int main(int argc, char* argv[]){
struct gengetopt_args_info args_info;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
cmdline_parser_print_help();
exit(1) ;
}
//get the dumpfile name and meta-data file name
std::string dumpFileName = args_info.input_arg;
std::string sele1;
std::string sele2;
// check the first selection argument, or set it to the environment
// variable, or failing that, set it to "select all"
if (args_info.sele1_given) {
sele1 = args_info.sele1_arg;
} else {
char* sele1Env= getenv("SELECTION1");
if (sele1Env) {
sele1 = sele1Env;
} else {
sele1 = "select all";
}
}
// check the second selection argument, or set it to the environment
// variable, or failing that, set it to the first selection
if (args_info.sele2_given) {
sele2 = args_info.sele2_arg;
} else {
char* sele2Env = getenv("SELECTION2");
if (sele2Env) {
sele2 = sele2Env;
} else {
//If sele2 is not specified, then the default behavior
//should be what is already intended for sele1
sele2 = sele1;
}
}
// use the memory string to figure out how much memory we can use:
char *end;
long long int memSize = memparse(args_info.memory_arg, &end);
sprintf( painCave.errMsg,
"Amount of memory being used: %llu bytes\n", memSize);
painCave.severity = OPENMD_INFO;
painCave.isFatal = 0;
simError();
//parse md file and set up the system
SimCreator creator;
SimInfo* info = creator.createSim(dumpFileName, false);
DynamicProperty* corrFunc = NULL;
if(args_info.sdcorr_given){
corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2,
memSize);
} else if (args_info.selecorr_given){
corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.dcorr_given){
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.rcorr_given) {
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
} else if (args_info.r_rcorr_given) {
corrFunc = new RCorrFuncR(info, dumpFileName, sele1, sele2);
} else if (args_info.thetacorr_given) {
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.drcorr_given) {
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2,
memSize);
} else if (args_info.rcorrZ_given) {
corrFunc = new RCorrFuncZ(info, dumpFileName, sele1, sele2,
args_info.nzbins_arg);
} else if (args_info.vcorr_given) {
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
} else if (args_info.vcorrZ_given) {
corrFunc = new VCorrFuncZ(info, dumpFileName, sele1, sele2);
} else if (args_info.vcorrR_given) {
corrFunc = new VCorrFuncR(info, dumpFileName, sele1, sele2);
} else if (args_info.bondcorr_given) {
corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
} else if (args_info.helfandEcorr_given){
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.stresscorr_given){
corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.momentum_given){
corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.freqfluccorr_given){
corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize);
} else if (args_info.lcorr_given) {
int order(0);
if (args_info.order_given)
order = args_info.order_arg;
else {
sprintf( painCave.errMsg,
"--order must be set if --lcorr is set\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order,
memSize);
} else if (args_info.lcorrZ_given) {
int order(0);
if (args_info.order_given)
order = args_info.order_arg;
else {
sprintf( painCave.errMsg,
"--order must be set if --lcorrZ is set\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order,
args_info.nzbins_arg, memSize);
} else if (args_info.cohZ_given) {
int order(0);
if (args_info.order_given)
order = args_info.order_arg;
else {
sprintf( painCave.errMsg,
