// Action_DihedralScan::IntervalAngles()
void Action_DihedralScan::IntervalAngles(Frame& currentFrame) {
Matrix_3x3 rotationMatrix;
double theta_in_radians = interval_ * Constants::DEGRAD;
// Write original frame
if (!outfilename_.empty())
outtraj_.WriteSingle(outframe_++, currentFrame);
for (std::vector<DihedralScanType>::iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
dih++)
{
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation((*dih).atom1, (*dih).atom2);
// Calculate rotation matrix for interval
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
if (debug_ > 0) {
mprintf("\tRotating Dih %s-%s by %.2f deg %i times.\n",
CurrentParm_->TruncResAtomName( (*dih).atom1 ).c_str(),
CurrentParm_->TruncResAtomName( (*dih).atom2 ).c_str(), interval_, maxVal_);
}
for (int rot = 0; rot < maxVal_; ++rot) {
// Rotate around axis
currentFrame.Rotate(rotationMatrix, (*dih).Rmask);
// Write output trajectory
if (!outfilename_.empty())
outtraj_.WriteSingle(outframe_++, currentFrame);
}
}
}
// -----------------------------------------------------------------------------
void Image::WrapToCell0(std::vector<double>& CoordsIn, Frame const& frmIn,
AtomMask const& maskIn,
Matrix_3x3 const& ucell, Matrix_3x3 const& recip)
{
double* uFrac = &CoordsIn[0];
int nUatoms = maskIn.Nselected();
int idx;
double* result;
const double* XYZ;
# ifdef _OPENMP
# pragma omp parallel private(idx, result, XYZ)
{
# pragma omp for
# endif
for (idx = 0; idx < nUatoms; idx++)
{
result = uFrac + idx*3;
XYZ = frmIn.XYZ( maskIn[idx] );
// Convert to frac coords
recip.TimesVec( result, XYZ );
// Wrap to primary unit cell
result[0] = result[0] - floor(result[0]);
result[1] = result[1] - floor(result[1]);
result[2] = result[2] - floor(result[2]);
// Convert back to Cartesian
ucell.TransposeMult( result, result );
}
# ifdef _OPENMP
} // END pragma omp parallel
# endif
}
/** \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;
}
/** \param Coord Coordinate to image.
* \param truncoct If true, image in truncated octahedral shape.
* \param origin If true, image w.r.t. coordinate origin.
* \param ucell Unit cell matrix.
* \param recip Reciprocal coordinates matrix.
* \param fcom If truncoct, image translated coordinate w.r.t. this coord.
* \return Vector containing image translation.
*/
Vec3 Image::Nonortho(Vec3 const& Coord, bool truncoct,
bool origin, Matrix_3x3 const& ucell, Matrix_3x3 const& recip,
Vec3 const& fcom, double min)
{
int ixyz[3];
Vec3 fc = recip * Coord;
if ( origin )
fc += 0.5;
Vec3 boxTransOut = ucell.TransposeMult( Vec3(floor(fc[0]), floor(fc[1]), floor(fc[2])) );
boxTransOut.Neg();
// Put into familiar trunc. oct. shape
if (truncoct) {
Vec3 TransCoord = recip * (Coord + boxTransOut);
Vec3 f2 = recip * fcom;
if (origin) {
TransCoord += 0.5;
f2 += 0.5;
}
DIST2_ImageNonOrthoRecip(TransCoord, f2, min, ixyz, ucell);
if (ixyz[0] != 0 || ixyz[1] != 0 || ixyz[2] != 0) {
boxTransOut += ucell.TransposeMult( ixyz );
//if (debug > 2)
// mprintf( " IMAGING, FAMILIAR OFFSETS ARE %i %i %i\n",
// ixyz[0], ixyz[1], ixyz[2]);
}
}
return boxTransOut;
}
// Action_Principal::DoAction()
Action::RetType Action_Principal::DoAction(int frameNum, ActionFrame& frm) {
Matrix_3x3 Inertia;
Vec3 Eval;
frm.Frm().CalculateInertia( mask_, Inertia );
// NOTE: Diagonalize_Sort_Chirality places sorted eigenvectors in rows.
Inertia.Diagonalize_Sort_Chirality( Eval, debug_ );
if (outfile_ != 0) {
int fn = frameNum+1;
outfile_->Printf("%i EIGENVALUES: %f %f %f\n%i EIGENVECTOR 0: %f %f %f\n%i EIGENVECTOR 1: %f %f %f\n%i EIGENVECTOR 2: %f %f %f\n",
fn, Eval[0], Eval[1], Eval[2],
fn, Inertia[0], Inertia[1], Inertia[2],
fn, Inertia[3], Inertia[4], Inertia[5],
fn, Inertia[6], Inertia[7], Inertia[8]);
//Eval.Print("PRINCIPAL EIGENVALUES");
//Inertia.Print("PRINCIPAL EIGENVECTORS (Rows)");
}
if (vecData_ != 0) {
vecData_->AddMat3x3( Inertia );
valData_->AddVxyz( Eval );
}
// Rotate - since Evec is already transposed (eigenvectors
// are returned in rows) just do plain rotation to affect an
// inverse rotation.
if (doRotation_) {
frm.ModifyFrm().Rotate( Inertia );
return Action::MODIFY_COORDS;
}
return Action::OK;
}
// MomentOfInertia()
static void MomentOfInertia(int natom, const double *X_, const double* Mass_, double* pmom)
{
Matrix_3x3 IVEC;
Vec3 eval;
// Center of mass
double cx = 0.0;
double cy = 0.0;
double cz = 0.0;
double sumMass = 0.0;
const double* mass = Mass_;
int natom3 = natom * 3;
for (int i = 0; i < natom3; i+=3) {
sumMass += (*mass);
cx += ( X_[i ] * (*mass) );
cy += ( X_[i+1] * (*mass) );
cz += ( X_[i+2] * (*mass) );
++mass;
}
cx /= sumMass;
cy /= sumMass;
cz /= sumMass;
// Moment of inertia
double xx = 0.0;
double yy = 0.0;
double zz = 0.0;
double xy = 0.0;
double xz = 0.0;
double yz = 0.0;
mass = Mass_;
for (int i = 0; i < natom3; i+=3) {
double dx = X_[i ] - cx;
double dy = X_[i+1] - cy;
double dz = X_[i+2] - cz;
xx += *mass * ( dy * dy + dz * dz );
yy += *mass * ( dx * dx + dz * dz );
zz += *mass * ( dx * dx + dy * dy );
xy -= *mass * dx * dy;
xz -= *mass * dx * dz;
yz -= *(mass++) * dy * dz;
}
IVEC[0] = xx;
IVEC[1] = xy;
IVEC[2] = xz;
IVEC[3] = xy;
IVEC[4] = yy;
IVEC[5] = yz;
IVEC[6] = xz;
IVEC[7] = yz;
IVEC[8] = zz;
// NOTE: Diagonalize sorts evals/evecs in descending order, but
// thermo() expects ascending.
