Calculations

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Electron Correlation methods
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@ECinit()

Initialize EC::ECInfo and add molecular system and/or fcidump if variables geometry::String and basis::Dict{String,Any} and/or fcidump::String are defined.

If EC is already initialized, it will be overwritten.

Examples

geometry="He 0.0 0.0 0.0"
basis = Dict("ao"=>"cc-pVDZ", "jkfit"=>"cc-pvtz-jkfit", "mpfit"=>"cc-pvdz-mpfit")
@ECinit
# output
Occupied orbitals:[1]

@bohf(opts_block=nothing)

Run bi-orthogonal HF calculation using FCIDUMP integrals.

The orbital rotations are stored to WfOptions.dump. For open-shell systems (or UHF FCIDUMPs), the BO-UHF energy is calculated.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

fcidump = "FCIDUMP"
@bohf
# with local options:
@bohf begin
  @set scf maxit=100
end

@bouhf(opts_block=nothing)

Run bi-orthogonal UHF calculation using FCIDUMP integrals.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

fcidump = "FCIDUMP"
@bouhf
# with local options:
@bouhf begin
  @set scf maxit=100
end

@cc(method, args...)

Run coupled cluster calculation.

The type of the method is determined by the first argument (ccsd/ccsd(t)/dcsd etc). The method can be specified as a string or as a variable, e.g., @cc CCSD or @cc "CCSD" or ccmethod="CCSD"; @cc ccmethod.

Optionally, a begin...end block can be provided as the last argument to set local options for this call. The options are reset after the call completes.

Keyword arguments

• fcidump::String: fcidump file (default: "", i.e., use integrals from EC).
• occa::String: occupied α orbitals (default: "-").
• occb::String: occupied β orbitals (default: "-").

The occupation strings can be given as a + separated list, e.g. occa = 1+2+3 or equivalently 1-3. Additionally, the spatial symmetry of the orbitals can be specified with the syntax orb.sym, e.g. occa = "-5.1+-2.2+-4.3".

Examples

geometry="bohr
O      0.000000000    0.000000000   -0.130186067
H1     0.000000000    1.489124508    1.033245507
H2     0.000000000   -1.489124508    1.033245507"
basis = Dict("ao"=>"cc-pVDZ", "jkfit"=>"cc-pvtz-jkfit", "mpfit"=>"cc-pvdz-mpfit")
@dfhf
@dfints
@cc ccsd
# with local options:
@cc ccsd begin
  @set wf charge=-1 ms2=1
  @set cc maxit=30
end

@check_molproinfo()

Check if MolproInterface.MolproInfo is initialized and return the files. If not initialized, throw an error.

@ciphi(args...)

Run CIPHI (CIΦ - CI via Perturbative and Heat-Bath Iterative selection) calculation.

Optionally, a begin...end block can be provided as the last argument to set local options for this call. The options are reset after the call completes.

Keyword arguments

• occa::String: occupied α orbitals (default: "-").
• occb::String: occupied β orbitals (default: "-").

The occupation strings can be given as a + separated list, e.g. occa = 1+2+3 or equivalently 1-3. Additionally, the spatial symmetry of the orbitals can be specified with the syntax orb.sym, e.g. occa = "-5.1+-2.2+-4.3".

@sci and @ciϕ are aliases for this macro.

Examples

geometry="bohr
O      0.000000000    0.000000000   -0.130186067
H1     0.000000000    1.489124508    1.033245507
H2     0.000000000   -1.489124508    1.033245507"
basis = Dict("ao"=>"6-31g", "jkfit"=>"vdz-jkfit", "mpfit"=>"vdz-mpfit")
@dfhf
@ciphi
# with local options:
@ciphi begin
  @set ciphi epsilon=1.e-4
end

@ciϕ(args...)

Alias for @ciphi.

@copyfile(from_file, to_file, kwargs...)

Copy file from_file to to_file in EC.scr directory.

Keyword arguments

• overwrite::Bool: overwrite existing file (default: false).

@copywf(to_file::AbstractString=""; start=false, state=0)

Copy wavefunction data from the current trexio dump file to another dump file.

If to_file is not provided, the wavefunction is copied to EC.options.wf.store file. Note: This does not check the contents of the files.

Keyword Arguments

• start::Bool=false: If true, copy from wf.start file instead of wf.dump.
• state::Int=0: State number for determinant files. If 0, copies the main dump file. If >0, copies the state-specific determinant file (e.g., file_state2.h5).

Examples

julia> @copywf  # copy dump to store
julia> @copywf "backup.h5"  # copy dump to backup file
julia> @copywf start=true  # copy start file to store
julia> @copywf "backup.h5" start=true  # copy start file to backup
julia> @copywf state=2  # copy state 2 determinant file to store
julia> @copywf "state2_backup.h5" state=2  # copy state 2 to specific file

@deletefile(filename)

Delete file filename from EC.scr directory.

@dfcc(method="svd-dcsd", opts_block=nothing)

Run coupled cluster calculation using density fitted integrals.

The type of the method is determined by the first argument. The method can be specified as a string or as a variable, e.g., @dfcc SVD-DCSD or @dfcc "SVD-DCSD" or ccmethod="SVD-DCSD"; @dfcc ccmethod.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

geometry="bohr
O      0.000000000    0.000000000   -0.130186067
H1     0.000000000    1.489124508    1.033245507
H2     0.000000000   -1.489124508    1.033245507"
basis = Dict("ao"=>"cc-pVDZ", "jkfit"=>"cc-pvtz-jkfit", "mpfit"=>"cc-pvdz-mpfit")
@dfhf
@dfcc svd-dcsd
# with local options:
@dfcc svd-dcsd begin
  @set cc maxit=30
end

@dfhf(opts_block=nothing)

Run DF-HF calculation. The orbitals are stored to WfOptions.dump.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

@dfhf
# with local options:
@dfhf begin
  @set scf maxit=100 thr=1.e-12
  @set wf charge=-1
end

@dfints()

Generate 2 and 4-idx MO integrals using density fitting. The MO coefficients are read from WfOptions.dump.

@dfmcscf(opts_block=nothing)

Run DF-MCSCF calculation. The orbitals are stored to WfOptions.dump.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

@dfmcscf
# with local options:
@dfmcscf begin
  @set scf maxit=100
  @set wf active="(4,4)"
end

@dfmp2(opts_block=nothing)

Run density-fitted MP2 calculation.

If save is set in CcOptions.save, the MP2 doubles amplitudes are saved to save*"_2" file.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

@dfmp2
# with local options:
@dfmp2 begin
  @set cc save="mp2_amplitudes"
end

@dfuhf(opts_block=nothing)

Run DF-UHF calculation. The orbitals are stored to WfOptions.dump.

Optionally, a begin...end block can be provided to set local options for this call. The options are reset after the call completes.

Examples

@dfuhf
# with local options:
@dfuhf begin
  @set scf maxit=100
end

@dummy(atoms)

Set atoms as dummy atoms in the system. atoms is a list of atom indices or atomic symbols.

After running the macro, only the atoms in the list are set as dummy atoms in the system.

Examples

@dummy [1,2,3]
@dummy ["H1","H2"]
@dummy [1,"H2",:H3]
@dummy [] # unset all dummy atoms

@export_molden(filename)

Export current orbitals to Molden file filename.

@fci(args...)

Run FCI calculation.

Optionally, a begin...end block can be provided as the last argument to set local options for this call. The options are reset after the call completes.

Keyword arguments

• occa::String: occupied α orbitals (default: "-").
• occb::String: occupied β orbitals (default: "-").

The occupation strings can be given as a + separated list, e.g. occa = 1+2+3 or equivalently 1-3. Additionally, the spatial symmetry of the orbitals can be specified with the syntax orb.sym, e.g. occa = "-5.1+-2.2+-4.3".

Examples

geometry="bohr
O      0.000000000    0.000000000   -0.130186067
H1     0.000000000    1.489124508    1.033245507
H2     0.000000000   -1.489124508    1.033245507"
basis = Dict("ao"=>"6-31g", "jkfit"=>"vdz-jkfit", "mpfit"=>"vdz-mpfit")
@dfhf
@fci
# with local options:
@fci begin
  @set wf charge=-1
end

@freeze_orbs(freeze_orbs)

Freeze orbitals in the integrals according to an array or range freeze_orbs.

Alternatively, the orbitals can be specified as a String with the +/- or :/; syntax, e.g., "1-5+7-8", or "1:5;7-8".

Examples

fcidump = "FCIDUMP"
@freeze_orbs 1:5
...
@ECinit
@freeze_orbs [1,2,20,21]

@import_matrix(filename)

Import matrix from file file.

The type of the matrix is determined automatically.

@loadfile(filename)

Read file filename from EC.scr directory.

Example

fock = @loadfile("f_mm")

@loadwf(what...; start=false, state=1)

Load wavefunction data from the trexio dump file.

The arguments what can be a vector of strings, a string variable or a list of arguments specifying what to load. Possible values are:

• all: load everything available (overrides other options)
• orbital_energies: molecular orbital energies
• orbital_occupations: molecular orbital occupations
• amplitudes: restricted CC amplitudes (T1, T2)
• unrestricted_amplitudes: unrestricted CC amplitudes (T1a, T1b, T2a, T2b, T2ab)
• determinants: selected CI determinants and coefficients

The loaded data are returned as a dictionary with keys corresponding to the requested data. basis, orbitals and orbital_type are always included in the output.

Keyword Arguments

• start::Bool=false: If true, read from wf.start file instead of wf.dump
• state::Int=1: State number for determinants (1 = ground state)
• OPattern::Type=UInt64: Orbital pattern type for determinants (use UInt128 for >64 orbitals)

Examples

julia> wf = @loadwf orbital_energies orbital_occupations
julia> wf["basis"]  # basis set information
julia> wf = @loadwf ["orbital_energies", "orbital_occupations"]
julia> wf = @loadwf amplitudes  # load CC amplitudes
julia> wf = @loadwf determinants state=2  # load determinants for excited state
julia> wf = @loadwf all start=true  # load everything from start file

@mainname(file)

Return the main name of a file, i.e. the part before the last dot and the extension.

