/** \param a1 First set of XYZ coordinates.
* \param a2 Second set of XYZ coordinates.
* \param ucell Unit cell vectors.
* \param recip Fractional cell vectors.
* \return the shortest vector from a1 to a2.
*/
Vec3 MinImagedVec(Vec3 const& a1, Vec3 const& a2,
Matrix_3x3 const& ucell, Matrix_3x3 const& recip)
{
Vec3 f1 = recip * a1;
Vec3 f2 = recip * a2;
// mprintf("DEBUG: a1= %g %g %g, f1= %g %g %g\n", a1[0], a1[1], a1[2], f1[0], f1[1], f1[2]);
// mprintf("DEBUG: a2= %g %g %g, f2= %g %g %g\n", a2[0], a2[1], a2[2], f2[0], f2[1], f2[2]);
for (unsigned int i = 0; i < 3; i++) {
f1[i] = f1[i] - floor(f1[i]);
f2[i] = f2[i] - floor(f2[i]);
}
// Self
Vec3 c1 = ucell.TransposeMult( f1 );
Vec3 c2 = ucell.TransposeMult( f2 );
Vec3 minVec = c2 - c1;
double minDist2 = minVec.Magnitude2();
// Images
for (int ix = -1; ix < 2; ix++) {
for (int iy = -1; iy < 2; iy++) {
for (int iz = -1; iz < 2; iz++) {
if (ix != 0 || iy != 0 || iz != 0) { // Ignore a2 self
Vec3 ixyz(ix, iy, iz);
c2 = ucell.TransposeMult(f2 + ixyz); // a2 image back in Cartesian space
Vec3 dxyz = c2 - c1;
double dist2 = dxyz.Magnitude2();
if (dist2 < minDist2) {
minDist2 = dist2;
minVec = dxyz;
}
}
}
}
}
return minVec;
}
// Action_ReplicateCell::Init()
Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Require imaging.
image_.InitImaging( true );
// Set up output traj
std::string trajfilename = actionArgs.GetStringKey("out");
parmfilename_ = actionArgs.GetStringKey("parmout");
bool setAll = actionArgs.hasKey("all");
std::string dsname = actionArgs.GetStringKey("name");
if (!dsname.empty()) {
coords_ = (DataSet_Coords*)init.DSL().AddSet(DataSet::COORDS, dsname, "RCELL");
if (coords_ == 0) return Action::ERR;
}
if (trajfilename.empty() && coords_ == 0) {
mprinterr("Error: Either 'out <traj filename> or 'name <dsname>' must be specified.\n");
return Action::ERR;
}
// Get Mask
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
// Determine which directions to set
if (setAll) {
for (int ix = -1; ix < 2; ix++)
for (int iy = -1; iy < 2; iy++)
for (int iz = -1; iz < 2; iz++) {
directionArray_.push_back( ix );
directionArray_.push_back( iy );
directionArray_.push_back( iz );
}
} else {
std::string dirstring = actionArgs.GetStringKey("dir");
while (!dirstring.empty()) {
std::vector<int> ixyz(3, -2);
std::vector<int>::iterator iptr = ixyz.begin();
for (std::string::const_iterator c = dirstring.begin();
c != dirstring.end(); ++c)
{
if (iptr == ixyz.end()) {
mprinterr("Error: 'dir' string has too many characters.\n");
return Action::ERR;
}
int sign = 1;
if (*c == '+') ++c;
else if (*c == '-') { sign = -1; ++c; }
if (isdigit( *c ))
*iptr = toDigit( *c ) * sign;
else {
mprinterr("Error: illegal character '%c' in 'dir' string '%s'; only numbers allowed.\n",
*c, dirstring.c_str());
return Action::ERR;
}
++iptr;
}
//mprintf("DEBUG: %s = %i %i %i\n", dirstring.c_str(), ixyz[0], ixyz[1], ixyz[2]);
directionArray_.push_back( ixyz[0] );
directionArray_.push_back( ixyz[1] );
directionArray_.push_back( ixyz[2] );
dirstring = actionArgs.GetStringKey("dir");
}
}
ncopies_ = (int)(directionArray_.size() / 3);
if (ncopies_ < 1) {
mprinterr("Error: No directions (or 'all') specified.\n");
