graph 1 nohead lt -1 set arrow 11 \ from graph 0. \ 1:(E($9)) t "17" with l ls 8.) #! /usr/bin/gnuplot reset set encoding iso_8859_1 set terminal postscript eps enhanced color dl 2 "Times-Roman. "K | U" x9_K.597934 x5_GM = 2.18" set output ’band. graph 1 nohead lt -1 4 from x4_K.dat’ x1_GM = 0.eps’ set lmargin 5. "L" x6_L. \ 1:(E($7)) t "15" with l ls 6. first E(LUCO) to graph 1. "W" x8_W. graph 0 to x6_L.512322 x6_L = 3. \ 1:(E($18)) t "26" with l ls 17.371738 10 10. \ 1:(E($17)) t "25" with l ls 16. graph 1 nohead lt -1 5 from x5_GM. graph 1 nohead lt -1 7 from x7_U. \ 1:(E($13)) t "21" with l ls 12. graph 1 nohead lt -1 3 from x3_W.786839 x8_W = 4. \ 1:(E($3)) t "11" with l ls 2. \ 1:(E($2)) t "10" with l ls 1 72 .293143 x4_K = 1. \ 1:(E($8)) t "16" with l ls 7. graph 1 nohead lt -1 2 from x2_X. \ 1:(E($11)) t "19" with l ls 10. "W" x3_W. graph 0 to x1_GM.371738 3.4 Band Structure: gpband Default The default gpband script for HSE optimized AlSb.048780 E(y) = y . \ 1:(E($15)) t "23" with l ls 14. \ 1:(E($14)) t "22" with l ls 13.058369 8. graph 1 nohead lt -1 8 from x8_W. \ 1:(E($5)) t "13" with l ls 4. graph 1 nohead lt -1 10 from x10_X.2 and 10. \ 1:(E($6)) t "14" with l ls 5.396424 x10_X = 4.3. graph 0 to x7_U. graph 0 to x2_X.Sec.5 set rmargin 4 set macros unset key unset colorbox set xlabel "k path" set ylabel "Energy (eV)" offset 1. (Discussed inSections 10.258914 x7_U = 3.091633 x9_K = 4. first E(LUCO) nohead lt 20 set yrange [*:*] plot \ data data data data data data data data data data data data data data data data data data using using using using using using using using using using using using using using using using using using 1:(E($19)) t "27" with l ls 18.701213 set xtics ( "{/Symbol G}" x1_GM. "{/Symbol G}" x5_GM.862114 x3_W = 1.E0 set set set set set set set set set set arrow arrow arrow arrow arrow arrow arrow arrow arrow arrow # energy shifting function 1 from x1_GM.405779 2. "U" x7_U.371738 11 12. 7.420518 10. "W" x3_W. \ 1:(E($14)) t "22" with l ls 5.00 tc rgbcolor ’dark-red’ 2 ’{2.2. \ 1:(E($9)) t "17-occ" with l ls 4. \ 1:(E($11)) t "19" with l ls 5.396424 x10_X = 4.701213 set xtics ( "{/Symbol G}" x1_GM. graph 0 to x6_L.eps’ data = ’AlSb-hiss.597934 x5_GM = 2. 13: Scripts 13.. graph 0 to x10_X.0 to 0. graph 0 to x1_GM. \ 1:(E($13)) t "21" with l ls 5..33 eV (I)}’ at 3.0 2.258914.258914 x7_U = 3.735264.. \ 1:(E($17)) t "25" with l ls 5.2. "{/Symbol G}" x5_GM.Sec. graph 1 nohead ls 1 5 from x5_GM.8 set yrange [-7:10] plot 0 w l lt E(LUCO) w l lt data using data using data using data using data using data using data using data using data using data using data using data using data using data using data using data using data using data using -1 not. graph 0 to x7_U..735264.862114 x3_W = 1. \ 1:(E($10)) t "18-occ" with l ls 4.5 lc rgb ’magenta’ front 1 ’{/Helvetica-Oblique=28 E_{F}}’ at 4.0 to 0.3.4.. \ 1:(E($18)) t "26" with l ls 5.. "L" x6_L.700369 E(y) = y . \ 1:(E($6)) t "14-occ" with l ls 4... "K | U" x9_K.371738 11 12...512322 x6_L = 3.0 to 3.. 0.5 lc lc lc lc lc rgbcolor rgbcolor rgbcolor rgbcolor rgbcolor ’dark-turquoise’ ’black’ ’black’ ’red’ ’blue’ #k-point Vertical LINESS # BORING BANDS thin black line # BANDS OF INTEREST thicker black line c # VB Max .371738 10 10.dat’ set rmargin 4 unset key set ylabel "Energy (eV)" offset 1.735264.405779 2.E(LUCO) size 0. graph 1 nohead ls 1 10 from x10_X.90 heads lw 2.5 2.3. "W" x8_W..E0 # energy shifting function # LINE STYLES set style set style set style set style set style set set set set set set set set set set arrow arrow arrow arrow arrow arrow arrow arrow arrow arrow line line line line line 1 2 3 4 5 lt lt lt lt lt 4 1 1 1 1 lw lw lw lw lw 0..E(LUCO) heads lw 1.. \ 1:(E($16)) t "24" with l ls 5... "X" x2_X. graph 1 nohead ls 1 2 from x2_X.. graph 0 to x2_X. graph 0 to x4_K.371738 3.058369 8. \ 1:(E($2)) t "10-occ" with l ls 4 73 .5 lc rgb ’green’ front 13 from x5_GM. \ 1:(E($7)) t "15-occ" with l ls 4. graph 1 nohead ls 1 9 from x9_K. graph 1 nohead ls 1 4 from x4_K. \ 1:(E($19)) t "27" with l ls 5.05 eV (I)}’ at 0.5 front 15 from x6_L. graph 1 nohead ls 1 6 from x6_L. graph 0 to x9_K..18" set output ’AlSb-hiss2. graph 1 nohead ls 1 # I-Bars and set arrow set arrow set arrow # Labels set label set label set label Transition Arrows 11 from 0.7 1. graph 1 nohead ls 1 3 from x3_W.048780 12. graph 0 to x3_W.E(UCO2) size 0.5 Band Structure: Modified AlSb (HISS) gpt File The modified gp file that produced Figure 16 in Section 10.000000 x2_X = 0.90 heads lw 2. reset set terminal postscript eps enhanced color dl 2 "Helvetica.091633 x9_K = 4. \ 1:(E($15)) t "23" with l ls 5.6 3 ’{2.