1. Running NWChem 단국대학교임석호차장환

2. OUTLINE Introduction Introduction Task Task Input file Input file Basis Set Basis Set Output Output Method of execution Method of execution Scratch file Scratch file Comparable Table (between Gaussian and NWChem) Comparable Table (between Gaussian and NWChem) Running NWChem

3. Introduction NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. NWChem is scalable, both in its ability to treat large problems efficiently, and in its utilization of available parallel computing resources. NWChem is scalable, both in its ability to treat large problems efficiently, and in its utilization of available parallel computing resources. Running NWChem

4. Introduction local disks: semidirect, with minimal usage of memory gpfs: semidirect, with minimal usage of memory no disk: direct if integrals do not fit into memory; in-core otherwise no disk + mem: tell NWchem to use up to 100MW local disk + mem: use local disks and 100MW buffer on every CPU. These pictures from High Performance Computing in COMPUTATIONAL CHEMISTRY (Sigismondo Boschi, CINECA) Running NWChem

5. Introduction These pictures from High Performance Computing in COMPUTATIONAL CHEMISTRY (Sigismondo Boschi, CINECA) Running NWChem

6. Task TASK Directive for Electronic Structure Calculations Scf – Hartree Fock mcscf – Multiconfiguration SCF MP2 – perturbation theory CCSD – Coupled-cluster single and double excitations DFT – Density functional theory for molecules md – Classical molecular dynamics simulation using nwARGOS sodft – Spin-Orbit DFT gapss – DFT for periodic systems pspw – Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW band – Pseudopotential plane-wave DFT for solids using NWPW

7. Task (Operation) Operation specifies the calculation that will be performed in the task energy – Evaluate the single point energy gradient – Evaluate the derivative of the energy with respect to nuclear coordinate optimize – Minimize the energy by varying the molecular structure. saddle – Conduct a search for a transition state using either Driver freq – Compute second derivatives and print out an analysis of molecular vibrations. dynamics – Compute molecular dynamics using nwARGOS thermodynamics – Perform multi-configuration thermodynamic integration using nwARGOS Running NWChem

8. Input file start start title title geometry geometry basis basis task task Running NWChem

9. Input (Print control) Running NWChem The print | noprint options control the level of output Name print level Description “total time” medium Print cpu and wall time at job end “task time” high Print cpu and wall time for each task “ma stats” high Print MA allocations at job end ---------------------in the DFT------------------------ “all vector symmetries” high symmetries of all molecular orbitals “convergence” default convergence of SCF procedure “intermediate evals” high intermediate orbital energies

10. Input (Example) Running NWChem title “Nitrogen cc-pvdz SCF geometry optimization” geometry n 0.0 0.0 0.0 n 0.0 0.0 1.08 end basis n library cc-pvdz end task scf optimize

11. Input (Example) start symmetry echo title " symmetry " geometry “symmetry" H 0.000000000 0.384100000 0.000000000 bqH 0.000000000 1.525925000 0.000000000 symmetry group c2v end basis H library cc-pVTZ bqH library H cc-pVTZ end SCF UHF thresh 1.0e-8 maxiter 1285 END set geometry " symmetry " task scf Running NWChem

12. Input (Example) Running NWChem start h2o_freq charge 1 Geometry unit angstroms O 0.0 0.0 0.0 H 0.0 0.0 0.1 H 0.0 0.1 0.0 end title “H2O+ : UMP2 geometry opt” task MP2 optimize mp2; print none; end scf; print none; end title “H2O+:6-31g** UMP2 freq” task mp2 freq Basis H library sto-3g O library sto-3g end scf uhf; doublet print low end title “H2O+ : STO-3G UHF geometry opt” task scf optimize basis H library 6-31g** O library 6-31g** end

13. Input (Example) Running NWChem start H2O_dimmer(BSSE) Geometry “H2O_dimmer” O -1.34 -0.11 0.02 H -0.36 -0.05 0.00 H -1.63 0.80 -0.14 O 1.14 0.01 -0.02 H 1.69 0.81 0.16 H 1.72 -0.80 -0.01 End Geometry “H2O+Ghost” O -1.34 -0.11 0.02 H -0.36 -0.05 0.00 H -1.63 0.80 -0.14 bqO 1.14 0.01 -0.02 bqH 1.69 0.81 0.16 bqH 1.72 -0.80 -0.01 End Basis H library sto-3g O library sto-3g bqH library H sto-3g bqO library O sto-3g End Set geometry “H2O_dimmer” Task scf Set geometry “H2O+Ghost” Task scf

