CIML: COLUMBUS Input Mark-up Language · 14 Integral (ARGOS) Input • requires one of the following. • • Uses a keyword for a database look up

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CIML: COLUMBUS Input Mark-up Language

Gary KedzioraANL

August 15, 2005

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Why New Input

• The IARGOS was difficult to use.• Mistakes were hard to overcome.• Had to start over for small modifications.

• Colinp menus.• Machine dependant glitches.• Did not save intermediate data and allow specific

modifications. • Legacy input was too difficult for a novice.

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CIML Program Design Goals

• Based on XML.• Standard format for parsing, sharing, and saving.• Provides a logical decomposition (hierarchical) of the input

data.• Compatible with web technology.

• Provide comfortable text user interface.• Easy to remember tag names.• Not everything is in tags.• Uses defacto standard chemistry formats inside tags.

• Eliminate redundant user input.• Provide feedback to the user.• Make it easy to fix mistakes or modify input.

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What Is XML?

• Extensible mark-up language.• Gives structure to data.• Is self describing.• Standard tools are available for processing

XML data.<molecule><atom><symbol> O </symbol><coordinate> <Bohrs/><x> 0.0 </x> <y> 0.0 </y> <z> 0.0 </z>

</coordinate></atom>. . .

</molecule>

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XML Basics

• Elements contain other elements or PCDATA.• Every start tag must have a matching end tag, or

be a self-closing tag.• Tags can’t overlap; elements must be properly

nested.• XML documents can have only one root element.• Element names obey XML conventions.• Case sensitive.• Preserves the white space in PCDATA (text data

in elements).• Comment delimiters: .

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Chemistry Markup Language: CML

<molecule id="allopurinol_CSD_CIF_ALOPUR"> <atomArray> <atom count="0.0" elementType="C" formalCharge="0" hydrogenCount="0" id="C1" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="0.0" x3="1.0359994" xFract="0.2837" y2="0.0" y3="-4.546476" yFract="-0.3096" z3="1.1487509" zFract="0.1245"></atom> <atom count="0.0" elementType="C" formalCharge="0" hydrogenCount="0" id="C2" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-1.299038" x3="1.1868163" xFract="0.325" y2="2.25" y3="-6.708108" yFract="-0.4568" z3="1.5726498" zFract="0.1675"></atom> <atom count="0.0" elementType="C" formalCharge="0" hydrogenCount="0" id="C3" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-2.598076" x3="1.9602555" xFract="0.5368" y2="1.5" y3="-6.5597897" yFract="-0.4467" z3="2.7217782" zFract="0.2887"></atom> <atom count="0.0" elementType="C" formalCharge="0" hydrogenCount="0" id="C4" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-2.598076" x3="2.313379" xFract="0.6335" y2="-2.220446E-16" y3="-5.2352023" yFract="-0.3565" z3="3.1315322" zFract="0.3329"></atom> <atom count="0.0" elementType="C" formalCharge="0" hydrogenCount="0" id="C5" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-3.7127934" x3="2.2023659" xFract="0.6031" y2="2.503696" y3="-7.877034" yFract="-0.5364" z3="3.1760104" zFract="0.3358"></atom> <atom count="0.0" elementType="H" formalCharge="0" hydrogenCount="0" id="H1" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-1.299038" x3="2.0084584" xFract="0.55" y2="-2.25" y3="-3.480345" yFract="-0.237" z3="2.3471053" zFract="0.253"></atom> <atom count="0.0" elementType="H" formalCharge="0" hydrogenCount="0" id="H2" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="1.299038" x3="0.6536619" xFract="0.179" y2="-0.75" y3="-3.75936" yFract="-0.256" z3="0.58496195" zFract="0.065"></atom> <atom count="0.0" elementType="H" formalCharge="0" hydrogenCount="0" id="H3" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-5.180015" x3="2.7607174" xFract="0.756" y2="2.1918285" y3="-8.208915" yFract="-0.559" z3="3.992211" zFract="0.422"></atom> <atom count="0.0" elementType="H" formalCharge="0" hydrogenCount="0" id="H4" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-0.60720974" x3="0.4199504" xFract="0.115" y2="4.8319387" y3="-8.502615" yFract="-0.579" z3="0.73942214" zFract="0.077"></atom> <atom count="0.0" elementType="N" formalCharge="0" hydrogenCount="0" id="N1" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-1.299038" x3="1.7878932" xFract="0.4896" y2="-0.75" y3="-4.279209" yFract="-0.2914" z3="2.2542732" zFract="0.2412"></atom> <atom count="0.0" elementType="N" formalCharge="0" hydrogenCount="0" id="N2" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="0.0" x3="0.68798834" xFract="0.1884" y2="1.5" y3="-5.72715" yFract="-0.39" z3="0.75586706" zFract="0.082"></atom> <atom count="0.0" elementType="N" formalCharge="0" hydrogenCount="0" id="N3" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-3.1026886" x3="1.6268513" xFract="0.4455" y2="3.8740141" y3="-8.758134" yFract="-0.5964" z3="2.3713465" zFract="0.2505"></atom> <atom count="0.0" elementType="N" formalCharge="0" hydrogenCount="0" id="N4" isotope="0.0" isotopeNumber="0" occupancy="0.0" spinMultiplicity="0" x2="-1.6109056" x3="1.0060551" xFract="0.2755" y2="3.7172215" y3="-8.032695" yFract="-0.547" z3="1.3827686" zFract="0.1468"></atom>

