NAME
mpqc - The Massively Parallel Quantum Chemistry program (MPQC)
SYNOPSIS
mpqc [options] [filename]
DESCRIPTION
MPQC computes the properties of molecules, ab initio, on a wide variety
of computer architectures.
It can compute closed shell and general restricted openshell
HartreeFock energies and gradients, second order openshell perturbation
theory (OPT2[2]) and Zaveraged perturbation theory (ZAPT2) energies,
and second order closed shell MoellerPlesset perturbation theory
energies and gradients. It also includes methods for optimizing
molecules in either Cartesian or internal coordinates.
MPQC is designed using objectoriented programming techniques and
implemented in the C++ programming language.
OPTIONS
MPQC can be given options followed by an optional input file name. If
the input file name is not given, it will default to ’mpqc.in’. The
following command line options are recognized:
-o Gives the name of the output file. The default is the console.
-i Convert a simple input file to an object oriented input file
and write the result to the output. No calculations are done.
-messagegrp
A ParsedKeyVal specification of a MessageGrp object. The
default depends on how MPQC was compiled.
-memorygrp
A ParsedKeyVal specification of a MemoryGrp object. The default
depends on how MPQC was compiled.
-threadgrp
A ParsedKeyVal specification of a ThreadGrp object. The default
depends on how MPQC was compiled.
-l Sets a limit on the number of basis functions. The default is
zero, which means an unlimited number of basis functions.
-W Sets the working directory. The default is the current
directory.
-c Check the input and exit.
-v Print the version number.
-w Print the warranty information (there is no warranty).
-d If a debugger object was given in the input, start the debugger
running as soon as MPQC is started.
-h Print a list of options.
-f The name of an object-oriented input file. The default is
mpqc.in. This cannot be used if another input file is
specified. This option is deprecated, as both input file
formats can be read by given the input file name on the command
line without any option flags.
Some MPI environments do not pass the command line to slave programs,
but supply it when MPI_Init is called. To make MPQC call MPI_Init on
start-up, instead of when an MPIMessageGrp is created, name the
executable mpqc-mpi.
ENVIRONMENTAL VARIABLES
MPQC looks at four environmental variables to set up communication and
find library files. Machine specific libraries and utilities to run
programs in parallel might look at other environment variables as well.
The four that apply on all platforms are:
SCLIBDIR
The name of the library directory.
MESSAGEGRP
A ParsedKeyVal specification of a MessageGrp object. The
default depends on how MPQC was compiled. See the MessageGrp
class documentation for more information.
MEMORYGRP
A ParsedKeyVal specification of a MemoryGrp object. The default
depends on how MPQC was compiled and the MessageGrp in use.
THREADGRP
A ParsedKeyVal specification of a ThreadGrp object. The default
depends on how MPQC was compiled.
By default, MPQC tries to find library files first in the lib
sub-directory of the installation directory and then the source code
directory. If the library files cannot be found, MPQC must be notified
of the new location with the environmental variable SCLIBDIR.
The other three keywords specify objects. This is done by giving a mini
ParsedKeyVal input in a string. The object is anonymous, that is, no
keyword is associated with it. Here is an example:
setenv MESSAGEGRP ’<ShmMessageGrp>:(n = 4)’
SHARED MEMORY MULTIPROCESSOR WITH SYSV IPC
By default, MPQC will run on only one CPU. To specify more, you can
give a ShmMessageGrp object on the command line. The following would
run mpqc in four processes:
mpqc -messagegrp ’<ShmMessageGrp>:(n = 4)’ input_file
Alternately, the ShmMessageGrp object can be given as an environmental
variable:
setenv MESSAGEGRP ’<ShmMessageGrp>:(n = 4)’
mpqc input_file
If MPQC should unexpectedly die, shared memory segments and semaphores
will be left on the machine. These should be promptly cleaned up or
other jobs may be prevented from running successfully. To see if you
have any of these resources allocated, use the ipcs command. The output
will look something like:
IPC status from /dev/kmem as of Wed Mar 13 14:42:18 1996
T ID KEY MODE OWNER GROUP
Message Queues:
Shared Memory:
m 288800 0x00000000 --rw------- cljanss user
Semaphores:
s 390 0x00000000 --ra------- cljanss user
s 391 0x00000000 --ra------- cljanss user
To remove the IPC resources used by cljanss in the above example on
IRIX, type:
ipcrm -m 288800
ipcrm -s 390
ipcrm -s 391
And on Linux, type:
ipcrm shm 288800
ipcrm sem 390
ipcrm sem 391
SHARED MEMORY MULTIPROCESSOR WITH POSIX THREADS
By default, MPQC will run with only one thread. To specify more, you
can give a PthreadThreadGrp object on the command line. MPQC is not
parallelized to as large an extent with threads as it is with the more
conventional distributed memory model, so you might not get the best
performance using this technique. On the other the memory overhead is
lower and no interprocess communication is needed.
