Developing Code Using SC

In addition to the executables, the Scientific Computing toolkit libraries and include files can be installed on your machine.

This is described in the Compiling section of this manual.

The `sc-config` program can be use to obtain the compilers, compiler options, and libraries needed to use the SC toolkit from your program. This utility is discussed below, along with how the SC toolkit must be initialized in your `main` subroutine.

- The sc-config Program
- Initializing SC
- MP2 Implementation Example
- Exception Handling in SC
- Adding Test Cases to the Verification Suite

# The sc-config Program

The sc-config program returns information about how SC was compiled and installed. See sc-config for more information.

# Initializing SC

First the execution environment must be initialized using the ExEnv init member.

      ExEnv::init(argc, argv);

By default, all output will go to the console stream, cout. To change this, use the following code:

      ostream *outstream = new ofstream(outputfilename);
      ExEnv::set_out(outstream);

MPI is allowed wait until MPI_Init is called to fill in argc and argv, so you may have to call MPI_Init before you even know that we ready to construct MPIMessageGrp. So if an MPIMessageGrp is needed, it is up to the developer to call MPI_Init to get the argument list for certain MPI implementations.

      MPI_Init(&argc, &argv);

When files are read and written, an extension is added to a basename to construct the file name. The default is "SC". To use another basename, make the following call, where `basename` is a `const char *`:

      SCFormIO::set_default_basename(basename);

If your job might run in parallel, then make the following call or the nodes will print redundant information. The `myproc` argument is the rank of the called node.

      SCFormIO::init_mp(myproc);

This segment of code sets up an object to provide multi-threading:

      RefThreadGrp thread = ThreadGrp::initial_threadgrp(argc, argv);
      ThreadGrp::set_default_threadgrp(thread);
      if (thread.nonnull())
        ThreadGrp::set_default_threadgrp(thread);
      else
        thread = ThreadGrp::get_default_threadgrp();

This segment of code sets up the message passing object:

      RefMessageGrp grp = MessageGrp::initial_messagegrp(argc, argv);
      if (grp.nonnull())
        MessageGrp::set_default_messagegrp(grp);
      else
        grp = MessageGrp::get_default_messagegrp();

# MP2 Implementation Example

This section illustrates how to add a new method a new method to MPQC.

## MP2 Implementation Example: Source

This example code illustrates a complete MP2 energy implementation using the SC Toolkit. First an MP2 class is declared and the necesary base class member functions are provided. Next a ClassDesc is defined. Finally, the member functions are defined.

Note that no main routine is provided. This is because this file is designed to be used to extend the functionality of the mpqc executable. To generate a new mpqc executable with the new class available for use, see the MP2 Implementation Example: Makefile section.