\ 2 lc rgbcolor "orange" not. graph 0 to x5_GM. "U" x7_U.9. "X" x10_X ) E0 cHOCO HOCO cLUCO LUCO EF mGap MGap iGap UCO2 = = = = = = = = = = 10. "K" x4_K. graph 1 nohead ls 1 7 from x7_U.. graph 0 to x8_W. \ 1:(E($4)) t "12-occ" with l ls 4.0. graph 1 nohead ls 1 8 from x8_W..0.0 x1_GM = 0.. \ 1:(E($8)) t "16-occ" with l ls 4. \ 1:(E($5)) t "13-occ" with l ls 4. # CB Min ----------------- 1 from x1_GM. \ 1:(E($3)) t "11-occ" with l ls 4.786839 x8_W = 4.293143 x4_K = 1. \ 1:(E($12)) t "20" with l ls 5.5 2.5. dat’ # SET MARGINS.2 Chunk 3: BS plot data-II: Plotting.1 Chunk 2: BS plot data-I: Set-up. Section 13.5 13.2 74 "Times-Roman.16" .gpt The Annoted Sections of the Gnuplot File: Chunk 1: Header.6.1 Header and Multiplot Set-Up # TERMINAL SET-UP reset set encoding iso_8859_1 set terminal postscript eps enhanced lw 2 color # SET INPUT AND OUTPUT FILE NAMES set output ’both.6. NO TITLE set multiplot layout 1.Sec.5 set rmargin 0 set xlabel "K-Path" set ylabel "Energy (eV)" offset 1. Section 13. 13: Scripts 13.0 unset key unset colorbox # SET MULTIPLOT # --> 1 ROW. Simply concatenate the parts discussed in the following pages to obtain a working script or scp the full version located at guscus:/projects/guscus/Manuals/scripts/both.6.6 BS and PDOS Multiplot Example This gnuplot script is modified gpband output → gpband will *not* produce this file.3 Chunk 4: PDOS plot data-I: Set-up. Section 13.3. Section 13.6.6. 2 COLUMNS. Section 13. AXES and DECORATIONS set lmargin 5.4 Chunk 5: PDOS plot data-II: Plotting. Note that the length of this template necessitates that it be broken into sections.6.eps’ data = ’band. dat file # The Lowest Unoccupied Crystal Orbital # The unscaled Fermi energy.0 lc rgbcolor ’gray50’ 15 lt 0 lc rgbcolor ’white’ 75 .5 lc rgbcolor ’black’ 4 lt 1 lw 1. "K" x3_K. "{/Symbol G}" x4_GM ) # RELEVANT ENERGY DATA E0 = -6.Sec.325276 E(y) = y . same as E0 for now # The minimum gap # The next gap # The indirect gap # The energy shifting (scaling) function # LINE STYLES & EXTRA COLORS FOR LABELING VARIOUS BANDS WHEN NECESSARY # -----> Note.225650 cLUCO = 11 LUCO = -3..0 lc rgbcolor ’forest-green’ 9 lt 4 lw 1.6.22565 # The cHOCO = 10 HOCO = -6.0 lc rgbcolor ’black’ 3 lt 1 lw 2.5 lc rgbcolor ’blue’ 6 lt 1 lw 1.0 lc rgbcolor ’yellow’ 8 lt 1 lw 1.529883 x4_GM = 2..000000 x2_M = 0.2 Band Structure Plot # X-TIC LABELS AND INFORMATION GENERATED BY gpband x1_GM = 0. there are more in the actual gpt file on guscus.138425 iGap = 2. set set set set set set set set set set set set set set set style style style style style style style style style style style style style style style line line line line line line line line line line line line line line line 1 lt 4 lw 0.969907 x3_K = 1.5 lc rgbcolor ’red’ 5 lt 1 lw 1.900374 EF = -6. 13: Scripts 13.0 lc rgbcolor ’orange’ 7 lt 1 lw 1.0 lc rgbcolor ’dark-salmon’ 14 lt 1 lw 1.0 lc rgbcolor ’green’ 11 lt 1 lw 1.649834 set xtics ( "{/Symbol G}" x1_GM.0 lc rgbcolor ’magenta’ 13 lt 1 lw 1.dat file # The Highest Occupied Crystal Orbital # The column containing the LUCO in the band.5 lc rgbcolor ’dark-turquoise’ 2 lt 1 lw 1.0 lc rgbcolor ’sea-green’ 10 lt 1 lw 2.225650 mGap = 2.0 lc rgbcolor ’cyan’ 12 lt 1 lw 1.325276 MGap = 4. "M" x2_M.E0 highest energy of the valence band # The column containing the HOCO in the band. graph 1 nohead ls 1 nohead ls 1 nohead ls 1 1 nohead ls 1 GAP INFOR (NOT PRODUCED BY gpband) = 1.0 lc rgb ’gray’ not. graph 0 to x3_K. \ data using 1:(E($19)) t "32" with l ls 5.3 Band Structure Plot–II # SET VERTICAL set arrow 1 set arrow 2 set arrow 3 set arrow 4 # LOWEST VBMx VBMy CBMx CBMy LINES FOR HIGH-SYMMETRY POINTS from x1_GM.3. first E(LUCO) nohead ls 9 set yrange [-8:12] set ytics -8. graph 1 from x4_GM. \ data using 1:(E($24)) t "37" with l ls 5. \ data using 1:(E($8)) t "21-occ" with l ls 4. 13: Scripts 13.Sec. \ data using 1:(E($15)) t "28" with l ls 5.225650-E0 # prescaled.Range from gpband (ls 5=blue. \ data using 1:(E($17)) t "30" with l ls 5. gpband gives [*:*] # PLOT THE BANDS . graph 0 to x4_GM.529883 = -6.6. \ data using 1:(E($14)) t "27" with l ls 5. \ data using 1:(E($4)) t "17-occ" with l ls 4. \ data using 1:(E($21)) t "34" with l ls 5.12 # Determine by hand.CBMy heads front set arrow 7 from 0.2. \ data using 1:(E($5)) t "18-occ" with l ls 4.VBMy to VBMx. graph from x2_M. \ data using 1:(E($2)) t "15-occ" with l ls 4 76 . \ data using 1:(E($20)) t "33" with l ls 5.900374-E0 # prescaled.first E(LUCO) to 5.90 ls 10 front set arrow 6 from VBMx. \ data using 1:(E($9)) t "22-occ" with l ls 4. \ data using 1:(E($23)) t "36" with l ls 5.scaled set arrow 5 from VBMx. \ data using 1:(E($22)) t "35" with l ls 5. \ data using 1:(E($16)) t "29" with l ls 5. \ data using 1:(E($11)) t "24" with l ls 5. \ data using 1:(E($12)) t "25" with l ls 5. \ data using 1:(E($18)) t "31" with l ls 5.scaled = 1. \ data using 1:(E($3)) t "16-occ" with l ls 4.529883 = -3. graph 0 to x1_GM. \ data using 1:(E($7)) t "20-occ" with l ls 4.2. ls 4=red) plot 0 w l lt 1 lw 3. \ data using 1:(E($10)) t "23-occ" with l ls 4.CBMy heads size . graph 0 to x2_M. \ data using 1:(E($6)) t "19-occ" with l ls 4. \ data using 1:(E($13)) t "26" with l ls 5. graph 1 from x3_K.VBMy to CBMx. 6.5 ’{/Helvetica=14 HSE Gap 2. -6. 