"--order must be set if --cohZ is set\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order,
args_info.nzbins_arg, memSize);
} else if (args_info.jumptime_given) {
int order(0);
if (args_info.order_given)
order = args_info.order_arg;
else {
sprintf( painCave.errMsg,
"--order must be specified when calculating Hydrogen Bond "
"Jump Statistics\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
corrFunc = new HBondJump(info, dumpFileName, sele1, sele2,
args_info.OOcut_arg,
args_info.thetacut_arg,
args_info.OHcut_arg,
order);
}
if (args_info.output_given) {
corrFunc->setOutputName(args_info.output_arg);
}
corrFunc->doCorrelate();
delete corrFunc;
delete info;
return 0;
}
int main(int argc, char* argv[]){
registerHydrodynamicsModels();
gengetopt_args_info args_info;
std::string dumpFileName;
std::string mdFileName;
std::string prefix;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name and meta-data file name
if (args_info.input_given){
dumpFileName = args_info.input_arg;
} else {
strcpy( painCave.errMsg,
"No input file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
if (args_info.output_given){
prefix = args_info.output_arg;
} else {
prefix = getPrefix(dumpFileName);
}
std::string outputFilename = prefix + ".diff";
//parse md file and set up the system
SimCreator creator;
SimInfo* info = creator.createSim(dumpFileName, true);
SimInfo::MoleculeIterator mi;
Molecule* mol;
Molecule::IntegrableObjectIterator ii;
StuntDouble* sd;
Mat3x3d identMat;
identMat(0,0) = 1.0;
identMat(1,1) = 1.0;
identMat(2,2) = 1.0;
Globals* simParams = info->getSimParams();
RealType temperature(0.0);
RealType viscosity(0.0);
if (simParams->haveViscosity()) {
viscosity = simParams->getViscosity();
} else {
sprintf(painCave.errMsg, "viscosity must be set\n");
painCave.isFatal = 1;
simError();
}
if (simParams->haveTargetTemp()) {
temperature = simParams->getTargetTemp();
} else {
sprintf(painCave.errMsg, "target temperature must be set\n");
painCave.isFatal = 1;
simError();
}
std::map<std::string, SDShape> uniqueStuntDoubles;
for (mol = info->beginMolecule(mi); mol != NULL;
mol = info->nextMolecule(mi)) {
for (sd = mol->beginIntegrableObject(ii); sd != NULL;
sd = mol->nextIntegrableObject(ii)) {
if (uniqueStuntDoubles.find(sd->getType()) == uniqueStuntDoubles.end()) {
sd->setPos(V3Zero);
sd->setA(identMat);
if (sd->isRigidBody()) {
RigidBody* rb = static_cast<RigidBody*>(sd);
rb->updateAtoms();
}
SDShape tmp;
tmp.shape = ShapeBuilder::createShape(sd);
tmp.sd = sd;
uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->getType(), tmp));
}
}
}
std::map<std::string, SDShape>::iterator si;
for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
HydrodynamicsModel* model;
Shape* shape = si->second.shape;
StuntDouble* sd = si->second.sd;;
if (args_info.model_given) {
model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
} else if (shape->hasAnalyticalSolution()) {
model = new AnalyticalModel(sd, info);
} else {
model = new BeadModel(sd, info);
}
model->init();
std::ofstream ofs;
std::stringstream outputBeads;
outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
ofs.open(outputBeads.str().c_str());
model->writeBeads(ofs);
ofs.close();
//if beads option is turned on, skip the calculation
if (!args_info.beads_flag) {
model->calcHydroProps(shape, viscosity, temperature);
std::ofstream outputDiff;
outputDiff.open(outputFilename.c_str());
model->writeHydroProps(outputDiff);
outputDiff.close();
}
delete model;
}
//MemoryUtils::deletePointers(shapes);
delete info;
}