#include <stddef.h>
#include <util/misc/autovec.h>
#include <util/misc/scexception.h>
#include <chemistry/qc/wfn/obwfn.h>
#include <chemistry/qc/scf/clhf.h>
using namespace std;
using namespace sc;
class MP2: public Wavefunction {
Ref<OneBodyWavefunction> ref_mp2_wfn_;
double compute_mp2_energy();
public:
MP2(const Ref<KeyVal> &);
MP2(StateIn &);
void save_data_state(StateOut &);
void compute(void);
void obsolete(void);
int nelectron(void);
RefSymmSCMatrix density(void);
int spin_polarized(void);
int value_implemented(void) const;
};
static ClassDesc MP2_cd(typeid(MP2), "MP2", 1, "public Wavefunction",
0, create<MP2>, create<MP2>);
MP2::MP2(const Ref<KeyVal> &keyval):Wavefunction(keyval) {
ref_mp2_wfn_ << keyval->describedclassvalue("reference");
if(ref_mp2_wfn_.null()) {
throw InputError("require a OneBodyWavefunction object",
__FILE__, __LINE__, "reference", 0,
class_desc());
}
}
MP2::MP2(StateIn &statein):Wavefunction(statein)
{
ref_mp2_wfn_ << SavableState::restore_state(statein);
}
void
MP2::save_data_state(StateOut &stateout) {
Wavefunction::save_data_state(stateout);
SavableState::save_state(ref_mp2_wfn_.pointer(),stateout);
}
void
MP2::compute(void)
{
if(gradient_needed()) {
throw FeatureNotImplemented("no gradients yet",
__FILE__, __LINE__, class_desc());
}
double extra_hf_acc = 10.;
ref_mp2_wfn_->set_desired_value_accuracy(desired_value_accuracy()
/ extra_hf_acc);
double refenergy = ref_mp2_wfn_->energy();
double mp2energy = compute_mp2_energy();
ExEnv::out0() << indent << "MP2 Energy = " << mp2energy << endl;
set_value(refenergy + mp2energy);
set_actual_value_accuracy(ref_mp2_wfn_->actual_value_accuracy()
* extra_hf_acc);
}
void
MP2::obsolete(void) {
Wavefunction::obsolete();
ref_mp2_wfn_->obsolete();
}
int
MP2::nelectron(void) {
return ref_mp2_wfn_->nelectron();
}
RefSymmSCMatrix
MP2::density(void) {
throw FeatureNotImplemented("no density yet",
__FILE__, __LINE__, class_desc());
return 0;
}
int
MP2::spin_polarized(void) {
return 0;
}
int
MP2::value_implemented(void) const {
return 1;
}
double
MP2::compute_mp2_energy()
{
if(molecule()->point_group()->char_table().order() != 1) {
throw FeatureNotImplemented("C1 symmetry only",
__FILE__, __LINE__, class_desc());
}
RefSCMatrix vec = ref_mp2_wfn_->eigenvectors();
int nao = vec.nrow();
int nmo = vec.ncol();
int nocc = ref_mp2_wfn_->nelectron()/2;
int nvir = nmo - nocc;
auto_vec<double> cvec_av(new double [vec.nrow() * vec.ncol()]);
double *cvec = cvec_av.get();
vec->convert(cvec);
auto_vec<double> pqrs_av(new double [nao * nao * nao * nao]);
double *pqrs = pqrs_av.get();
for(int n = 0; n < nao*nao*nao*nao; n++) pqrs[n] = 0.0;
Ref<TwoBodyInt> twoint = integral()->electron_repulsion();
const double *buffer = twoint->buffer();
Ref<GaussianBasisSet> basis = this->basis();
int nshell = basis->nshell();
for(int P = 0; P < nshell; P++) {
int nump = basis->shell(P).nfunction();
for(int Q = 0; Q < nshell; Q++) {
int numq = basis->shell(Q).nfunction();
for(int R = 0; R < nshell; R++) {
int numr = basis->shell(R).nfunction();
for(int S = 0; S < nshell; S++) {
int nums = basis->shell(S).nfunction();
twoint->compute_shell(P,Q,R,S);
int index = 0;
for(int p=0; p < nump; p++) {
int op = basis->shell_to_function(P)+p;
for(int q = 0; q < numq; q++) {
int oq = basis->shell_to_function(Q)+q;
for(int r = 0; r < numr; r++) {
int oor = basis->shell_to_function(R)+r;
for(int s = 0; s < nums; s++,index++) {
int os = basis->shell_to_function(S)+s;
int ipqrs = (((op*nao+oq)*nao+oor)*nao+os);
pqrs[ipqrs] = buffer[index];
}
}
}
}
}
}
}
}
twoint = 0;
auto_vec<double> ijkl_av(new double [nmo * nmo * nmo * nmo]);
double *ijkl = ijkl_av.get();
int idx = 0;
for(int i = 0; i < nmo; i++) {
for(int j = 0; j < nmo; j++) {
for(int k = 0; k < nmo; k++) {
for(int l = 0; l < nmo; l++, idx++) {
ijkl[idx] = 0.0;
int index = 0;
for(int p = 0; p < nao; p++) {
for(int q = 0; q < nao; q++) {
for(int r = 0; r < nao; r++) {
for(int s = 0; s < nao; s++,index++) {
ijkl[idx] += cvec[p*nmo + i] * cvec[q*nmo +j]
* cvec[r*nmo + k] * cvec[s*nmo + l]
* pqrs[index];
}
}
}
}
}
}
}
}
pqrs_av.release(); pqrs = 0;
cvec_av.release(); cvec = 0;
auto_vec<double> evals_av(new double [nmo]);
double *evals = evals_av.get();
ref_mp2_wfn_->eigenvalues()->convert(evals);
double energy = 0.0;
for(int i=0; i < nocc; i++) {
for(int j=0; j < nocc; j++) {
for(int a=nocc; a < nmo; a++) {
for(int b=nocc; b < nmo; b++) {
int iajb = (((i*nmo+a)*nmo+j)*nmo+b);
int ibja = (((i*nmo+b)*nmo+j)*nmo+a);
energy += (2 * ijkl[iajb] - ijkl[ibja]) * ijkl[iajb]/
(evals[i] + evals[j] - evals[a] - evals[b]);
}
}
}
}
ijkl_av.release(); ijkl = 0;
evals_av.release(); evals = 0;
return energy;
}

## MP2 Implementation Example: Makefile

This example Makefile demonstrates how to link in a new class to form a new mpqc executable, here named mp2. The code is given in the MP2 Implementation Example: Source section. The sc-config command is used to obtain information about how the SC toolkit was compiled and installed. The library specified with -lmpqc provides the main routine from mpqc.