<atom count="0.0" elementType="O" formalCharge="0" hydrogenCount="0" id="O1" isotooccupancy="0.0" spinMultiplicity="0" x2="-3.8971143" x3="2.9918728" xFract="0.8193" 0.3335" z3="4.097068" zFract="0.4351"></atom> </atomArray> <bondArray> <bond atomRefs2="C1 H2" id="C1_H2" order="S"></bond> <bond atomRefs2="C1 N1" id="C1_N1" order="S"></bond> <bond atomRefs2="C1 N2" id="C1_N2" order="D"> <bondStereo atomRefs4="N1 C1 N2 C2">C </bondStereo></bond> <bond atomRefs2="C2 C3" id="C2_C3" order="D"> <bondStereo atomRefs4="N2 C2 C3 C4">C </bondStereo></bond> <bond atomRefs2="C2 N2" id="C2_N2" order="S"></bond> <bond atomRefs2="C2 N4" id="C2_N4" order="S"></bond> <bond atomRefs2="C3 C4" id="C3_C4" order="S"></bond> <bond atomRefs2="C3 C5" id="C3_C5" order="S"></bond> <bond atomRefs2="C4 N1" id="C4_N1" order="S"></bond> <bond atomRefs2="C4 O1" id="C4_O1" order="D"></bond> <bond atomRefs2="C5 H3" id="C5_H3" order="S"></bond> <bond atomRefs2="C5 N3" id="C5_N3" order="D"> <bondStereo atomRefs4="C3 C5 N3 N4">C </bondStereo></bond> <bond atomRefs2="H1 N1" id="H1_N1" order="S"></bond> <bond atomRefs2="H4 N4" id="H4_N4" order="S"></bond> <bond atomRefs2="N3 N4" id="N3_N4" order="S"></bond> </bondArray> </molecule>

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CIML Tag Conventions

• Tag names are lower case.• No attributes are used:

<tag_name att=“not_used”>.

• Full words or common abbreviations are ususallyused. Abbreviations are harder to remember.

• Words are combined with an underscore, e.g. <initial_orbitals>.

• We try to maintain a balance of concision and descriptiveness.