14. Input (Example) Running NWChem start Ti-C2H6 echo title "Ti-C2H6" geometry "TiC2H6" C 6.755830000 7.348640000 1.123030000 C 8.243390000 7.348630000 1.122730000 Ti 7.500000000 7.500000000 3.000000000 H 6.248260000 8.233750000 0.706360000 H 6.245880000 6.411440000 0.848070000 H 8.753470000 6.411620000 0.847510000 H 8.751220000 8.233390000 0.705720000 H 7.500000000 7.118970000 7.000000000 H 7.500000000 7.887170000 7.000000000 end basis C library cc-pVTZ H library cc-pVTZ Ti library "NASA Ames cc-pVTZ" end SCF UHF thre`h 1.0e-8 maxiter 1285 END CCSD freeze core atomic thresh 1.0e-8 maxiter 1285 End set geometry "TiC2H6" task CCSD(T)

15. Input (Basis Set) Running NWChem Standard all-electron basis sets: Basis Set "STO-2G" (number of atoms 21) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sr ) Basis Set "STO-3G" (number of atoms 53) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I ) Basis Set "STO-6G" (number of atoms 36) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr ) Basis Set "STO-3G*" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "3-21G" (number of atoms 55) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs ) Basis Set "3-21++G" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "3-21G*" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "3-21++G*" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "3-21GSP" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar )

16. Input (Basis Set) Running NWChem Basis Set "4-22GSP" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "4-31G" (number of atoms 13) (H He Li Be B C N O F Ne P S Cl ) Basis Set "6-31G" (number of atoms 30) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn ) Basis Set "6-31G*" (number of atoms 30) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn ) Basis Set "6-31G**" (number of atoms 30) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn ) Basis Set "6-31++G" (number of atoms 20) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca ) Basis Set "6-31++G*" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "6-31++G**" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "6-31+G*" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar ) Basis Set "6-31G(3df,3pd)" (number of atoms 18) (H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar )

17. Input (Basis Set) Running NWChem basis O library cc-pVDZ Ti library cc-pVDZ end basis * library cc-pVDZ end basis * library cc-pVDZ except Ti Ti library “NASA cc-pVTZ” end

18. Input (Basis Set) geometry “example" C 6.755830000 7.348640000 1.123030000 C 8.243390000 7.348630000 1.122730000 H1 6.248260000 8.233750000 0.706360000 H1 6.245880000 6.411440000 0.848070000 H1 8.753470000 6.411620000 0.847510000 H1 8.751220000 8.233390000 0.705720000 H2 7.500000000 7.118970000 7.000000000 H2 7.500000000 7.887170000 7.000000000 end basis C library cc-pVTZ H1 library cc-pVTZ H2 library cc-pVTZ end geometry “example" C 6.755830000 7.348640000 1.123030000 C 8.243390000 7.348630000 1.122730000 H 6.248260000 8.233750000 0.706360000 H 6.245880000 6.411440000 0.848070000 H 8.753470000 6.411620000 0.847510000 H 8.751220000 8.233390000 0.705720000 H 7.500000000 7.118970000 7.000000000 H 7.500000000 7.887170000 7.000000000 end basis C library cc-pVTZ H library cc-pVTZ end

19. OUTPUT Running NWChem Grep ‘functions’ 1.out

20. OUTPUT Running NWChem Grep ‘iter’ 1.out

21. OUTPUT Running NWChem Grep ‘Total CCSD(T)’ 1.out Grep ‘Total times’ 1.out

22. OUTPUT Running NWChem

23. Method of execution (HOSTinfo.p) Running NWChem User Node execution place Scratch

24. Method of execution Running NWChem Only Single node!!! How many do you want??

25. Scratch Name.aoints.0 Name.aoints.0 Name.b Name.b Name.b^_1 Name.b^_1 Name.c Name.c Name.db Name.db Name.movecs Name.movecs Name.p Name.p Name.zmat Name.zmat Running NWChem

26. Comparative Table Running NWChem

27. Comparative Table Running NWChem

28. Comparative Table Running NWChem

29. Comparative Table Running NWChem

30. …………SCF …… …… END………… Self-Consistent Field (SCF)

