mpqcoo.dox

大型并行量子化学软件；支持密度泛函（DFT）。可以进行各种量子化学计算。支持CHARMM并行计算。非常具有应用价值。

      energy = $..:..:mole
    )
  )
)
</pre>

\subsection mpqcoosampfixopt Fixed Coordinate Optimization

 This example shows how to selectively fix internal coordinates in an
optimization.  Any number of linearly independent coordinates can be given.
These coordinates must remain linearly independent throughout the
optimization, a condition that might not hold since the coordinates can be
nonlinear.

 By default, the initial fixed coordinates' values are taken from the
cartesian geometry given by the Molecule object; however, the
molecule will be displaced to the internal coordinate values given with the
fixed internal coordinates if have_fixed_values keyword is set to
true, as shown in this example.  In this case, the initial cartesian
geometry should be reasonably close to the desired initial geometry and all
of the variable coordinates will be frozen to their original values during
the initial displacement.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = CS
  { atoms geometry } = {
    H [  3.04 -0.69 -1.59 ]
    H [  3.04 -0.69  1.59 ]
    N [  2.09 -0.48 -0.00 ]
    C [ -0.58 -0.15  0.00 ]
    H [ -1.17  1.82  0.00 ]
    H [ -1.41 -1.04 -1.64 ]
    H [ -1.41 -1.04  1.64 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "4-31G*"
  molecule = $:molecule
)
mpqc: (
  checkpoint = no
  savestate = no
  % molecular coordinates for optimization
  coor<SymmMolecularCoor>: (
    molecule = $:molecule
    generator<IntCoorGen>: (
      molecule = $:molecule
    )
    have_fixed_values = yes
    fixed<SetIntCoor>: [
      <OutSimpleCo>: ( value = -0.1
                       label = "N-inversion"
                       atoms = [4 3 2 1] )
      ]
  )
  % method for computing the molecule's energy
  mole<CLHF>: (
    molecule = $:molecule
    basis = $:basis
    coor = $..:coor
    memory = 16000000
  )
  % optimizer object for the molecular geometry
  opt<QNewtonOpt>: (
    max_iterations = 20
    function = $..:mole
    update<BFGSUpdate>: ()
    convergence<MolEnergyConvergence>: (
      cartesian = yes
      energy = $..:..:mole
    )
  )
)
</pre>

\subsection mpqcoosampts Transition State Optimization

This example shows a transition state optimization of the N-inversion in
\f$\mathrm{CH}_3\mathrm{NH}_2\f$ using mode following.  The initial geometry
was obtained by doing a few fixed coordinate optimizations along the
inversion coordinate.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = CS
  { atoms geometry } = {
    H [  3.045436 -0.697438 -1.596748 ]
    H [  3.045436 -0.697438  1.596748 ]
    N [  2.098157 -0.482779 -0.000000 ]
    C [ -0.582616 -0.151798  0.000000 ]
    H [ -1.171620  1.822306  0.000000 ]
    H [ -1.417337 -1.042238 -1.647529 ]
    H [ -1.417337 -1.042238  1.647529 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "4-31G*"
  molecule = $:molecule
)
mpqc: (
  checkpoint = no
  savestate = no
  % molecular coordinates for optimization
  coor<SymmMolecularCoor>: (
    molecule = $:molecule
    generator<IntCoorGen>: (
      molecule = $:molecule
    )
    followed<OutSimpleCo> = [ "N-inversion" 4 3 2 1 ]
  )  
  % method for computing the molecule's energy
  mole<CLHF>: (
    molecule = $:molecule
    basis = $:basis
    coor = $..:coor
    memory = 16000000
  )
  % optimizer object for the molecular geometry
  opt<EFCOpt>: (
    transition_state = yes
    mode_following = yes
    max_iterations = 20
    function = $..:mole
    update<PowellUpdate>: ()
    convergence<MolEnergyConvergence>: (
      cartesian = yes
      energy = $..:..:mole
    )
  )
)
</pre>