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Correspondences Between Tags And Programs/Legacy Input

CIML Tags COLUMBUS Programs Legacy Input files

ARGOS

SCFPQ

MCSCF, MCDRT, MCUFT

CIDRT, TRAN, CISRT, CIUDG

CIDRT, TRAN, CISRT, CIUDG

<molecule> <basis>,<ecp>,<so_potential>

argosin

<scf> scfin

<mcscf>mcdrtin, mcuftin, mcscfin

<ci>cidrtin, tranin, cisrtin, ciudgin

<soci>cidrtin, tranin, cisrtin, ciudgin

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ciml.x Program Architecture

Expat XML Parsing Library written in C

CIML User Input

Transfer to Fortran

SCFMolecular Integrals MCSCF CI and

Correlation Properties

CIML Outputargosin scfinmcdrtin,mcdrtflmcscfin

cidrtin,cidrtfl, etc.

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Work Bench/Atelier Concept

Run CIML,other codes

Examine output

Prepare/ adjust input

• User interacts with CIML, refining calculation based on output.

• MR-CI is usually not a model chemistry; it requires too much user interaction because of scaling.

• Good for exploration.• Refinements with legacy

input or colinp.

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3P C and 2Π CH Examples

C atom H atomCH

1s2p

1s

2s

π

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Integral (ARGOS) Input

• <molecule> contains information about atoms, coordinates and symmetry.

• <basis> contains the basis set specification.• <ecp> contains the effective core potential

(ECP) information.• <so_potential> contains the spin-orbit

potiental (SOP).• <molecule> and <basis> are required.

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3P Carbon Example

<molecule>

<point_group> c2v </point_group>

<geometry>

C 0.0 0.0 0.0

</geometry>

<charge> 0 </charge>

</molecule>

Default is c1. You can leave out</point_group> if you wantc1 (C1) symmetry specified.

Required! XYZ format (don’t need to specify number of atoms)

Default is charge is 0. This can beLeft out.

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• <basis> requires one of the following.• <standard>

• Uses a keyword for a database look up.• The database is currently only minimally implemented.• Available basis sets can be listed with <standard>list</standard>.

• <general>• Uses NWChem format.• Cut and paste from “EMSL Gaussian Basis Set Order Form.”• For now this is the recommended method of basis set

specification.

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3P Carbon Example<basis><general><!–-http://www.chemistry.ohio-state.edu/~pitzer/docs/arep_pvdz/c-->

C s25.0400000 -0.0107539 0.0000000 0.00000003.3580000 -0.1374153 0.0000000 0.00000000.4836000 0.5764853 0.0000000 1.00000000.1519000 0.5356447 1.0000000 0.0000000

C p9.4300000 0.0381521 0.00000002.0010000 0.2094554 0.00000000.5451000 0.5089666 0.00000000.1516000 0.4683787 1.0000000

C d0.5578000 1.0000000

</general></basis>

Hydrogen atom angular momentum term symbol

Atom labels—can have numbers

General Basis Set

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Integral (ARGOS) Input3P Carbon Example



<ecp><general>C 1 2

3 / p1 51.6159000 -1.43484602 18.0668000 -4.07455002 5.3528000 -0.55931304 / s-p0 12.2112000 3.03797001 6.2707000 -4.67536402 4.1732000 71.58925802 3.8191000 -47.0982150

</general></ecp>

Atom label, angular momentum of first type of shell not included in the core, and charge of core.

Number of functions in potential expansion and optional label.

General Effective Core Potential

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Integral (ARGOS) Input3P Carbon Example

General Spin-Orbit Potential

<so_potential><general>C 13 / p2 5.352800 .0042482 18.066800 -.0056001 51.615900 .028402

</general></so_potential>

Atom label and highest angular momentum for shells with spin-orbit potentials

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SCF Input

• <initial_orbitals> The SCF orbital guess is required. Currently no automatic guess.

• The child tags are• <atomic_orbitals> Uses specific atomic orbitals

read off of the ARGOS output file argosls.• <core_hamiltonian> Less work; more automatic.

Does not require specific orbitals, just numbers of orbtials.

• <molecular_orbitals> Uses specific MOs from previous SCF run. Not implemented yet.