int main(int argc, char* argv[]){
gengetopt_args_info args_info;
string dumpFileName;
string outFileName;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name and meta-data file name
if (args_info.input_given){
dumpFileName = args_info.input_arg;
} else {
strcpy( painCave.errMsg,
"No input file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
if (args_info.output_given){
outFileName = args_info.output_arg;
} else {
strcpy( painCave.errMsg,
"No output file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
Vector3i repeat = Vector3i(args_info.repeatX_arg,
args_info.repeatY_arg,
args_info.repeatZ_arg);
Mat3x3d repeatD = Mat3x3d(0.0);
repeatD(0,0) = repeat.x();
repeatD(1,1) = repeat.y();
repeatD(2,2) = repeat.z();
Vector3d translate = Vector3d(args_info.translateX_arg,
args_info.translateY_arg,
args_info.translateZ_arg);
//parse md file and set up the system
SimCreator oldCreator;
SimInfo* oldInfo = oldCreator.createSim(dumpFileName, false);
Globals* simParams = oldInfo->getSimParams();
std::vector<Component*> components = simParams->getComponents();
std::vector<int> nMol;
for (vector<Component*>::iterator i = components.begin();
i !=components.end(); ++i) {
int nMolOld = (*i)->getNMol();
int nMolNew = nMolOld * repeat.x() * repeat.y() * repeat.z();
nMol.push_back(nMolNew);
}
createMdFile(dumpFileName, outFileName, nMol);
SimCreator newCreator;
SimInfo* newInfo = newCreator.createSim(outFileName, false);
DumpReader* dumpReader = new DumpReader(oldInfo, dumpFileName);
int nframes = dumpReader->getNFrames();
DumpWriter* writer = new DumpWriter(newInfo, outFileName);
if (writer == NULL) {
sprintf(painCave.errMsg, "error in creating DumpWriter");
painCave.isFatal = 1;
simError();
}
SimInfo::MoleculeIterator miter;
Molecule::IntegrableObjectIterator iiter;
Molecule::RigidBodyIterator rbIter;
Molecule* mol;
StuntDouble* sd;
StuntDouble* sdNew;
RigidBody* rb;
Mat3x3d oldHmat;
Mat3x3d newHmat;
Snapshot* oldSnap;
Snapshot* newSnap;
Vector3d oldPos;
Vector3d newPos;
for (int i = 0; i < nframes; i++){
cerr << "frame = " << i << "\n";
dumpReader->readFrame(i);
oldSnap = oldInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap = newInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap->setID( oldSnap->getID() );
newSnap->setTime( oldSnap->getTime() );
oldHmat = oldSnap->getHmat();
newHmat = repeatD*oldHmat;
newSnap->setHmat(newHmat);
newSnap->setThermostat( oldSnap->getThermostat() );
newSnap->setBarostat( oldSnap->getBarostat() );
int newIndex = 0;
for (mol = oldInfo->beginMolecule(miter); mol != NULL;
mol = oldInfo->nextMolecule(miter)) {
for (int ii = 0; ii < repeat.x(); ii++) {
for (int jj = 0; jj < repeat.y(); jj++) {
for (int kk = 0; kk < repeat.z(); kk++) {
Vector3d trans = Vector3d(ii, jj, kk);
for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
sd = mol->nextIntegrableObject(iiter)) {
oldPos = sd->getPos() + translate;
oldSnap->wrapVector(oldPos);
newPos = oldPos + trans * oldHmat;
sdNew = newInfo->getIOIndexToIntegrableObject(newIndex);
sdNew->setPos( newPos );
sdNew->setVel( sd->getVel() );
if (sd->isDirectional()) {
sdNew->setA( sd->getA() );
sdNew->setJ( sd->getJ() );
}
newIndex++;
}
}
}
}
}
//update atoms of rigidbody
for (mol = newInfo->beginMolecule(miter); mol != NULL;
mol = newInfo->nextMolecule(miter)) {
//change the positions of atoms which belong to the rigidbodies
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
rb->updateAtomVel();
}
}
writer->writeDump();
}
// deleting the writer will put the closing at the end of the dump file.