# Change this to the path to your installed sc-config script.
SCCONFIG = /usr/local/mpqc/current/bin/sc-config
CXX := $(shell $(SCCONFIG) --cxx)
CXXFLAGS := $(shell $(SCCONFIG) --cxxflags)
CPPFLAGS := $(shell $(SCCONFIG) --cppflags)
LIBS := $(shell $(SCCONFIG) --libs)
LIBDIR := $(shell $(SCCONFIG) --libdir)
LTLINK := $(shell $(SCCONFIG) --ltlink)
LTLINKBINOPTS := $(shell $(SCCONFIG) --ltlinkbinopts)
mp2: mp2.o
$(LTLINK) $(CXX) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS)

## MP2 Implementation Example: Input

This input file can be used with the program illustrated in the MP2 Implementation Example: Source section. It will compute the MP2 energy using the new MP2 class. Note that only the object-oriented input format can be used with user provided classes.

% emacs should use -*- KeyVal -*- mode
molecule<Molecule>: (
symmetry = C1
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: (
checkpoint = no
savestate = no
% MP2 is the new class. Change MP2 to MBPT2 to test
% against the standard MP2 code
mole<MP2>: (
molecule = $:molecule
basis = $:basis
reference<CLHF>: (
molecule = $:molecule
basis = $:basis
memory = 16000000
)
)
)

# Exception Handling in SC

The development of SC began before exception handling was available in C++. A retrofit of the code to use exceptions is in progress. It is difficult to retrofit a code, especially a parallel code, to do exception handling. There will be some limitations: exception handling will not work well for parallel jobs, objects whose members throw might be left in a questionable state, etc. However, it is intended that SC objects will be usable in an interactive environment. It is also planned that exceptions be used internally to facilitate recover from certain problems.

All new code should use exceptions instead of exit or abort and allocate resources in such a way that, if an exception occurs, all resources such as memory or locks are released. A hierarchy of exception classes has been created that maps better to scientific computing than the standard exceptions. More information is below, as well as in the documentation for the SCException class and its derivatives.

- Exceptions and Memory Allocation
- Exceptions and Locks
- Exceptions and Region Timers
- Using the SC Exception Classes
- Debugging Code with Exceptions

## Exceptions and Memory Allocation

Consider the following code fragment:

    Object *obj = new Object;
    double *array = new double[n];

    f(obj, array, mol);

    delete obj;
    delete[] array;

If an exception is thrown in the function f(), then storage for array and obj will not be released. The standard C++ library provides a class, auto_ptr, to deal with obj, and the SC toolkit provides a class, auto_vec, to deal with array.

The include files for these two classes are:

    #include <memory>
    #include <util/misc/autovec.h>

the code would be modified as follows:

    std::auto_ptr<Object> obj(new Object);
    sc::auto_vec<double> array(new double[n]);

    f(obj.get(), array.get());

    obj.release();  // or just let the destructor release it
    array.release();  // or just let the destructor release it

Note that when sc::Ref is used to store pointers, the storage will automatically be released when necessary. No special treatment is needed to deal with exceptions.

## Exceptions and Locks

Consider the following code fragment:

    g(const sc::Ref<sc::ThreadLock> &lock)
    {
      lock->lock();
      f();
      lock->unlock();
    }

If f() throws, then the lock is never released. The ThreadLock lock() and unlock() members should not be used anymore. Now do the following:

    g(const sc::Ref<sc::ThreadLock> &lock)
    {
      sc::ThreadLockHolder lockholder(lock);
      f();
      lockholder->unlock(); // or let the destructor unlock it
    }

## Exceptions and Region Timers

Consider the following code fragment:

    g(const sc::Ref<sc::RegionTimer> &regtim)
    {
      regtim->enter("f()");
      f();
      regtim->exit();
    }

If f() throws, then the "f()" timing region is never exited. Instead use the following:

    g(const sc::Ref<sc::RegionTimer> &regtim)
    {
      sc::Timer timer(regtim, "f()");
      f();
      timer.reset(); // or let the destructor exit the region
    }

## Using the SC Exception Classes

The SC exceptions provide information that can be used into two ways. First, text information is provided so that if the exception is not caught at a lower level, then the mpqc executable will catch it and write information about the problem to the terminal or an output file. Second, information about the nature of the problem is provided, to permit developers to catch the exception and deal with it in some way. The documentation for sc::SCException and all of its derivatives gives more information about the exceptions that are available. As an example, consider the following loop, where a maximum number of iterations is permitted:

    XYZ::update()
    {
      for (int i=0; i<maxiter; i++) {
        // ... compute xyz update ...
        if (residual < threshold) return;
      }
      throw MaxIterExceeded("too many iterations xyz computation",
                            __FILE__, __LINE__, maxiter, class_desc());
    }

The first argument to the exception class is a brief description of the error. Additional information can be provided, see SCException::elaborate() description below. The next two arguments are the filename and line number. The C preprocessor provides these for you with the FILE and LINE macros. The next argument is specific to the MaxIterExceeded exception; it is the maximum number of iterations. Finally, a ClassDesc* can be given, which will be used to print out the class name of the object that failed. All of these arguments are optional; however, the first three should always be given.