4.33 eV (D)}’ tc rgb ’dark-red’ 77 .2.4 The Rotated PDOS Plot-I # SET UP PDOS PLOT pdosdata = ’pdos.E(LUCO) heads lw 0. -2.0 to 2.0. 13: Scripts 13.Sec.dat’ set rmargin 5.12 set y2tics (-8.90 ls 10 lw 2 front # ARROW set arrow 2 from 2.1.6 set y2range [-8:12] set y2tics -8.8 front # LABEL: SYSTEM & CALCULATION TYPE set label 1 at 3.3.E(HOCO) to 2.5 set lmargin 0 unset xlabel unset ylabel set xlabel ’PDOS (states/eV/unit cell)’ unset ytics unset xtics set xrange [*:*] # Use until you know your system. set xrange [-0. ’{/Times-ItalicBold E_F}’ 0. -4. 8.6.1:6] # Adjust as is necessary set xtics 1. overwritten by line below.-0.5 ’{/Helvetica=14 MoS_{2} Monolayer SPE}’ tc rgb ’navy’ # LABEL: FUNCTIONAL AND BAND GAP set label 2 at 3.E(LUCO) heads size . 12) set key # GAP LABELS FOR PDOS SIDE unset arrow unset label # I-BAR set arrow 1 from 2. 2. 10. 0 lc rgbcolor ’blue’ set style line 5 lt 4 lw 1. SET UP THE LEGEND/KEY plot 0 w l lt pdosdata using pdosdata using pdosdata using pdosdata using pdosdata using pdosdata using pdosdata using unset multiplot 1 lw 3.0 lc rgbcolor ’goldenrod’ set style line 16 lt 1 lw 1. 13: Scripts 13.7 lc rgbcolor ’#00abff’ set style line 28 lt 3 lw 0.0 lc rgbcolor ’blue’ set style line 4 lt 1 lw 1.8 lc rgbcolor ’forest-green’ set style line 9 lt 4 lw 1.0 lc rgbcolor ’#ab00ab’ set style line 27 lt 1 lw 0.0 lc rgb ’gray’ not.0 lc rgbcolor ’forest-green’ set style line 7 lt 1 lw 1.0 lc rgbcolor ’orange’ set style line 15 lt 4 lw 1.\ 8:1 w l ls 1 t ’Total’ # ALWAYS USE THIS FOR A MULTIPLOT PLOT 78 .0 lc rgbcolor ’spring-green’ set style line 8 lt 2 lw 0.0 lc rgbcolor ’pink’ set style line 21 lt 1 lw 1.0 lc rgbcolor ’khaki’ set style line 22 lt 1 lw 1.\ 5:1 w l ls 28 t ’Mo_{/Helvetica-Italic s}’.0 lc rgbcolor ’gold’ set style line 14 lt 1 lw 1.7 lc rgbcolor ’#00abff’ set style line 29 lt 0 lc rgbcolor ’white’ # PLOT THE PDOS DATA.0 lc rgbcolor ’dark-green’ set style line 17 lt 1 lw 1.0 lc rgbcolor ’red’ set style line 12 lt 4 lw 1.\ 6:1 w l ls 27 t ’Mo_{/Helvetica-Italic p}’.0 lc rgbcolor ’plum’ set style line 20 lt 1 lw 1.\ 7:1 w l ls 26 t ’Mo_{/Helvetica-Italic d}’.0 lc rgbcolor ’green’ set style line 24 lt 1 lw 1.0 lc rgbcolor ’navy’ set style line 19 lt 1 lw 1.0 lc rgbcolor ’cyan’ set style line 25 lt 1 lw 1.0 lc rgbcolor ’royalblue’ set style line 6 lt 4 lw 1.0 lc rgbcolor ’dark-khaki’ set style line 18 lt 1 lw 1.\ 2:1 w l ls 13 t ’S_{/Helvetica-Italic s}’.6.5 The Rotated PDOS Plot-II # PDOS PLOT COLORS set style line 1 lt 1 lw 1.5 lc rgbcolor ’black’ set style line 2 lt 1 lw 1.0 lc rgbcolor ’sea-green’ set style line 23 lt 3 lw 1.0 lc rgbcolor ’brown’ set style line 13 lt 1 lw 1.\ 3:1 w l ls 14 t ’S_{/Helvetica-Italic p}’.0 lc rgbcolor ’dark-magenta’ set style line 10 lt 4 lw 1.Sec.0 lc rgbcolor ’skyblue’ set style line 3 lt 2 lw 1.0 lc rgbcolor ’red’ set style line 11 lt 1 lw 1.0 lc rgbcolor ’magenta’ set style line 26 lt 1 lw 1.\ 4:1 w l ls 15 t ’S_{/Helvetica-Italic d}’. 13: Scripts 79 .Sec. HISSb HISS-a HISS-a [11] [12] [12] Use this! G09-B.. SR=Short -range. 6] G09-B1 and higher HSE. (Not an exhaustive list. gdv-h11 (PBC) Use this gdv-h1 (PBC) Don’t use. 9] [8. HISSb [11] HISS. HSE06H HSE.. HSE06 HSE03 [7.1 PBC Functionals Scuseria Functionals Table 5: Functionals developed in the Scuseria Group sorted according to type.. yet. discussed and compared in the literature. gdv-h11 (PBC) Don’t use. Note that availability is variable.) Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes — — — — PBEPBE + 3/74=5050 AMO5 HSEsol HTBS MBJLDA PBEsol [17] [18] [19] [20] [14. Just-For-Solids Functionals Table 6: Functionals developed explicitly for solids. 80 . yet. gdv-h1 (PBC) LC-ωPBE [13] G09-B1 and higher Semilocal PBEPBE + 3/74=5050 PBEsol TPSSTPSS TPSS 14. no PBC. and LR=Long-range. MR=Middle-range. 8.14 14. 9] [10] Use this *always* HISS.. Keyword and/or IOp Acronym(s) Global Hybrids TPSSh TPSSh SR Screened Hybrids HSEh1HSE HSE1PBE HSE2PBE MR Screened Hybrids 3/74=-61 3/74=-56 3/74=-62 3/74=-57 LR Screened Hybrids LC-wPBE Citation(s) [5. 15] Not available Not available Not available Not available gdv-h11-sol. no PBC. but not necessarily implemented widely.2 Availability/Notes [14. 15] [16] gdv-h11-sol. a BibTex file. LDA M06L PBE PW91 PW92 TPSS revTPSS WC [23] [24] [25.bib file with all of the citations used here and more is provided at guscus:/projects/guscus/Manuals/functionals.1. 