delete writer;
delete oldInfo;
}
int main(int argc, char *argv []) {
registerLattice();
gengetopt_args_info args_info;
std::string latticeType;
std::string inputFileName;
std::string outputFileName;
MoLocator* locator;
int nComponents;
double latticeConstant;
RealType rodRadius;
RealType rodLength;
Mat3x3d hmat;
DumpWriter *writer;
// Parse Command Line Arguments
if (cmdline_parser(argc, argv, &args_info) != 0)
exit(1);
/* get lattice type */
latticeType = "FCC";
/* get input file name */
if (args_info.inputs_num)
inputFileName = args_info.inputs[0];
else {
sprintf(painCave.errMsg, "No input .omd file name was specified "
"on the command line");
painCave.isFatal = 1;
cmdline_parser_print_help();
simError();
}
/* parse md file and set up the system */
SimCreator oldCreator;
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
latticeConstant = args_info.latticeConstant_arg;
rodRadius = args_info.radius_arg;
rodLength = args_info.length_arg;
Globals* simParams = oldInfo->getSimParams();
vector<Vector3d> sites;
vector<Vector3d> orientations;
if (args_info.ellipsoid_flag) {
shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
rodLength, rodRadius);
sites = nanoEllipsoid.getSites();
orientations = nanoEllipsoid.getOrientations();
} else {
/* Create nanorod */
shapedLatticeRod nanoRod(latticeConstant, latticeType,
rodRadius, rodLength);
/* Build a lattice and get lattice points for this lattice constant */
sites = nanoRod.getSites();
orientations = nanoRod.getOrientations();
}
std::vector<std::size_t> vacancyTargets;
vector<bool> isVacancy;
Vector3d myLoc;
RealType myR;
for (std::size_t i = 0; i < sites.size(); i++)
isVacancy.push_back(false);
// cerr << "checking vacancyPercent" << "\n";
if (args_info.vacancyPercent_given) {
// cerr << "vacancyPercent given" << "\n";
if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
sprintf(painCave.errMsg,
"vacancyPercent was set to a non-sensical value.");
painCave.isFatal = 1;
simError();
} else {
RealType vF = args_info.vacancyPercent_arg / 100.0;
// cerr << "vacancyPercent = " << vF << "\n";
RealType vIR;
RealType vOR;
if (args_info.vacancyInnerRadius_given) {
vIR = args_info.vacancyInnerRadius_arg;
} else {
vIR = 0.0;
}
if (args_info.vacancyOuterRadius_given) {
vOR = args_info.vacancyOuterRadius_arg;
} else {
vOR = rodRadius;
}
if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
for (std::size_t i = 0; i < sites.size(); i++) {
myLoc = sites[i];
myR = myLoc.length();
if (myR >= vIR && myR <= vOR) {
vacancyTargets.push_back(i);
}
}
std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
std::size_t nTargets = vacancyTargets.size();
vacancyTargets.resize((int)(vF * nTargets));
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
"\tsites between %lf and %lf.", (int) vacancyTargets.size(),
vIR, vOR);
painCave.isFatal = 0;
painCave.severity = OPENMD_INFO;
simError();
isVacancy.clear();
for (std::size_t i = 0; i < sites.size(); i++) {
bool vac = false;
for (std::size_t j = 0; j < vacancyTargets.size(); j++) {
if (i == vacancyTargets[j]) vac = true;
}
isVacancy.push_back(vac);
}
} else {
sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
"\tinner or outer radii. Check their values.");
painCave.isFatal = 1;
simError();
}
}
}
/* Get number of lattice sites */
std::size_t nSites = sites.size() - vacancyTargets.size();
// cerr << "sites.size() = " << sites.size() << "\n";
// cerr << "nSites = " << nSites << "\n";
// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";
std::vector<Component*> components = simParams->getComponents();
std::vector<RealType> molFractions;
std::vector<RealType> shellRadii;
std::vector<int> nMol;
std::map<int, int> componentFromSite;
nComponents = components.size();
// cerr << "nComponents = " << nComponents << "\n";
if (args_info.molFraction_given && args_info.shellRadius_given) {
sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
"arguments, but not both!");
painCave.isFatal = 1;
simError();
}
