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    + +

    Keywords for adcc

    -
    +

    CUTOFF_AMPS_PRINT

    Tolerance for extracted or printed amplitudes. This option is only available for the adcc backend.

    @@ -168,8 +169,8 @@

    +

    +

    KIND

    The kind of states to compute.

    @@ -179,8 +180,8 @@

    +

    +

    MAX_NUM_VECS

    Maximum number of subspace vectors. A negative value uses * the adcc default (roughly between 20 and 5 * N_GUESSES). This option is only available for the adcc backend.

    @@ -189,8 +190,8 @@

    +

    +

    MAXITER

    Maximum number of iterations

    @@ -199,8 +200,8 @@

    +

    +

    NUM_CORE_ORBITALS

    Number of orbitals to place in the core. This option is only available for the adcc backend.

    @@ -209,8 +210,8 @@

    +

    +

    NUM_GUESSES

    Number of guess vectors to generate and use. Negative values keep * the adcc default (currently 2 * ROOTS_PER_IRREP). This option is only available for the adcc backend.

    @@ -219,8 +220,8 @@

    +

    +

    R_CONVERGENCE

    Convergence threshold for ADC matrix diagonalisation. Negative values keep the * adcc default (1e-6)

    @@ -229,8 +230,8 @@

    +

    +

    REFERENCE

    Reference wavefunction type

    @@ -240,8 +241,8 @@

    +

    +

    ROOTS_PER_IRREP

    The number of poles / excited states to obtain per irrep vector

    @@ -250,9 +251,9 @@

    +

    +
    +

    How to configure adcc for building Psi4

    Role and Dependencies

    @@ -404,7 +405,7 @@

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  • subset ['h2o', 'nh3', 'ch4']

  • - +
    -
    +

    BAKERJCC96

    Geometries from Baker and Chan J. Comput. Chem. 17 888 (1996),
    @@ -167,9 +168,9 @@

    'off'

  • rlxd 'off'

  • -

    +

    -
    +

    S66by8

    Database (Hobza) of interaction energies for bimolecular complexes.
    @@ -190,9 +191,9 @@

    -
    +

    HSG

    Database (Merz) of interaction energies for bimolecular complexes from protein-indinavir reaction site.
    @@ -215,9 +216,9 @@

    -
    +

    RGC10

    Database (Sherrill) of interaction energies for dissociation curves of rare-gas biatomic complexes.
    @@ -244,9 +245,9 @@

    -
    +

    BENCH12

    Database of <description of members and reference energy type>.
    @@ -277,9 +278,9 @@

    -
    +

    ACENES

    Database of Ed and Rob’s favorite linear acene dimers.
    @@ -298,9 +299,9 @@

    -
    +

    HTBH

    Database (Truhlar) of hydrogen-transfer barrier height reactions.
    @@ -317,9 +318,9 @@

    -
    +

    S66

    Database (Hobza) of interaction energies for bimolecular complexes.
    @@ -338,9 +339,9 @@

    -
    +

    SSI

    Database (Merz) of interaction energies for protein sidechain-sidechain interactions.
    @@ -352,9 +353,9 @@

    'off' || 'on'

  • rlxd 'off'

  • -

    +

    -
    +

    HTR40

    Database of Hydrogen transfer reactions.
    @@ -376,9 +377,9 @@

    -
    +

    S22

    Database (Hobza) of interaction energies for bimolecular complexes.
    @@ -408,9 +409,9 @@

    -
    +

    NCB31

    Database (Truhlar) of several classes of noncovalent interactions.
    @@ -439,9 +440,9 @@

    -
    +

    S22by5

    Database (Hobza) of interaction energies for dissociation curves of bimolecular complexes.
    @@ -462,9 +463,9 @@

    -
    +

    CORE

    Database of Pulay corannulene structures. Subsumed into CFLOW.
    @@ -473,9 +474,9 @@

    'off' || 'on'

  • rlxd 'off'

  • -

    +

    -
    +

    A24

    Database (Hobza) of interaction energies for bimolecular complexes.
    @@ -499,9 +500,9 @@

