Running NWChemRunning NWChem

단국대학교단국대학교임석호임석호차장환차장환

Running NWChem

OUTLINEOUTLINE IntroductionIntroduction TaskTask Input fileInput file Basis SetBasis Set OutputOutput Method of execution Method of execution Scratch fileScratch file Comparable Table Comparable Table (between Gaussian and NWChem)(between Gaussian and NWChem)

Running NWChem

IntroductionIntroduction NWChem is a computational chemistry package tNWChem is a computational chemistry package t

hat is designed to run on high-performance parallhat is designed to run on high-performance parallel supercomputers as well as conventional worksel supercomputers as well as conventional workstation clusters. tation clusters.

NWChem is scalable, both in its ability to treat laNWChem is scalable, both in its ability to treat large problems efficiently, and in its utilization of arge problems efficiently, and in its utilization of available parallel computing resources.vailable parallel computing resources.

Running NWChem

IntroductionIntroduction

local disks: semidirect, with minimal usage of memorygpfs: semidirect, with minimal usage of memoryno disk: direct if integrals do not fit into memory; in-core otherwiseno disk + mem: tell NWchem to use up to 100MWlocal 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

IntroductionIntroduction

These pictures from High Performance Computing in COMPUTATIONAL CHEMISTRY (Sigismondo Boschi, CINECA)

Running NWChem

TaskTaskRunning NWChem

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 moleculesmd – Classical molecular dynamics simulation using nwARGOSsodft – 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

Task (Operation)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

Input fileInput file startstart

titletitle

geometrygeometry

basisbasis

tasktask

Running NWChem

Input (Print control)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

Input (Example)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

Input (Example)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 c2vend

basis H library cc-pVTZ bqH library H cc-pVTZ end

SCF UHF thresh 1.0e-8 maxiter 1285END

set geometry " symmetry "task scf

Running NWChem

Input (Example)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-3gendscf uhf; doublet print lowend

title “H2O+ : STO-3G UHF geometry opt”task scf optimizebasis H library 6-31g** O library 6-31g**end

Input (Example)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 -0.01EndGeometry “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 -0.01EndBasis H library sto-3g O library sto-3g bqH library H sto-3g bqO library O sto-3gEndSet geometry “H2O_dimmer”Task scfSet geometry “H2O+Ghost”Task scf

Input (Example)Input (Example)Running NWChem

start Ti-C2H6 echotitle "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 7.000000000endbasis C library cc-pVTZ H library cc-pVTZ Ti library "NASA Ames cc-pVTZ"endSCF UHF thre`h 1.0e-8 maxiter 1285ENDCCSD freeze core atomic thresh 1.0e-8 maxiter 1285End

set geometry "TiC2H6"task CCSD(T)

Input (Basis Set)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 )

Input (Basis Set)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 )

Input (Basis Set)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

Input (Basis Set)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 7.000000000end

basis C library cc-pVTZ H1 library cc-pVTZ H2 library cc-pVTZend

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 7.000000000end

basis C library cc-pVTZ H library cc-pVTZend

OUTPUTOUTPUTRunning NWChem

Grep ‘functions’ 1.out

OUTPUTOUTPUTRunning NWChem

Grep ‘iter’ 1.out

OUTPUTOUTPUTRunning NWChem

Grep ‘Total CCSD(T)’ 1.out

Grep ‘Total times’ 1.out

OUTPUTOUTPUTRunning NWChem

Method of executionMethod of execution(HOSTinfo.p)(HOSTinfo.p)

Running NWChem

User Node execution place Scratch

Method of executionMethod of executionRunning NWChem

Only Single node!!!How many do you want??

ScratchScratch Name.aoints.0Name.aoints.0 Name.bName.b Name.b^_1Name.b^_1 Name.cName.c Name.dbName.db Name.movecsName.movecs Name.pName.p Name.zmatName.zmat

Running NWChem

Comparative TableComparative TableMP2 Binding energy with BSSE corrected

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Mg- coronene

eV

6- 31G*6- 311G*6- 311+G**6- 311++G**6- 311+G(2d,2p)6- 311++G(2d,2p)- Gau6- 311++G(2d,2p)- NWC6- 311+G(2df,2p)cc- PVTZ- NWC

Running NWChem

Comparative TableComparative TableJob CPU Time

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Mg- coronene

Tim

e(s)

6- 31G*6- 311G*6- 311+G**6- 311++G**6- 311+G(2d,2p)6- 311++G(2d,2p)- Gau6- 311++G(2d,2p)- NWC6- 311+G(2df,2p)cc- PVTZ- NWC

Running NWChem

Comparative TableComparative TableRunning NWChem

MP2 Binding energy with BSSE corrected

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Ca- coronene

eV

6- 31G*6- 311G*6- 311+G**6- 311++G**6- 311+G(2d,2p)6- 311++G(2d,2p)- Gau6- 311++G(2d,2p)- NWC6- 311+G(2df,2p)

Comparative TableComparative TableRunning NWChem

Job CPU Time

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6- 31G*6- 311G*6- 311+G**6- 311++G**6- 311+G(2d,2p)6- 311++G(2d,2p)- Gau6- 311++G(2d,2p)- NWC6- 311+G(2df,2p)

……………………

SCFSCF …… …… …… …… …… ……ENDEND……………………

Self-Consistent Field (SCF)Self-Consistent Field (SCF)

RHFRHF - closed-shell restricted HF- closed-shell restricted HF UHFUHF - spin-unrestricted HF- spin-unrestricted HF ROHFROHF - restricted high-spin open-shell HF- restricted high-spin open-shell HF

Self-Consistent Field (SCF)Self-Consistent Field (SCF)

