/** Set angle up for this parmtop. Get masks etc.
*/
Action::RetType Action_Energy::Setup(Topology* currentParm, Topology** parmAddress) {
if (currentParm->SetupCharMask(Mask1_)) return Action::ERR;
if (Mask1_.None()) {
mprinterr("Warning: Mask '%s' selects no atoms.\n", Mask1_.MaskString());
return Action::ERR;
}
Mask1_.MaskInfo();
Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
currentParm_ = currentParm;
return Action::OK;
}
/** Set angle up for this parmtop. Get masks etc.
*/
Action::RetType Action_Energy::Setup(ActionSetup& setup) {
if (setup.Top().SetupCharMask(Mask1_)) return Action::ERR;
if (Mask1_.None()) {
mprintf("Warning: Mask '%s' selects no atoms.\n", Mask1_.MaskString());
return Action::SKIP;
}
Mask1_.MaskInfo();
Imask_ = AtomMask(Mask1_.ConvertToIntMask(), Mask1_.Natom());
// Check for LJ terms
for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
if ((*calc == N14 || *calc == NBD) && !setup.Top().Nonbond().HasNonbond())
{
mprinterr("Error: Nonbonded energy calc requested but topology '%s'\n"
"Error: does not have non-bonded parameters.\n", setup.Top().c_str());
return Action::ERR;
}
currentParm_ = setup.TopAddress();
return Action::OK;
}
/** Set up masks. */
int Cpptraj::MaskArray::SetupMasks(AtomMask const& maskIn, Topology const& topIn)
{
if (type_ == BY_MOLECULE && topIn.Nmol() < 1) {
mprintf("Warning: '%s' has no molecule information, cannot setup by molecule.\n",
topIn.c_str());
return 1;
}
masks_.clear();
if ( maskIn.None() ) {
mprintf("Warning: Nothing selected by mask '%s'\n", maskIn.MaskString());
return 0;
}
int last = -1;
int current = 0;
maxAtomsPerMask_ = 0;
sameNumAtomsPerMask_ = true;
for (AtomMask::const_iterator atm = maskIn.begin(); atm != maskIn.end(); ++atm)
{
switch (type_) {
case BY_ATOM : current = *atm; break;
case BY_RESIDUE : current = topIn[*atm].ResNum(); break;
case BY_MOLECULE : current = topIn[*atm].MolNum(); break;
}
if (current != last) {
if (!masks_.empty())
checkAtomsPerMask( masks_.back().Nselected() );
masks_.push_back( AtomMask() );
masks_.back().SetNatoms( topIn.Natom() );
}
masks_.back().AddSelectedAtom( *atm );
last = current;
}
if (!masks_.empty())
checkAtomsPerMask( masks_.back().Nselected() );
return 0;
}
// -----------------------------------------------------------------------------
// Action_NMRrst::Init()
Action::RetType Action_NMRrst::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
if (init.TrajComm().Size() > 1) {
mprinterr("Error: 'nmrrst' action does not work with > 1 thread (%i threads currently).\n",
init.TrajComm().Size());
return Action::ERR;
}
# endif
debug_ = debugIn;
// Get Keywords
Image_.InitImaging( !(actionArgs.hasKey("noimage")) );
useMass_ = !(actionArgs.hasKey("geom"));
findNOEs_ = actionArgs.hasKey("findnoes");
findOutput_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("findout"), "Found NOEs",
DataFileList::TEXT, true);
specOutput_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("specout"), "Specified NOEs",
DataFileList::TEXT, true);
if (findOutput_ == 0 || specOutput_ == 0) return Action::ERR;
resOffset_ = actionArgs.getKeyInt("resoffset", 0);
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
max_cut_ = actionArgs.getKeyDouble("cut", 6.0);
strong_cut_ = actionArgs.getKeyDouble("strongcut", 2.9);
medium_cut_ = actionArgs.getKeyDouble("mediumcut", 3.5);
weak_cut_ = actionArgs.getKeyDouble("weakcut", 5.0);
series_ = actionArgs.hasKey("series");
std::string rstfilename = actionArgs.GetStringKey("file");
viewrst_ = actionArgs.GetStringKey("viewrst");
setname_ = actionArgs.GetStringKey("name");
if (setname_.empty())
setname_ = init.DSL().GenerateDefaultName("NMR");
nframes_ = 0;
// Atom Mask
Mask_.SetMaskString( actionArgs.GetMaskNext() );
// Pairs specified on command line.
std::string pair1 = actionArgs.GetStringKey("pair");
while (!pair1.empty()) {
std::string pair2 = actionArgs.GetStringNext();
if (pair2.empty()) {
mprinterr("Error: Only one mask specified for pair (%s)\n", pair1.c_str());
return Action::ERR;
}
Pairs_.push_back( MaskPairType(AtomMask(pair1), AtomMask(pair2)) );
pair1 = actionArgs.GetStringKey("pair");
}
// Check that something will be done
if (!findNOEs_ && rstfilename.empty() && Pairs_.empty()) {
mprinterr("Error: Must specify restraint file, 'pair', and/or 'findnoes'.\n");
return Action::ERR;
}
// Read in NMR restraints.
if (!rstfilename.empty()) {
if (ReadNmrRestraints( rstfilename )) return Action::ERR;
}
// Set up distances.