6] G09-B1 and higher PBE hybrid → HSE Truhlar Suite Variation of above Variation of above Not sure which 14.bib.Sec.PBE0 M06 M06HF M062X TPSSh [33] [34. Table 8: Global hybrid functionals that have been applied to the extended systems.use the LSDA with SVWN5” Never use Use this rather than PW91 Less-clean version of PBE Not sure what this is Jian-Min says “eh.4 Availability/Notes G09-B1 and higher “. anyway. Last Modified March 26. but continue to be used. why? Seriously. Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes B3LYP PBEh1PBE M06 M06HF M062X TPSSh B3LYP PBEh. 14: PBC Functionals 14.[21] Keyword and/or IOp Acronym(s) Citation(s) SVWN5 LSDA [22] LSDA M06L PBEPBE PW91 PW92 TPSSTPSS revTPSS WC LSDA.3 (Semi)Local Functionals Table 7: Functionals commonly encountered by the solid state theoretician that are known not to work well.” Not sure about any of this Global Hybrids OMG. 30. 2012 81 . see the commentary by GES in Section 11. 35] [36] [37] [38] [5.5 Functional Bibliography For LaTex users... 26] [27] [28] [16] [29. 31] [32] 14. Arranged roughly according to the rungs of the functional Jacob’s Ladder. functionals. Note: expect to expend extensive amounts of CPU time. 2333250 0. F.1145360 0.00 11427. • Scale Factor (#) refers to the shell scale factor. • The type/constraint specification is for shells: S. Generally.1390000 33. respectively.0137419 0. • Comments are made using an exclamation point 15.3500000 395..2374510 0.6026000 4.. and the scale factor. 0.15 Basis Sets for Extended Systems The format for PBC basis sets is the same as that for molecular basis sets. for s-.3218920 **** <—. the number of primitive gaussians..9190100 SP 3 1. shells. D.2995050 0.4 asterisks after blank space (Mandatory) <—.1 Example: The 6-311G Basis Set for Fluorine **** F 0 S 6 1. n total primitive gaussian lines.8204580 1. p-.Mandatory 4 asterisks terminating basis set <—.7460000 115. The shell descriptor line contains: the shell type..00180093 0.7175600 SP 1 1.Indicates this is a Fluorine basis set The first shell (S) descriptor line The first (S) exponent and contract coeffcients The second ...0354609 0.0000000 The second (SP ) shell descriptor The first set of SP exponent and contract coeffcients The second SP )shell descriptor The second SP shell descriptor <—. P.00 55. if #=2.0681334 0. See the G09 Basis Set and Gen/GenECP pages for more details.1000000 1722. DP.Mandatory blank space after Tv’s <—. 1. e.Mandatory blank space terminating input file 82 .0000000 1. SPD. αn nGauss d1µ d2µ d3µ dnµ ScaleFactor # # # # # The the “Shell Descriptor Line” n primitive gaussian specifications αk exponent and dkµ contraction coefficient. • NGauss specifies the number of primitive gaussian shells (the degree of contraction) for the shell being defined.0000000 1.5890860 0.6323000 3. G. the basis sets will be called externally via Gen/GenECP(or Pseudo=Read) or by specifying the path to the basis set preceded by an @ and terminated with a /N to prevent writing to the output file.1654500 SP 1 1. dp.00 1.4441000 12. all primitive exponents are scaled by 2..00 0.00337804 0.9205120 -0. 2. (As in Section 3) The anatomy of a G09 basis set file is as follows: Type/Constraint α1 α2 α3 . The remaining lines are primitive gaussian specifications • There are nGauss of them • Each line defines the exponents αk and dkµ contraction coefficients.0000000 1. d−.g.. • See also Sections 11. followed by a step-by-step example for chlorine. Run the LSDA/GGA calculation with the modified PBC gaussian basis set in G09 3. To address this potential issue: 1. the PDOS will usually indicate which basis set should be re-adjusted. 41.e. more detailed discussion. a basis set developed for atoms/molecules is reasonable for extended systems. Keep in mind that the reference planewave calculation must be of reasonable quality. (within 3-5 eV) then the modified PBC basis set is sufficient.2. 42] for additional. the next two sections include annotated examples of PBC-optimized basis sets with and without effective core potentials (ECPs).. (They slow the Coulomb near field of the fast multipole method. A copy is also kept at: gusucs:/projects/guscus/Manuals/Towler. Compare the results: • If they are similar. • A periodic system in 3-D does not need these tails.2 and References [40. • If the gap is too large. which will slow down your jobs.) WHY? Molecular basis sets typically contain one or more few diffuse basis functions (bfs) in order to properly describe atomic tails. The Gaussian Basis Set FAQ prepared by Mike Towler provides a nice introduction to the use of gaussian basis sets in PBC calculations. and the basis sets for two or more atoms were modified.1. In the case of no decent standard.)[39] • There are are some tails in lower dimensions.Sec. (Basis sets are generally downloaded from the EMSL or a similar ES database – see Section 15. it is important to ensure that the chosen MOLECULAR basis set i. 15: Basis Sets for Extended Systems 15. Find an LSDA or GGA planewave calculation with PDOS or band gap data for the system of interest 2. common sense and experience must be employed. 