It is possible to provide additional information using the SCException::elaborate() member. This will return a ostream, and the additional information can be written to this stream. However, if for some reason it is not possible to write to this stream (say, there wasn't enough memory to allocate it), then an exception will be thrown. For this reason, the string description given as the first argument should be informative since the additional information might not be available, and attempts to use elaborate() should be in a try block. So, for example, the elaborate() member could be used in the above example as follows:

    XYZ::update()
    {
      for (int i=0; i<maxiter; i++) {
        // ... compute xyz update ...
        if (residual < threshold) return;
      }
      MaxIterExceeded ex("too many iterations in xyz computation",
                         __FILE__, __LINE__, maxiter, class_desc());
      try {
        ex.elaborate() << "this can happen when the stepsize is too small"
                       << std::endl
                       << "the stepsize is " << stepsize
                       << std::endl;
      }
      catch (...) {}
      throw ex;
    }

Note that writing to stream returned by elaborate() won't necessarily cause anything to get written to the terminal or an output file. The information will be available when the what() member is called, if writing to the stream succeeds. If the exception is caught by the mpqc main routine, then it will be printed for the user to see. If the program catches the exception and determines that it is possible to proceed in a different way, then the user will never see the text.

## Debugging Code with Exceptions

Usually, exceptions are not the desired behaviour in a program, and it is necessary to debug a program that throws an exception. This was easy when abort was called, because abort would raise a signal that was caught by the debugger and the code is stopped at the appropriate place. With exceptions the matter is more complex, because the stack is unwound when an exception is thrown and most debugging information is lost. To work around this problem, a breakpoint can be set in code that will be reached only in an exception, and will be run before the stack unwind begins. A useful place to do this when GCC is used as the compiler is in the routine __cxa_allocate_exception(). So, in gdb, the following could be done:

    $ gdb ./scextest
    (gdb) b main
    (gdb) run
    Breakpoint 1, main () at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:172
    172           f();
    (gdb) b __cxa_allocate_exception
    (gdb) cont
    Breakpoint 2, 0x40582d46 in __cxa_allocate_exception ()
       from /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.5/libstdc++.so.5
    (gdb) where
    #0  0x40582d46 in __cxa_allocate_exception ()
       from /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.5/libstdc++.so.5
    #1  0x0804b3f7 in f () at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:60
    #2  0x0804b9e9 in main ()
        at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:172

Giving gdb "b main" followed by "run" was required before gdb could find the __cxa_allocate_exception symbol.

# Adding Test Cases to the Verification Suite

There are two ways to test an MPQC build. The `testbuild` and `testrun` make targets can be used to run test programs in various library directories, and the `check` and related make targets can be used to run MPQC on sets of input files. See Validating MPQC for more information about how to run the tests.

Test programs can be added to the library directories by providing a source file with a main routine. The set of test programs that is to be built and run by `testbuild` and `testrun`, respectively, is given by the `TESTPROGS` variable in the library's `Makefile`. It may be necessary for an explicit rule to be given for building the test program to ensure that necessary libraries are linked in. If a file named after the test program with a `.out` suffix is found in the source directory, then `testrun` fail if the command's output differs from that file. Care must be taken to ensure that the output is architecture independent in this case. Otherwise, `testrun` will fail only if running the command results in a nonzero return code.

Additional MPQC test inputs can be added in the `src/bin/mpqc/validate` directory. These inputs can be provided in one of two ways. An input which is used to automatically generate multiple test cases can be written (with a `.qci` suffix), or a subdirectory with each input can be made. See `Makefile`, `basis1.qci`, and `input` in the `src/bin/mpqc/validate` directory for examples.

After you have added new inputs and modified the Makefile, change into the `src/bin/mpqc/validate` subdirectory of your object directory (where you compiled MPQC) and type `make inputs`. This will create a `input` subdirectory containing MPQC input files with a `.in` suffix. Files ending with a `.qci` suffix will also be placed in the `input` directory. These contain a description of the calculation that is used by the utility program that checks the results of the validation suite. Both the `.in` and `.qci` files for the new test cases must be copied into the `ref` directory in the source tree. Note that inputs that are not useful in your build environment are not created by `make inputs`.