simple.cc

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

/* simple.cc -- implementation of the simple internal coordinate classes
 *
 *      THIS SOFTWARE FITS THE DESCRIPTION IN THE U.S. COPYRIGHT ACT OF A
 *      "UNITED STATES GOVERNMENT WORK".  IT WAS WRITTEN AS A PART OF THE
 *      AUTHOR'S OFFICIAL DUTIES AS A GOVERNMENT EMPLOYEE.  THIS MEANS IT
 *      CANNOT BE COPYRIGHTED.  THIS SOFTWARE IS FREELY AVAILABLE TO THE
 *      PUBLIC FOR USE WITHOUT A COPYRIGHT NOTICE, AND THERE ARE NO
 *      RESTRICTIONS ON ITS USE, NOW OR SUBSEQUENTLY.
 *
 *  Author:
 *      E. T. Seidl
 *      Bldg. 12A, Rm. 2033
 *      Computer Systems Laboratory
 *      Division of Computer Research and Technology
 *      National Institutes of Health
 *      Bethesda, Maryland 20892
 *      Internet: [e-mail]
 *      February, 1993
 */

#ifdef __GNUC__
#pragma implementation
#endif

#include <string.h>
#include <math.h>

#if defined(SGI) && !defined(__GNUC__)
#include <bstring.h>
#endif

#include <util/misc/formio.h>
#include <util/state/stateio.h>
#include <chemistry/molecule/simple.h>
#include <chemistry/molecule/localdef.h>

#include <util/container/bitarray.h>

using namespace std;
using namespace sc;

//////////////////////////////////////////////////////////////////////

static ClassDesc SimpleCo_cd(
  typeid(SimpleCo),"SimpleCo",1,"public IntCoor",
  0, 0, 0);

SimpleCo::SimpleCo():
  natoms_(0),
  atoms(0)
{
}

SimpleCo::SimpleCo(int na, const char *re) :
  IntCoor(re),
  natoms_(na), atoms(0)
{
  atoms=new int[na]; memset(atoms,'\0',sizeof(int)*na);
}

SimpleCo::SimpleCo(const Ref<KeyVal>&kv,int na) :
  IntCoor(kv),
  natoms_(na), atoms(0)
{
  atoms=new int[na];
  memset(atoms,'\0',sizeof(int)*na);

  if (kv->count() == 0) {
      int i;
      for (i=0; i<na; i++) {
          atoms[i] = kv->intvalue("atoms",i);
          if (kv->error() != KeyVal::OK) break;
        }
      if (i == 0) {
          // couldn't find any atoms so look for a molecule and atom labels
          Ref<Molecule> mol; mol << kv->describedclassvalue("molecule");
          if (mol.nonnull()) {
              for (i=0; i<na; i++) {
                  char *label = kv->pcharvalue("atom_labels", i);
                  if (kv->error() != KeyVal::OK) break;
                  atoms[i] = mol->atom_label_to_index(label) + 1;
                  delete[] label;
                  if (atoms[i] == 0) break;
                }
            }
        }
      if (i != na) {
          ExEnv::err0() << indent
               << scprintf(
                   "%s::%s(const Ref<KeyVal>&): missing one of the atoms "
                   "or atom_labels (requires a molecule too) "
                   "or an atom label was invalid\n",
                   class_name(),class_name());
          kv->errortrace();
          abort();
        }
    }
  else {
      // This is a shorthand form for the input that doesn't allow
      // the specification of a value.
      if (label_) delete[] label_;
      label_=kv->pcharvalue(0);
      for (int i=0; i<na; i++) {
          atoms[i]=kv->intvalue(i+1);
          if (kv->error() != KeyVal::OK) {
              ExEnv::err0() << indent
                   << scprintf("%s::%s(const Ref<KeyVal>&): missing an atom\n",
                               class_name(),class_name());
              kv->errortrace();
              abort();
            }
        }
    }
}

SimpleCo::~SimpleCo()
{
  if(atoms) delete[] atoms; atoms=0;
  natoms_=0;
}

void
SimpleCo::save_data_state(StateOut& s)
{
  IntCoor::save_data_state(s);
  s.put(natoms_);
  s.put(atoms,natoms_);
}

SimpleCo::SimpleCo(StateIn& si):
  IntCoor(si)
{
  si.get(natoms_);
  si.get(atoms);
}

int
SimpleCo::natoms() const
{
  return natoms_;
}

int
SimpleCo::operator[](int i) const
{
  return atoms[i];
}

int
SimpleCo::operator!=(SimpleCo&u)
{
  return !(*this==u);
}

int
SimpleCo::operator==(SimpleCo& sc)
{
  if(label_ && !sc.label_ || !label_ && sc.label_) return 0;
  if(label_ && strcmp(label_,sc.label_)) return 0;

  if(atoms && !sc.atoms || !atoms && sc.atoms) return 0;
  if(atoms)
    for(int i=0; i < natoms_; i++) if (atoms[i]!=sc.atoms[i]) return 0;

  return 1;
}

double
SimpleCo::force_constant(Ref<Molecule>&mol)
{
  return calc_force_con(*mol);
}

// this updates the values before it computes the bmatrix,
// which is not quite what I wanted--but close enough
void
SimpleCo::bmat(const Ref<Molecule>&mol,RefSCVector&bmat,double coef)
{
  int i;
  int n = bmat.dim().n();

  double* v = new double[n];
  for (i=0; i<n; i++) v[i] = bmat(i);

  calc_intco(*mol,v,coef);

  for (i=0; i<n; i++) {
      bmat(i) = v[i];
    }
  
  delete[] v;
}

void
SimpleCo::update_value(const Ref<Molecule>&mol)
{
  calc_intco(*mol);
}

void
SimpleCo::print_details(const Ref<Molecule> &mol, ostream& os) const
{
  os << indent
     << scprintf("%-5s %7s %11.5f", ctype(), (label()?label():""),
                 preferred_value());
  
  int i;
  for (i=0; i<natoms(); i++)
      os << scprintf(" %4d", atoms[i]);

  if (mol.nonnull()) {
      char *separator = " ";
      os << "  ";
      for (i=0; i<(4-natoms()); i++) {
          os << "   ";
        }
      for (i=0; i<natoms(); i++) {
          os << separator << AtomInfo::symbol(mol->Z(atoms[i]-1));
          separator = "-";
        }
    }

  os << endl;
  
}

// this doesn't catch all cases, it would be best for each subclass
// to override this
int
SimpleCo::equivalent(Ref<IntCoor>&c)
{
  if (class_desc() != c->class_desc()) {
      return 0;
    }
  SimpleCo* sc = dynamic_cast<SimpleCo*>(c.pointer());
  if (natoms_ != sc->natoms_) return 0; // this should never be the case
  for (int i=0; i<natoms_; i++) {
      if (atoms[i] != sc->atoms[i]) return 0;
    }
  return 1;
}

/////////////////////////////////////////////////////////////////////////////

// Local Variables:
// mode: c++
// c-file-style: "CLJ"
// End: