Merge changes from development repository

.gitignore

@@ -8,3 +8,4 @@ docs/equations/*.log
 docs/equations/*.out
 docs/equations/*.toc
 docs/src/release-notes.md
+LocalPreferences.toml

CHANGELOG.md

@@ -1,5 +1,32 @@
 # Release notes
 
+## Version [v0.13.0] - 2024.07.09
+
+### Breaking
+
+* `DIIS.perform` has been changed to `DIIS.perform!` in order to allow to read the vectors and residuals as `Vector{}`.
+* The signature of `newmmap` function has changed (the type specification is now the last argument and defaults to `Float64`.
+* The `FciDump` module has been renamed to `FciDumps`.
+* The `FDump` type has been changed to `FDump{N}` with N=3 (for triangular storage of 2-electron integrals) or 4. The logical variable `triang` has been removed (there is a function `is_triang(::FDump)` now). Aliases `TFDump = FDump{3}` and `QFDump = FDump{4}` have been introduced. 
+* The `ECInfo` type now accepts only `FDump{3}`. The `FDump{4}` objects have to be transformed first (the transformation functions are not implemented yet).
+* The triangular functions have been moved to a separate file `utensors.jl`, part of the `QMTensors` module. `uppertriangular` function has been renamed to `uppertriangular_index`.
+* The driver functions and macros now return energies in an ordered descriptive dictionary `OutDict=ODDict{String,Float64}`. Use `last_energy` function to access the last energy (or `last` to access the whole entry including the key and the description).
+
+### Changed
+
+* Save the memory using in Hessian matrix calculation in dfmcscf function.
+* `dfdump` stores the MO integrals internally in mmaped files.
+* The header of the `FDump` is now stored in a type-stable structure `FDumpHeader`.
+
+### Added
+
+* Export of molden files (`@export_molden`). At the moment the orbital energies and occupations are not exported.
+* Add dfmcscf part in documentation
+* CCSDT and DC-CCSDT closed-shell implementations generated with Quantwo.
+* `QMTensors.SpinMatrix` struct for one-electron matrices (e.g., MO coefficients)
+* An ordered descriptive dictionary for energy outputs (`ODDict`) has been implemented. Each key-value entry can have a description.
+* `DIIS.perform!` now accepts a tuple of functions to calculate cusomized dot-products (e.g., involving contravariants etc).
+
 ## Version [v0.12.0] - 2024.05.28
 
 ### Breaking

Project.toml

@@ -1,7 +1,7 @@
 name = "ElemCo"
 uuid = "094d408e-8508-40f4-9646-a254980d91ac"
 authors = ["Daniel Kats <d.kats@fkf.mpg.de> and contributors"]
-version = "0.12.0"
+version = "0.12.0+"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -13,6 +13,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TensorOperations = "6aa20fa7-93e2-5fca-9bc0-fbd0db3c71a2"
@@ -26,14 +27,15 @@ AtomsBase = "0.3.5 - 0.3"
 DocStringExtensions = "0.9"
 ITensors = "0.4.0 - 0.7"
 IterativeSolvers = "0.9"
-MKL = "0.6"
+MKL = "0.6 - 0.7"
 NPZ = "0.4"
-TensorOperations = "3.2.5 - 4"
+PrecompileTools = "1"
 StaticArrays = "1.4"
+TensorOperations = "3.2.5 - 4"
 Unitful = "1"
 UnitfulAtomic = "1"
-libcint_jll = "5.1"
 julia = "1.8.5"
+libcint_jll = "5.1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