IVEC.Diagonalize_Sort( eval );
pmom[0] = eval[2];
pmom[1] = eval[1];
pmom[2] = eval[0];
}
/** Set box from unit cell matrix. */
void Box::SetBox(Matrix_3x3 const& ucell) {
Vec3 x_axis = ucell.Row1();
Vec3 y_axis = ucell.Row2();
Vec3 z_axis = ucell.Row3();
box_[0] = x_axis.Normalize(); // A
box_[1] = y_axis.Normalize(); // B
box_[2] = z_axis.Normalize(); // C
box_[3] = y_axis.Angle( z_axis ) * Constants::RADDEG; // alpha
box_[4] = x_axis.Angle( z_axis ) * Constants::RADDEG; // beta
box_[5] = x_axis.Angle( y_axis ) * Constants::RADDEG; // gamma
SetBoxType();
}
/** Use box coordinates to calculate unit cell and fractional matrix for use
* with imaging routines. Return cell volume.
*/
double Box::ToRecip(Matrix_3x3& ucell, Matrix_3x3& recip) const {
double u12x,u12y,u12z;
double u23x,u23y,u23z;
double u31x,u31y,u31z;
double volume,onevolume;
// If box lengths are zero no imaging possible
if (box_[0]==0.0 || box_[1]==0.0 || box_[2]==0.0) {
ucell.Zero();
recip.Zero();
return -1.0;
}
ucell[0] = box_[0]; // u(1,1)
ucell[1] = 0.0; // u(2,1)
ucell[2] = 0.0; // u(3,1)
ucell[3] = box_[1]*cos(Constants::DEGRAD*box_[5]); // u(1,2)
ucell[4] = box_[1]*sin(Constants::DEGRAD*box_[5]); // u(2,2)
ucell[5] = 0.0; // u(3,2)
ucell[6] = box_[2]*cos(Constants::DEGRAD*box_[4]);
ucell[7] = (box_[1]*box_[2]*cos(Constants::DEGRAD*box_[3]) - ucell[6]*ucell[3]) / ucell[4];
ucell[8] = sqrt(box_[2]*box_[2] - ucell[6]*ucell[6] - ucell[7]*ucell[7]);
// Get reciprocal vectors
u23x = ucell[4]*ucell[8] - ucell[5]*ucell[7];
u23y = ucell[5]*ucell[6] - ucell[3]*ucell[8];
u23z = ucell[3]*ucell[7] - ucell[4]*ucell[6];
u31x = ucell[7]*ucell[2] - ucell[8]*ucell[1];
u31y = ucell[8]*ucell[0] - ucell[6]*ucell[2];
u31z = ucell[6]*ucell[1] - ucell[7]*ucell[0];
u12x = ucell[1]*ucell[5] - ucell[2]*ucell[4];
u12y = ucell[2]*ucell[3] - ucell[0]*ucell[5];
u12z = ucell[0]*ucell[4] - ucell[1]*ucell[3];
volume=ucell[0]*u23x + ucell[1]*u23y + ucell[2]*u23z;
onevolume = 1.0 / volume;
recip[0] = u23x*onevolume;
recip[1] = u23y*onevolume;
recip[2] = u23z*onevolume;
recip[3] = u31x*onevolume;
recip[4] = u31y*onevolume;
recip[5] = u31z*onevolume;
recip[6] = u12x*onevolume;
recip[7] = u12y*onevolume;
recip[8] = u12z*onevolume;
return volume;
}
void Action_Vector::Principal(Frame const& currentFrame) {
Matrix_3x3 Inertia;
Vec3 Eval;
// Origin is center of atoms in mask_
Vec3 OXYZ = currentFrame.CalculateInertia( mask_, Inertia );
// NOTE: Diagonalize_Sort_Chirality places sorted eigenvectors in rows.
Inertia.Diagonalize_Sort_Chirality( Eval, 0 );
// Eval.Print("PRINCIPAL EIGENVALUES");
// Inertia.Print("PRINCIPAL EIGENVECTORS (Rows)");
if ( mode_ == PRINCIPAL_X )
Vec_->AddVxyz( Inertia.Row1(), OXYZ ); // First row = first eigenvector
else if ( mode_ == PRINCIPAL_Y )
Vec_->AddVxyz( Inertia.Row2(), OXYZ ); // Second row = second eigenvector
else // PRINCIPAL_Z
Vec_->AddVxyz( Inertia.Row3(), OXYZ ); // Third row = third eigenvector
}
/** Fill the translate vector array with offset values based on this
* unit cell. Only need forward direction, so no -Z.
*/
void PairList::FillTranslateVec(Matrix_3x3 const& ucell) {
int iv = 0;
for (int i3 = 0; i3 < 2; i3++)
for (int i2 = -1; i2 < 2; i2++)
for (int i1 = -1; i1 < 2; i1++)
translateVec_[iv++] = ucell.TransposeMult( Vec3(i1, i2, i3) );
//for (int i = 0; i < 18; i++)
// mprintf("TRANVEC %3i%12.5f%12.5f%12.5f\n", i+1, translateVec_[i][0],
// translateVec_[i][1], translateVec_[i][2]);
}
/** Calculate direct space energy. This is the slow version that doesn't
* use a pair list; for debug purposes only.