    -
    +

    A24alt

    Database (Hobza) of interaction energies for bimolecular complexes.
    @@ -525,9 +526,9 @@

    -
    +

    RSE42

    Database of radical stabilization energies.
    @@ -550,9 +551,9 @@

    -
    +

    NHTBH

    Database (Truhlar) of non-hydrogen-transfer barrier height reactions.
    @@ -568,9 +569,9 @@

    -
    +

    BBI

    Database (Merz) of protein backbone-backbone interactions.
    @@ -582,9 +583,9 @@

    'off' || 'on'

  • rlxd 'off'

  • -

    +

    -
    +

    NBC10

    Database (Sherrill) of interaction energies for dissociation curves of dispersion-bound bimolecular complexes.
    @@ -626,9 +627,9 @@

    -
    +

    HBC6

    Database (Sherrill) of interaction energies for dissociation curves of doubly hydrogen-bonded bimolecular complexes.
    @@ -659,9 +660,9 @@

    -
    +

    JSCH

    Database (Hobza) of interaction energies for nucelobase pairs.
    @@ -682,7 +683,7 @@

    -

    +
    @@ -809,7 +810,7 @@

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    Decontracted Basis Sets

    Decontraction of the basis set can be useful in certain situations. In order to decontract a given basis set, simply add “-decon” to the name @@ -289,8 +290,8 @@

    Navigation

    Obviously this will add significantly to the computational cost of any given calculation, however it can be useful when checking the basis set dependence of a particular calculated property or in certain situations where a large basis set is critical. Currently it is recommended that a decontracted basis is always used when performing relativistic calculations using the X2C Hamiltonian.

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    User-Defined Basis Sets

    Note

    @@ -403,8 +404,8 @@

    Navigation

    The test case mints2 provides a complete example of user-specified basis sets.

    -
    -
    + +

    Inputting effective core potentials (ECPs)

    For ECP containing basis sets, all of the above mechanisms may still be used to input the basis set; simply place the ECP definitions (in G94 format) in the @@ -415,8 +416,8 @@

    Navigation

    Effective core potentials (ECPs) for more information about using ECPs and the Def2-TZVP basis set definition for an example of their input syntax.

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    @@ -527,7 +528,7 @@

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    Keywords

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    BRIANQC_ENABLE

    Whether to enable using the BrianQC GPU module

    @@ -241,9 +242,9 @@

    @@ -361,7 +362,7 @@

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    Configuring, Building, and Installing PSI4 via Source

    1. Planning: how to configure Psi4 and invoke CMake

    2. @@ -159,8 +160,8 @@

      Configuring, Building, and Installing How to save configuration settings for a future compilation

    3. How to configure a Psi4 build on Cray

    -
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    +
    +

    Non-QC Dependencies

    1. What are the tools and dependencies strictly required for building Psi4

    2. @@ -175,8 +176,8 @@

      Non-QC DependenciesWhat Fortran compilers are approved

    3. How to obtain a Fortran compiler for Mac without Fink, MacPorts, or Homebrew

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    QC Dependencies and Extensions

    1. What are the add-on capabilities for Psi4 and what are their dependencies

    2. @@ -190,8 +191,8 @@

      QC Dependencies and ExtensionsHow to configure Libint for building Psi4

    3. How to configure PCMSolver for building Psi4

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    Testing

    1. How to see CTest testing errors

    2. @@ -199,8 +200,8 @@

      TestingHow to run a minute’s worth of tests

    3. How to test a Psi4 installation

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    Runtime Setup

    1. How to run Psi4 as executable after compilation

    2. @@ -212,8 +213,8 @@

      Runtime SetupHow to configure paths for PsiAPI

    3. How to solve ModuleNotFoundError: No module named 'psi4'

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    Running PSI4

    1. What command line options does Psi4 have

    2. @@ -223,8 +224,8 @@

      Running

      How to use Psi4 within a PBS queue

    3. How do I retain specific Psi4 scratch files

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    Runtime Errors and Debugging

    1. How to use gdb and lldb with Psi4

    2. @@ -232,23 +233,23 @@

      Runtime Errors and DebuggingHow to fix “undefined symbol: _Py_FalseStruct”

    3. How to fix error “RuntimeError: value for ERI”

    -
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    Managing Code

    1. What is the directory layout of the installed or staged Psi4

    2. What is the suggested GitHub workflow

    3. How to highlight git merge conflicts in vi

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    -
    + +

    Miscellaneous

    1. How to refer to Psi4

    2. How to get a Psi4 logo file

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    @@ -365,7 +366,7 @@

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  • Tarball from GitHub Repository

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    Find-the-code Quiz

    A better decision tree is available at psicode.org/installs/latest, though the below remains valid.

