mpqc - The Massively Parallel Quantum Chemistry program (MPQC)

mpqc [options] [filename]

MPQC computes the properties of molecules, ab initio, on a wide variety of computer architectures.

It can compute closed shell and general restricted open-shell Hartree-Fock energies and gradients, second order open-shell perturbation theory (OPT2[2]) and Z-averaged perturbation theory (ZAPT2) energies, and second order closed shell Moeller-Plesset perturbation theory energies and gradients. It also includes methods for optimizing molecules in either Cartesian or internal coordinates.

MPQC is designed using object-oriented programming techniques and implemented in the C++ programming language.

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 ouput. 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.

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 subdirectory 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)'

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

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

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.

MPQC supports two input formats. The primary input is an object oriented format which gives users access to all of MPQC's options. The second format allows access to a subset of MPQC's 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.

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

Specificies the charge on the molecule. The default is 0.

method

Specifices 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

Specifices 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.

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.

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.

) )

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

MP2 Energy

Hartree-Fock Optimization

Optimization with a Computed Guess Hessian

Optimization Using Newton's Method

Hartree-Fock Frequencies

Giving Coordinates and a Guess Hessian

Optimization with a Hydrogen Bond

Fixed Coordinate Optimization

Transition State Optimization

Transition State Optimization with a Computed Guess Hessian