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SCF Initial Orbitals

<scf>

<initial_orbitals>

<core_hamiltonian>

</core_hamiltonian>

</initial_orbitals>

</scf>

<scf>

<initial_orbitals>

<noninteracting_electrons>

<noninteracting_electrons>

</initial_orbitals>

</scf>

=

• The core Hamiltonian is the non-interacting electron Hamiltonian. It has no electron-electron repulsion.

• Using this option the initial orbitals are the lowest energy eigenfunctions.

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<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep></occupied_orbitals_per_irrep></core_hamiltonian>

</initial_orbitals></scf>

2Π CH Example

Now we must determine how many occupied orbitals there are in each irrep for the 2Π state of CH. There are two ways:

1) Run your favorite SCF program that uses automatic guesses and post-convergence symmetry analysis.

2) Analyze the AOs your self with the help of ARGOS output.

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ZX

Y

E C2RC2

σv

Rσv

σv'

Rσv' R Bases

A1 1 1 1 1 1

1

1

1

-2

z

A2 1 1 -1 -1 Rz

B1 1 -1 1 -1 x, Ry

B2 1 -1 -1 1 y, Rx

E1/2 2 0 0 0 (α,β)

C H

2px 2py 2pz

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3P C and 2Π CH Example

C atom H atomCH

A1 2pz

B2 2py

B1 πx

B2 πy

B1 2px

A1

1s2p

1s

2s

π

A1

A1

ZX

Y

C H

2pz2px 2py

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Group And Irrep Names

Adopted CIML character representation of group and irrep names

Group Irreducible Representation (Irrep) Namesd2h ag b1g b2g b3g au b1u b2u b3uc2v a1 a2 b1 b2c2h ag bg au bud2 a b1 b2 b3cs a’ a”c2 a bci ag auc1 a

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<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1> <b1>1</b1> <b2>1</b2></occupied_orbitals_per_irrep></core_hamiltonian>


2Π CH Example

By default the occupied orbitals are doubly occupied. We can override the occupation number with the <open_shell> tag.

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<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1> <b1>1</b1> <b2>1</b2></occupied_orbitals_per_irrep><open_shell>(1b1 1b2)^1</open_shell></core_hamiltonian>


2Π CH Example

An open shell is defined by a list of orbitals and a shell occupation separated by a ^ (the superscript operator)

Next we need to specify the open-shell coupling coefficients.

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2Π CH Example<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1> <b1>1</b1> <b2>1</b2></occupied_orbitals_per_irrep><open_shell>(1b1 1b2)^1</open_shell></core_hamiltonian>

</initial_orbitals><open_shell_coefficients>(1,1)

</open_shell_coefficients></scf>

α and β open-shell coefficients are entered for each open shell (intra-shell) and pairs of open shells (inter-shell). Here we have one open shell.

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3P C v 2Π CHersus

<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1><b1>1</b1><b2>1</b2></occupied_orbitals_per_irrep><open_shell>(1b1 1b2)^1</open_shell>

</core_hamiltonian></initial_orbitals><open_shell_coefficients>

(1,1)</open_shell_coefficients></scf>

<scf><initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1><b1>1</b1><b2>1</b2></occupied_orbitals_per_irrep><open_shell>

(2a1 1b1 1b2)^2</open_shell>

</core_hamiltonian></initial_orbitals><open_shell_coefficients>

(1/4,-1/2)</open_shell_coefficients></scf>

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Core Hamiltonian guess

Atomic orbital guess

<initial_orbitals><core_hamiltonian><occupied_orbitals_per_irrep><a1>2</a1><b1>1</b1><b2>1</b2></occupied_orbitals_per_irrep><open_shell>(1b1 1b2)^1</open_shell>

</core_hamiltonian></initial_orbitals>

<initial_orbitals><atomic_orbitals>

<doubly_occupied>1a1 4a1

</doubly_occupied><open_shell>(1b1 1b2)^1</open_shell>

</atomic_orbitals></initial_orbitals>

The indices for these AOs must be found in the argos output, argosls.