*/
double Ewald::Direct(Matrix_3x3 const& ucell, Topology const& tIn, AtomMask const& mask)
{
t_direct_.Start();
double cut2 = cutoff_ * cutoff_;
double Eelec = 0.0;
Varray const& Image = pairList_.ImageCoords();
Varray const& Frac = pairList_.FracCoords();
unsigned int maxidx = Image.size();
for (unsigned int idx1 = 0; idx1 != maxidx; idx1++)
{
// Set up coord for this atom
Vec3 const& crd1 = Image[idx1];
// Set up exclusion list for this atom
int atom1 = mask[idx1];
Atom::excluded_iterator excluded_atom = tIn[atom1].excludedbegin();
for (unsigned int idx2 = idx1 + 1; idx2 != maxidx; idx2++)
{
int atom2 = mask[idx2];
// If atom is excluded, just increment to next excluded atom.
if (excluded_atom != tIn[atom1].excludedend() && atom2 == *excluded_atom) {
++excluded_atom;
//mprintf("ATOM: Atom %4i to %4i excluded.\n", atom1+1, atom2+1);
} else {
// Only need to check nearest neighbors.
Vec3 const& frac2 = Frac[idx2];
for (Varray::const_iterator ixyz = Cells_.begin(); ixyz != Cells_.end(); ++ixyz)
{
Vec3 dxyz = ucell.TransposeMult(frac2 + *ixyz) - crd1;
double rij2 = dxyz.Magnitude2();
if ( rij2 < cut2 ) {
double rij = sqrt( rij2 );
// Coulomb
double qiqj = Charge_[idx1] * Charge_[idx2];
t_erfc_.Start();
//double erfc = erfc_func(ew_coeff_ * rij);
double erfc = ERFC(ew_coeff_ * rij);
t_erfc_.Stop();
double e_elec = qiqj * erfc / rij;
Eelec += e_elec;
//mprintf("EELEC %4i%4i%12.5f%12.5f%12.5f%3.0f%3.0f%3.0f\n",
// mprintf("EELEC %6i%6i%12.5f%12.5f%12.5f\n", atom1, atom2, rij, erfc, e_elec);
// TODO can we break here?
} //else
//mprintf("ATOM: Atom %4i to %4i outside cut, %6.2f > %6.2f %3.0f%3.0f%3.0f\n",
//mprintf("ATOM: Atom %4i to %4i outside cut, %6.2f > %6.2f\n",
// atom1, atom2,sqrt(rij2),cutoff_);
}
}
}
}
t_direct_.Stop();
return Eelec;
}
// Action_MakeStructure::DoAction()
Action::RetType Action_MakeStructure::DoAction(int frameNum, Frame* currentFrame,
Frame** frameAddress)
{
Matrix_3x3 rotationMatrix;
for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
ss != secstruct_.end(); ++ss)
{
std::vector<float>::iterator theta = ss->thetas_.begin();
std::vector<AtomMask>::iterator Rmask = ss->Rmasks_.begin();
for (DihedralSearch::mask_it dih = ss->dihSearch_.begin();
dih != ss->dihSearch_.end(); ++dih, ++theta, ++Rmask)
{
double theta_in_radians = (double)*theta;
// Calculate current value of dihedral
double torsion = Torsion( currentFrame->XYZ( (*dih).A0() ),
currentFrame->XYZ( (*dih).A1() ),
currentFrame->XYZ( (*dih).A2() ),
currentFrame->XYZ( (*dih).A3() ) );
// Calculate delta needed to get to theta
double delta = theta_in_radians - torsion;
// Set axis of rotation
Vec3 axisOfRotation = currentFrame->SetAxisOfRotation((*dih).A1(), (*dih).A2());
// Calculate rotation matrix for delta
rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
if (debug_ > 0) {
std::string a0name = CurrentParm_->TruncResAtomName( (*dih).A0() );
std::string a1name = CurrentParm_->TruncResAtomName( (*dih).A1() );
std::string a2name = CurrentParm_->TruncResAtomName( (*dih).A2() );
std::string a3name = CurrentParm_->TruncResAtomName( (*dih).A3() );
mprintf("\tRotating Dih %i:%s (%i-%i-%i-%i) (@%.2f) by %.2f deg to get to %.2f.\n",
(*dih).ResNum()+1, (*dih).Name().c_str(),
(*dih).A0() + 1, (*dih).A1() + 1, (*dih).A2() + 1, (*dih).A3() + 1,
torsion*Constants::RADDEG, delta*Constants::RADDEG, theta_in_radians*Constants::RADDEG);
}
// Rotate around axis
currentFrame->Rotate(rotationMatrix, *Rmask);
}
}
return Action::OK;
}
// -----------------------------------------------------------------------------
// Exec_PermuteDihedrals::IntervalAngles()
void Exec_PermuteDihedrals::IntervalAngles(Frame const& frameIn, Topology const& topIn,
double interval_in_deg)
{
Matrix_3x3 rotationMatrix;
double theta_in_radians = interval_in_deg * Constants::DEGRAD;
int maxVal = (int) (360.0 / interval_in_deg);
if (maxVal < 0) maxVal = -maxVal;
// Write original frame
if (outtraj_.IsInitialized())
outtraj_.WriteSingle(outframe_++, frameIn);
if (crdout_ != 0)
crdout_->AddFrame( frameIn );
Frame currentFrame = frameIn;
for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
++dih)
{
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation(dih->atom1, dih->atom2);
// Calculate rotation matrix for interval
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
if (debug_ > 0) {
mprintf("\tRotating Dih %s-%s by %.2f deg %i times.\n",
topIn.TruncResAtomName( dih->atom1 ).c_str(),
topIn.TruncResAtomName( dih->atom2 ).c_str(), interval_in_deg, maxVal);
}
for (int rot = 0; rot != maxVal; ++rot) {
// Rotate around axis
currentFrame.Rotate(rotationMatrix, dih->Rmask);
// Write output trajectory
if (outtraj_.IsInitialized())
outtraj_.WriteSingle(outframe_++, currentFrame);
if (crdout_ != 0)
crdout_->AddFrame( currentFrame );
}
}
}
/** \param frameIn Frame to image.
* \param origin If true image w.r.t. coordinate origin.
* \param fcom If truncoct is true, calc distance w.r.t. this coordinate.
* \param ucell Unit cell matrix.
* \param recip Reciprocal coordinates matrix.
* \param truncoct If true imaging will occur using truncated octahedron shape.
* \param center If true image w.r.t. center coords, otherwise use first atom coords.
* \param useMass If true use COM, otherwise geometric center.
* \param AtomPairs Atom pairs to image.
