Exemplo n.º 1
0
void ComputeGridForce::doForce(FullAtom* p, Results* r)
{
    SimParameters *simParams = Node::Object()->simParameters;
    Molecule *mol = Node::Object()->molecule;
    
    Force *forces = r->f[Results::normal];
    BigReal energy = 0;
    Force extForce = 0.;
    Tensor extVirial;
    
    int numAtoms = homePatch->getNumAtoms();

    if ( mol->numGridforceGrids < 1 ) NAMD_bug("No grids loaded in ComputeGridForce::doForce()");
    
    for (int gridnum = 0; gridnum < mol->numGridforceGrids; gridnum++) {
	GridforceGrid *grid = mol->get_gridfrc_grid(gridnum);
	
	if (homePatch->flags.step % GF_OVERLAPCHECK_FREQ == 0) {
	    // only check on node 0 and every GF_OVERLAPCHECK_FREQ steps
	  if (simParams->langevinPistonOn || simParams->berendsenPressureOn) {
		// check for grid overlap if pressure control is on
		// not needed without pressure control, since the check is also performed on startup
      if (!grid->fits_lattice(homePatch->lattice)) {
        char errmsg[512];
        if (simParams->gridforcechecksize) {
          sprintf(errmsg, "Warning: Periodic cell basis too small for Gridforce grid %d.  Set gridforcechecksize off in configuration file to ignore.\n", gridnum);
          NAMD_die(errmsg);      
        }
      }
	 }
	}
	
	Position center = grid->get_center();
	
	if (homePatch->flags.step % 100 == 1) {
	    DebugM(3, "center = " << center << "\n" << endi);
	    DebugM(3, "e = " << grid->get_e() << "\n" << endi);
	}
	
	if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeFull) {
	    GridforceFullMainGrid *g = (GridforceFullMainGrid *)grid;
	    do_calc(g, gridnum, p, numAtoms, mol, forces, energy, extForce, extVirial);
	} else if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeLite) {
	    GridforceLiteGrid *g = (GridforceLiteGrid *)grid;
	    do_calc(g, gridnum, p, numAtoms, mol, forces, energy, extForce, extVirial);
	}
    }
    reduction->item(REDUCTION_MISC_ENERGY) += energy;
    ADD_VECTOR_OBJECT(reduction,REDUCTION_EXT_FORCE_NORMAL,extForce);
    ADD_TENSOR_OBJECT(reduction,REDUCTION_VIRIAL_NORMAL,extVirial);
    reduction->submit();
}
Exemplo n.º 2
0
void ComputeGlobal::recvResults(ComputeGlobalResultsMsg *msg) {
  DebugM(3,"Receiving results (" << msg->aid.size() << " forces, "
	 << msg->newgdef.size() << " new group atoms) on client\n");

  // set the forces only if we aren't going to resend the data
  int setForces = !msg->resendCoordinates;

  if(setForces) { // we are requested to 
    // Store forces to patches
    PatchMap *patchMap = PatchMap::Object();
    int numPatches = patchMap->numPatches();
    AtomMap *atomMap = AtomMap::Object();
    const Lattice & lattice = patchList[0].p->lattice;
    ResizeArrayIter<PatchElem> ap(patchList);
    Force **f = new Force*[numPatches];
    FullAtom **t = new FullAtom*[numPatches];
    for ( int i = 0; i < numPatches; ++i ) { f[i] = 0; t[i] = 0; }
    Force extForce = 0.;
    Tensor extVirial;

    for (ap = ap.begin(); ap != ap.end(); ap++) {
      (*ap).r = (*ap).forceBox->open();
      f[(*ap).patchID] = (*ap).r->f[Results::normal];
      t[(*ap).patchID] = (*ap).p->getAtomList().begin();
    }

    AtomIDList::iterator a = msg->aid.begin();
    AtomIDList::iterator a_e = msg->aid.end();
    ForceList::iterator f2 = msg->f.begin();
    for ( ; a != a_e; ++a, ++f2 ) {
      DebugM(1,"processing atom "<<(*a)<<", F="<<(*f2)<<"...\n");
      /* XXX if (*a) is out of bounds here we get a segfault */
      LocalID localID = atomMap->localID(*a);
      if ( localID.pid == notUsed || ! f[localID.pid] ) continue;
      Force f_atom = (*f2);
      f[localID.pid][localID.index] += f_atom;
      Position x_orig = t[localID.pid][localID.index].position;
      Transform trans = t[localID.pid][localID.index].transform;
      Position x_atom = lattice.reverse_transform(x_orig,trans);
      extForce += f_atom;
      extVirial += outer(f_atom,x_atom);
    }
    DebugM(1,"done with the loop\n");

  // calculate forces for atoms in groups
    Molecule *mol = Node::Object()->molecule;
    AtomIDList::iterator g_i, g_e;
    g_i = gdef.begin(); g_e = gdef.end();
    ResizeArray<BigReal>::iterator gm_i = gmass.begin();
    ForceList::iterator gf_i = msg->gforce.begin();
    //iout << iDEBUG << "recvResults\n" << endi;
    for ( ; g_i != g_e; ++g_i, ++gm_i, ++gf_i ) {
      //iout << iDEBUG << *gf_i << '\n' << endi;
      Vector accel = (*gf_i) / (*gm_i);
      for ( ; *g_i != -1; ++g_i ) {
	//iout << iDEBUG << *g_i << '\n' << endi;
	LocalID localID = atomMap->localID(*g_i);
	if ( localID.pid == notUsed || ! f[localID.pid] ) continue;
	Force f_atom = accel * mol->atommass(*g_i);
	f[localID.pid][localID.index] += f_atom;
        Position x_orig = t[localID.pid][localID.index].position;
        Transform trans = t[localID.pid][localID.index].transform;
        Position x_atom = lattice.reverse_transform(x_orig,trans);
        extForce += f_atom;
        extVirial += outer(f_atom,x_atom);
      }
    }
    DebugM(1,"done with the groups\n");

    for (ap = ap.begin(); ap != ap.end(); ap++) {
      (*ap).forceBox->close(&((*ap).r));
    }

    delete [] f;
    delete [] t;

    ADD_VECTOR_OBJECT(reduction,REDUCTION_EXT_FORCE_NORMAL,extForce);
    ADD_TENSOR_OBJECT(reduction,REDUCTION_VIRIAL_NORMAL,extVirial);
    reduction->submit();
  }
  // done setting the forces

  // Get reconfiguration if present
  if ( msg->reconfig ) configure(msg->newaid, msg->newgdef);

  // send another round of data if requested

  if(msg->resendCoordinates) {
    DebugM(3,"Sending requested data right away\n");
    sendData();
  }

  delete msg;
  DebugM(3,"Done processing results\n");
}