ComputeMsmSerialMgr Class Reference

Inheritance diagram for ComputeMsmSerialMgr:

Public Member Functions
	ComputeMsmSerialMgr ()
	~ComputeMsmSerialMgr ()
void	setCompute (ComputeMsmSerial *c)
void	recvCoord (MsmSerialCoordMsg *)
void	recvForce (MsmSerialForceMsg *)

Detailed Description

Definition at line 54 of file ComputeMsmSerial.C.

Constructor & Destructor Documentation

ComputeMsmSerialMgr()

ComputeMsmSerialMgr::ComputeMsmSerialMgr

(

)

Definition at line 81 of file ComputeMsmSerial.C.

                                         :
  msmProxy(thisgroup), msmCompute(0), numSources(0), numArrived(0),
  coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0),
  msmsolver(0), msmcoord(0), msmforce(0)
{
  CkpvAccess(BOCclass_group).computeMsmSerialMgr = thisgroup;
}

~ComputeMsmSerialMgr()

ComputeMsmSerialMgr::~ComputeMsmSerialMgr

(

)

Definition at line 89 of file ComputeMsmSerial.C.

References NL_msm_destroy().

{
  for (int i=0;  i < numSources;  i++)  delete coordMsgs[i];
  delete [] coordMsgs;
  delete [] coord;
  delete [] force;
  delete oldmsg;
  if (msmsolver) NL_msm_destroy(msmsolver);
  if (msmcoord) delete[] msmcoord;
  if (msmforce) delete[] msmforce;
}

Member Function Documentation

recvCoord()

void ComputeMsmSerialMgr::recvCoord

(

MsmSerialCoordMsg *

msg

)

Definition at line 308 of file ComputeMsmSerial.C.

References Lattice::a(), Lattice::a_p(), Lattice::a_r(), Lattice::b(), Lattice::b_p(), Lattice::b_r(), Lattice::c(), Lattice::c_p(), Lattice::c_r(), ComputeMsmSerialAtom::charge, MsmSerialCoordMsg::coord, COULOMB, MsmSerialForceMsg::energy, MsmSerialForceMsg::force, ComputeMsmSerialAtom::id, MsmSerialCoordMsg::lattice, Node::molecule, NAMD_die(), NL_msm_compute_force(), NL_MSM_COMPUTE_LONG_RANGE, NL_msm_configure(), NL_msm_create(), NL_MSM_PERIODIC_ALL, NL_MSM_PERIODIC_VEC1, NL_MSM_PERIODIC_VEC2, NL_MSM_PERIODIC_VEC3, NL_msm_setup(), MsmSerialCoordMsg::numAtoms, Molecule::numAtoms, PatchMap::Object(), Node::Object(), Lattice::origin(), ComputeMsmSerialAtom::position, rescale_nonperiodic_cell(), Node::simParameters, simParams, MsmSerialCoordMsg::sourceNode, split(), MsmSerialForceMsg::virial, Vector::x, Vector::y, and Vector::z.

                                                          {
  if ( ! numSources ) {
    numSources = (PatchMap::Object())->numNodesWithPatches();
    coordMsgs = new MsmSerialCoordMsg*[numSources];
    for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
    numArrived = 0;
    numAtoms = Node::Object()->molecule->numAtoms;
    coord = new ComputeMsmSerialAtom[numAtoms];
    force = new MsmSerialForce[numAtoms];
  }

  int i;
  for ( i=0; i < msg->numAtoms; ++i ) {
    coord[msg->coord[i].id] = msg->coord[i];
  }

  coordMsgs[numArrived] = msg;
  ++numArrived;

  if ( numArrived < numSources ) return;
  numArrived = 0;

  // ALL DATA ARRIVED --- CALCULATE FORCES
  Lattice lattice = msg->lattice;
  SimParameters *simParams = Node::Object()->simParameters;

  double energy = 0;
  double virial[3][3];