*/
void Image::Nonortho(Frame& frameIn, bool origin, Vec3 const& fcom, Vec3 const& offIn,
Matrix_3x3 const& ucell, Matrix_3x3 const& recip,
bool truncoct, bool center,
bool useMass, PairType const& AtomPairs)
{
Vec3 Coord;
Vec3 offset = ucell.TransposeMult( offIn );
double min = -1.0;
if (truncoct)
min = 100.0 * (frameIn.BoxCrd().BoxX()*frameIn.BoxCrd().BoxX()+
frameIn.BoxCrd().BoxY()*frameIn.BoxCrd().BoxY()+
frameIn.BoxCrd().BoxZ()*frameIn.BoxCrd().BoxZ());
// Loop over atom pairs
for (PairType::const_iterator atom = AtomPairs.begin();
atom != AtomPairs.end(); ++atom)
{
int firstAtom = *atom;
++atom;
int lastAtom = *atom;
//if (debug>2)
// mprintf( " IMAGE processing atoms %i to %i\n", firstAtom+1, lastAtom);
// Set up Coord with position to check for imaging based on first atom or
// center of mass of atoms first to last.
if (center) {
if (useMass)
Coord = frameIn.VCenterOfMass(firstAtom,lastAtom);
else
Coord = frameIn.VGeometricCenter(firstAtom,lastAtom);
} else
Coord = frameIn.XYZ( firstAtom );
// boxTrans will hold calculated translation needed to move atoms back into box
Vec3 boxTrans = Nonortho(Coord, truncoct, origin, ucell, recip, fcom, min) + offset;
frameIn.Translate(boxTrans, firstAtom, lastAtom);
} // END loop over atom pairs
}
/** Place selected atoms into grid cells. Convert to fractional coords, wrap
* into primary cell, then determine grid cell.
*/
void PairList::GridUnitCell(Frame const& frmIn, Matrix_3x3 const& ucell,
Matrix_3x3 const& recip, AtomMask const& maskIn)
{
// Clear any existing atoms in cells.
for (Carray::iterator cell = cells_.begin(); cell != cells_.end(); ++cell)
cell->ClearAtoms();
Frac_.clear();
Frac_.reserve( maskIn.Nselected() );
if (frmIn.BoxCrd().Type() == Box::ORTHO) {
// Orthogonal imaging
for (AtomMask::const_iterator atom = maskIn.begin(); atom != maskIn.end(); ++atom)
{
const double* XYZ = frmIn.XYZ(*atom);
Vec3 fc( XYZ[0]*recip[0], XYZ[1]*recip[4], XYZ[2]*recip[8] );
Vec3 fcw(fc[0]-floor(fc[0]), fc[1]-floor(fc[1]), fc[2]-floor(fc[2]));
Vec3 ccw(fcw[0]*ucell[0], fcw[1]*ucell[4], fcw[2]*ucell[8] );
# ifdef DEBUG_PAIRLIST
mprintf("DBG: o %6i fc=%7.3f%7.3f%7.3f fcw=%7.3f%7.3f%7.3f ccw=%7.3f%7.3f%7.3f\n",
*atom+1, fc[0], fc[1], fc[2], fcw[0], fcw[1], fcw[2], ccw[0], ccw[1], ccw[2]);
# endif
GridAtom( atom-maskIn.begin(), fcw, ccw );
}
} else {
// Non-orthogonal imaging
for (AtomMask::const_iterator atom = maskIn.begin(); atom != maskIn.end(); ++atom)
{
Vec3 fc = recip * Vec3(frmIn.XYZ(*atom));
Vec3 fcw(fc[0]-floor(fc[0]), fc[1]-floor(fc[1]), fc[2]-floor(fc[2]));
Vec3 ccw = ucell.TransposeMult( fcw );
# ifdef DEBUG_PAIRLIST
mprintf("DBG: n %6i fc=%7.3f%7.3f%7.3f fcw=%7.3f%7.3f%7.3f ccw=%7.3f%7.3f%7.3f\n",
*atom+1, fc[0], fc[1], fc[2], fcw[0], fcw[1], fcw[2], ccw[0], ccw[1], ccw[2]);
# endif
GridAtom( atom-maskIn.begin(), fcw, ccw );
}
}
}
/** Given the structure of a molecule and its normal mode vibrational
* frequencies this routine uses standard statistical mechanical
* formulas for an ideal gas (in the canonical ensemble, see,
* for example, d. a. mcquarrie, "statistical thermodynamics",
* harper & row, new york, 1973, chapters 5, 6, and 8) to compute
* the entropy, heat capacity, and internal energy.
* The si system of units is used internally. Conversion to units
* more familiar to most chemists is made for output.
*
* \param outfile output file, should already be open.
* \param temp temperature
* \param patm pressure, in atmospheres
*/
int DataSet_Modes::Thermo( CpptrajFile& outfile, int ilevel, double temp, double patm) const
{
// avgcrd_ Contains coordinates in Angstroms
// mass_ Contains masses in amu.
// nmodes_ Number of eigenvectors (already converted to frequencies)
// evalues_ vibrational frequencies, in cm**-1 and in ascending order
double rtemp, rtemp1, rtemp2, rtemp3;
// ----- Constants -------------------
const double thresh = 900.0; // vibrational frequency threshold
const double tokg = 1.660531e-27; // kilograms per amu.
const double boltz = 1.380622e-23; // boltzman constant, in joules per kelvin.
const double planck = 6.626196e-34; // planck constant, in joule-seconds.
// const double avog = 6.022169e+23; // avogadro constant, in mol**(-1).
const double jpcal = 4.18674e+00; // joules per calorie.
const double tomet = 1.0e-10; // metres per Angstrom.
const double hartre = 4.35981e-18; // joules per hartree.
const double pstd = 1.01325e+05; // Standard pressure in pascals
// compute the gas constant, pi, pi**2, and e.
// compute the conversion factors cal per joule and kcal per joule.
// const double gas = avog * boltz;
// pi = four * datan(one)
const double pipi = Constants::PI * Constants::PI;
const double e = exp(1.0);
const double tocal = 1.0 / jpcal;
const double tokcal = tocal / 1000.0;
if (!outfile.IsOpen()) {
mprinterr("Internal Error: DataSet_Modes::Thermo(): output file is not open.\n");
return 1;
}
// print the temperature and pressure.
outfile.Printf("\n *******************\n");
outfile.Printf( " - Thermochemistry -\n");
outfile.Printf( " *******************\n\n");
outfile.Printf("\n temperature %9.3f kelvin\n pressure %9.5f atm\n",temp,patm);
double pressure = pstd * patm;
double rt = Constants::GASK_J * temp;
// compute and print the molecular mass in amu, then convert to
// kilograms.
double weight = 0.0;
for (Darray::const_iterator m = mass_.begin(); m != mass_.end(); ++m)
weight += *m;
outfile.Printf(" molecular mass (principal isotopes) %11.5f amu\n", weight);
weight *= tokg;
//trap non-unit multiplicities.