int num_noe = 1;
for (noeDataArray::iterator noe = NOEs_.begin(); noe != NOEs_.end(); ++noe, ++num_noe) {
// Translate any ambiguous atom names
TranslateAmbiguous( noe->aName1_ );
TranslateAmbiguous( noe->aName2_ );
// Create mask expressions from resnum/atom name
noe->dMask1_.SetMaskString( MaskExpression( noe->resNum1_, noe->aName1_ ) );
noe->dMask2_.SetMaskString( MaskExpression( noe->resNum2_, noe->aName2_ ) );
// Dataset to store distances
AssociatedData_NOE noeData(noe->bound_, noe->boundh_, noe->rexp_);
MetaData md(setname_, "NOE", num_noe);
md.SetLegend( noe->dMask1_.MaskExpression() + " and " + noe->dMask2_.MaskExpression());
md.SetScalarMode( MetaData::M_DISTANCE );
md.SetScalarType( MetaData::NOE );
noe->dist_ = init.DSL().AddSet(DataSet::DOUBLE, md);
if (noe->dist_==0) return Action::ERR;
noe->dist_->AssociateData( &noeData );
// Add dataset to data file
if (outfile != 0) outfile->AddDataSet( noe->dist_ );
}
masterDSL_ = init.DslPtr();
mprintf("Warning: *** THIS ACTION IS EXPERIMENTAL. ***\n");
mprintf(" NMRRST: %zu NOEs from NMR restraint file.\n", NOEs_.size());
mprintf("\tShifting residue numbers in restraint file by %i\n", resOffset_);
// DEBUG - print NOEs
for (noeDataArray::const_iterator noe = NOEs_.begin(); noe != NOEs_.end(); ++noe)
mprintf("\t'%s' %f < %f < %f\n", noe->dist_->legend(),
noe->bound_, noe->rexp_, noe->boundh_);
if (findNOEs_) {
mprintf("\tSearching for potential NOEs. Max cutoff is %g Ang.\n", max_cut_);
mprintf("\tNOE distance criteria (Ang.): S= %g, M= %g, W= %g\n",
strong_cut_, medium_cut_, weak_cut_);
if (series_)
mprintf("\tDistance data for NOEs less than cutoff will be saved as '%s[foundNOE]'.\n",
setname_.c_str());
mprintf("\tFound NOEs will be written to '%s'\n", findOutput_->Filename().full());
}
if (!Pairs_.empty()) {
mprintf("\tSpecified NOE pairs:\n");
for (MaskPairArray::const_iterator mp = Pairs_.begin(); mp != Pairs_.end(); ++mp)
mprintf("\t\t[%s] to [%s]\n", mp->first.MaskString(), mp->second.MaskString());
mprintf("\tSpecified NOE data will be written to '%s'\n", specOutput_->Filename().full());
}
if (!Image_.UseImage())
mprintf("\tNon-imaged");
else
mprintf("\tImaged");
if (useMass_)
mprintf(", center of mass.\n");
else
mprintf(", geometric center.\n");
if (!viewrst_.empty())
mprintf("\tTopologies corresponding to found NOEs will be written to '%s'\n", viewrst_.c_str());
return Action::OK;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
else if (actionArgs.hasKey("mass") ) property_ = MASS;
else if (actionArgs.hasKey("charge") ) property_ = CHARGE;
else if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
binType_ = CENTER;
if (actionArgs.hasKey("bincenter")) binType_ = CENTER;
else if (actionArgs.hasKey("binedge") ) binType_ = EDGE;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
if (delta_ <= 0) {
mprinterr("Error: Delta must be > 0.0\n");
return Action::ERR;
}
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
// If no masks assume we want total system density.
if (dsname.empty())
dsname = actionArgs.GetStringNext();
density_ = init.DSL().AddSet(DataSet::DOUBLE, dsname, "DENSITY");
if (density_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( density_ );
image_.InitImaging( true );
// Hijack delta for storing sum of masses
delta_ = 0.0;
} else {
// Density selected by mask(s) along an axis
density_ = 0;
histograms_.resize(masks_.size() );
}
mprintf(" DENSITY:");
if (density_ == 0) {
const char* binStr[] = {"center", "edge"};
mprintf(" Determining %s density for %zu masks.\n", PropertyStr_[property_], masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
mprintf("\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n");
mprintf("\tBin coordinates will be to bin %s.\n", binStr[binType_]);
} else {
mprintf(" No masks specified, calculating total system density in g/cm^3.\n");
mprintf("\tData set name is '%s'\n", density_->legend());
}
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
/** 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;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
if (init.TrajComm().Size() > 1) {
mprinterr("Error: 'density' action does not work with > 1 thread (%i threads currently).\n",
init.TrajComm().Size());
return Action::ERR;
}
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
if (actionArgs.hasKey("mass") ) property_ = MASS;
if (actionArgs.hasKey("charge") ) property_ = CHARGE;
if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
mprinterr("Error: No masks specified.\n");
return Action::ERR;
}
minus_histograms_.resize(masks_.size() );
plus_histograms_.resize(masks_.size() );
mprintf(" DENSITY: Determining %s density for %zu masks.\n", PropertyStr_[property_],
masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