return Action::ERR;
}
// Initialize output trajectory with remaining arguments
if (!trajfilename.empty()) {
outtraj_.SetDebug( debugIn );
if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(),
TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) )
return Action::ERR;
writeTraj_ = true;
# ifdef MPI
outtraj_.SetTrajComm( init.TrajComm() );
# endif
} else
writeTraj_ = false;
mprintf(" REPLICATE CELL: Replicating cell in %i directions:\n", ncopies_);
mprintf("\t\t X Y Z\n");
for (unsigned int i = 0; i != directionArray_.size(); i += 3)
mprintf("\t\t%2i %2i %2i\n", directionArray_[i],
directionArray_[i+1], directionArray_[i+2]);
mprintf("\tUsing atoms in mask '%s'\n", Mask1_.MaskString());
if (writeTraj_)
mprintf("\tWriting to trajectory %s\n", outtraj_.Traj().Filename().full());
if (!parmfilename_.empty())
mprintf("\tWriting topology %s\n", parmfilename_.c_str());
if (coords_ != 0)
mprintf("\tSaving coords to data set %s\n", coords_->legend());
return Action::OK;
}
// Action_Diffusion::DoAction()
Action::RetType Action_Diffusion::DoAction(int frameNum, ActionFrame& frm) {
Matrix_3x3 ucell, recip;
// Load initial frame if necessary
if (initial_.empty()) {
initial_ = frm.Frm();
# ifdef MPI
if (trajComm_.Size() > 1) {
if (trajComm_.Master())
for (int rank = 1; rank < trajComm_.Size(); ++rank)
initial_.SendFrame( rank, trajComm_ );
else
initial_.RecvFrame( 0, trajComm_ );
}
# endif
for (AtomMask::const_iterator atom = mask_.begin(); atom != mask_.end(); ++atom)
{
const double* XYZ = initial_.XYZ(*atom);
previous_.push_back( XYZ[0] );
previous_.push_back( XYZ[1] );
previous_.push_back( XYZ[2] );
}
}
// Diffusion calculation
if (image_.ImageType() != NOIMAGE) {
boxcenter_ = frm.Frm().BoxCrd().Center();
if (image_.ImageType() == NONORTHO)
frm.Frm().BoxCrd().ToRecip(ucell, recip);
}
// For averaging over selected atoms
double average2 = 0.0;
double avgx = 0.0;
double avgy = 0.0;
double avgz = 0.0;
unsigned int idx = 0; // Index into previous_ and delta_
for (AtomMask::const_iterator at = mask_.begin(); at != mask_.end(); ++at, idx += 3)
{ // Get current and initial coords for this atom.
const double* XYZ = frm.Frm().XYZ(*at);
const double* iXYZ = initial_.XYZ(*at);
// Calculate distance from initial position.
double delx, dely, delz;
if ( image_.ImageType() == ORTHO ) {
// Orthorhombic imaging
// Calculate distance to previous frames coordinates.
delx = XYZ[0] - previous_[idx ];
dely = XYZ[1] - previous_[idx+1];
delz = XYZ[2] - previous_[idx+2];
// If the particle moved more than half the box, assume it was imaged
// and adjust the distance of the total movement with respect to the
// original frame.
if (delx > boxcenter_[0]) delta_[idx ] -= frm.Frm().BoxCrd().BoxX();
else if (delx < -boxcenter_[0]) delta_[idx ] += frm.Frm().BoxCrd().BoxX();
if (dely > boxcenter_[1]) delta_[idx+1] -= frm.Frm().BoxCrd().BoxY();
else if (dely < -boxcenter_[1]) delta_[idx+1] += frm.Frm().BoxCrd().BoxY();
if (delz > boxcenter_[2]) delta_[idx+2] -= frm.Frm().BoxCrd().BoxZ();
else if (delz < -boxcenter_[2]) delta_[idx+2] += frm.Frm().BoxCrd().BoxZ();
// Calculate the distance between this "fixed" coordinate
// and the reference (initial) frame.