//if (multip != 1) {
// outfile.Printf("\n Warning-- assumptions made about the electronic partition function\n");
// outfile.Printf( " are not valid for multiplets!\n\n");
//}
// compute contributions due to translation:
// etran-- internal energy
// ctran-- constant v heat capacity
// stran-- entropy
double dum1 = boltz * temp;
double dum2 = pow(Constants::TWOPI, 1.5);
double arg = pow(dum1, 1.5) / planck;
arg = (arg / pressure) * (dum1 / planck);
arg = arg * dum2 * (weight / planck);
arg = arg * sqrt(weight) * exp(2.5);
double stran = Constants::GASK_J * log(arg);
double etran = 1.5 * rt;
double ctran = 1.5 * Constants::GASK_J;
// Compute contributions due to electronic motion:
// It is assumed that the first electronic excitation energy
// is much greater than kt and that the ground state has a
// degeneracy of one. Under these conditions the electronic
// partition function can be considered to be unity. The
// ground electronic state is taken to be the zero of
// electronic energy.
// for monatomics print and return.
if (avgcrd_.size() <= 3){
outfile.Printf("\n internal energy: %10.3f joule/mol %10.3f kcal/mol\n",
etran, etran * tokcal);
outfile.Printf( " entropy: %10.3f joule/k-mol %10.3f cal/k-mol\n",
stran, stran * tocal);
outfile.Printf( " heat capacity cv: %10.3f joule/k-mol %10.3f cal/k-mol\n",
ctran, ctran * tocal);
return 0;
}
Frame AVG;
AVG.SetupFrameXM( avgcrd_, mass_ );
// Allocate workspace memory
// vtemp vibrational temperatures, in kelvin.
// evibn contribution to e from the vibration n.
// cvibn contribution to cv from the vibration n.
// svibn contribution to s from the vibration n.
double* WorkSpace = new double[ 4 * nmodes_ ];
double* vtemp = WorkSpace;
double* evibn = WorkSpace + nmodes_;
double* cvibn = WorkSpace + nmodes_*2;
double* svibn = WorkSpace + nmodes_*3;
// compute contributions due to rotation.
// Compute the principal moments of inertia, get the rotational
// symmetry number, see if the molecule is linear, and compute
// the rotational temperatures. Note the imbedded conversion
// of the moments to SI units.
Matrix_3x3 Inertia;
AVG.CalculateInertia( AtomMask(0, AVG.Natom()), Inertia );
// NOTE: Diagonalize_Sort sorts evals/evecs in descending order, but
// thermo() expects ascending.
// pmom principal moments of inertia, in amu-bohr**2 and in ascending order.
Vec3 pmom;
Inertia.Diagonalize_Sort( pmom );
rtemp = pmom[0];
pmom[0] = pmom[2];
pmom[2] = rtemp;
outfile.Printf("\n principal moments of inertia (nuclei only) in amu-A**2:\n");
outfile.Printf( " %12.2f%12.2f%12.2f\n", pmom[0], pmom[1], pmom[2]);
bool linear = false;
// Symmetry number: only for linear molecules. for others symmetry number is unity
double sn = 1.0;
if (AVG.Natom() <= 2) {
linear = true;
if (AVG.Mass(0) == AVG.Mass(1)) sn = 2.0;
}
outfile.Printf("\n rotational symmetry number %3.0f\n", sn);
double con = planck / (boltz*8.0*pipi);
con = (con / tokg) * (planck / (tomet*tomet));
if (linear) {
rtemp = con / pmom[2];
if (rtemp < 0.2) {
outfile.Printf("\n Warning-- assumption of classical behavior for rotation\n");
outfile.Printf( " may cause significant error\n");
}
outfile.Printf("\n rotational temperature (kelvin) %12.5f\n", rtemp);
} else {
rtemp1 = con / pmom[0];
rtemp2 = con / pmom[1];
rtemp3 = con / pmom[2];
if (rtemp1 < 0.2) {
outfile.Printf("\n Warning-- assumption of classical behavior for rotation\n");
outfile.Printf( " may cause significant error\n");
}
outfile.Printf("\n rotational temperatures (kelvin) %12.5f%12.5f%12.5f\n",
rtemp1, rtemp2, rtemp3);
}
// erot-- rotational contribution to internal energy.
// crot-- rotational contribution to cv.
// srot-- rotational contribution to entropy.
double erot, crot, srot;
if (linear) {
erot = rt;
crot = Constants::GASK_J;
arg = (temp/rtemp) * (e/sn);
srot = Constants::GASK_J * log(arg);
} else {
erot = 1.5 * rt;
crot = 1.5 * Constants::GASK_J;
arg = sqrt(Constants::PI*e*e*e) / sn;
double dum = (temp/rtemp1) * (temp/rtemp2) * (temp/rtemp3);
arg = arg * sqrt(dum);
srot = Constants::GASK_J * log(arg);
}
// compute contributions due to vibration.
// compute vibrational temperatures and zero point vibrational
// energy. only real frequencies are included in the analysis.
// ndof = 3*natoms - 6 - nimag
// if (nimag .ne. 0) write(iout,1210) nimag
// if (linear) ndof = ndof + 1
int ndof = nmodes_;
// (---iff is the first frequency to include in thermo:)
int iff;
if (ilevel != 0)
iff = 0;
else if (linear)
iff = 5;
else
iff = 6;
con = planck / boltz;
double ezpe = 0.0;
for (int i = 0; i < ndof; ++i) {
vtemp[i] = evalues_[i+iff] * con * 3.0e10;
ezpe += evalues_[i+iff] * 3.0e10;
}
ezpe = 0.5 * planck * ezpe;
outfile.Printf("\n zero point vibrational energy %12.1f (joules/mol) \n"
" %12.5f (kcal/mol)\n"
" %12.7f (hartree/particle)\n",
ezpe*Constants::NA, ezpe*tokcal*Constants::NA, ezpe/hartre);
// compute the number of vibrations for which more than 5% of an
// assembly of molecules would exist in vibrational excited states.