31. RHF RHF - closed-shell restricted HF - closed-shell restricted HF UHF UHF - spin-unrestricted HF - spin-unrestricted HF ROHF ROHF - restricted high-spin open-shell HF - restricted high-spin open-shell HF Self-Consistent Field (SCF)

32. SCF Module UHF RHF ROHF UHFROHF RHF

33. UHF UHF : alpha MO + beta MO ROHF ROHF : closed + open shell

34. Wavefunction type SINGLETDOUBLETTRIPLETQUARTETSEXTETSEPTETOCTET NOPEN 0 NOPEN 1 NOPEN 2 NOPEN 3 NOPEN 4 NOPEN 5 NOPEN 6

35. SCF TRIPLET TRIPLET UHF UHF …… …… END Self-Consistent Field (SCF)

36. SYM – use of symmetry SCF …… …… SYM ON/OFF SYM ON/OFF …… ……END SYM ON SYM OFF

37. ADAPT – symmetry adaptaion of MOs SCF …… …… ADAPT ON/OFF ADAPT ON/OFF …… ……END ADPAT OFF ADAPT ON

38. SCF …… …… TOL2E 10e-4 TOL2E 10e-4 …… …… END TOL2E – integral screening threshold

39. SCF …… …… THRESH 10e-6 THRESH 10e-6 …… ……END THRESH – convergence threshold

40. SCF …… …… MAXITER 100 MAXITER 100 …… ……END MAXITER – iteration limit

41. MP2 There are (at least) three algorithms within NWChem that compute the Møller- Plesset (or many-body) perturbation theory second-order correction to the Hartree-Fock energy (MP2). Semi-direct -- this is recommended for most large applications. Partially transformed integrals are stored on disk, multi-passing as necessary. RHF and UHF references may be treated including computation of analytic derivatives. TASK MP2 Fully-direct -- this is of utility if only limited I/O resources are available. Only RHF references and energies are available. This is selected by specifying direct_mp2 on the task directive. TASK DIRECT_MP2 Resolution of the identity (RI) approximation MP2 (RI-MP2) -- this uses the RI approximation and is therefore only exact in the limit of a complete fitting basis. However, with some care, high accuracy may be obtained with relatively modest fitting basis sets. An RI-MP2 calculation can cost over 40 times less than the corresponding exact MP2 calculation. RHF and UHF references with only energies are available. TASK RIMP2

42. Freezing orbitals The atomic keyword causes orbitals to be frozen according to the rules in Table. Note that no orbitals are frozen on atoms on which the nuclear charge has been modified either by the user or due to the presence of an ECP. The actual input would be freeze atomic The user may also specify the number of orbitals to be frozen by atom. Following the example, the user could specify freeze atomic O 1 Si 3

43. Increased precision The TIGHT directive can be used to increase the precision in the MP2 energy and gradients. By default the MP2 gradient package should compute energies accurate to better than a micro-Hartree, and gradients accurate to about five decimal places (atomic units). For computing very accurate geometries or numerical frequencies, greater precision may be desirable. This option increases the precision to which both the SCF (from to ) and CPHF (from to ) are solved, and also tightens thresholds for computation of the AO and MO integrals (from to ) within the MP2 code.

44. CO 2 Total Energy Basis set Nwchem v5.0 Energy (eV) Nwchem v5.1 Energy (eV) V5.1 - v5.0 Energy (eV) cc-pVDZ-5117.725743491530-5117.725743664250-0.000000172720 cc-pVTZ-5123.413221066000-5123.413221068230-0.000000002230 cc-pVQZ-5126.756506122170-5126.756506123480-0.000000001306 aug-cc-pVDZ-5119.010146595770-5119.0101465801300.000000015641 aug-cc-pVTZ-5124.378382812610-5124.378382870980-0.000000058371 aug-cc-pVQZ-5127.171583447550-5127.171583495040-0.000000047490

45. CO 2 Caculation Time Basis set Nwchem v5.0 Time (s) Nwchem v5.1 Time (s) V5.1 - v5.0 Time (s) CPU Time Wall Time CPU Time Wall Time CPU Time Wall Time cc-pVDZ20.960.918.348.2-2.6-12.7 cc-pVTZ100.1175.9101.0178.50.92.6 cc-pVQZ965.21216.1970.31219.75.13.6 aug-cc-pVDZ55.9117.647.196.0-8.8-21.6 aug-cc-pVTZ458.8627.2459.6632.60.85.4 aug-cc-pVQZ4964.06873.54878.97469.8-85.1596.3

46. CO 2 Caculation Time