The indices for these are assumed to be the highest in each irrep.

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MCSCF

• Basic template:

<mcscf><doubly_occupied> [orbital list] </doubly_occupied><active_subspace><group_occupations> <!– orbital groups with group occupations -->

</group_occupations></active_subspace></mcscf>

• We also have <occmin>/<occmax> and <bmin>/<bmax> for <mcscf>

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Methane Wavefunctions

( )84321 1H,1H,1H,1H,2C,2C,2C,2C ssssppps zyx

8 electron 8 orbital full valence complete active space (CAS):

RCI-GVB Wavefuncion:

C H

C H

σCH∗σCH∗∗ == iiiii σσσσ CHandCH

( ) ( ) ( ) ( )2442

332

222

11∗∗∗∗ ⊗⊗⊗ σσσσσσσσ

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MCSCF

Methane Example

<mcscf><initial_orbitals> mocoef </initial_orbitals><doubly_occupied> 1a </doubly_occupied><active_subspace><group_occupations> (2a 3a 4a 5a 6a 7a 8a 9a)^8 </group_occupations></active_subspace><orbital_resolution> natural orbital </orbital_resolution></mcscf>

8 electron 8 orbital CASMOs from previous SCF

Useful for RCI-GVB starting guess.

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MCSCF/MR-CI

Methane Example

<mcscf><initial_orbitals> restart </initial_orbitals><doubly_occupied> 1a </doubly_occupied><active_subspace><group_occupations>(2a 6a)^2 (3a 7a)^2 (4a 8a)^2 (5a 9a)^2

</group_occupations></active_subspace><orbital_resolution> natural orbital </orbital_resolution></mcscf>

Use orbitals from previous MCSCF restart file

RCI-GVB wave function.

<ci/> This generates all the input necessary for an MR-CISD.

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MCSCF/MR-CI

Methane Example

Wavefunction Number of CSFs Energy

SCF 1 -40.198709

RCI-GVB 150 -40.269265

8x8 CAS 1764 -40.279787

RCI-GVB/CISD 1142998 -40.381352

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Spin-Orbit CI

ii

N

iiSO

elec

rH SL •= ∑=

)(1ξ

LSversus

CH π shellC p shell3P2

SO2Π3/2SO

3P1 2Π1/2π1 π-12p1 2p0 2p-1 3P0

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Spin-Orbit CI

• <soci> is the name of the spin-orbit CI tag• <highest_multiplicity>

• Highest multiplicity of interacting spin states in CI expansion• Required currently

• <reference_space> is required for SCF only reference space.• <doubly_occupied> list of doubly occupied orbitals in reference

space• <group_occupations>

• List of orbitals and group occupations• Similar to the open-shell tag for SCF.

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Spin-Orbit CI

Required Tags

<soci><highest_multiplicity>5</highest_multiplicity><reference_space><group_occupations> (2a1 1b1 1b2)^2 </group_occupations><doubly_occupied> 1a1 </doubly_occupied>

</reference_space></soci>

<reference_space> defaults to <mcscf> <active_space>, but currently no default for open-shell SCF wavefunctions.

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Spin-Orbit CI

3P C Example

<soci><highest_multiplicity>5</highest_multiplicity><state_symmetry> a1 </state_symmetry><reference_space><group_occupations> (2a1 1b1 1b2)^2 </group_occupations><doubly_occupied> 1a1 </doubly_occupied>

</reference_space><number_roots> 6 </number_roots><convergence_tolerance> 1e-5 </convergence_tolerance><maximum_excitation> 0 </maximum_excitation></soci>

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Spin-Orbit CI

3P C Example

Irrep Total Energy

a1 -5.3173236a2 -5.3172464b1 -5.3172464b2 -5.3172464a1 -5.3170930a1 -5.3170930a2 -5.3170930b1 -5.3170930b2 -5.3170930a1 -5.2584888a1 -5.2584888a2 -5.2584888b1 -5.2584888b2 -5.2584888a1 -5.1704677