docs/equations/references.bib

@@ -185,3 +185,48 @@ @article{aroeiraFermi2022
   issn = {1549-9618},
   doi = {10.1021/acs.jctc.1c00719},
 }
+
+@article{kreplinMCSCF2020,
+  author = {Kreplin, David A. and Knowles, Peter J. and Werner, Hans-Joachim},
+  title = "{MCSCF optimization revisited. II. Combined first- and second-order orbital optimization for large molecules}",
+  journal = jcp,
+  volume = {152},
+  number = {7},
+  pages = {074102},
+  year = {2020},
+  month = {02},
+  doi = {10.1063/1.5142241},
+  urldate = {2020-02-21},    
+  issn = {0021-9606},
+  doi = {10.1063/1.5142241},
+}
+
+
+  @article{SCI1989,
+  author = {Meier, U. and Staemmler, V.},
+	date = {1989/03/01},
+	date-added = {2024-04-26 10:53:27 +0200},
+	date-modified = {2024-04-26 10:53:27 +0200},
+	doi = {10.1007/BF00532127},
+	id = {Meier1989},
+	isbn = {1432-2234},
+	journal = tcac,
+	number = {2},
+	pages = {95--111},
+	title = {An efficient first-order CASSCF method based on the renormalized Fock-operator technique},
+	volume = {76},
+	year = {1989},
+  }
+
+  @article{augmentedHessian1981,
+  title = {Comment on the use of the augmented matrix in MCSCF theory},
+  journal = cpl,
+  volume = {77},
+  number = {3},
+  pages = {634-635},
+  year = {1981},
+  issn = {0009-2614},
+  doi = {https://doi.org/10.1016/0009-2614(81)85223-2},
+  author = {David R. Yarkony},
+  abstract = {The augmented matrix (AM) approach to the solution of the system of linear equations occurring in second-order MCSCF theory is discussed. It is shown that the AM approach provides a damped solution to this system of equations which eliminates the appropriate number of negative eigenvalues of the hessian and that the intermediate normalization is appropriate for the eigenvector of the AM.}
+  }

docs/make.jl

@@ -53,10 +53,13 @@ makedocs(
       "mnpy.md",
       "msystem.md",
       "orbtools.md",
+      "qmtensors.md",
       "tensortools.md",
+      "descdict.md",
       "utils.md",
       "interfaces.md",
-      "molpro.md"
+      "molpro.md",
+      "molden.md"
     ],
     "release-notes.md", 
   ],

docs/src/descdict.md

@@ -0,0 +1,21 @@
+# Ordered descriptive dictionary
+
+```@docs
+ElemCo.DescDict
+```
+
+## Exported types and functions
+
+```@autodocs
+Modules = [ElemCo.DescDict]
+Private = false
+Order = [:type, :macro, :function]
+```
+
+## Internal functions
+
+```@autodocs
+Modules = [ElemCo.DescDict]
+Public = false
+Order = [:type, :macro, :function]
+```

docs/src/dump.md

@@ -1,31 +1,38 @@
 # FCIDump files
 
 ```@meta
-CurrentModule = ElemCo.FciDump
+CurrentModule = ElemCo.FciDumps
 ```
 
 ```@docs
-FciDump
+FciDumps
 ```
 
 The FCIDump file format is a simple text file format for storing molecular integrals. It is used by many quantum chemistry programs. 
 
 ## Storage of molecular integrals
+
 ```@docs
 FDump
 ```
 
+
 ## Exported functions
 
 ```@autodocs
-Modules = [FciDump]
+Modules = [FciDumps]
 Private = false
 Order = [:function]
 ```
 
 ## Internal functions
+
+```@docs
+FDumpHeader
+```
+
 ```@autodocs
-Modules = [FciDump]
+Modules = [FciDumps]
 Public = false
 Order = [:function]
 ```

docs/src/elemco.md

@@ -18,27 +18,42 @@ Various macros are defined and exported to simplify running calculations. The ma
 | `EC::ECInfo` | A global information object containing options, molecular system description, integrals and orbital spaces information, see [`ElemCo.ECInfo`](@ref). |
 | `geometry::String` | Molecular coordinates, either in the `xyz` format or the file containing the xyz coordinates, see [`ElemCo.MSystem`](@ref). |
 | `basis::Dict` | Basis set information, see [`ElemCo.MSystem`](@ref) |
-| `fcidump::String` | File containing the integrals in the FCIDUMP format, see [`ElemCo.FciDump`](@ref). |
+| `fcidump::String` | File containing the integrals in the FCIDUMP format, see [`ElemCo.FciDumps`](@ref). |
 
-The driver routines and macros return energies as `NamedTuple`. The last energy is always the total energy (can be accessed using `last(energies)`). The following table lists the keys and their meanings.
+The driver routines and macros return energies as ordered descriptive dictionaries [`ElemCo.ODDict`](@ref). The last energy is always the total energy (can be accessed using `last_energy(energies)`). The following table lists the keys and their meanings.
 