if (nComponents == 1) {
molFractions.push_back(1.0);
shellRadii.push_back(rodRadius);
} else if (args_info.molFraction_given) {
if ((int)args_info.molFraction_given == nComponents) {
for (int i = 0; i < nComponents; i++) {
molFractions.push_back(args_info.molFraction_arg[i]);
}
} else if ((int)args_info.molFraction_given == nComponents-1) {
RealType remainingFraction = 1.0;
for (int i = 0; i < nComponents-1; i++) {
molFractions.push_back(args_info.molFraction_arg[i]);
remainingFraction -= molFractions[i];
}
molFractions.push_back(remainingFraction);
} else {
sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
"for all of the components in the <MetaData> block.");
painCave.isFatal = 1;
simError();
}
} else if ((int)args_info.shellRadius_given) {
if ((int)args_info.shellRadius_given == nComponents) {
for (int i = 0; i < nComponents; i++) {
shellRadii.push_back(args_info.shellRadius_arg[i]);
}
} else if ((int)args_info.shellRadius_given == nComponents-1) {
for (int i = 0; i < nComponents-1; i++) {
shellRadii.push_back(args_info.shellRadius_arg[i]);
}
shellRadii.push_back(rodRadius);
} else {
sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
"\tshell radii for all of the components in the <MetaData> block.");
painCave.isFatal = 1;
simError();
}
} else {
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
"\tbut have not specified either molFraction or shellRadius arguments.");
painCave.isFatal = 1;
simError();
}
if (args_info.molFraction_given) {
RealType totalFraction = 0.0;
/* Do some simple sanity checking*/
for (int i = 0; i < nComponents; i++) {
if (molFractions.at(i) < 0.0) {
sprintf(painCave.errMsg, "One of the requested molFractions was"
" less than zero!");
painCave.isFatal = 1;
simError();
}
if (molFractions.at(i) > 1.0) {
sprintf(painCave.errMsg, "One of the requested molFractions was"
" greater than one!");
painCave.isFatal = 1;
simError();
}
totalFraction += molFractions.at(i);
}
if (abs(totalFraction - 1.0) > 1e-6) {
sprintf(painCave.errMsg,
"The sum of molFractions was not close enough to 1.0");
painCave.isFatal = 1;
simError();
}
int remaining = nSites;
for (int i=0; i < nComponents-1; i++) {
nMol.push_back(int((RealType)nSites * molFractions.at(i)));
remaining -= nMol.at(i);
}
nMol.push_back(remaining);
// recompute actual mol fractions and perform final sanity check:
std::size_t totalMolecules = 0;
for (int i=0; i < nComponents; i++) {
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
totalMolecules += nMol.at(i);
}
if (totalMolecules != nSites) {
sprintf(painCave.errMsg,
"Computed total number of molecules is not equal "
"to the number of lattice sites!");
painCave.isFatal = 1;
simError();
}
} else {
for (unsigned int i = 0; i < shellRadii.size(); i++) {
if (shellRadii.at(i) > rodRadius + 1e-6 ) {
sprintf(painCave.errMsg,
"One of the shellRadius values exceeds the rod Radius.");
painCave.isFatal = 1;
simError();
}
if (shellRadii.at(i) <= 0.0 ) {
sprintf(painCave.errMsg,
"One of the shellRadius values is smaller than zero!");
painCave.isFatal = 1;
simError();
}
}
}
vector<int> ids;
if ((int)args_info.molFraction_given){
// cerr << "molFraction given 2" << "\n";
sprintf(painCave.errMsg,
"Creating a randomized spherically-capped nanorod.");
painCave.isFatal = 0;
painCave.severity = OPENMD_INFO;
simError();
/* Random rod is the default case*/
for (std::size_t i = 0; i < sites.size(); i++)
if (!isVacancy[i]) ids.push_back(i);
std::random_shuffle(ids.begin(), ids.end());
} else{
sprintf(painCave.errMsg, "Creating an fcc nanorod.");
painCave.isFatal = 0;
painCave.severity = OPENMD_INFO;
simError();
// RealType smallestSoFar;
int myComponent = -1;
nMol.clear();
nMol.resize(nComponents);
// cerr << "shellRadii[0] " << shellRadii[0] << "\n";
// cerr << "rodRadius " << rodRadius << "\n";
for (unsigned int i = 0; i < sites.size(); i++) {
myLoc = sites[i];
myR = myLoc.length();
// smallestSoFar = rodRadius;
// cerr << "vac = " << isVacancy[i]<< "\n";
if (!isVacancy[i]) {