Irrep Total Energy

a1 -5.3173236 a1 -5.3170930 a1 -5.3170930 a1 -5.2584888 a1 -5.2584888 a1 -5.1704677 a2 -5.3172464 a2 -5.3170930 a2 -5.2584888 b1 -5.3172464 b1 -5.3170930 b1 -5.2584888 b2 -5.3172464 b2 -5.3170930 b2 -5.2584888

3P0

3P1sort

3P2

1D2

1S0

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Spin-Orbit CI

3P C Example

Level (cm-1) Configuration Term J Experiment Ref

Space CISD

2s2 2p2 3P 0 0.00 0.0 0.0 1 16.40 16.9 15.8 2 43.40 50.6 47.2

2s2 2p2 1D 2 10 192.63 12 914 12120

2s2 2p2 1S 0 21 648.01 32 234 23324

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Spin-Orbit CI

S even M Spin function Irrep Spin function Irrep 0 0S Ag 0S Rz

−SM Rx −SM Ry 1,3,5,… +SM Ry +SM Rx −SM Rz −SM Ag 2,4,6… +SM Ag +SM Rz

Real spherical spatial symmetry adapted spin functions.

( )[ ]

( )( )[ ]MSMSiSM

MMSMSiSM

M

M

S

MS

,1,12

0,,1,2

0

1

−+−+

=+

>−−−=−+

δ

From Yabushita, Zhang, and Pitzer, J. Phys. Chem. A 103, 5791 (1999)

41

Spin-Orbit CI

3P C Exampleinternal orbitals

level 1 2 3 4orbital 1 2 9 12symmetry a1 a1 b1 b2

p 2S+1 M+- csf# c(i) ext. orb.(sym)z* 3 1+ 2 0.577350 +- + +z* 3 1- 3 -0.577350 +- + +z* 3 0+ 5 0.577350 +- + +

total energy( 1) = -5.3173235518

internal orbitals

level 1 2 3 4orbital 1 2 9 12symmetry a1 a1 b1 b2

p 2S+1 M+- csf# c(i) ext. orb.(sym)z* 3 1+ 2 0.804781 +- + +z* 3 1- 3 0.283040 +- + +z* 3 0+ 5 -0.521740 +- + +

total energy( 2) = -5.3170929980

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CIML Features

• Input is a singe file that provides documentation for the calculation.

• Can be archived.• Easy to understand.• Easy to modify. • Provides user feed-back.• Compatible with runc and colinp.

43

Future Directions

• Add automatic symmetry detection.• Add automatic SCF orbital guess.• Incorporate more COLUMBUS features.

• State averaged MCSCF MRCI.• Geometry optimization.• Non-adiabatic coupling.

• Add graphical support.• Refine data logic.• Fix bugs.• Wavefunction symmetry analysis.

44

Acknowledgements

• Jean Blaudeau• Eric Stahlberg• Scott Brozell• Authors of iargos.• Ron Shepard (mcdrt.x and cidrt.x)

45

GUI With XUL

• XUL is XML User Interface Library.• It work with the Mozilla Development Platform.• The Firefox browser and Thunderbird email

programs’ GUIs are written with XUL

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Hello XUL

<?xml version="1.0"?>

<windowxmlns="http://www.mozilla.org/keymaster/gatekeeper/there.is.only.xul">

<box><description style="color: red; font-size:36pt;">Hello, world!</description></box>

</window>

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XUL Tab Box

<tabbox><tabs>

<tab label="Geometry"/><tab label="Basis Set"/>

</tabs><tabpanels>

<tabpanel><description>Enter Geometry Information</description>

</tabpanel><tabpanel><description>Enter Basis Set Information</description>

</tabpanel></tabpanels>

</tabbox>

Documents

CIML: COLUMBUS Input Mark-up Language · 14 Integral (ARGOS) Input • requires one of the following. • • Uses a keyword for a database look up