    @@ -191,8 +192,8 @@

    Obtaining sourceforge, but you’re on your own.

    -

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    Binary Installer

    +

    Conda Binary Package

    +

    Clone from GitHub Repository

    +

    Fork from GitHub Repository

    -
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    Tarball from GitHub Repository

    +

    What is the suggested GitHub workflow

    _images/prflow.001.jpeg _images/prflow.002.jpeg _images/prflow.003.jpeg -
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    @@ -452,7 +453,7 @@

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    How to fix error “RuntimeError: value for ERI

    You will need to rebuild Libint. Reissue cmake or edit CMakeCache.txt with larger MAX_AM_ERI and rebuild.

    @@ -602,8 +603,8 @@

    Navigation

  • How to configure code to use high angular momentum basis sets

  • How to get high angular momentum integrals from conda

  • -
    -
    + +

    How to choose the compilation directory, {objdir}

    -
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    How to save configuration settings for a future compilation

    Create a file like do-configure with the cmake command and options on one line.

    @@ -633,8 +634,8 @@

    Navigation

    >>> ./do-configure
    - -
    + +

    What is the directory layout of the installed or staged Psi4

    After compilation (cd objdir && make), a directory structure like the below will exist at objdir/stage. This may be tested and used @@ -683,8 +684,8 @@

    Navigation

  • PYTHONPATH pointing to lib (ordinary) or lib/pythonX.X/site-packages (conda)

  • PSIDATADIR pointing to share/psi4

  • -
    -
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    How to run Psi4 as executable after compilation

    Substituting the full installation directory prefix and a suitable scratch directory, issue the following commands directly in your @@ -713,15 +714,15 @@

    Navigation

    todo how to check if current py is compatible with compilation

    - -
    + +

    How to solve ModuleNotFoundError: No module named 'psi4'

    You’re using PSI4 in PsiAPI mode (python input.py where input.py contains import psi4) but the Python interpreter can’t find the PSI4 Python module. Follow the directions at How to configure paths for PsiAPI.

    -
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    How to configure paths for PsiAPI

    If you know the location of the PSI4 executable (bin/psi4) for Psithon mode and want to know the corresponding location to add to @@ -739,8 +740,8 @@

    Navigation

    >>> python -c "import psi4"
    - -
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    How to run Psi4 as Python module after compilation

    Substituting the full installation directory prefix and a suitable scratch directory, issue the following commands directly in your @@ -772,8 +773,8 @@

    Navigation

    SCF E.............................................................PASSED
    - -
    + +

    How to run Psi4 as executable or Python module from conda installation

    The configuration commands below are generic versions of the ones printed to your screen as advice upon installing PSI4 into a Anaconda, @@ -829,8 +830,8 @@

    Navigation

    SCF E.............................................................PASSED
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    How to run Psi4 as executable after compilation using driver from source

    When developing python driver code, it can be annoying to keep makeing to test the code. PSI4 can be run “inplace” through the following procedure. To be clear, this is running compiled C++ from the @@ -841,8 +842,8 @@

    Navigation

    >>> python ../psi4/run_psi4.py --inplace input.dat
    - -
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    Why not to set PSIDATADIR

    PSIDATADIR is an environment variable containing the location of the text resource parts of the PSI4 codebase (e.g., basis sets, @@ -865,8 +866,8 @@

    Navigation

    export PSIDATADIR={top-level-psi4-dir}/psi4/share/psi4
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    How to configure C++ and C compilers for building Psi4

    Role and Dependencies

    - -
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    What C and C++ compilers and versions are approved

    On Linux, the following work nicely.