// for (int j = 0; j < nComponents; j++) {
// if (myR <= shellRadii[j]) {
// if (shellRadii[j] <= smallestSoFar) {
// smallestSoFar = shellRadii[j];
// myComponent = j;
// }
// }
// }
myComponent = 0;
componentFromSite[i] = myComponent;
nMol[myComponent]++;
// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
}
}
}
// cerr << "nMol = " << nMol.at(0) << "\n";
outputFileName = args_info.output_arg;
//creat new .omd file on fly which corrects the number of molecule
createMdFile(inputFileName, outputFileName, nMol);
delete oldInfo;
SimCreator newCreator;
SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
// Place molecules
Molecule* mol;
SimInfo::MoleculeIterator mi;
mol = NewInfo->beginMolecule(mi);
int l = 0;
for (int i = 0; i < nComponents; i++){
locator = new MoLocator(NewInfo->getMoleculeStamp(i),
NewInfo->getForceField());
// cerr << "nMol = " << nMol.at(i) << "\n";
if (!args_info.molFraction_given) {
for (unsigned int n = 0; n < sites.size(); n++) {
if (!isVacancy[n]) {
if (componentFromSite[n] == i) {
mol = NewInfo->getMoleculeByGlobalIndex(l);
locator->placeMol(sites[n], orientations[n], mol);
l++;
}
}
}
} else {
for (int n = 0; n < nMol.at(i); n++) {
mol = NewInfo->getMoleculeByGlobalIndex(l);
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
l++;
}
}
}
//fill Hmat
hmat(0, 0)= 10.0*rodRadius;
hmat(0, 1) = 0.0;
hmat(0, 2) = 0.0;
hmat(1, 0) = 0.0;
hmat(1, 1) = 10.0*rodRadius;
hmat(1, 2) = 0.0;
hmat(2, 0) = 0.0;
hmat(2, 1) = 0.0;
hmat(2, 2) = 5.0*rodLength + 2.0*rodRadius;
//set Hmat
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
//create dumpwriter and write out the coordinates
writer = new DumpWriter(NewInfo, outputFileName);
if (writer == NULL) {
sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
painCave.isFatal = 1;
simError();
}
writer->writeDump();
// deleting the writer will put the closing at the end of the dump file
delete writer;
// cleanup a by calling sim error.....
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
"generated.\n", outputFileName.c_str());
painCave.isFatal = 0;
painCave.severity = OPENMD_INFO;
simError();
return 0;
}
int main(int argc, char* argv[]){
gengetopt_args_info args_info;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name
std::string dumpFileName = args_info.input_arg;
std::string sele1;
std::string sele2;
std::string sele3;
// check the first selection argument, or set it to the environment
// variable, or failing that, set it to "select all"
if (args_info.sele1_given) {
sele1 = args_info.sele1_arg;
} else {
char* sele1Env= getenv("SELECTION1");
if (sele1Env) {
sele1 = sele1Env;
} else {
sele1 = "select all";
}
}
// check the second selection argument, or set it to the environment
// variable, or failing that, set it to the first selection
if (args_info.sele2_given) {
sele2 = args_info.sele2_arg;
} else {
char* sele2Env = getenv("SELECTION2");
if (sele2Env) {
sele2 = sele2Env;
} else {
//If sele2 is not specified, then the default behavior
//should be what is already intended for sele1
sele2 = sele1;
}
}
// check the third selection argument, which is only set if
// requested by the user
if (args_info.sele3_given) sele3 = args_info.sele3_arg;
bool batchMode(false);
if (args_info.scd_given){
if (args_info.sele1_given &&
args_info.sele2_given && args_info.sele3_given) {
batchMode = false;
} else if (args_info.molname_given &&
args_info.begin_given && args_info.end_given) {
if (args_info.begin_arg < 0 ||
args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
sprintf( painCave.errMsg,
"below conditions are not satisfied:\n"
"0 <= begin && 0<= end && begin <= end-2\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
batchMode = true;
} else{
sprintf( painCave.errMsg,
"either --sele1, --sele2, --sele3 are specified,"
" or --molname, --begin, --end are specified\n");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
}
//parse md file and set up the system
SimCreator creator;