4. For illustrative purposes. 83 .2 Modifying Basis Sets for PBC Calculations Before running a PBC job.1 and 11.pdf CAUTION: → A basis set properly optimized for previous PBC calculations may not work as well when applied to a different system. but these calculations are not as sensitive. 00000000 1.9199990 -0.0000000 1.237594000 0.00 0.619879000 0.0402487 0.25 1.919999000 -0.00 1.0761269 0.00000000 1.1778810 0.2.00000000 .00000000 1.6308070 12.303068000E-02 0.7321170 0.00 335.00 77.626000000 **** 0.12 1.250000000 P 1 1.4553000 13.cam.pnl.6211400 1.682990000E-01 0.0000000 0.8033100 1.4593300 SP 1 1.82773000 SP 3 1. Si p− shell exponents are edited as in Reference [44].00 20.9268660 S 1 1.00 0.00000000 1.00 0.9881500 9.00000000 0.00000000 1. 43] and many other papers.9642000 4.815854000 1.45933000 SP 1 1.6291680 S 3 1.00 0.1249670 0.4391480 1.00000000 0.0000000 1.45131000 P 1 1.1429500 214.00000000 1.9400000 2333.8158540 1.256234000 S 1 1.Sec.4513100 P 1 1.221006000 0.0654320 D 1 1.it/Basis_Sets/Ptable.1 Basis Set Databases Sites from which gaussian-type basis sets may be downloaded prior to modification include: EMSL https://bse.8796000 657.0000000 1.00 0.00 69379.0088660 0.00 0.124967000 0.247623000 1.45234300 S 1 1. As is clear from the arrows.2562340 S 1 1.5049770 P 1 1. but nothing is modified in the C basis set.4523430 S 1 1.00 69379.2608010 0.00 0. 11.62114000 1.00 3.00 0.732117000 0.0007570 0.00 0.24000 682.260801000 0.0152306 0.8012950 S 1 1.0942790 P 4 1.00000000 1.00 3.crystal.00 20.2 Example 1: Modified PBC Basis Sets with No ECPs This example contains the basis sets for β-SiC (zincblende polytype) used in References [12.114660000 0.4831900 78.616462000 0.html Crystal Periodic Table http://www.reset to 0.00 0.554888000 0.1455850 D 1 1.00 3.6198790 0.177881000 0.9881500 9. 15: Basis Sets for Extended Systems 15.0000000 84 0.00 4563.ac.9003660 24.00000000 1.2909580 0.402487000E-01 0.6164620 0.120000000 D 1 1. MODIFIED Si and C m-6-311G* basis sets ORIGINAL Si and C 6-311G* basis sets from the EMSL **** Si 0 S 6 1.00 0.0000000 1.00 1.145585000 D 1 1.757000000E-03 0.152306000E-01 0.483456000 SP 1 1.301130 77.0000000 1.310880000E-01 0.5548880 0.4834560 SP 1 1.4553000 13.1863170 P 1 1.00 0.8012950 S 1 1.0290000 1.92686600 S 1 1.2476230 1.2300 10354.0310880 0.0240000 154.3011300 77.uk/ mdt26/crystal.2197110 P 2 1.450000000 **** C 0 S 6 1.0059320 0.00 3.886600000E-02 0.2375940 0.196665000E-02 0.0290000 1.1146600 0.593200000E-02 0.html 15.87960 657.00303068 0.0000000 1.4500000 **** C 0 S 6 1.6308070 12.9730000 44.21971100 P 2 1.00 77.00 0.00 4563.0000000 1.unito.973000 44.9400 2333.761269000E-01 0.0000000 0.tcm.6291680 S 3 1.627765000 0.00 0.8277300 SP 3 1.6260000 **** **** S 0 S 6 1.00 0.6291680 30.00000000 1.6277650 0.439148000 1.2300000 10354.9003660 24.0000000 1.120000000 P 4 1.00 335.00 0.gov/bse/portal Mike Towler’s Page http://www.142950 214.386897000 0.290958000 0.phy.6291680 30.00 0.2400000 682.80331000 1.2.3868970 0.0000000 <---.00196665 0.00000000 1.00 0.0682990 0.9642000 4.024000 154.0000000 <---.2210060 0.504977000 P 1 1.reset to 0.483190 78. 199410000E-01 -0.5601000 1.6763840 <-------. MODIFIED As m-pVDZ-PP basis set ORIGINAL As cc-pVDZ-PP basis set from the EMSL 0 8 1.6893000 5.8100000 381.00 0.76116000 1.00 <-------2542.deleted 1.851010000E-01 0.42096000 S 6 1.0000000 <-------- set to 0.53909000 2 18.3078000 D 1 1.1195000 5.00 <-------113.219000000E-02 -0.876100000E-02 0.00 2542.87146400 -18.77523000 -2.00 113.712926000 0.5349000 24.3214430 0.15725900 .8872000 13.76768100 P-G POTENTIAL 4 2 45.00 <-------99.107210000 -0.00 0.00 0.00000000 0.1009720 P 1 1.30788000 28.3373910 0.00000000 370.5601000 1.1840120 0.0021900 -0.184012000 0.00 0.1217000 3.00 99.3214430 S 1 1.4733760 0.deleted 1.605500000E-02 0.67222300 2 3.84196000 2.0011370 0.00000000 S-G POTENTIAL 2 2 28.1167350 S 8 1.0795440 0.12 1.2018900 1.120000000 P 6 1.0000000 1.14210300 198.5356530 <-------.81350200 F-G POTENTIAL 2 2 11.0308000 D 7 1.136878000 -0.119800000E-01 0.00 0.deleted 0.2.deleted Goes from 8 to 6 bc of deletions -0.4047620 0.4209600 0.236755000 0.3 Example 2: Modified Arsenic Basis Set + ECP Note the modifications marked in the original As basis set (right) downloaded from the EMSL.33106400 2 44.00 0.0268530 0.169000 40.00 2542.56010000 1.0000000 1.404762000 0.2342000 16.0038570 -0.0199410 -0.3184240 0.1217000 3.Sec.2342000 16.11402500 9.307800000 **** AS 0 AS-ECP 4 10 G POTENTIAL 1 2 1.11353000 -1.5349800 <-------.72512200 2 6.0000000 <-------.169000 40.1722590 0.48514500 -28.8100000 381.97347100 D-G POTENTIAL 6 2 51.268530000E-01 0.0060550 0.deleted Goes from 7 to 6 bc of