    @@ -995,8 +996,8 @@

    Navigation

    -
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    How to obtain C and C++ compilers for Mac without Fink, MacPorts, or Homebrew

    The easiest compiler to obtain is clang which is a drop-in replacement for gcc and g++. Just install XCode. Some old versions @@ -1033,8 +1034,8 @@

    Navigation

    # Configure and build
    - -
    + +

    How to satisfy the GCC >= 4.9 requirement on Linux without updating the OS

    # See if GCC too old (in this case, yes)
     >>> gcc --version
    @@ -1088,8 +1089,8 @@ 

    Navigation

    >>> export LD_LIBRARY_PATH=${GCC7}/lib:$LD_LIBRARY_PATH
    -
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    How to configure a Psi4 build on Cray

    Cray systems strongly prefer to build static libraries, but PSI4 needs to be dynamic to function as a Python module. Courtesy of @misha @@ -1099,8 +1100,8 @@

    Navigation

    CRAYPE_LINK_TYPE=dynamic CRAY_ADD_RPATH=yes cmake ...
     
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    How to configure Fortran compilers for building Psi4

    Role and Dependencies

    - -
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    What Fortran compilers are approved

    On Linux and Mac, the following work nicely.

    @@ -1153,15 +1154,15 @@

    Navigation

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    How to obtain a Fortran compiler for Mac without Fink, MacPorts, or Homebrew

    Xcode does not provide a Fortran compiler. A way to get one is to download the gfortran_osx-64 conda package. This provides gfortran compilers for Mac. The version is 4.8.5, which is quite old, but the Fortran compiler will work.

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    How to configure BLAS/LAPACK for building Psi4

    Role and Dependencies

    -
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    How to configure Python for building Psi4

    Role and Dependencies

    - -
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    What Python is Psi4 running

    The Python detected at build-time is embedded into the PSI4 executable. That is, the top line of bin/psi4 is something like @@ -1378,14 +1379,14 @@

    Navigation

    edit the shebang line.

    If you’re using PSI4 as a Python module, then PSI4 is running the Python of which python.

    -
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    How to fix “undefined symbol: _Py_FalseStruct

    You’re probably loading a Py3-compiled Psi4 in Py2. Switch interpreters and re-run. A python of proper Py2 or Py3-ness is baked into the PSI4 “executable”, so you’ll see this error only for Psi4 as Python module.

    -
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    How to use gdb and lldb with Psi4

    Debugging PSI4 has gotten a little confusing now that it’s running through Python. Here’s the syntax

    >>> cd {objdir}
    @@ -1398,14 +1399,14 @@ 

    Navigation

    >>> (gdb) run
    -
    -
    + +

    How to see the actual compiling commands (or errors) with cmake

    CMake by default hides a lot of useful debugging information to make the compilation cleaner. Issue make VERBOSE=1 to display the full compilation commands and errors.

    -
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    How to highlight git merge conflicts in vi

    Edit your ~/.vimrc file to include the lines below. Hitting the F7 key will toggle highlighting of git’s conflict markers.

    @@ -1414,8 +1415,8 @@

    Navigation

    map <F7> :/\(<<<<<<<\\|=======\\|>>>>>>>\)<CR>
    - -
    + +

    How to handle “runtime library may be hidden” when building with Anaconda Python

    When building against Ana/Miniconda python (e.g., cmake -DPython_EXECUTABLE=/path/to/conda/bin/python), the warning below often @@ -1430,8 +1431,8 @@

    Navigation

    Some of these libraries may not be found correctly.
    - -
    + +

    How to set up the scratch directory

    The scratch directory is where Psi4 stores potentially large files during computation. It should thus be on a local, fast disk to minimize any @@ -1446,21 +1447,21 @@

    Navigation

    See also the more general scratch documentation.

    - -
    + +

    How do I retain specific Psi4 scratch files

    You can set up a specific path for PSI4 scratch file and keep them for later use through the psi4_io handler.

    -
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    How to use Psi4 within a PBS queue

    You will usually need to set up a PBS job script that is setting all necessary environment variables, making sure the scratch directories are set up, and invokes the executable. An example PBS script is provided in the manual, but make sure to also consult your own PBS documentation for appropriate setup.