SimInfo* info = creator.createSim(dumpFileName);
RealType maxLen;
RealType zmaxLen(0.0);
if (args_info.length_given) {
maxLen = args_info.length_arg;
if (args_info.zlength_given){
zmaxLen = args_info.zlength_arg;
}
} else {
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
zmaxLen = hmat(2,2);
}
RealType nanglebins, nrbins;
// in case we override nbins with nrbins:
if (args_info.nrbins_given) {
nrbins = args_info.nrbins_arg;
} else {
nrbins = args_info.nbins_arg;
}
// in case we override nbins with nrbins:
if (args_info.nanglebins_given) {
nanglebins = args_info.nanglebins_arg;
} else {
nanglebins = args_info.nbins_arg;
}
StaticAnalyser* analyser;
if (args_info.gofr_given){
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
nrbins);
} else if (args_info.gofz_given) {
analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
args_info.nbins_arg);
} else if (args_info.r_z_given) {
analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
nrbins, args_info.nbins_z_arg);
} else if (args_info.r_theta_given) {
if (args_info.sele3_given)
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
nrbins, nanglebins);
else
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
nrbins, nanglebins);
} else if (args_info.r_omega_given) {
if (args_info.sele3_given)
analyser = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
nrbins, nanglebins);
else
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
nrbins, nanglebins);
} else if (args_info.theta_omega_given) {
if (args_info.sele3_given)
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
nanglebins);
else
analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
nanglebins);
} else if (args_info.gxyz_given) {
if (args_info.refsele_given) {
analyser= new GofXyz(info, dumpFileName, sele1, sele2,
args_info.refsele_arg, maxLen, args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"--refsele must set when --gxyz is used");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.twodgofr_given){
if (args_info.dz_given) {
analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
args_info.dz_arg, nrbins);
} else {
sprintf( painCave.errMsg,
"A slab width (dz) must be specified when calculating TwoDGofR");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.p2_given) {
if (args_info.sele1_given) {
if (args_info.sele2_given)
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
else
if (args_info.seleoffset_given)
analyser = new P2OrderParameter(info, dumpFileName, sele1,
args_info.seleoffset_arg);
else
analyser = new P2OrderParameter(info, dumpFileName, sele1);
} else {
sprintf( painCave.errMsg,
"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.rp2_given){
analyser = new RippleOP(info, dumpFileName, sele1, sele2);
} else if (args_info.bo_given){
if (args_info.rcut_given) {
analyser = new BondOrderParameter(info, dumpFileName, sele1,
args_info.rcut_arg,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.multipole_given){
analyser = new MultipoleSum(info, dumpFileName, sele1,
maxLen, args_info.nbins_arg);
} else if (args_info.tet_param_given) {
if (args_info.rcut_given) {
analyser = new TetrahedralityParam(info, dumpFileName, sele1,
args_info.rcut_arg,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.tet_param_z_given) {
if (args_info.rcut_given) {
analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
args_info.rcut_arg,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.tet_param_xyz_given) {
if (!args_info.rcut_given) {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating"
" Tetrahedrality Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
if (!args_info.voxelSize_given) {
sprintf( painCave.errMsg,
"A voxel size must be specified when calculating"
" volume-resolved Tetrahedrality Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
if (!args_info.gaussWidth_given) {
sprintf( painCave.errMsg,
"A gaussian width must be specified when calculating"
" volume-resolved Tetrahedrality Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
