/** Like the strip action, closest will modify the current parm keeping info
* for atoms in mask plus the closestWaters solvent molecules. Set up the
* vector of MolDist objects, one for every solvent molecule in the original
* parm file. Atom masks for each solvent molecule will be set up.
*/
Action_Closest::RetType Action_Closest::Setup(Topology const& topIn, CoordinateInfo const& cInfoIn)
{
// If there are no solvent molecules this action is not valid.
if (topIn.Nsolvent()==0) {
mprintf("Warning: Parm %s does not contain solvent.\n",topIn.c_str());
return Action_Closest::SKIP;
}
// If # solvent to keep >= solvent in this parm the action is not valid.
if (closestWaters_ >= topIn.Nsolvent()) {
mprintf("Warning: # solvent to keep (%i) >= # solvent molecules in '%s' (%i)\n",
closestWaters_, topIn.c_str(), topIn.Nsolvent());
return Action_Closest::SKIP;
}
image_.SetupImaging( cInfoIn.TrajBox().Type() );
if (image_.ImagingEnabled())
mprintf("\tDistances will be imaged.\n");
else
mprintf("\tImaging off.\n");
// LOOP OVER MOLECULES
// 1: Check that all solvent molecules contain same # atoms. Solvent
// molecules must be identical for the command to work properly;
// the prmtop strip occurs only once so the solvent params become fixed.
// 2: Set up a mask for all solvent molecules.
SolventMols_.clear();
// NOTE: May not be necessary to init 'solvent'
MolDist solvent;
solvent.D = 0.0;
solvent.mol = 0;
SolventMols_.resize(topIn.Nsolvent(), solvent);
std::vector<MolDist>::iterator mdist = SolventMols_.begin();
// 3: Set up the soluteMask for all non-solvent molecules.
int molnum = 1;
int nclosest = 0;
int NsolventAtoms = -1;
for (Topology::mol_iterator Mol = topIn.MolStart();
Mol != topIn.MolEnd(); ++Mol)
{
if ( Mol->IsSolvent() ) {
// Solvent, check for same # of atoms.
if (NsolventAtoms == -1)
NsolventAtoms = Mol->NumAtoms();
else if ( NsolventAtoms != Mol->NumAtoms() ) {
mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n"
"Error: First solvent mol = %i atoms, solvent mol %i = %i atoms.\n",
topIn.c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms());
return Action_Closest::ERR;
}
// mol here is the output molecule number which is why it starts from 1.
mdist->mol = molnum;
// Solvent molecule mask
mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() );
// Atoms in the solvent molecule to actually calculate distances to.
if (firstAtom_) {
mdist->solventAtoms.assign(1, Mol->BeginAtom() );
} else {
mdist->solventAtoms.clear();
mdist->solventAtoms.reserve( Mol->NumAtoms() );
for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++)
mdist->solventAtoms.push_back( svatom );
}
if (debug_ > 0) {
mprintf("DEBUG:\tSet up mol %i:", mdist->mol); // DEBUG
mdist->mask.PrintMaskAtoms("solvent"); // DEBUG
mprintf("\n"); // DEBUG
}
++mdist;
}
++molnum;
}
// Setup distance atom mask
// NOTE: Should ensure that no solvent atoms are selected!
if ( topIn.SetupIntegerMask(distanceMask_) ) return Action_Closest::ERR;
if (distanceMask_.None()) {
mprintf("Warning: Distance mask '%s' contains no atoms.\n",
distanceMask_.MaskString());
return Action_Closest::SKIP;
}
distanceMask_.MaskInfo();
// Check the total number of solvent atoms to be kept.