deletion -0.0180130 <-------.3214430 0.576400000E-02 -0.00 0.321443000 S 1 1.00000000 1.deleted 1.12 1.00 0.00 0.1072100 -0.42096000 S 1 1.0007720 0.1217000 3.17033800 -0.00 2542.0003900 -0.320457000 -0.120000000 D 6 1.0000000 Goes from 7 to 6 bc of deletion 0.05715200 2 50.0119800 0.20189000 1.531478000 0.1195000 5.1000000 **** As S As S 0.38307300 56.1195000 5.337391000 1.0087610 0.76741500 2 19.1167350 S 1 1.0804600 0.0841250 -0.84196000 2. The basis set modification for gaussian PBC calculations (left) is discussed in Reference [44] and is acompanied by the appropriate ECP at the bottom.8872000 13.20189000 1.406686000 0.5349000 24.4066860 0.7375680 0.1167350 S 1 1.0087300 <-------.4209600 0.0057640 -0.772000000E-03 0.0000000 <-------- set to 0.00000000 0.00 0.405285000 0. 15: Basis Sets for Extended Systems 15.00 0.0851010 0.0930800 0.737568000 D 1 1.1731620 0.81000 381.1009720 P 1 1.2367550 0.3184240 0.00 99.390000000E-03 -0.3078000 D 1 1.3204570 -0.0000000 0 6 <-------.5349000 24.deleted Goes from 7 to 6 bc of deletion 0.56010000 1.8419600 2.0037200 <-------.1195000 5.10175700 0.81000 381.318424000 P 1 1.2342000 16.00 <-------99.4052850 0.5090000 36.15134000 2 16.3896400 2.8419600 2.09308000 0.94058400 2 17.08046000 0.0930800 0.5349000 24.5697440 0.113700000E-02 0.09308000 0.deleted -0.38964000 2.6893000 5.2018900 1.172259000 0.34929600 99.841250000E-01 -0.0003520 <-------.509000 36.318424000 P 6 1.10893600 2 14.401534000 0.4015340 0.deleted 85 0.5314780 0.85192700 2 3.00000000 0.385700000E-02 -0.569744000 1.1690000 40.1368780 -0.173162000 1.1009720 P 7 1.2342000 16.795440000E-01 0.7129260 0.0370000 P 7 1.1217000 3.22389500 -1.473376000 -0.1690000 40.34576500 0. Sec. 15: Basis Sets for Extended Systems 15.2.4 Example 3: Step-by-Step Modification for Cl General Procedure: 1. Reset some of the diffuse functions to a minimum value: • Generally, the minimum exponent for s-type functions should be less than αmin = 2/d2 , where d is the smallest distance between two atoms. • In gaussian, d is expressed in Bohr. • 0.15 is a reasonable value. (See Sections 11.1 and 11.2.) 2. Remove any redundancies. On the left is the original 6-311++G(3df) basis set for chlorine: all exponents with values of 0.15 have been marked with arrows. (Note that in Section 15.2.3, 0.12 is the minimum.) In the column to the right, the values of the 2 marked exponents have been changed to 0.15. 1st MODIFICATION Cl 6-311++G(3df ) basis set ORIGINAL Cl 6-311++G(3df ) basis set from the EMSL Cl 0 S 6 1.00 105819.0000000 15872.0000000 3619.6500000 1030.8000000 339.9080000 124.5380000 S 3 1.00 124.5380000 49.5135000 20.8056000 S 1 1.00 6.5834600 S 1 1.00 2.5646800 S 1 1.00 0.5597630 S 1 1.00 0.1832730 P 5 1.00 589.7760000 139.8490000 45.1413000 16.8733000 6.7411000 P 2 1.00 6.7411000 2.7715200 P 1 1.00 1.0238700 P 1 1.00 0.3813680 P 1 1.00 0.1094370 SP 1 1.00 0.0483000 D 1 1.00 3.0000000 D 1 1.00 0.7500000 D 1 1.00 0.1875000 F 1 1.00 0.7000000 **** Cl 0 S 6 1.00 0.0007380 105819.0000000 0.0057180 15872.0000000 0.0294950 3619.6500000 0.1172860 1030.8000000 0.3629490 339.9080000 0.5841490 124.5380000 S 3 1.00 0.1341770 124.5380000 0.6242500 49.5135000 0.2917560 20.8056000 S 1 1.00 1.0000000 6.5834600 S 1 1.00 1.0000000 2.5646800 S 1 1.00 1.0000000 0.5597630 S 1 1.00 1.0000000 0.1832730 P 5 1.00 0.0023910 589.7760000 0.0185040 139.8490000 0.0813770 45.1413000 0.2215520 16.8733000 0.7725690 6.7411000 P 2 1.00 -1.5722440 6.7411000 0.9923890 2.7715200 P 1 1.00 1.0000000 1.0238700 P 1 1.00 1.0000000 0.3813680 P 1 1.00 1.0000000 <---------------------------------------> 0.1500000 SP 1 1.00 1.0000000 1.0000000 <----------------------> 0.1500000 D 1 1.00 1.0000000 3.0000000 D 1 1.00 1.0000000 0.7500000 D 1 1.00 1.0000000 0.1875000 F 1 1.00 1.0000000 0.7000000 **** 86 0.0007380 0.0057180 0.0294950 0.1172860 0.3629490 0.5841490 0.1341770 0.6242500 0.2917560 1.0000000 1.0000000 1.0000000 1.0000000 0.0023910 0.0185040 0.0813770 0.2215520 0.7725690 -1.5722440 0.9923890 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 Sec. 15: Basis Sets for Extended Systems Now look for redundancies: • The 1st modification (left column) results in a basis set with P (Sim1) and SP (Sim2) functions with values of 0.15. • There is also an S function at 0.1832, which is very close, Marked Sim3. • Since they are virtually the same, pull out the SP function. (Marked *** YANKED *** in the right column.) • Notice a similar logic was used for the As basis set in Section 15.2.3. 