The following would run MPQC in four threads:
mpqc -threadgrp ’<PthreadThreadGrp>:(num_threads = 4)’ input_file
Alternately, the PthreadThreadGrp object can be given as an
environmental variable:
setenv THREADGRP ’<PthreadThreadGrp>:(n = 4)’
mpqc input_file
SHARED OR DISTRIBUTED MEMORY MULTIPROCESSOR WITH MPI
A MPIMessageGrp object is used to run using MPI. The number of nodes
used is determined by the MPI run-time and is not specified as input
data to MPIMessageGrp.
mpqc -messagegrp ’<MPIMessageGrp>:()’ input_file
Alternately, the MPIMessageGrp object can be given as an environmental
variable:
setenv MESSAGEGRP ’<MPIMessageGrp>:()’
mpqc input_file
Usually, a special command is needed to start MPI jobs; typically it is
named mpirun.
INPUT
MPQC supports two input formats. The primary input is an object
oriented format which gives users access to all of MPQCs options. The
second format allows access to a subset of MPQCs capabilities, but is
more intuitive and easier to learn. New users are advised to start with
the simplified format. MPQC can be used to convert the simplified
format to the full object-oriented format with the -i option.
Simple Input
The simple input format consists of keywords followed by a ’:’ followed
by a value. The keywords are case sensitive. The values might be
modified by options found in parenthesis. For example, the following
input performs an optimization of water using density functional theory
with the B3LYP exchange-correlation functional:
% B3LYP optimization of water
optimize: yes
method: KS (xc = B3LYP)
basis: 3-21G*
molecule:
O 0.172 0.000 0.000
H 0.745 0.000 0.754
H 0.745 0.000 -0.754
Comments begin with a % and continue to the end of the line. Basis set
names containing special characters, such as a space or parentheses,
must be quoted inside a pair of double quotes. The accepted keywords
are:
molecule
Gives the atoms types and coordinates. The following options can
be used
bohr
The coordinates are given in Bohr.
angstrom
The coordinates are given in Angstroms.
charge
This option can be given after an ’element x y z’ quadruple. This
will override the charge on the atom. For example, (charge = 0) can
be given for the ghost atoms in a counterpoise correction
calculation.
multiplicity
Gives the multiplicity of the molecule. The default is 1.
optimize
If yes, then an optimization will be performed. The default is no.
The following options can be given.
cartesian
Use Cartesian coordinates.
internal
Use internal coordinates.
redundant
Use redundant internal coordinates.
gradient
If yes, then a gradient calculation will be performed. The default
is no.
frequencies
If yes, then the frequencies will be obtained. The default is no.
charge
Specifies the charge on the molecule. The default is 0.
method
Specif ices the method. There is no default and the possible
values are:
HF Hartree-Fock. Unrestricted HF is used if multiplicity > 1
RHF
Restricted Hartree-Fock.
UHF
Unrestricted Hartree-Fock.
KS Kohn-Sham. Unrestricted KS is used if multiplicity > 1
RKS
Restricted Kohn-Sham.
UKS
Unrestricted Kohn-Sham.
MP2
Second order Moeller-Plesset perturbation theory. Only available
for multiplicity = 1.
ZAPT2
Z-averaged perturbation theory. Only available for multiplicity >
1. No gradient, optimization, or frequencies are possible.
The following options are valid with the KS, RKS, and UKS methods:
grid
Specifies the grid to be used for numerical integrations. The
following values can be given:
xcoarse
coarse
medium
fine
xfine
ultrafine
xc Specifies the exchange-correlation functional. There is no
default. See the table in the StdDenFunctional class documentation
for the possible values.
basis
Specifies the basis set. There is no default. See the table in the
GaussianBasisSet class documentation for the available basis sets.
restart
Set to yes to restart an optimization. The default is no.
checkpoint
Set to no to not save checkpoint files during an optimization. The
default is yes.