\subsection mpqcoosamptshess Transition State Optimization with a Computed Guess Hessian

This example shows a transition state optimization of the N-inversion in
\f$\mathrm{CH}_3\mathrm{NH}_2\f$ using mode following.  The initial geometry
was obtained by doing a few fixed coordinate optimizations along the
inversion coordinate.  An approximate guess Hessian will be computed, which
makes the optimiziation converge much faster in this case.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = CS
  { atoms geometry } = {
    H [  3.045436 -0.697438 -1.596748 ]
    H [  3.045436 -0.697438  1.596748 ]
    N [  2.098157 -0.482779 -0.000000 ]
    C [ -0.582616 -0.151798  0.000000 ]
    H [ -1.171620  1.822306  0.000000 ]
    H [ -1.417337 -1.042238 -1.647529 ]
    H [ -1.417337 -1.042238  1.647529 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "4-31G*"
  molecule = $:molecule
)
mpqc: (
  checkpoint = no
  savestate = no
  % molecular coordinates for optimization
  coor<SymmMolecularCoor>: (
    molecule = $:molecule
    generator<IntCoorGen>: (
      molecule = $:molecule
    )
    followed<OutSimpleCo> = [ "N-inversion" 4 3 2 1 ]
  )  
  % method for computing the molecule's energy
  mole<CLHF>: (
    molecule = $:molecule
    basis = $:basis
    coor = $..:coor
    memory = 16000000
    guess_hessian<FinDispMolecularHessian>: (
      molecule = $:molecule
      only_totally_symmetric = yes
      eliminate_cubic_terms = no
      checkpoint = no
      energy<CLHF>: (
        molecule = $:molecule
        memory = 16000000
        basis<GaussianBasisSet>: (
          name = "3-21G"
          molecule = $:molecule
        )
      )
    )
  )
  % optimizer object for the molecular geometry
  opt<EFCOpt>: (
    transition_state = yes
    mode_following = yes
    max_iterations = 20
    function = $..:mole
    update<PowellUpdate>: ()
    convergence<MolEnergyConvergence>: (
      cartesian = yes
      energy = $..:..:mole
    )
  )
)
</pre>


\subsection mpqcoosamphfckpt Hartree-Fock energy with intermediate checkpointing

The following two sections demonstrate how MPQC can be used to save the <tt>mole</tt> object
periodically.
This input will compute the Hartree-Fock energy of water while saving
the <tt>mole</tt> object every 3 iterations.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = C2V
  unit = angstrom
  { atoms geometry } = {
    O     [     0.00000000     0.00000000     0.37000000 ]
    H     [     0.78000000     0.00000000    -0.18000000 ]
    H     [    -0.78000000     0.00000000    -0.18000000 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "STO-3G"
  molecule = $:molecule
)
mpqc: (
  checkpoint = yes
  filename = "h2o-rhf-STO3G"
  checkpoint_freq = 3
  savestate = no
  % method for computing the molecule's energy
  mole<CLHF>: (
    molecule = $:molecule
    basis = $:basis
    memory = 16000000
  )
)
</pre>

The <tt>mole</tt> object will be saved to files named "h2o-rhf-STO3G.wfn.<iter#>.tmp"
where <iter#> is the SCF iteration number (3, 6, etc.). Only the most recent file is kept,
files from previous iterations are removed automatically. Keyword <tt>filename</tt>
here is used to set the default file name prefix.