Examples

julia> @mainname("~/test.xyz")
("test", "xyz")

@molpro_input(filename="elemcoil")

Initialize the Molpro interface with the given filename.

It relies on the Molpro XML file to set up the molecule and basis set. If the basis variable exists, it will be updated with the AO basis set from the XML file.

See MolproInterface for more details on the Molpro interface.

@molpro_output(ecvariables, kwargs...)

Save key-value pairs from ecvariables to a ECVARIABLES file in the MolproInterface.MolproInfo object.

The ecvariables is a dictionary with the variables to be included in the output. The keyword arguments are passed to the MolproInterface.save_ecvariables_to_file function. Possible keyword arguments include:

• prefix::String: prefix for each variable in the output file (default: "")
• new::Bool: if true, create a new file, otherwise append to the existing file (default: true)

@opt(opt, kwargs...)

Alias for @set.

@print_input(print_init=false)

Print the input file content.

Can be used to print the input file content to the output.

@reset(opt)

Reset options for opt to default values.

@rotate_orbs(orb1, orb2, angle, kwargs...)

Rotate orbitals orb1 and orb2 from WfOptions.dump by angle (in degrees). For UHF, spin can be :α or :β (keyword argument).

The orbitals are stored to WfOptions.store.

Keyword arguments

• spin::Symbol: spin of the orbitals (default: :α).

Examples

@dfhf
# swap orbitals 1 and 2
@rotate_orbs 1, 2, 90

general runner

@savefile(filename, arr, kwargs...)

Save array or tuple of arrays arr to file filename in EC.scr directory.

Keyword arguments

• description::String: description of the file (default: "tmp").
• overwrite::Bool: overwrite existing file (default: false).

@savewf(wf::AbstractDict; state=1)

Save wavefunction data to the trexio dump file.

The argument wf is a dictionary with the data to be saved. Possible keys are:

Orbital data:

• "basis": basis set information
• "orbitals": molecular orbitals
• "rotations": orbital rotations (alternative to "orbitals")
• "orbital_type": type of the orbitals (e.g., "RHF", "UHF", "ROHF", "MCSCF")
• "orbital_energies": molecular orbital energies
• "orbital_occupations": molecular orbital occupations

Restricted CC amplitudes:

• "T1": singles amplitudes (nvirt × nocc)
• "T2": doubles amplitudes (nvirt × nvirt × nocc × nocc)

Unrestricted CC amplitudes:

• "T1a", "T1b": α and β singles amplitudes
• "T2a", "T2b", "T2ab": αα, ββ, and αβ doubles amplitudes

Selected CI (CIPHI) data:

• "determinants": vector of determinants
• "ci_coefficients": CI coefficients (vector for single state, matrix for multi-state)

Keyword Arguments

• state::Int=1: State number for determinants (used when ci_coefficients is a vector)

Examples

julia> wf = @loadwf orbital_energies orbital_occupations
julia> orbs = wf["orbitals"]
[...]
julia> wf1 = Dict("basis"=>wf["basis"], "orbitals"=>orbs, "orbital_type"=>"modified RHF") 
julia> @savewf wf1

julia> # Save amplitudes
julia> @savewf Dict("T1"=>T1, "T2"=>T2)

julia> # Save determinants for excited state
julia> @savewf Dict("determinants"=>dets, "ci_coefficients"=>coeffs) state=2

@sci(args...)

Alias for @ciphi.

@set(opt, kwargs...)

Set options for EC::ECInfo.

The first argument opt is the name of the option (e.g., scf, cc, cholesky), see ECInfos.Options. The keyword arguments are the options to be set (e.g., thr=1.e-14, maxit=10). The current state of the options can be stored in a variable, e.g., opt_cc = @set cc. The state can then be restored by @set cc opt_cc. If EC is not already initialized, it will be done.

Examples

optscf = @set scf thr=1.e-14 maxit=10
@set cc maxit=100
...
@set scf optscf

@setupEC()

Setup EC::ECInfo with geometry, basis, and fcidump if defined.

@show_orbs(range=nothing)

Show orbitals in the integrals according to an array or range range.

Examples

@dfhf
@show_orbs 1:5

@transform_ints()

Rotate FCIDump integrals using rotations from WfOptions.dump as transformation matrices.

The orbital rotations are read from WfOptions.dump. If type of the rotations contains the word biorthogonal, the bi-orthogonal orbitals are used.

@tryECinit()

If EC::ECInfo is not yet initialized, run @ECinit macro.

@write_ints(file="FCIDUMP", kwargs...)

Write FCIDump integrals to file file.

Keyword arguments

• tol::Float64: tolerance for writing integrals (default: -1.0 - all integrals are written).
• format::Symbol: format for writing integrals (default: :ascii). Can be :npy for NumPy format.

__init__()

Print the header with the version and the git hash of the current commit.