Running Psi 3 from MPQC

Psi 3 is a suite of ab initio codes related to the original Psi package started in Prof. Fritz Schaefer's group at Berkeley. From now on we will refer to Psi 3 as simply Psi. Psi is written primarily in C and executes in serial mode only. The interface between Psi and MPQC is intended mainly for Psi users who wish to exploit MPQC's geometry optimization and frequency analyses capabilities with Psi energies and gradients.

This chapter explains how to use Psi from MPQC.

• How the MPQC-Psi interface works
• Environmental Variables
• Preparing an input file
• Psi Execution Environment
• PsiWavefunction specializations
• More examples

How the MPQC-Psi interface works

The current version of the interface is rather slim. It is only possible to import energies and gradients computed with Psi into MPQC, i.e. wave functions cannot be imported. All MPQC-Psi interaction happens via text files and system calls. MPQC generates input file for Psi, calls appropriate Psi modules, and then parses the output files for energies and gradients.

Environmental Variables

Several environmental variables are used to control MPQC-Psi interaction:

PSIBIN

By default, MPQC will try to find Psi binaries under /usr/local/psi/bin. Use PSIBIN environmental variable to point to the right location.

The rest of the Psi environment is job specific and specified in the input file.

Preparing an input file

As noted above, MPQC parses the input file, and as such the input file has to be in the MPQC OO input format. All features of usual MPQC input files are there (mpqc section, mole MolecularEnergy object, etc.). In addition the following rules apply:

• instead of using MPQC Wavefunction objects (CLHF, MBPT2, etc.), the Psi specific Wavefunction types (i.e. specializations of PsiWavefunction) have to be used. Presently the following specializations are supported: PsiCLHF, PsiHSOSHF, PsiUHF, PsiCCSD, PsiCCSD_T . The first three are directly analogous to MPQC Wavefunction types CLHF, HSOSHF, and UHF. The latter two do not have MPQC analogs yet. See appropriate class documentation on how to specify them properly.
• each Psi-specific Wavefunction object has to have a member object psienv of type PsiExEnv. PsiExEnv contains job specific information, such as the directory in which Psi input, output, and checkpoint files will be kept, filename prefix, scratch directories, etc. It makes sense to define one such object and simply refer to it from all PsiWavefunction objects. See PsiExEnv class documentation for more info.

Psi Execution Environment

Each PsiWavefunction-derived class has to have a member object called psienv of type PsiExEnv. The following keywords are used by its KeyVal constructor:

cwd

The directory where to keep Psi input, checkpoint, stdout, stderr, and other files. Default is /tmp.

fileprefix

The file prefix to use for Psi checkpoint and scratch files. Equivalent to keyword name in Psi default:files:default section. Defaults to psi.

stdout

The file into which to redirect standard output of Psi modules. Defaults to psi.stdout.

stderr

The file into which to redirect standard error of Psi modules. Defaults to psi.stderr.

nscratch

The number of locations over which to stripe Psi binary files. Equivalent to keyword nvolume in Psi default:files:default section. Default is 1.

scratch

The locations over which to stripe Psi binary files. Equivalent to keyword volumex in Psi default:files:default section. There's no default.

Here's an example:

  psienv<PsiExEnv>: (
    cwd = ./
    fileprefix = psi.test
    nscratch = 2
    scratch = [ "/scratch1/" "/scratch2/" ]
  )

PsiWavefunction specializations

Class PsiWavefunction is derived from class Wavefunction, hence its KeyVal constructor uses all keywords that Wavefunction's KeyVal constructor uses (basis, molecule, etc.). In addition, PsiWavefunction's KeyVal constructor looks for the following keywords in the input file:

psienv

The PsiExEnv object that provides job specific Psi environment. There's no default.

docc

An optional array of integers that specifies the number of doubly-occupied orbitals in each irrep.

socc

An optional array of integers that specifies the number of singly-occupied orbitals in each irrep.

frozen_docc

An optional array of integers that specifies the number of doubly-occupied orbitals in each irrep frozen in correlated computations.

frozen_uocc

An optional array of integers that specifies the number of unoccupied orbitals in each irrep frozen in correlated computations.

total_charge

The total charge of the system. This keyword is queried only if neither docc nor socc are given.

multiplicity

The spin multiplicity of the system (2*M_S+1). This keyword is queried only if neither docc nor socc are given.

memory

The number of bytes of memory Psi modules associated with this PsiWavefunction are allowed to use. Default is 2000000 (2 million bytes, approximately 2 MB).