args_info.rcut_arg,
args_info.voxelSize_arg,
args_info.gaussWidth_arg);
} else if (args_info.ior_given){
if (args_info.rcut_given) {
analyser = new IcosahedralOfR(info, dumpFileName, sele1,
args_info.rcut_arg,
nrbins, maxLen);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.for_given){
if (args_info.rcut_given) {
analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
nrbins, maxLen);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.bad_given){
if (args_info.rcut_given) {
analyser = new BondAngleDistribution(info, dumpFileName, sele1,
args_info.rcut_arg,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.scd_given) {
if (batchMode) {
analyser = new SCDOrderParameter(info, dumpFileName,
args_info.molname_arg,
args_info.begin_arg, args_info.end_arg);
} else{
analyser = new SCDOrderParameter(info, dumpFileName,
sele1, sele2, sele3);
}
}else if (args_info.density_given) {
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
args_info.nbins_arg);
} else if (args_info.count_given) {
analyser = new ObjectCount(info, dumpFileName, sele1 );
} else if (args_info.slab_density_given) {
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
} else if (args_info.rnemdz_given) {
analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
} else if (args_info.rnemdr_given) {
analyser = new RNEMDR(info, dumpFileName, sele1, nrbins);
} else if (args_info.rnemdrt_given) {
analyser = new RNEMDRTheta(info, dumpFileName, sele1, nrbins, nanglebins);
} else if (args_info.nitrile_given) {
analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
args_info.nbins_arg);
} else if (args_info.p_angle_given) {
if (args_info.sele1_given) {
if (args_info.sele2_given)
analyser = new pAngle(info, dumpFileName, sele1, sele2,
args_info.nbins_arg);
else
if (args_info.seleoffset_given) {
if (args_info.seleoffset2_given) {
analyser = new pAngle(info, dumpFileName, sele1,
args_info.seleoffset_arg,
args_info.seleoffset2_arg,
args_info.nbins_arg);
} else {
analyser = new pAngle(info, dumpFileName, sele1,
args_info.seleoffset_arg,
args_info.nbins_arg);
}
} else
analyser = new pAngle(info, dumpFileName, sele1,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"At least one selection script (--sele1) must be specified when "
"calculating P(angle) distributions");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
}else if (args_info.hxy_given) {
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
args_info.nbins_y_arg, args_info.nbins_arg);
#endif
}else if(args_info.gcn_given){
analyser = new GCN(info, dumpFileName, sele1, sele2, args_info.nbins_arg);
}
else if (args_info.surfDiffusion_given){
analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
}else if (args_info.rho_r_given) {
if (args_info.radius_given){
analyser = new RhoR(info, dumpFileName, sele1, maxLen, nrbins,
args_info.radius_arg);
}else{
sprintf( painCave.errMsg,
"A particle radius (radius) must be specified when calculating Rho(r)");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.hullvol_given) {
analyser = new NanoVolume(info, dumpFileName, sele1);
} else if (args_info.rodlength_given) {
analyser = new NanoLength(info, dumpFileName, sele1);
} else if (args_info.angle_r_given) {
analyser = new AngleR(info, dumpFileName, sele1, maxLen, nrbins);
} else if (args_info.hbond_given){
if (args_info.rcut_given) {
if (args_info.thetacut_given) {
analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
args_info.rcut_arg,
args_info.thetacut_arg,
args_info.nbins_arg);
} else {
sprintf( painCave.errMsg,
"A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else {
sprintf( painCave.errMsg,
"A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
} else if (args_info.potDiff_given) {
analyser = new PotDiff(info, dumpFileName, sele1);
}
if (args_info.output_given) {
analyser->setOutputName(args_info.output_arg);
}
if (args_info.step_given) {
analyser->setStep(args_info.step_arg);
}
analyser->process();
delete analyser;
delete info;
return 0;
}