delx = XYZ[0] + delta_[idx ] - iXYZ[0];
dely = XYZ[1] + delta_[idx+1] - iXYZ[1];
delz = XYZ[2] + delta_[idx+2] - iXYZ[2];
} else if ( image_.ImageType() == NONORTHO ) {
// Non-orthorhombic imaging
// Calculate distance to previous frames coordinates.
delx = XYZ[0] - previous_[idx ];
dely = XYZ[1] - previous_[idx+1];
delz = XYZ[2] - previous_[idx+2];
// If the particle moved more than half the box, assume it was imaged
// and adjust the distance of the total movement with respect to the
// original frame.
if (fabs(delx) > boxcenter_[0] ||
fabs(dely) > boxcenter_[1] ||
fabs(delz) > boxcenter_[2])
{
// Previous position in Cartesian space
Vec3 pCart( previous_[idx], previous_[idx+1], previous_[idx+2] );
// Current position in fractional coords
Vec3 cFrac = recip * Vec3( XYZ[0], XYZ[1], XYZ[2] );
// Look for imaged distance closer to previous than current position
double minDist2 = frm.Frm().BoxCrd().BoxX() *
frm.Frm().BoxCrd().BoxY() *
frm.Frm().BoxCrd().BoxZ();
Vec3 minCurr(0.0);
for (int ix = -1; ix < 2; ix++) {
for (int iy = -1; iy < 2; iy++) {
for (int iz = -1; iz < 2; iz++) {
if (ix != 0 || iy != 0 || iz != 0) { // Ignore current position
Vec3 ixyz(ix, iy, iz);
// Current position shifted and back in Cartesian space
Vec3 IMG = ucell.TransposeMult(cFrac + ixyz);
// Distance from previous position to imaged current position
Vec3 dxyz = IMG - pCart;
double dist2 = dxyz.Magnitude2();
if (dist2 < minDist2) {
minDist2 = dist2;
minCurr = IMG;
}
}
}
}
}
// Update the delta for this atom
delta_[idx ] += minCurr[0] - XYZ[0]; // cCart
delta_[idx+1] += minCurr[1] - XYZ[1];
delta_[idx+2] += minCurr[2] - XYZ[2];
}
// Calculate the distance between this "fixed" coordinate
// and the reference (initial) frame.
delx = XYZ[0] + delta_[idx ] - iXYZ[0];
dely = XYZ[1] + delta_[idx+1] - iXYZ[1];
delz = XYZ[2] + delta_[idx+2] - iXYZ[2];
} else {
// No imaging. Calculate distance from current position to initial position.
delx = XYZ[0] - iXYZ[0];
dely = XYZ[1] - iXYZ[1];
delz = XYZ[2] - iXYZ[2];
}
// Calc distances for this atom
double distx = delx * delx;
double disty = dely * dely;
double distz = delz * delz;
double dist2 = distx + disty + distz;
// Accumulate averages
avgx += distx;
avgy += disty;
avgz += distz;
average2 += dist2;
// Store distances for this atom
if (printIndividual_) {
float fval = (float)distx;
atom_x_[*at]->Add(frameNum, &fval);
fval = (float)disty;
atom_y_[*at]->Add(frameNum, &fval);
fval = (float)distz;
atom_z_[*at]->Add(frameNum, &fval);
fval = (float)dist2;
atom_r_[*at]->Add(frameNum, &fval);
dist2 = sqrt(dist2);
fval = (float)dist2;
atom_a_[*at]->Add(frameNum, &fval);
}
// Update the previous coordinate set to match the current coordinates
previous_[idx ] = XYZ[0];
previous_[idx+1] = XYZ[1];
previous_[idx+2] = XYZ[2];
} // END loop over selected atoms
// Calc averages
double dNselected = 1.0 / (double)mask_.Nselected();
avgx *= dNselected;
avgy *= dNselected;
avgz *= dNselected;
average2 *= dNselected;
// Save averages
avg_x_->Add(frameNum, &avgx);
avg_y_->Add(frameNum, &avgy);
avg_z_->Add(frameNum, &avgz);
avg_r_->Add(frameNum, &average2);
average2 = sqrt(average2);
avg_a_->Add(frameNum, &average2);
return Action::OK;
}
// Action_ReplicateCell::Init()
Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
// Require imaging.