SCF ModuleSCF Module

UHFRHF ROHF

UHFUHFROHROHFF

RHFRHF

UHFUHF : alpha MO + beta MO

ROHFROHF : closed + open shell

Wavefunction typeWavefunction type

SINGLETSINGLETDOUBLETDOUBLETTRIPLETTRIPLETQUARTETQUARTETSEXTETSEXTETSEPTETSEPTETOCTETOCTET

NOPEN 0NOPEN 0NOPEN 1NOPEN 1NOPEN 2NOPEN 2NOPEN 3NOPEN 3NOPEN 4NOPEN 4NOPEN 5NOPEN 5NOPEN 6NOPEN 6

SCFSCF TRIPLETTRIPLET <Default : SINGLET><Default : SINGLET> UHFUHF <Default : RHF><Default : RHF> ………… …… ……ENDEND

Self-Consistent Field (SCF)Self-Consistent Field (SCF)

SYM SYM – use of symmetry– use of symmetry

SCFSCF …… …… SYM ON/OFF SYM ON/OFF <default : ON><default : ON> …… ……ENDEND

SYM SYM ONON

SYM SYM OFFOFF

ADAPT ADAPT – symmetry adaptaion of MOs– symmetry adaptaion of MOs

SCFSCF …… …… ADAPT ON/OFF ADAPT ON/OFF <default : ON><default : ON> …… ……ENDEND

ADPAT ADPAT OFFOFF

ADAPT ADAPT ONON

SCFSCF …… …… TOL2E 10e-4TOL2E 10e-4 …… …… <Default : 10e-7 or <Default : 10e-7 or

0.01*thresh>0.01*thresh>ENDEND

TOL2E TOL2E – integral screening – integral screening thresholdthreshold

SCFSCF …… …… THRESH 10e-6 THRESH 10e-6 <Default : 10e-<Default : 10e-

4>4> …………ENDEND

THRESH THRESH – convergence – convergence thresholdthreshold

SCFSCF …… …… MAXITER 100 MAXITER 100 <Default : 8><Default : 8> …………ENDEND

MAXITER MAXITER – iteration limit– iteration limit

MP2 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

Freezing orbitals 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

Increased precision 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.

COCO22 Total Energy Total EnergyBasis setBasis set Nwchem v5.0 Energy (eV)Nwchem v5.0 Energy (eV) Nwchem v5.1 Energy (eV)Nwchem v5.1 Energy (eV) V5.1 - v5.0 Energy (eV)V5.1 - v5.0 Energy (eV)

cc-pVDZcc-pVDZ -5117.725743491530 -5117.725743491530 -5117.725743664250 -5117.725743664250 -0.000000172720 -0.000000172720 cc-pVTZcc-pVTZ -5123.413221066000 -5123.413221066000 -5123.413221068230 -5123.413221068230 -0.000000002230 -0.000000002230 cc-pVQZcc-pVQZ -5126.756506122170 -5126.756506122170 -5126.756506123480 -5126.756506123480 -0.000000001306 -0.000000001306 aug-cc-pVDZaug-cc-pVDZ -5119.010146595770 -5119.010146595770 -5119.010146580130 -5119.010146580130 0.000000015641 0.000000015641 aug-cc-pVTZaug-cc-pVTZ -5124.378382812610 -5124.378382812610 -5124.378382870980 -5124.378382870980 -0.000000058371 -0.000000058371 aug-cc-pVQZaug-cc-pVQZ -5127.171583447550 -5127.171583447550 -5127.171583495040 -5127.171583495040 -0.000000047490 -0.000000047490

v5.1 - v 5.0 Energy

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cc- pVDZ cc- pVTZ cc- pVQZ aug- cc- pVDZ aug- cc- pVTZ aug- cc-pVQZ

Basis set

Ener

gy (1

0 -9

eV) .

COCO22 Caculation Time Caculation TimeBasis setBasis set

Nwchem v5.0 Time (s)Nwchem v5.0 Time (s) Nwchem v5.1 Time (s)Nwchem v5.1 Time (s) V5.1 - v5.0 Time (s)V5.1 - v5.0 Time (s)CPU TimeCPU Time Wall TimeWall Time CPU TimeCPU Time Wall TimeWall Time CPU TimeCPU Time Wall TimeWall Time

cc-pVDZcc-pVDZ 20.9 20.9 60.9 60.9 18.3 18.3 48.2 48.2 -2.6 -2.6 -12.7 -12.7

cc-pVTZcc-pVTZ 100.1 100.1 175.9 175.9 101.0 101.0 178.5 178.5 0.9 0.9 2.6 2.6

cc-pVQZcc-pVQZ 965.2 965.2 1216.1 1216.1 970.3 970.3 1219.7 1219.7 5.1 5.1 3.6 3.6 aug-cc-pVDZaug-cc-pVDZ 55.9 55.9 117.6 117.6 47.1 47.1 96.0 96.0 -8.8 -8.8 -21.6 -21.6 aug-cc-pVTZaug-cc-pVTZ 458.8 458.8 627.2 627.2 459.6 459.6 632.6 632.6 0.8 0.8 5.4 5.4 aug-cc-pVQZaug-cc-pVQZ 4964.0 4964.0 6873.5 6873.5 4878.9 4878.9 7469.8 7469.8 -85.1 -85.1 596.3 596.3

v5.1 - v5.0 Time

- 25- 20- 15- 10- 505

10

cc- pVDZ cc- pVTZ cc- pVQZ aug- cc- pVDZ aug- cc- pVTZ

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) .

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COCO22 Caculation Time Caculation TimeCPU Time

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nwchem v5.0nwchem v5.1

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nwchem v5.0nwchem v5.1