symmetry
Specif ices the Schoenflies symbol of the point group of the
molecule. The default is auto, which will cause to program to find
the highest order Abelian subgroup of the molecule.
docc
Gives the number of doubly occupied orbitals in each each
irreducible representation in a parenthesized list. The symmetry
must be specified and not be auto. The method must be restricted.
socc
Gives the number of single occupied orbitals in each each
irreducible representation in a parenthesized list. The symmetry
must be specified and not be auto. The method must be restricted.
alpha
Gives the number of alpha occupied orbitals in each each
irreducible representation in a parenthesized list. The symmetry
must be specified and not be auto. The method must be unrestricted.
beta
Gives the number of beta occupied orbitals in each each
irreducible representation in a parenthesized list. The symmetry
must be specified and not be auto. The method must be unrestricted.
frozen_docc
Gives the number of frozen core orbitals. Can be either a single
integer or a parenthesized list giving the frozen core orbitals in
each irreducible representation. In the latter case the symmetry
must be given and not be auto.
frozen_uocc
Gives the number of frozen virtual orbitals. Can be either a
single integer or a parenthesized list giving the frozen virtual
orbitals in each irreducible representation. In the latter case the
symmetry must be given and not be auto.
Object-Oriented Input
MPQC is an object-oriented program that directly allows the user to
specify objects that MPQC then manipulates to obtain energies,
properties, etc. This makes the input very flexible, but very complex.
However, most calculations should be quite similar to the one of the
examples given later in this chapter. The best way to get started is to
use one of the example input files and modify it to meet your needs.
MPQC starts off by creating a ParsedKeyVal object that parses the input
file specified on the command line. The format of the input file is
documented in . It is basically a free format input that associates
keywords and logical groupings of keywords with values. The values can
be scalars, arrays, or objects.
The keywords recognized by MPQC begin with the mpqc prefix. That is,
they must be nested between an mpqc:( and a ). Alternately, each
keyword can be individually prefixed by mpqc:. The primary keywords are
given below. Some of the keywords specify objects, in which case the
object will require more ParsedKeyVal input. These objects are created
from the input by using their ParsedKeyVal constructors. These
constructors are documented with the source code documentation for the
class.
mole
This is the most important keyword for MPQC. It specifies the
MolecularEnergy object. This is an object that knows how to compute
the energy of a molecule. The specializations of MolecularEnergy
that are most commonly used are CLKS, HSOSKS, UKS, CLHF, HSOSHF,
UHF, and MBPT2.
opt
This keyword must be specified for optimizations. It specifies an
Optimize object. Usually, QNewtonOpt is best for finding minima and
EFCOpt is best for transition states.
freq
This keyword must be specified to compute frequencies. It
specifies a MolecularFrequencies object.
thread
This specifies an object of type ThreadGrp that can be used to
advantage on shared-memory multiprocessor machines for certain
types of calculations. This keyword can be overridden by giving the
ThreadGrp in the environment or command line. See the section on
running MPQC for more information.
checkpoint
The value of this keyword is Boolean. If true, then optimizations
will be checkpointed after each iteration. The checkpoint file
suffice is .ckpt. The default is to checkpoint.
savestate
The value of this keyword is Boolean. If true, then the states of
the optimizer and wavefunction objects will be saved after the
calculation completes. The output file suffix is .wfn. The default
is to save state.
restart
The value of this keyword is Boolean. If true, mpqc will attempt
to restart the calculation. If the checkpoint file is not found,
the calculation will continue as if the value were false. The
default is true.
restart_file
This gives the name of a file from which restart information is
read. If the file name ends in .wfn the MolecularEnergy object will
be restored. Otherwise, the Optimize object will be restored. The
default file name is formed by appending .ckpt to the input file
name with the extension removed.
do_energy
The value of this keyword is Boolean. If true a single point
energy calculation will be done for the MolecularEnergy object
given with the mole keyword. The default is true.
do_gradient
The value of this keyword is Boolean. If true a single point
gradient calculation will be done for the MolecularEnergy object
given with the mole keyword. The default is false.
optimize
The value of this keyword is Boolean. If true and the opt keyword
was set to a valid value, then an optimization will be performed.
The default is true.
write_pdb
The value of this keyword is Boolean. If true a PDB file with the
molecular coordinates will be written.
filename
The value of this keyword is a string that gives a name from which
checkpoint and other filenames are constructed. The default is the
basename of the input file.
print_timings
If this is true, timing information is printed at the end of the
run. The default is true.