 ----------------------
 | Key | Meaning |
 |:---:|:--------|
-| `:HF` | Hartree-Fock energy |
-| `:MP2` | MP2 energy |
-| `:CCSD` | CCSD energy |
-| `:DCSD` | DCSD energy |
-| `:SING2D_DCSD` | singlet 2D-DCSD energy |
-| `:TRIP2D_DCSD` | triplet 2D-DCSD energy |
+| `E` | Total energy |
+| `Ec` | Correlation energy |
+| `HF` | Hartree-Fock energy |
+| `MP2` | MP2 energy |
+| `CCSD` | CCSD energy |
+| `DCSD` | DCSD energy |
+| `SING2D-DCSD` | singlet 2D-DCSD energy |
+| `TRIP2D-DCSD` | triplet 2D-DCSD energy |
 | etc. ||
 
-One can print the keys of the returned `NamedTuple` to see all the available keys:
+One can print the keys of the returned `ODDict` to see all the available keys:
 
 ```julia
 julia> println(keys(energies))
 ```
 
+or display the complete dictionary together with the descriptions as
+
+```julia
+julia> display(energies)
+```
+
+The values and the descriptions can be accessed using the keys as
+
+```julia
+julia> energies["E"] # Total energy
+julia> energies("E") # Description of the total energy
+```
+
 ## [Macros](@id list_of_macros)
 
 ```@autodocs

docs/src/molden.md

@@ -0,0 +1,21 @@
+# Molden Interface
+
+```@docs
+ElemCo.MoldenInterface
+```
+
+## Exported functions and types
+
+```@autodocs
+Modules = [ElemCo.MoldenInterface]
+Private = false
+Order = [:function, :type, :macro, :constant]
+```
+
+## Internal functions and types
+
+```@autodocs
+Modules = [ElemCo.MoldenInterface]
+Public = false
+Order = [:function, :type, :macro, :constant]
+```

docs/src/outputs.md

@@ -0,0 +1,21 @@
+# Outputs
+
+```@docs
+ElemCo.Outputs
+```
+
+## Exported functions
+
+```@autodocs
+Modules = [ElemCo.Outputs]
+Private = false
+Order = [:type, :macro, :function]
+```
+
+## Internal functions
+
+```@autodocs
+Modules = [ElemCo.Outputs]
+Public = false
+Order = [:type, :macro, :function]
+```

docs/src/qmtensors.md

@@ -0,0 +1,21 @@
+# QMTensors
+
+```@docs
+ElemCo.QMTensors
+```
+
+## Exported types and functions
+
+```@autodocs
+Modules = [ElemCo.QMTensors]
+Private = false
+Order = [:type, :macro, :function]
+```
+
+## Internal types and functions
+
+```@autodocs
+Modules = [ElemCo.QMTensors]
+Public = false
+Order = [:type, :macro, :function]
+```

docs/src/tensortools.md

@@ -30,7 +30,7 @@ ints2
 ```@docs
 sqrtinvchol
 invchol
-rotate_eigenvectors_to_real!
+rotate_eigenvectors_to_real
 ```
 
 ## Other exported functions
@@ -39,7 +39,7 @@ rotate_eigenvectors_to_real!
 Modules = [TensorTools]
 Private = false
 Order = [:function]
-Filter = t -> t ∉ [ElemCo.save!, ElemCo.load, ElemCo.mmap, ElemCo.newmmap, ElemCo.closemmap, ElemCo.ints1, ElemCo.ints2, ElemCo.sqrtinvchol, ElemCo.invchol, ElemCo.rotate_eigenvectors_to_real! ]
+Filter = t -> t ∉ [ElemCo.save!, ElemCo.load, ElemCo.mmap, ElemCo.newmmap, ElemCo.closemmap, ElemCo.ints1, ElemCo.ints2, ElemCo.sqrtinvchol, ElemCo.invchol, ElemCo.rotate_eigenvectors_to_real ]
 ```
 
 ## Internal functions

docs/src/utils.md

@@ -13,7 +13,7 @@ Utils
 ```@autodocs
 Modules = [Utils]
 Private = false
-Order = [:function]
+Order = [:function, :type]
 ```
 
 ## Internal functions

profile/LocalPreferences.toml

@@ -0,0 +1,2 @@
+[ElemCo]
+precompile_workload = false