1st MODIFICATION Cl 6-311++G(3df ) basis set Cl 0 S 6 1.00 105819.0000000 15872.0000000 3619.6500000 1030.8000000 339.9080000 124.5380000 S 3 1.00 124.5380000 49.5135000 20.8056000 S 1 1.00 6.5834600 S 1 1.00 2.5646800 S 1 1.00 0.5597630 S 1 1.00 0.1832730 P 5 1.00 589.7760000 139.8490000 45.1413000 16.8733000 6.7411000 P 2 1.00 6.7411000 2.7715200 P 1 1.00 1.0238700 P 1 1.00 0.3813680 P 1 1.00 0.1500000 SP 1 1.00 0.1500000 D 1 1.00 3.0000000 D 1 1.00 0.7500000 D 1 1.00 0.1875000 F 1 1.00 0.7000000 **** 0.0007380 0.0057180 0.0294950 0.1172860 0.3629490 0.5841490 0.1341770 0.6242500 0.2917560 1.0000000 1.0000000 1.0000000 1.0000000 0.0023910 0.0185040 0.0813770 0.2215520 0.7725690 -1.5722440 0.9923890 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 2nd MODIFICATION Cl 6-311++G(3df ) basis set Cl 0 S 6 1.00 105819.0000000 15872.0000000 3619.6500000 1030.8000000 339.9080000 124.5380000 S 3 1.00 124.5380000 49.5135000 20.8056000 S 1 1.00 6.5834600 S 1 1.00 2.5646800 S 1 1.00 0.5597630 S 1 1.00 <------------------ Sim3 ---------------------> 0.1832730 P 5 1.00 589.7760000 139.8490000 45.1413000 16.8733000 6.7411000 P 2 1.00 6.7411000 2.7715200 P 1 1.00 1.0238700 P 1 1.00 0.3813680 P 1 1.00 <----------------- Sim1 ----------------------> 0.1500000 <----------------- Sim2 ----------------> # SP 1 1.00 1.0000000 <------ Sim2 ------> # 0.1500000 D 1 1.00 3.0000000 D 1 1.00 0.7500000 D 1 1.00 0.1875000 F 1 1.00 0.7000000 **** 0.0007380 0.0057180 0.0294950 0.1172860 0.3629490 0.5841490 0.1341770 0.6242500 0.2917560 1.0000000 1.0000000 1.0000000 1.0000000 0.0023910 0.0185040 0.0813770 0.2215520 0.7725690 -1.5722440 0.9923890 1.0000000 1.0000000 1.0000000 1.0000000 (*** YANKED ***) 1.0000000 (*** YANKED ***) 1.0000000 1.0000000 1.0000000 1.0000000 A contribution from Professor Edwards Brothers at Texas A&M-Qatar Locally access the *gbs files via: guscus:/projects/Manuals/examples/Cl-ori.gbs or Cl-mod.gbs Last Modified April 19, 2012 87 Sec. 15: Basis Sets for Extended Systems 15.3 Using the EMSL The EMSL site is very easy to use. The key features of the homepage are shown below. 1. Use the periodic table (red arrow) to select one (or more) elements. 2. The program window (green arrow) allows selction of the appropriate format for common ES codes. 3. The basis set window (blue arrow)for choosing the basis set. 4. Information about the basis set (purple arrow). 15.3.1 Example: Ge The process for acquiring the Ge 6-311G* basis set for use in gaussian is illustrated in Figure 18. Specifically: 1. Ensure Gaussian94 is the ES code format selected (red oval). 2. Click Ge (green oval). 3. Select 6-311G* in the basis set window (blue oval). Notice that information about the basis set chosen appears in the bottom section (purple rectangle). Figure 18: The process for acquiring the Ge 6-311G* basis set in gaussian format. 88 3847 0.gbs file using the gbsutil script written by Cris Diaconu.072 0.001927 0.9980000000 3.394 0.0210000000E-02 39.Sec.390 0 3 3 1.011094 0.2500000000E-04 29700. • All references and notes information moved from the bottom in Step 1.0000000000 2.4490000000E-01 SP 6 1.2000000000 2. M.2129 0. Move all of the information at the bottom of the *.4028 0. they must be converted into the gaussian format. ORIGINAL Crystal09 (cry) Basis Set CONVERTED gaussian09 (gbs) Basis Set Sc_864-11G*_harrison_2006 ! Sc_864-11G*_harrison_2006 ! N.04997 0. 1.000225 0.4520000000 SP 1 1.53 39.0 208000.9270000000E-03 6280.406 N.0180000000 1. 25. The gbsutil script is too long to include in Section 13.3600000000E-01 -7.183 -0. Remove ALL extra spaces at the top or bottom.0738 -0.9790000000 -7.20 6.6200000000 -1.160 0. B.0 1.0 499. or copy it locally.4000000000 -5.0 1.0 SP 1 1. Notice the differences in format.1300000000E-01 0. 89 . 1.452 1.3800000000E-02 6. The Sc_864-11G*_harrison_2006 Crystal basis set *. 1.4650000000E-01 1.0100000000 -1.1160 0. unpublished.3100000000E-02 9. 0./gbsutil Sc-864-11G*. Harrison. 1.4029 0.0720000000 3. M. It is being used for Sc@C82 and Sc@C82@SWNT (single-wall carbon nanotube).4 Converting cry to gbs Files: gbsutil After downloading gaussian basis sets from Mike Towler’s or the Crystal web sites. either by deletion or ! 4.0 D 3 1.9970000000E-02 494.01 15.0 0.0 1642. 29700.0 0.4 118.7800000000 1.3900000000 1.7059 1.313 0.0000000000 4.323 0. 1.7014000000E-01 170.1360 -0. Ling Ge. for Scandium.64 170.979 1. 1.0900000000 1. 208000.6000000000E-03 -3.17014 0.7200000000 1. Ling Ge.780 0 1 1 0. Montanari.0 494.8470000000E-01 6. Harrison.0 25.06021 0. 6280.5800000000E-03 8. 3.511 1. Montanari. 1.1449 -0. ! It is being used for Sc@C82 and Sc@C82@SWNT ! (single-wall carbon nanotube).5110000000 6.3940000000 4. 3. Run the script: [sgu1@login2]$ .3688 0.4930000000E-01 3. 0.00558 -0.1290000000E-01 15.cry file to the TOP 2. so a copy is available at guscus:/projects/guscus/Manuals/scripts/gbsutil.940 1. Sc 0 S 8 1.5100000000E-03 118.1300000000E-02 3.9400000000 1.5300000000 -7.0713 0.6400000000 1.0 3. To use this script: 1.6985 0.6200000000 4. unpublished. 2006.72 0 1 6 8.0000000000 1.2300000000E-01 1.1094000000E-02 1642.gbs Download the original Sc. B. 15: Basis Sets for Extended Systems 15. 