image_.InitImaging( true );
// Set up output traj
trajfilename_ = actionArgs.GetStringKey("out");
parmfilename_ = actionArgs.GetStringKey("parmout");
Topology* tempParm = PFL->GetParm( actionArgs );
bool setAll = actionArgs.hasKey("all");
std::string dsname = actionArgs.GetStringKey("name");
if (!dsname.empty()) {
coords_ = (DataSet_Coords*)DSL->AddSet(DataSet::COORDS, dsname, "RCELL");
if (coords_ == 0) return Action::ERR;
}
if (trajfilename_.empty() && coords_ == 0) {
mprinterr("Error: Either 'out <traj filename> or 'name <dsname>' must be specified.\n");
return Action::ERR;
}
// Get Mask
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
// Determine which directions to set
if (setAll) {
for (int ix = -1; ix < 2; ix++)
for (int iy = -1; iy < 2; iy++)
for (int iz = -1; iz < 2; iz++) {
directionArray_.push_back( ix );
directionArray_.push_back( iy );
directionArray_.push_back( iz );
}
} else {
std::string dirstring = actionArgs.GetStringKey("dir");
while (!dirstring.empty()) {
std::vector<int> ixyz(3, -2);
std::vector<int>::iterator iptr = ixyz.begin();
for (std::string::const_iterator c = dirstring.begin();
c != dirstring.end(); ++c)
{
if (iptr == ixyz.end()) {
mprinterr("Error: 'dir' string has too many characters.\n");
return Action::ERR;
}
int sign = 1;
if (*c == '+') ++c;
else if (*c == '-') { sign = -1; ++c; }
if (*c == '1') *iptr = 1 * sign;
else if (*c == '0') *iptr = 0;
++iptr;
}
mprintf("DEBUG: %s = %i %i %i\n", dirstring.c_str(), ixyz[0], ixyz[1], ixyz[2]);
directionArray_.push_back( ixyz[0] );
directionArray_.push_back( ixyz[1] );
directionArray_.push_back( ixyz[2] );
dirstring = actionArgs.GetStringKey("dir");
}
}
ncopies_ = (int)(directionArray_.size() / 3);
if (ncopies_ < 1) {
mprinterr("Error: No directions (or 'all') specified.\n");
return Action::ERR;
}
// Set up output trajectory
if (!trajfilename_.empty()) {
if (tempParm == 0) {
mprinterr("Error: Could not get topology for %s\n", trajfilename_.c_str());
return Action::ERR;
}
outtraj_.SetDebug( debugIn );
// Initialize output trajectory with remaining arguments
trajArgs_ = actionArgs.RemainingArgs();
ensembleNum_ = DSL->EnsembleNum();
}
mprintf(" REPLICATE CELL: Replicating cell in %i directions:\n", ncopies_);
mprintf("\t\t X Y Z\n");
for (unsigned int i = 0; i != directionArray_.size(); i += 3)
mprintf("\t\t%2i %2i %2i\n", directionArray_[i],
directionArray_[i+1], directionArray_[i+2]);
mprintf("\tUsing atoms in mask '%s'\n", Mask1_.MaskString());
if (!trajfilename_.empty())
mprintf("\tWriting to trajectory %s\n", trajfilename_.c_str());
if (!parmfilename_.empty())
mprintf("\tWriting topology %s\n", parmfilename_.c_str());
if (coords_ != 0)
mprintf("\tSaving coords to data set %s\n", coords_->legend());
return Action::OK;
}