// special printing for these modes is done to allow the user to
// easily take internal rotations into account. the criterion
// corresponds roughly to a low frequency of 1.9(10**13) hz, or
// 625 cm**(-1), or a vibrational temperature of 900 k.
int lofreq = 0;
for (int i = 0; i < ndof; ++i)
if (vtemp[i] < thresh)
++lofreq;
if (lofreq != 0) {
outfile.Printf("\n Warning-- %3i vibrations have low frequencies and may represent hindered \n",
lofreq);
outfile.Printf( " internal rotations. The contributions printed below assume that these \n");
outfile.Printf( " really are vibrations.\n");
}
// compute:
// evib-- the vibrational component of the internal energy.
// cvib-- the vibrational component of the heat capacity.
// svib-- the vibrational component of the entropy.
double evib = 0.0;
double cvib = 0.0;
double svib = 0.0;
double scont;
for (int i = 0; i < ndof; ++i) {
// compute some common factors.
double tovt = vtemp[i] / temp;
double etovt = exp(tovt);
double em1 = etovt - 1.0;
// compute contributions due to the i'th vibration.
double econt = tovt * (0.5 + 1.0/em1);
double ccont = etovt * pow(tovt/em1,2.0);
double argd = 1.0 - 1.0/etovt;
if (argd > 1.0e-7)
scont = tovt/em1 - log(argd);
else {
scont = 0.0;
outfile.Printf(" warning: setting vibrational entropy to zero for mode %i with vtemp = %f\n",
i+1, vtemp[i]);
}
// if (lofreq .ge. i) then
evibn[i] = econt * rt;
cvibn[i] = ccont * Constants::GASK_J;
svibn[i] = scont * Constants::GASK_J;
// end if
evib += econt;
cvib += ccont;
svib += scont;
}
evib *= rt;
cvib *= Constants::GASK_J;
svib *= Constants::GASK_J;
// the units are now:
// e-- joules/mol
// c-- joules/mol-kelvin
// s-- joules/mol-kelvin
double etot = etran + erot + evib;
double ctot = ctran + crot + cvib;
double stot = stran + srot + svib;
// print the sum of the hartree-fock energy and the thermal energy.
// call tread(501,gen,47,1,47,1,0)
// esum = gen(32) + etot/avog/hartre
// write(iout,1230) esum
// convert to the following and print
// e-- kcal/mol
// c-- cal/mol-kelvin
// s-- cal/mol-kelvin
etran = etran * tokcal;
ctran = ctran * tocal;
stran = stran * tocal;
erot = erot * tokcal;
crot = crot * tocal;
srot = srot * tocal;
evib = evib * tokcal;
cvib = cvib * tocal;
svib = svib * tocal;
etot = etran + erot + evib;
ctot = ctran + crot + cvib;
stot = stran + srot + svib;
for (int i = 0; i < ndof; ++i) {
evibn[i] *= tokcal;
cvibn[i] *= tocal;
svibn[i] *= tocal;
}
outfile.Printf("\n\n freq. E Cv S\n");
outfile.Printf( " cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin\n");
outfile.Printf( "--------------------------------------------------------------------------------\n");
outfile.Printf( " Total %11.3f %11.3f %11.3f\n",etot,ctot,stot);
outfile.Printf( " translational %11.3f %11.3f %11.3f\n",etran,ctran,stran);
outfile.Printf( " rotational %11.3f %11.3f %11.3f\n",erot,crot,srot);
outfile.Printf( " vibrational %11.3f %11.3f %11.3f\n",evib,cvib,svib);
for (int i = 0; i < iff; ++i)
outfile.Printf(" %5i%10.3f\n", i+1, evalues_[i]);
for (int i = 0; i < ndof; ++i) {
outfile.Printf(" %5i%10.3f %11.3f %11.3f %11.3f\n",i+iff+1,
evalues_[i+iff], evibn[i], cvibn[i], svibn[i]);
}
delete[] WorkSpace;
return 0;
}
// -----------------------------------------------------------------------------
// Image::UnwrapNonortho()
void Image::UnwrapNonortho( Frame& tgtIn, Frame& refIn, PairType const& AtomPairs,
Matrix_3x3 const& ucell, Matrix_3x3 const& recip,
bool center, bool useMass )
{
Vec3 vtgt, vref, boxTrans;
// Loop over atom pairs
for (PairType::const_iterator atom = AtomPairs.begin();
atom != AtomPairs.end(); ++atom)
{
int firstAtom = *atom;
++atom;
int lastAtom = *atom;
if (center) {
// Use center of coordinates between first and last atoms.
if (useMass) {
vtgt = tgtIn.VCenterOfMass(firstAtom, lastAtom);
vref = refIn.VCenterOfMass(firstAtom, lastAtom);
} else {
vtgt = tgtIn.VGeometricCenter(firstAtom, lastAtom);
vref = refIn.VGeometricCenter(firstAtom, lastAtom);
}
} else {
// Use position first atom only.
vtgt = tgtIn.XYZ( firstAtom );
vref = refIn.XYZ( firstAtom );
}
boxTrans.Zero();
// Calculate original distance from the ref (previous) position.
Vec3 vd = vtgt - vref; // dx dy dz
double minDistanceSquare = vd.Magnitude2();
// Reciprocal coordinates
vd = recip * vd ; // recip * dxyz
double cx = floor(vd[0]);
double cy = floor(vd[1]);
double cz = floor(vd[2]);
// Loop over all possible translations
for (int ix = -1; ix < 2; ++ix) {
for (int iy = -1; iy < 2; ++iy) {
for (int iz = -1; iz < 2; ++iz) {
// Calculate the translation.