There are also some utility keywords that tell mpqc some technical
details about how to do the calculation:
debug
This optional keyword gives a Debugger object which can used to
help find the problem if MPQC encounters a catastrophic error.
matrixkit
This optional keyword gives a SCMatrixKit specialization which is
used to produce matrices of the desired type. The default is a
ReplSCMatrixKit which replicates matrices on all of the nodes.
Other choices are not thoroughly tested.
EXAMPLES
This example input does a Hartree-Fock calculation on water. Following
is the entire input, followed by a breakdown with descriptions.
% This input does a Hartree-Fock calculation on water.
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<GaussianBasisSet>: (
name = ’STO-3G’
molecule = $:molecule
)
mpqc: (
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
)
)
We start with a descriptive comment. Comments begin with a %.
Everything from the % to the end of the line is ignored.
% This input does a Hartree-Fock calculation on water.
Now lets set up a Molecule object. The name of the object comes first,
it is molecule. Then, in angle brackets, comes the type of the
molecule, which is the class Molecule. The keyword and class name are
followed by a : and then several pieces of input grouped between a pair
of matching parentheses. These parentheses contain the information that
will be given to Molecule KeyVal constructor.
molecule<Molecule>: (
The point group of the molecule is needed. This is done by assigning
symmetry to a case insensitive Schoenflies symbol that is used to
initialize a PointGroup object. An Abelian point group should be used.
symmetry = C2V
The default unit for the Cartesian coordinates is Bohr. You can specify
other units by assigned unit to a string that will be used to
initialize a Units object.
unit = angstrom
Finally, the atoms and coordinates are given. This can be given in the
shorthand table syntax shown below. The headings of the table are the
keywords between the first pair of brackets. These are followed by an =
and another pair of brackets that contain the data. The first datum is
assigned to the first element of the array that corresponds to the
first heading, atom. The second datum is assigned to the first element
of the array associated with the second heading, geometry, and so on.
Here the second datum is actually a vector: the x, y and z coordinates
of the first atom.
{ atoms geometry } = {
O [ 0.00000000 0.00000000 0.37000000 ]
H [ 0.78000000 0.00000000 -0.18000000 ]
H [ -0.78000000 0.00000000 -0.18000000 ]
}
)
Next, a basis set object is given.
basis<GaussianBasisSet>: (
name = ’STO-3G’
molecule = $:molecule
)
Now we will give the main body of input. All the subsequent keywords
will be grouped in the mpqc section of the input (that is, each keyword
will be prefixed with mpqc:).
mpqc: (
Next we give the mole keyword which provides a specialization of the
MolecularEnergy class. In this case we will do a closed-shell
Hartree-Fock calculation. That is done with an object of type CLHF. The
keywords that CLHF accepts are given with the documentation for the
CLHF class, usually in the description of the const RefKeyVal&
constructor for the class. Also with the CLHF documentation is a list
of parent classes. Each of the parent classes may also have input. This
input is included with the rest of the input for the child class.
mole<CLHF>: (
The next line specifies the molecule to be used. There are two things
to note, first that this is actually a reference to complete molecule
specification elsewhere in the input file. The $ indicates that this is
a reference and the keyword following the $ is the actual location of
the molecule. The : in front of the keyword means that the keyword is
not relative to the current location in the input, but rather relative
to the root of the tree of keywords. Thus, this line grabs the molecule
that was specified above. The molecule object could have been placed
here, but frequently it is necessary that several objects refer to the
exact same object and this can only be done using references.
The second point is that if you look at the documentation for CLHF, you
will see that it doesn’t read molecule keyword. However, if you follow
its parent classes up to MolecularEnergy, you’ll find that molecule is
indeed read.
molecule = $:molecule
Just as we gave molecule, specify the basis set with the basis keyword
as follows:
basis = $:basis
Now we close off the parentheses we opened above and we are finished.
)
)
Sample Object-Oriented Input Files
The easiest way to get started with mpqc is to start with one of sample
inputs that most nearly matches your problem. All of the samples inputs
shown here can be found in the directory src/bin/mpqc/samples.
Hartree-Fock Energy
The following input will compute the Hartree-Fock energy of water.
% 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 = no
% method for computing the molecule’s energy
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
)
)
MP2 Energy
The following input will compute the MP2 energy of water.
% 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 = no
% method for computing the molecule’s energy
mole<MBPT2>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
% reference wavefunction
reference<CLHF>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
)
)
)
Hartree-Fock Optimization
The following input will optimize the geometry of water using the
quasi-Newton method.
% 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 = ’6-31G*’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
% molecular coordinates for optimization
coor<SymmMolecularCoor>: (
molecule = $:molecule
generator<IntCoorGen>: (
molecule = $:molecule
)
)
% 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>: (
function = $..:mole
update<BFGSUpdate>: ()
convergence<MolEnergyConvergence>: (
cartesian = yes
energy = $..:..:mole
)
)
)
Optimization with a Computed Guess Hessian
The following input will optimize the geometry of water using the
quasi-Newton method. The guess Hessian will be computed at a lower
level of theory.
% 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 = ’6-31G*’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
% molecular coordinates for optimization
coor<SymmMolecularCoor>: (
molecule = $:molecule
generator<IntCoorGen>: (
molecule = $:molecule
)
)
% 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<QNewtonOpt>: (
function = $..:mole
update<BFGSUpdate>: ()
convergence<MolEnergyConvergence>: (
cartesian = yes
energy = $..:..:mole
)
)
)
Optimization Using Newton’s Method
The following input will optimize the geometry of water using the
Newton’s method. The Hessian will be computed at each step in the
optimization. However, Hessian recomputation is usually not worth the
cost; try using the computed Hessian as a guess Hessian for a
quasi-Newton method before resorting to a Newton optimization.
% Emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
symmetry = c2v
unit = angstrom
{ atoms geometry } = {
O [ 0.00000000 0.00000000 0.36937294 ]
H [ 0.78397590 0.00000000 -0.18468647 ]
H [ -0.78397590 0.00000000 -0.18468647 ]
}
)
% basis set specification
basis<GaussianBasisSet>: (
name = ’3-21G’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
restart = no
% molecular coordinates for optimization
coor<SymmMolecularCoor>: (
molecule = $:molecule
generator<IntCoorGen>: (
molecule = $:molecule
)
)
do_energy = no
do_gradient = no
% method for computing the molecule’s energy
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
coor = $..:coor
guess_wavefunction<CLHF>: (
molecule = $:molecule
total_charge = 0
basis<GaussianBasisSet>: (
molecule = $:molecule
name = ’STO-3G’
)
memory = 16000000
)
hessian<FinDispMolecularHessian>: (
only_totally_symmetric = yes
eliminate_cubic_terms = no
checkpoint = no
)
)
optimize = yes
% optimizer object for the molecular geometry
opt<NewtonOpt>: (
print_hessian = yes
max_iterations = 20
function = $..:mole
convergence<MolEnergyConvergence>: (
cartesian = yes
energy = $..:..:mole
)
)
)
Hartree-Fock Frequencies
The following input will compute Hartree-Fock frequencies by finite
displacements. A thermodynamic analysis will also be performed. If
optimization input is also provided, then the optimization will be run
first, then the frequencies.
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
symmetry = C1
{ atoms geometry } = {
O [ 0.0000000000 0.0000000000 0.8072934188 ]
H [ 1.4325589285 0.0000000000 -0.3941980761 ]
H [ -1.4325589285 0.0000000000 -0.3941980761 ]
}
)
% basis set specification
basis<GaussianBasisSet>: (
name = ’STO-3G’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
% method for computing the molecule’s energy
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
)
% vibrational frequency input
freq<MolecularFrequencies>: (
molecule = $:molecule
)
)
Giving Coordinates and a Guess Hessian
The following example shows several features that are really
independent. The variable coordinates are explicitly given, rather than
generated automatically. This is especially useful when a guess Hessian
is to be provided, as it is here. This Hessian, as given by the user,
is not complete and the QNewtonOpt object will fill in the missing
values using a guess the Hessian provided by the MolecularEnergy
object. Also, fixed coordinates are given in this sample input.