    -
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    How to update and rebuild Psi4

    Obtain code updates as appropriate from Binary Installer, Clone from GitHub Repository, or Fork from GitHub Repository. Move into @@ -1468,8 +1469,8 @@

    Navigation

    will only rebuild objects and libraries depending on changed files. It is scarcely ever necessary for the user to reinvoke cmake to update objdir.

    -
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    How to run a minute’s worth of tests

    When you want to do a very minimal test of the build and have CTest installed, the following command can be useful.

    @@ -1480,8 +1481,8 @@

    Navigation

    >>> make pytest
     
    -
    -
    + +

    How to run a subset of tests

    CTest allows flexibly partitioned running of the test suite. In the examples below, testname are regex of test names, @@ -1498,8 +1499,8 @@

    Navigation

  • Run tests matching by label: ctest -L testlabel

  • Run tests excluding those by label: ctest -LE testlabel

  • -
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    + +

    How to see CTest testing errors

    >>> ctest
     Test project /your/path/2/psi4/build/directory/tests
    @@ -1516,8 +1517,8 @@ 

    Navigation

    .tmp extension, depending on whether the last test was interrupted and a few other factors. Either way, this file should contain CMake’s testing output, as well as everything that was printed to the screen.

    -
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    +
    +

    How to test a Psi4 installation

    ctest requires a connection to source files and cmake machinery and so can only be performed from objdir @@ -1572,8 +1573,8 @@

    Navigation

    test_psi4.py::test_psi4_scfproperty PASSED
    - -
    + +

    How to refer to Psi4

    Ways to refer to PSI4 in text, in order of decreasing goodness:

    @@ -1594,12 +1595,12 @@

    Navigation

  • NOT PSI4 or PSI

  • - -
    + +

    How to get a Psi4 logo file

    All image files are stored in https://github.com/psi4/psi4media

    -
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    How to use a local Add-On repository in the Psi4 build

    For each Add-On, PSI4 pulls source from a specific online Git repository and a specific tag/branch/commit in it. This ensures success @@ -1641,8 +1642,8 @@

    Navigation

    to your dev AddOn dynamic lib and update automatically when you rebuild the AddOn lib. Naturally, you may need to delete core.so and remake as needed.

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  • Sphinx Docs

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    Math in the Codebase

    It is often useful to have mathematical expressions in docstrings or comments in the code that are auto-documented into the manual. Such @@ -249,8 +250,8 @@

    Math in the Codebase -

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    The Map of the Sphinx

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  • The scripts discussed below are located in psi4/psi4/share/psi4/fsapt.

    -
    +

    F-SAPT: A Representative Example

    Below, we show an example of using F-SAPT0/jun-cc-pVDZ to analyze the distribution of the intermolecular interaction energy components between the @@ -274,8 +275,8 @@

    F-SAPT: A Representative Example +

    +

    Order-1 Visualization with PyMol

    The fsapt.py script above also generates a number of order-1 .pdb files that can be used to get a quick qualitative picture of the F-SAPT partition. The @@ -297,8 +298,8 @@

    Order-1 Visualization with PyMol.pymol files require some small tweaks to permit publication-quality renderings.

    Total Order-1 F-SAPT0 -

    -
    + +

    Difference F-SAPT Analysis

    For those interested in taking the differences between two F-SAPT partitions (e.g., to see how a substituent modulates a noncovalent interaction), we have @@ -311,8 +312,8 @@

    Difference F-SAPT Analysis\(E^{\Delta} = E^{1} - E^{2}\), and the geometries for order-1 .pdb visualization files are taken from system 1.

    -

    -
    + +

    I-SAPT: A Representative Example

    Caution

    @@ -390,8 +391,8 @@

    I-SAPT: A Representative Example +

    +

    Cube File Visualization with PyMol

    Setting FISAPT_DO_PLOT true above generates a set of .cube files containing the densities and ESPs of the various subsystems in the I-SAPT @@ -413,8 +414,8 @@

    Cube File Visualization with PyMol.pymol files require some small tweaks to permit publication-quality renderings.