  int rc = 0;  // return code

  if ( ! msmsolver ) {
    //
    // setup MSM solver
    //
    msmsolver = NL_msm_create();
    if ( ! msmsolver ) NAMD_die("unable to create MSM solver");
    double dielectric = simParams->dielectric;
    double cutoff = simParams->cutoff;
    double gridspacing = simParams->MSMGridSpacing;
    double padding = simParams->MSMPadding;
    int approx = simParams->MSMApprox;
    int split = simParams->MSMSplit;
    int nlevels = simParams->MSMLevels;
    int msmflags = 0;
    msmflags |= (lattice.a_p() ? NL_MSM_PERIODIC_VEC1 : 0);
    msmflags |= (lattice.b_p() ? NL_MSM_PERIODIC_VEC2 : 0);
    msmflags |= (lattice.c_p() ? NL_MSM_PERIODIC_VEC3 : 0);
    msmflags |= NL_MSM_COMPUTE_LONG_RANGE;  // compute only long-range part
    //msmflags |= NL_MSM_COMPUTE_ALL;
    //printf("msmflags = %x\n", msmflags);
    rc = NL_msm_configure(msmsolver, gridspacing, approx, split, nlevels);
    if (rc) NAMD_die("unable to configure MSM solver");
    Vector u=lattice.a(), v=lattice.b(), w=lattice.c(), c=lattice.origin();
    Vector ru=lattice.a_r(), rv=lattice.b_r(), rw=lattice.c_r();
    if ((msmflags & NL_MSM_PERIODIC_ALL) != NL_MSM_PERIODIC_ALL) {
      // called only if there is some non-periodic boundary
      int isperiodic = (msmflags & NL_MSM_PERIODIC_ALL);
      //printf("calling rescale\n");
      rescale_nonperiodic_cell(u, v, w, c, ru, rv, rw,
          isperiodic, numAtoms, coord, padding, gridspacing);
    }
    double vec1[3], vec2[3], vec3[3], center[3];
    vec1[0] = u.x;
    vec1[1] = u.y;
    vec1[2] = u.z;
    vec2[0] = v.x;
    vec2[1] = v.y;
    vec2[2] = v.z;
    vec3[0] = w.x;
    vec3[1] = w.y;
    vec3[2] = w.z;
    center[0] = c.x;
    center[1] = c.y;
    center[2] = c.z;
#if 0
    printf("dielectric = %g\n", dielectric);
    printf("vec1 = %g %g %g\n", vec1[0], vec1[1], vec1[2]);
    printf("vec2 = %g %g %g\n", vec2[0], vec2[1], vec2[2]);
    printf("vec3 = %g %g %g\n", vec3[0], vec3[1], vec3[2]);
    printf("center = %g %g %g\n", center[0], center[1], center[2]);
    printf("cutoff = %g\n", cutoff);
    printf("numatoms = %d\n", numAtoms);
#endif
    rc = NL_msm_setup(msmsolver, cutoff, vec1, vec2, vec3, center, msmflags);
    if (rc) NAMD_die("unable to set up MSM solver");
    msmcoord = new double[4*numAtoms];
    msmforce = new double[3*numAtoms];
    if (msmcoord==0 || msmforce==0) NAMD_die("can't allocate MSM atom buffers");
    // scale charges - these won't change
    double celec = sqrt(COULOMB / simParams->dielectric);
    for (i = 0;  i < numAtoms;  i++) {
      msmcoord[4*i+3] = celec * coord[i].charge;
    }
  }

  // evaluate long-range MSM forces
  for (i = 0;  i < numAtoms;  i++) {
    msmcoord[4*i  ] = coord[i].position.x;
    msmcoord[4*i+1] = coord[i].position.y;
    msmcoord[4*i+2] = coord[i].position.z;
  }
  for (i = 0;  i < numAtoms;  i++) {
    msmforce[3*i  ] = 0;
    msmforce[3*i+1] = 0;
    msmforce[3*i+2] = 0;
  }
  rc = NL_msm_compute_force(msmsolver, msmforce, &energy, msmcoord, numAtoms);
  if (rc) NAMD_die("error evaluating MSM forces");
  for (i = 0;  i < numAtoms;  i++) {
    force[i].x = msmforce[3*i  ];
    force[i].y = msmforce[3*i+1];
    force[i].z = msmforce[3*i+2];
  }
  // MSM does not yet calculate virial
  for (int k=0;  k < 3;  k++) {
    for (int l=0;  l < 3;  l++) {
      virial[k][l] = 0;
    }
  }

  // distribute forces
  for (int j=0;  j < numSources;  j++) {
    MsmSerialCoordMsg *cmsg = coordMsgs[j];
    coordMsgs[j] = 0;
    MsmSerialForceMsg *fmsg = new (cmsg->numAtoms, 0) MsmSerialForceMsg;

    for (int i=0;  i < cmsg->numAtoms;  i++) {
      fmsg->force[i] = force[cmsg->coord[i].id];
    }

    if ( ! j ) {  // set virial and energy only for first message
      fmsg->energy = energy;
      for (int k=0;  k < 3;  k++) {
        for (int l=0;  l < 3;  l++) {
          fmsg->virial[k][l] = virial[k][l];
        }
      }
    }
    else {  // set other messages to zero, add into reduction only once
      fmsg->energy = 0;
      for (int k=0;  k < 3;  k++) {
        for (int l=0;  l < 3;  l++) {
          fmsg->virial[k][l] = 0;
        }
      }
    }

    msmProxy[cmsg->sourceNode].recvForce(fmsg);
    delete cmsg;
  }
}

recvForce()

void ComputeMsmSerialMgr::recvForce

(

MsmSerialForceMsg *

msg

)

Definition at line 461 of file ComputeMsmSerial.C.

References ComputeMsmSerial::saveResults().

                                                          {
  msmCompute->saveResults(msg);
  delete oldmsg;
  oldmsg = msg;
}

setCompute()

void ComputeMsmSerialMgr::setCompute ( ComputeMsmSerial *  c )

inline

Definition at line 59 of file ComputeMsmSerial.C.

{ msmCompute = c; }

---

The documentation for this class was generated from the following file:

• ComputeMsmSerial.C