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
symmetry = C1
{ atoms geometry } = {
H [ 0.088 2.006 1.438 ]
O [ 0.123 3.193 0.000 ]
H [ 0.088 2.006 -1.438 ]
O [ 4.502 5.955 -0.000 ]
H [ 2.917 4.963 -0.000 ]
H [ 3.812 7.691 -0.000 ]
}
)
% basis set specification
basis<GaussianBasisSet>: (
name = ’STO-3G’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
% method for computing the molecule’s energy
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
coor = $..:coor
memory = 16000000
)
% molecular coordinates for optimization
coor<SymmMolecularCoor>: (
molecule = $:molecule
generator<IntCoorGen>: (
molecule = $:molecule
extra_bonds = [ 2 5 ]
)
% use these instead of generated coordinates
variable<SetIntCoor>: [
<StreSimpleCo>:( atoms = [ 2 5 ] )
<BendSimpleCo>:( atoms = [ 2 5 4 ] )
<OutSimpleCo>: ( atoms = [ 5 2 1 3 ] )
<SumIntCoor>: (
coor: [
<StreSimpleCo>:( atoms = [ 1 2 ] )
<StreSimpleCo>:( atoms = [ 2 3 ] )
]
coef = [ 1.0 1.0 ]
)
<SumIntCoor>: (
coor: [
<StreSimpleCo>:( atoms = [ 4 5 ] )
<StreSimpleCo>:( atoms = [ 4 6 ] )
]
coef = [ 1.0 1.0 ]
)
<BendSimpleCo>:( atoms = [ 1 2 3 ] )
<BendSimpleCo>:( atoms = [ 5 4 6 ] )
]
% these are fixed by symmetry anyway,
fixed<SetIntCoor>: [
<SumIntCoor>: (
coor: [
<StreSimpleCo>:( atoms = [ 1 2 ] )
<StreSimpleCo>:( atoms = [ 2 3 ] )
]
coef = [ 1.0 -1.0 ]
)
<SumIntCoor>: (
coor: [
<StreSimpleCo>:( atoms = [ 4 5 ] )
<StreSimpleCo>:( atoms = [ 4 6 ] )
]
coef = [ 1.0 -1.0 ]
)
<TorsSimpleCo>:( atoms = [ 2 5 4 6] )
<OutSimpleCo>:( atoms = [ 3 2 6 4 ] )
<OutSimpleCo>:( atoms = [ 1 2 6 4 ] )
]
)
% optimizer object for the molecular geometry
opt<QNewtonOpt>: (
function = $..:mole
update<BFGSUpdate>: ()
convergence<MolEnergyConvergence>: (
cartesian = yes
energy = $..:..:mole
)
% give a partial guess hessian in internal coordinates
% the missing elements will be filled in automatically
hessian = [
[ 0.0109261670 ]
[ -0.0004214845 0.0102746106 ]
[ -0.0008600592 0.0030051330 0.0043149957 ]
[ 0.0 0.0 0.0 ]
[ 0.0 0.0 0.0 ]
[ 0.0 0.0 0.0 ]
[ 0.0 0.0 0.0 ]
]
)
)
Optimization with a Hydrogen Bond
The automatic internal coordinate generator will fail if it cannot find
enough redundant internal coordinates. In this case, the internal
coordinate generator must be explicitly created in the input and given
extra connectivity information, as is shown below.
% emacs should use -*- KeyVal -*- mode
% molecule specification
molecule<Molecule>: (
symmetry = C1
{ atoms geometry } = {
H [ 0.088 2.006 1.438 ]
O [ 0.123 3.193 0.000 ]
H [ 0.088 2.006 -1.438 ]
O [ 4.502 5.955 -0.000 ]
H [ 2.917 4.963 -0.000 ]
H [ 3.812 7.691 -0.000 ]
}
)
% basis set specification
basis<GaussianBasisSet>: (
name = ’STO-3G’
molecule = $:molecule
)
mpqc: (
checkpoint = no
savestate = no
% method for computing the molecule’s energy
mole<CLHF>: (
molecule = $:molecule
basis = $:basis
coor = $..:coor
memory = 16000000
)
% molecular coordinates for optimization
coor<SymmMolecularCoor>: (
molecule = $:molecule
% give an internal coordinate generator that knows about the
% hydrogen bond between atoms 2 and 5
generator<IntCoorGen>: (
molecule = $:molecule
extra_bonds = [ 2 5 ]
)
)
% optimizer object for the molecular geometry
opt<QNewtonOpt>: (
function = $..:mole
update<BFGSUpdate>: ()
convergence<MolEnergyConvergence>: (
cartesian = yes
energy = $..:..:mole
)
)
)
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.
% 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
)
)
)
Transition State Optimization
This example shows a transition state optimization of the N-inversion
in using mode following. The initial geometry was obtained by doing a
few fixed coordinate optimizations along the inversion coordinate.
% 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
)
)
)
Transition State Optimization with a Computed Guess Hessian
This example shows a transition state optimization of the N-inversion
in 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
optimization converge much faster in this case.
% 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
)
)
)