Vec3 vcc = ucell.TransposeMult( Vec3( cx+(double)ix,
cy+(double)iy,
cz+(double)iz ) ); // ucell^T * ccxyz
// Calc. the potential new coordinate for tgt
Vec3 vnew = vtgt - vcc;
// Calc. the new distance from the ref (previous) position
Vec3 vr = vref - vnew;
double distanceSquare = vr.Magnitude2();
// If the orig. distance is greater than the new distance, unwrap.
if ( minDistanceSquare > distanceSquare ) {
minDistanceSquare = distanceSquare;
boxTrans = vcc;
}
}
}
}
// Translate tgt atoms
boxTrans.Neg();
tgtIn.Translate( boxTrans, firstAtom, lastAtom );
// Save new ref positions
int i3 = firstAtom * 3;
std::copy( tgtIn.xAddress()+i3, tgtIn.xAddress()+(lastAtom*3), refIn.xAddress()+i3 );
} // END loop over atom pairs
}
int notmain(void)
{
int i,j,k;
Matrix_3x3 id;
Matrix_3x3 invid;
Vector vec(1,2,3);
Vector res, res2;
for(i=0;i<3;i++) for(j=0;j<3;j++) id.set(i,j,(float)((i*4)+j));
for(k=0;k<100;k++)
{
for(i=0;i<3;i++) //col
for(j=0;j<3;j++) //lin
{
/* if(i<j)
id.set(i,j,0.0);
else*/
id.set(i,j, (float)( (((i*j*k)%7 + ((k+1)%3) + (i+j))+1) * (((k+i+j)%2)==0 ? -1 : 1) ));
};
printf("\n\nTEST #%d\n",k);
if(id.is_invertable())
{
printf("Det==%g\n",id.det());
res=Vector(1.0,1.0,1.0);
res=id.solve(res);
printf("solve erg = %g,%g,%g\n",res[0],res[1],res[2]);
res2=id*res;
printf("solve test = %g,%g,%g\n",res2[0],res2[1],res2[2]);
id.dump(" M");
invid=id.invert();
invid.dump("M^-1");
(id*invid).dump("mul");
};
};
id.dump("id");
printf("vec = ");
dvec(vec);
printf("\n");
res=id*vec;
printf("res = ");
dvec(res);
printf("\n");
return 0;
}
// Exec_PermuteDihedrals::RandomizeAngles()
void Exec_PermuteDihedrals::RandomizeAngles(Frame& currentFrame, Topology const& topIn) {
Matrix_3x3 rotationMatrix;
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
int debugframenum=0;
Trajout_Single DebugTraj;
DebugTraj.PrepareTrajWrite("debugtraj.nc",ArgList(),(Topology*)&topIn,
CoordinateInfo(), BB_dihedrals_.size()*max_factor_,
TrajectoryFile::AMBERNETCDF);
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
int next_resnum;
int bestLoop = 0;
int number_of_rotations = 0;
// Set max number of rotations to try.
int max_rotations = (int)BB_dihedrals_.size();
max_rotations *= max_factor_;
// Loop over all dihedrals
std::vector<PermuteDihedralsType>::const_iterator next_dih = BB_dihedrals_.begin();
next_dih++;
for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
++dih, ++next_dih)
{
++number_of_rotations;
// Get the residue atom of the next dihedral. Residues up to and
// including this residue will be checked for bad clashes
if (next_dih != BB_dihedrals_.end())
next_resnum = next_dih->resnum;
else
next_resnum = dih->resnum - 1;
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation(dih->atom1, dih->atom2);
// Generate random value to rotate by in radians
// Guaranteed to rotate by at least 1 degree.
// NOTE: could potentially rotate 360 - prevent?
// FIXME: Just use 2PI and rn_gen, get everything in radians
double theta_in_degrees = ((int)(RN_.rn_gen()*100000) % 360) + 1;
double theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for random theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
int loop_count = 0;
double clash = 0;
double bestClash = 0;
if (debug_>0) mprintf("DEBUG: Rotating dihedral %zu res %8i:\n", dih - BB_dihedrals_.begin(),
dih->resnum+1);
bool rotate_dihedral = true;
while (rotate_dihedral) {
if (debug_>0) {
mprintf("\t%8i %12s %12s, +%.2lf degrees (%i).\n",dih->resnum+1,
topIn.AtomMaskName(dih->atom1).c_str(),
topIn.AtomMaskName(dih->atom2).c_str(),
theta_in_degrees,loop_count);
}
// Rotate around axis
currentFrame.Rotate(rotationMatrix, dih->Rmask);
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
// If we dont care about sterics exit here
if (!check_for_clashes_) break;
// Check resulting structure for issues
int checkresidue;
if (!checkAllResidues_)
checkresidue = CheckResidue(currentFrame, topIn, *dih, next_resnum, clash);
else
checkresidue = CheckResidue(currentFrame, topIn, *dih, topIn.Nres(), clash);
if (checkresidue==0)
rotate_dihedral = false;
else if (checkresidue==-1) {
if (dih - BB_dihedrals_.begin() < 2) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
dih--; // 0
dih--; // -1
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous again.\n");
}
break;
}
if (clash > bestClash) {bestClash = clash; bestLoop = loop_count;}
//n_problems = CheckResidues( currentFrame, second_atom );
//if (n_problems > -1) {
// mprintf("%i\tCheckResidues: %i problems.\n",frameNum,n_problems);
// rotate_dihedral = false;
//} else if (loop_count==0) {
if (loop_count==0 && rotate_dihedral) {
if (debug_>0)
mprintf("\tTrying dihedral increments of +%i\n",increment_);
// Instead of a new random dihedral, try increments
theta_in_degrees = (double)increment_;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for new theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
}
++loop_count;
if (loop_count == max_increment_) {
if (debug_>0)
mprintf("%i iterations! Best clash= %.3lf at %i\n",max_increment_,
sqrt(bestClash),bestLoop);
if (dih - BB_dihedrals_.begin() < backtrack_) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
for (int bt = 0; bt < backtrack_; bt++)
dih--;
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous %i again.\n",
backtrack_ - 1);
}
break;
// Calculate how much to rotate back in order to get to best clash
/*int num_back = bestLoop - 359;
theta_in_degrees = (double) num_back;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for theta
calcRotationMatrix(rotationMatrix, axisOfRotation, theta_in_radians);
// Rotate back to best clash
frm.Frm().RotateAroundAxis(rotationMatrix, theta_in_radians, dih->Rmask);
