This is the command mpqc that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
)
)
)
Use mpqc online using onworks.net services