NsolventAtoms *= closestWaters_;
mprintf("\tKeeping %i solvent atoms.\n",NsolventAtoms);
if (NsolventAtoms < 1) {
mprintf("Warning: # of solvent atoms to be kept is < 1.\n");
return Action_Closest::SKIP;
}
NsolventMolecules_ = (int)SolventMols_.size();
return Action_Closest::OK;
}
/** Each rank only sets up file that it will process. */
int TrajIOarray::SetupIOarray(ArgList& argIn, TrajFrameCounter& counter,
CoordinateInfo& cInfo, Topology* trajParm,
Parallel::Comm const& ensComm, Parallel::Comm const& trajComm)
{
// Sanity check
if (!IOarray_.empty()) {
mprinterr("Internal Error: SetupIOarray() has been called twice.\n");
return 1;
}
// Detect format
FileName const& repFname = replica_filenames_[ensComm.Rank()];
TrajectoryFile::TrajFormatType repformat = TrajectoryFile::UNKNOWN_TRAJ;
TrajectoryIO* replica0 = TrajectoryFile::DetectFormat( repFname, repformat );
if ( replica0 == 0 ) {
mprinterr("Error: Could not set up replica file %s\n", repFname.full());
return 1;
}
mprintf("\tReading '%s' as %s\n", repFname.full(), TrajectoryFile::FormatString(repformat));
replica0->SetDebug( debug_ );
// Construct the IOarray_ with blanks for all except this rank.
for (int member = 0; member != ensComm.Size(); member++)
if (member == ensComm.Rank())
IOarray_.push_back( replica0 );
else
IOarray_.push_back( 0 );
// Process format-specific read args.
replica0->processReadArgs( argIn );
// Set up replica for reading and get # frames
int nframes = replica0->setupTrajin( repFname, trajParm );
if (nframes == TrajectoryIO::TRAJIN_ERR) {
mprinterr("Error: Could not set up %s for reading.\n", repFname.full());
return 1;
}
// Set coordinate info
cInfo = replica0->CoordInfo();
int totalFrames = nframes;
if (cInfo.ReplicaDimensions().Ndims() > 0) { // TODO put in common routine
mprintf("\tReplica dimensions:\n");
for (int rd = 0; rd < cInfo.ReplicaDimensions().Ndims(); rd++)
mprintf("\t\t%i: %s\n", rd+1, cInfo.ReplicaDimensions().Description(rd));
}
// Check # frames in all files, use lowest.
Parallel::World().AllReduce( &totalFrames, &nframes, 1, MPI_INT, MPI_MIN );
if (totalFrames != nframes) {
rprintf("Warning: Replica '%s' frames (%i) is > # frames in shortest replica.\n",
repFname.full(), nframes);
mprintf("Warning: Setting total # of frames to read from replica ensemble to %i\n",
totalFrames);
}
if (trajComm.Master()) {
static const int iSize = 6;
static const char* iTitle[iSize] = {"box", "velocity", "temperature", "time", "force",
"replica dimensions"};
// Check coordinate info of all files 0 1 2 3 4 5
std::vector<int> Info( iSize * ensComm.Size() ); // box, vel, temp, time, force, nRepDims
int rank_info[iSize];
rank_info[0] = (int)cInfo.TrajBox().Type();
rank_info[1] = (int)cInfo.HasVel();
rank_info[2] = (int)cInfo.HasTemp();
rank_info[3] = (int)cInfo.HasTime();
rank_info[4] = (int)cInfo.HasForce();
rank_info[5] = cInfo.ReplicaDimensions().Ndims();
ensComm.AllGather( rank_info, iSize, MPI_INT, &Info[0] );
// TODO Should mismatches be errors instead?
for (int midx = 0; midx != iSize; midx++) {
for (int ridx = midx + iSize; ridx < (int)Info.size(); ridx += iSize) {
if (Info[midx] != Info[ridx]) {
rprintf("Warning: Replica %i %s info does not match first replica.\n",
ridx/iSize, iTitle[midx]);
}
}
}
}
// TODO: Put code below into a common routine with serial version
// Check how many frames will actually be read
if (counter.CheckFrameArgs( totalFrames, argIn )) return 1;
// SANITY CHECK
if (IOarray_.size() != replica_filenames_.size()) {
mprinterr("Error: Not all replica files were set up.\n");
return 1;
}
// Update ensemble size
cInfo.SetEnsembleSize( (int)IOarray_.size() );
if (debug_ > 0)
cInfo.PrintCoordInfo( repFname.full(), trajParm->c_str() );
return 0;
}