// DEBUG
DebugTraj.WriteFrame(debugframenum++,currentParm,*currentFrame);
// Sanity check
CheckResidue(currentFrame, *dih, second_atom, &clash);
rotate_dihedral=false;*/
//DebugTraj.EndTraj();
//return 1;
}
} // End dihedral rotation loop
// Safety valve - number of defined dihedrals times * maxfactor
if (number_of_rotations > max_rotations) {
mprinterr("Error: # of rotations (%i) exceeds max rotations (%i), exiting.\n",
number_of_rotations, max_rotations);
//# ifdef DEBUG_PERMUTEDIHEDRALS
// DebugTraj.EndTraj();
//# endif
// Return gracefully for now
break;
//return 1;
}
} // End loop over dihedrals
# ifdef DEBUG_PERMUTEDIHEDRALS
DebugTraj.EndTraj();
mprintf("\tNumber of rotations %i, expected %u\n",number_of_rotations,BB_dihedrals_.size());
# endif
}
// Exec_RotateDihedral::Execute()
Exec::RetType Exec_RotateDihedral::Execute(CpptrajState& State, ArgList& argIn) {
// Get input COORDS set
std::string setname = argIn.GetStringKey("crdset");
if (setname.empty()) {
mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
return CpptrajState::ERR;
}
if (CRD->Size() < 1) {
mprinterr("Error: COORDS set is empty.\n");
return CpptrajState::ERR;
}
int frame = argIn.getKeyInt("frame", 0);
if (frame < 0 || frame >= (int)CRD->Size()) {
mprinterr("Error: Specified frame %i is out of range.\n", frame+1);
return CpptrajState::ERR;
}
mprintf(" ROTATEDIHEDRAL: Using COORDS '%s', frame %i\n", CRD->legend(), frame+1);
// Get target frame
Frame FRM = CRD->AllocateFrame();
CRD->GetFrame(frame, FRM);
// Save as reference
Frame refFrame = FRM;
// Create output COORDS set if necessary
DataSet_Coords* OUT = 0;
int outframe = 0;
std::string outname = argIn.GetStringKey("name");
if (outname.empty()) {
// This will not work for TRAJ data sets
if (CRD->Type() == DataSet::TRAJ) {
mprinterr("Error: Using TRAJ as input set requires use of 'name' keyword for output.\n");
return CpptrajState::ERR;
}
OUT = CRD;
outframe = frame;
} else {
// Create new output set with 1 empty frame.
OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, outname );
if (OUT == 0) return CpptrajState::ERR;
OUT->Allocate( DataSet::SizeArray(1, 1) );
OUT->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
OUT->AddFrame( CRD->AllocateFrame() );
mprintf("\tOutput to set '%s'\n", OUT->legend());
}
// Determine whether we are setting or incrementing.
enum ModeType { SET = 0, INCREMENT };
ModeType mode = SET;
if (argIn.Contains("value"))
mode = SET;
else if (argIn.Contains("increment"))
mode = INCREMENT;
else {
mprinterr("Error: Specify 'value <value>' or 'increment <increment>'\n");
return CpptrajState::ERR;
}
double value = argIn.getKeyDouble(ModeStr[mode], 0.0);
switch (mode) {
case SET: mprintf("\tDihedral will be set to %g degrees.\n", value); break;
case INCREMENT: mprintf("\tDihedral will be incremented by %g degrees.\n", value); break;
}
// Convert to radians
value *= Constants::DEGRAD;
// Select dihedral atoms
int A1, A2, A3, A4;
if (argIn.Contains("type")) {
// By type
ArgList typeArg = argIn.GetStringKey("type");
if (typeArg.empty()) {
mprinterr("Error: No dihedral type specified after 'type'\n");
return CpptrajState::ERR;
}
DihedralSearch dihSearch;
dihSearch.SearchForArgs( typeArg );
if (dihSearch.NoDihedralTokens()) {
mprinterr("Error: Specified dihedral type not recognized.\n");
return CpptrajState::ERR;
}
// Get residue
int res = argIn.getKeyInt("res", -1);
if (res <= 0) {
mprinterr("Error: If 'type' specified 'res' must be specified and > 0.\n");
return CpptrajState::ERR;
}
// Search for dihedrals. User residue #s start from 1.
if (dihSearch.FindDihedrals(CRD->Top(), Range(res-1)))
return CpptrajState::ERR;
DihedralSearch::mask_it dih = dihSearch.begin();
A1 = dih->A0();
A2 = dih->A1();
A3 = dih->A2();
A4 = dih->A3();
} else {
// By masks
AtomMask m1( argIn.GetMaskNext() );
AtomMask m2( argIn.GetMaskNext() );
AtomMask m3( argIn.GetMaskNext() );
AtomMask m4( argIn.GetMaskNext() );
if (CRD->Top().SetupIntegerMask( m1 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m2 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m3 )) return CpptrajState::ERR;
if (CRD->Top().SetupIntegerMask( m4 )) return CpptrajState::ERR;
if (m1.Nselected() != 1) return MaskError( m1 );
if (m2.Nselected() != 1) return MaskError( m2 );
if (m3.Nselected() != 1) return MaskError( m3 );
if (m4.Nselected() != 1) return MaskError( m4 );
A1 = m1[0];
A2 = m2[0];
A3 = m3[0];
A4 = m4[0];
}
mprintf("\tRotating dihedral defined by atoms '%s'-'%s'-'%s'-'%s'\n",
CRD->Top().AtomMaskName(A1).c_str(),
CRD->Top().AtomMaskName(A2).c_str(),
CRD->Top().AtomMaskName(A3).c_str(),
CRD->Top().AtomMaskName(A4).c_str());
// Set mask of atoms that will move during dihedral rotation
AtomMask Rmask = DihedralSearch::MovingAtoms(CRD->Top(), A2, A3);
// Calculate current value of dihedral
double torsion = Torsion( FRM.XYZ(A1), FRM.XYZ(A2), FRM.XYZ(A3), FRM.XYZ(A4) );
// Calculate delta needed to get to target value.
double delta;
switch (mode) {
case SET: delta = value - torsion; break;
case INCREMENT: delta = value; break;
}
mprintf("\tOriginal torsion is %g, rotating by %g degrees.\n",
torsion*Constants::RADDEG, delta*Constants::RADDEG);
// Set axis of rotation
Vec3 axisOfRotation = FRM.SetAxisOfRotation( A2, A3 );
// Calculate rotation matrix for delta.
Matrix_3x3 rotationMatrix;
rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
// Rotate around axis
FRM.Rotate(rotationMatrix, Rmask);
// RMS-fit the non-moving part of the coords back on original
AtomMask refMask = Rmask;
refMask.InvertMask();
FRM.Align( refFrame, refMask );
// Update coords
OUT->SetCRD( outframe, FRM );
return CpptrajState::OK;
}