Note that keywords docc, socc, frozen_docc, frozen_uocc, total_charge, and multiplicity are used by appropriate specializations of PsiWavefunctions, i.e. PsiCLHF only checks for docc, etc.

PsiWavefunction specializations PsiCCSD and PsiCCSD_T also look for keyword reference which specifies the reference wave function (an object of type PsiSCF). All classes for correlated Psi wave functions will require such an object.

Here are a few examples of PsiWavefunctions:

  
   ROHF DZ on F atom
  
  mole<PsiHSOSHF>: (
    docc = [ 2 0 0 0 0 1 1 0 ] socc = [ 0 0 0 0 0 0 0 1]
    memory = 10000000

     Psi Environment data
    psienv<PsiExEnv>: (
      cwd = ./
      fileprefix = f.dz.test
      stdout = f.dz.test.stdout
      stderr = f.dz.test.stderr
      nscratch = 1
      scratch = [ "/scratch/mpqc/" ]
    )

     MolecularEnergy input
    molecule<Molecule>: (
        {atoms geometry} = {
          F  [   0.0  0.0   0.0 ]
         }
      )

     Basis input
    basis<GaussianBasisSet>: (
        molecule = $..:molecule
        name = "DZ (Dunning)"
      )

  )

  
   RHF CCSD/cc-pVDZ on water
  
  mole<PsiCCSD>: (
    frozen_docc = [1 0 0 0]
    memory = 40000000

     Psi Environment data
    psienv<PsiExEnv>: (
      cwd = ./
      fileprefix = h2o.ccpvdz.ccsd.test
      nscratch = 1
      scratch = [ "/tmp/" ]
    )

     MolecularEnergy input
    molecule<Molecule>: (
        {atoms geometry} = {
          H  [  -1.5  0.0  -0.3 ]
          H  [   1.5  0.0  -0.3 ]
          O  [   0.0  0.0   1.0 ]
         }
      )

     Basis input
    basis<GaussianBasisSet>: (
        molecule = $..:molecule
        name = "cc-pVDZ"
      )

    reference<PsiCLHF>: (
      psienv = $..:psienv
      molecule = $..:molecule
      basis = $..:basis
      total_charge = 0
      multiplicity = 1
    )
  )

More examples

This section contains some examples of complete inputs that specify an MPQC/Psi computations.

Here's an optimization + subsequent frequency analysis on water molecule at the RHF CCSD 6-311G** level:

 Emacs should use -*- KeyVal -*- mode
 this file was automatically generated
 label: water test series
 molecule specification
molecule<Molecule>: (
  symmetry = C2V
  unit = angstrom
  { atoms geometry } = {
     O     [     0.000000000000     0.000000000000     0.369372944000 ]
     H     [     0.783975899000     0.000000000000    -0.184686472000 ]
     H     [    -0.783975899000     0.000000000000    -0.184686472000 ]
  }
)
 basis set specification
basis<GaussianBasisSet>: (
  name = "6-311G**"
  molecule = $:molecule
)
 Psi environment specification
psienv<PsiExEnv>: (
      cwd = ./
      fileprefix = mpqcpsi
      stdout = mpqcpsi.stdout
      stderr = mpqcpsi.stderr
      nscratch = 1
      scratch = [ "/scratch/evaleev/" ]
)

mpqc: (
  checkpoint = no
  savestate = no
  restart = no
  coor<SymmMolecularCoor>: (
    molecule = $:molecule
    generator<IntCoorGen>: (
      molecule = $:molecule
    )
  )
   molecular coordinates for optimization  do_energy = yes
  do_gradient = no
   method for computing the molecule's energy
  mole<PsiCCSD>: (
    molecule = $:molecule
    basis = $:basis
    coor = $..:coor
    psienv = $:psienv
    memory = 32000000
    reference<PsiCLHF>: (
      psienv = $:psienv
      molecule = $:molecule
      total_charge = 0
      multiplicity = 1
      basis = $:basis
      memory = 32000000
    )
    hessian<FinDispMolecularHessian>: (
      point_group<PointGroup>: symmetry = C2V
      checkpoint = no
      restart = no
    )
  )
  optimize = yes
   optimizer object for the molecular geometry
  opt<QNewtonOpt>: (
    max_iterations = 20
    function = $..:mole
    update<BFGSUpdate>: ()
    convergence<MolEnergyConvergence>: (
      cartesian = yes
      energy = $..:..:mole
    )
  )
 vibrational frequency input
  freq<MolecularFrequencies>: (
    point_group<PointGroup>: symmetry = C2V
    molecule = $:molecule
  )
)

---