499. 1.cry file at the link above.cry Sc-864-11G*. along with the Sc. 2006. below.0290000000E-01 27.00851 0.2493 0.62 27.0590000000E-01 1.0600000000E-01 **** 21 6 0 0 8 2.0331 -0.0016 -0.998 0 1 4 8.1600000000E-01 2.0280000000E-01 1.62 3.6120000000 1.1465 1.0000000000 1.018 0.612 0 1 1 2. 0.gbs file from: guscus:/projects/guscus/Manuals/examples/.8300000000E-01 SP 4 1. 1.9850000000E-01 4.6200000000 3.6000000000E-01 1. Comment out all non-basis set data using exclamation points: • The basis set description line (already at the top).6880000000E-01 66.cry on the left was converted to a gaussianformatted *.62 66.09 9. archive. Using the format above will mirror sgu1’s directories in /shared.hard links.scratch/sgu1/ .scratch/sgu1/ .scratch/ on STIC (2) Alternatively. preserve hard links V .g..verbose. large chk files for unfinished jobs and anything else not needing to be saved.1 Using rsync: Examples (1) Assume user sgu1 has directories for each of the clusters on guscus. same as rlptgoD (no -H) H ./ 90 . The easiest and fasted way to accomplish routine backups is via the rsync command: rsync -aHVhu. e.: [sgu1@guscus ~]$ ls Bluebiou Davinci STIC Sugar 1. 4. pdos. This is useful to prevent backing up all *err files.log pdos. the gjf . u . an exclude file may be used./ 3. check man rsync rsync –help –OR– the Official rsync Page for advanced scripts and more.: cd STIC 2.16 Backing Up Your Data Given that the state-of-the-art filesystems can crash and there are monthly purges of /shared. chk and all BS and PDOS dat files may be of import later. Add the names of the files and/or directories for which backups are undesirable on separate lines.chk *err fort* mkpdos.update.d directories. e. Especially since PBC jobs tend to run long. e. archive mode. The tmp/ directory is not backed up as it contains gaussian scratch files and should be purged regularly. Type rsync -aHvhu sgu1@stic:/shared. where a . “xclude” 2. output numbers in a human readable format For more information. skip files that are newer on the receiver 16.scratch/ on all Rice clusters (See Section 12) it is a good idea to back up all data you might want. For completed jobs. use the bzip2 command to zip and compress the chk files for transfer and storage. The rsync command to use is now: rsync -aHvhu -˙ -exclude-from /users/sgu1/xclud sgu1@stic:/shared. out.g.g.d/ zpratl* 1. [sgu1@guscus ~]$ vi xclude tmp/ *. Create a text file in the home directory. increase verbosity h . cd to the directory corresponding to the cluster to be backed up. 3.human readable. out InP-B3LYP/InP-z-B3LYPx.out MgO/TPSS/Readme-2-this-is-weird Si-TPSS/Si-d-TPSSx. etc.out AlAs-wuPBE/band. png).bz2 InP-B3LYP/InP-z-B3LYPx. InP-B3LYP and MgO is shown below.pbs InP-B3LYP/band.scratch/sgu1/ sgu1@stic’s password: receiving file list .txt MgO/ MgO/HSE/XTAL/ MgOHSE/XTAL/deleteme MgO/HSE/OPT/ MgO/HSE/OPT/MgO-rs_o.dat AlAs-wu2PBE/pdos.dat MgO/HSE/OPT/pdos.chk.gpt CdSe-wu/OPT/pdos.legend.gjf MgO/HSE/OPT/MgO-rs_o. CdSe-wu.chk.dat CdSe-wu/OPT/pdos.dat InP-B3LYP/bandk.dat InP-B3LYP/pdos.out CdSe-wu/OPT/band.chk.dat InP-B3LYP/ InP-B3LYP/InP-z-B3LYPx.dat CdSe-wu/OPT/bandk. rsync cmds as aliases are very convenient. image (eps.gjf MgO/TPSS/MgO-TPSSx.).out MgO/HSE/OPT/MgO-rs_o.out Notice that none of the files or directories specified in the xclud file on the previous page are downloaded.dat GaN-wu/LSDA/OPT/bandk. e.bz2 GaN-wu/LSDA/OPT/GaN-w2-LSDAo. Gnuplot (gpt).pbs MgO/HSE/OPT/pdos./’ 91 .dat InP-B3LYP/pdos. and BS/PDOS dat files are all copied recursively. done AlAs-wu2PBE/ AlAs-wu2PBE_x. GaN-wu.out GaN-wu/LSDA/OPT/band.scratch/sgu1/ ..bashrc file: alias stics=’rsync -aHvhu -˙ -exclude-from /users/sgu1/xclud sgu1@stic:/shared. [sgu1@guscus STIC]$ rsync -aHvhu --exclude-from /users/sgu1/xclud sgu1@stic:/shared.Sec.txt CdSe-wu/ CdSe-wu/OPT/ CdSe-wu/OPT/CdSe-wu_o.bz2 MgO/HSE/OPT/MgO-rs_o.txt MgO/TPSS/ MgO/TPSS/MgO-TPSSx. deleteme.legend.bz2 MgO/TPSS/MgO-TPSSx.legend.gjf InP-B3LYP/InP-z-B3LYPx. while non-gaussian-generated files including text (README.g.chk.legend..txt GaN-wu/LSDA/XTAL/ GaN-wu/LSDA/XTAL/README GaN-wu/LSDA/OPT/GaN-w2-LSDAo. 16: Backing Up Your Data The output from adding the -˙ -exclude-from /users/sgu1/xclud option to the rsync command to back up a STIC directory with subdirectories AlAs-wu2PBE.dat CdSe-wu/OPT/pdos..eps CdSe-wu/OPT/pdos. in the .dat AlAs-wu2PBE/bandk.png CdSe-wu/OPT/pdos. Izmaylov. Heyd. 118. A. J. 2010. B 12. Savin. A. B 83. Phys. Rev. G. Joullie. I. E. Scuseria. E. Perdew. Scuseria. B. E. and G. [11] T. Blaha. E. Phys. G. [2] E. Lett. Girault. M. G. Specifically. Rev. [19] P. 12129 (2003). Phys. A. E. Chem. Vydrov and G. Heyd. Ruzsinszky. 92 . 085108 (2005). 085108 (2005). 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