    ESP of monomer A -

    -
    + +

    F/I-SAPT Keywords

    The input files described above cover roughly 90% of all F/I-SAPT analyses. For more delicate or involved problems, there are a large number of user options @@ -422,8 +423,8 @@

    F/I-SAPT Keywordsvideo tutorial devoted to F/I-SAPT Options . Direct source-code documentation on these options is available here.

    -

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    Additional Notes

    Caution

    @@ -437,8 +438,8 @@

    Additional NotesDF_BASIS_ELST option in Ed’s code to provide an accurate result.

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    Density Cumulant Theory (DCT)

    PSI4 features several formulations of newly-developed density cumulant theory (DCT), also known as density cumulant functional theory (DCFT). @@ -264,8 +265,8 @@

    Density Cumulant Theory (DCT)10.1063/1.4892946).

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    Configuration Interaction (CI)

    PSI has a highly optimized code for full configuration interaction and highly correlated configuration interaction, as described in

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    Configuration Interaction (CI)10.1016/S0065-3276(08)60532-8).

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    Coupled Cluster (CC)

    A general discussion of coupled cluster theory is given in

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    Mukherjee State-Specific Multi-Reference Coupled Cluster (Mk-MRCC)

    PSI4 features production-level Mukherjee-style state-specific coupled-cluster theory, including perturbative triples and also associated @@ -370,8 +371,8 @@

    Mukherjee State-Specific Multi-Reference Coupled Cluster (Mk-MRCC)10.1039/b822910d).

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    Symmetry-Adapted Perturbation Theory (SAPT)

    PSI4 features an extremely efficient code to perform wavefunction-based Symmetry Adapted Perturbation Theory (SAPT). A good review article for this @@ -475,8 +476,8 @@

    Symmetry-Adapted Perturbation Theory (SAPT)10.1080/00268976.2013.827253)

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    Orbital-Optimized Post-Hartree–Fock Methods

    Orbital-optimized second-order perturbation theory (OMP2)

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    Algebraic-Diagrammatic Construction methods (ADC)

    General ADC theory

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    Density Matrix Renormalization Group (DMRG)

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    Scalar Relativistic Corrections

    General theory for the exact two-component approach (X2C)

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    Supported Systems

    Architectures

    The majority of PSI4 was developed on Mac and Linux machines; in @@ -649,16 +650,16 @@

    Scalar Relativistic CorrectionsPSI4 1.3 supports Python 3.6 and 3.7.

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    License

    PSI4 is distributed under the GNU Lesser General Public License version 3, LGPL-3.0. Its required dependencies and add-ons have their own licenses, ranging from BSD-2-Clause to GPL-2.0+. It is possible to build PSI4 without any GPL dependencies.

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    Capabilities

    PSI4 can perform ab initio computations employing basis sets of contracted Gaussian-type functions of virtually arbitrary @@ -1101,8 +1102,8 @@

    CapabilitiesPSI4 can also compute an extensive list of one-electron properties.

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    Technical Support

    The PSI4 package is distributed for free and without any guarantee of reliability, accuracy, or suitability for any particular purpose. No @@ -1158,8 +1159,8 @@

    Capabilities

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    How to name keywords in psi4/src/read_options.cc

    A few guidelines for standardizing option names among modules.

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  • Copy meta.yaml and build.sh of at least psi4-multiout and psi4-rt to e.g., v121-build.sh files for easy reference or rebuilding as dependencies in master change.

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    Publish to main conda label

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    Build Psi4conda set

    Installers are build using the project constructor and build binary bash scripts, one per OS per Python version. In analogy to Miniconda, they’re called Psi4Conda. They can be built anywhere (Mac can be built on Linux) and get served from vergil (cdsgroup webserver).

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    Finalize release

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    Reset psi4meta for nightly operation

    On both Linux and Mac:

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    Output

    The progress of a geometry optimization can be monitored by grepping the output file for the tilde character (~). This produces a table like the one below that shows @@ -777,8 +778,8 @@

    OutputOPTKING.

    Information on the Psithon function that drives geometry optimizations is provided at optimize().

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