\subsection mpqcoosampmp2r12ckpt MP2-R12 energy with intermediate checkpointing

The following input will compute the MP2-R12 energy of water in standard approximation A'
(MP2-R12/A') while saving the <tt>mole</tt> object at intermediate checkpoints.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = C2V
  unit = angstrom
  { atoms geometry } = {
    O     [     0.00000000     0.00000000     0.37000000 ]
    H     [     0.78000000     0.00000000    -0.18000000 ]
    H     [    -0.78000000     0.00000000    -0.18000000 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "cc-pVDZ"
  molecule = $:molecule
)
% auxiliary basis set specification
abasis<GaussianBasisSet>: (
  name = "aug-cc-pVDZ"
  molecule = $:molecule
)
mpqc: (
  checkpoint = yes
  filename = "h2o-mp2r12ap-vdz-avdz"
  savestate = no
  % method for computing the molecule's energy
  mole<MBPT2_R12>: (
    molecule = $:molecule
    basis = $:basis
    aux_basis = $:abasis
    stdapprox = "A'"
    nfzc = 1
    memory = 16000000
    integrals<IntegralCints>:()
    % reference wavefunction
    reference<CLHF>: (
      molecule = $:molecule
      basis = $:basis
      memory = 16000000
      integrals<IntegralCints>:()
    )
  )
)
</pre>

The <tt>mole</tt> object will be saved to a file named <tt>h2o-mp2r12ap-vdz-avdz.wfn"</tt>.
Keyword <tt>filename</tt> here is used to set the default file name prefix.
Objects of the <tt>MBPT2_R12</tt> type are checkpointed after the HF procedure,
after the first integrals (SBS) transformation, and after the optional second (ABS)
transformation.

\subsection mpqcoosamphfgradfromwfn HF gradient computed from a previously computed HF wave funtion

The following will illustrate how to reuse previously computed <tt>MolecularEnergy</tt> objects
in subsequent computations. The first input computes Hartree-Fock energy for water
and saves the <tt>mole</tt> object to file <tt>h2o-rhf-sto3g.wfn</tt>.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = C2V
  unit = angstrom
  { atoms geometry } = {
    O     [     0.00000000     0.00000000     0.37000000 ]
    H     [     0.78000000     0.00000000    -0.18000000 ]
    H     [    -0.78000000     0.00000000    -0.18000000 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "STO-3G"
  molecule = $:molecule
)
mpqc: (
  checkpoint = no
  savestate = yes
  filename = "h2o-rhf-sto3g"
  % method for computing the molecule's energy
  mole<CLHF>: (
    molecule = $:molecule
    basis = $:basis
    memory = 16000000
  )
)
</pre>

The second input reuses the <tt>mole</tt> object from the previous run
to compute the gradient of the Hartree-Fock energy.

<pre>
% emacs should use -*- KeyVal -*- mode
mpqc: (
  checkpoint = no
  savestate = no
  restart = yes
  restart_file = "h2o-rhf-sto3g.wfn"
  do_gradient = yes
)
</pre>

\subsection mpqcoosampmp2usinghfwfn MP2 Energy computed using precomputed Hartree-Fock wave function

The following input will compute the MP2 energy of water using a saved Hartree-Fock wave function
obtained using the first input from \ref mpqcoosamphfgradfromwfn.

<pre>
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
  symmetry = C2V
  unit = angstrom
  { atoms geometry } = {
    O     [     0.00000000     0.00000000     0.37000000 ]
    H     [     0.78000000     0.00000000    -0.18000000 ]
    H     [    -0.78000000     0.00000000    -0.18000000 ]
  }
)
% basis set specification
basis<GaussianBasisSet>: (
  name = "STO-3G"
  molecule = $:molecule
)
% wave function file object specification
wfnfile<BcastStateInBin>:file = "h2o-rhf-sto3g.wfn"
mpqc: (
  checkpoint = no
  savestate = no
  % method for computing the molecule's energy
  mole<MBPT2>: (
    molecule = $:molecule
    basis = $:basis
    memory = 16000000
    % reference wavefunction
    reference<SavableStateProxy>: (
      statein = $:wfnfile
      object = "CLHF"
    )
  )
)
</pre>

Note that now object <tt>reference</tt> is of type <tt>SavableStateProxy</tt>,
rather than <tt>CLHF</tt>. <tt>SavableStateProxy</tt> is a special object type
that can be converted at runtime into the desired type (in this case, <tt>CLHF</tt>,
as indicated by <tt>object</tt>).

*/