void setMembers(const std::vector<int>& members) {
members_ = members;
if (members_.size() < 3 || members_.size() > 4) {
std::ostringstream oss;
oss << "members" << containerToString(members) << " is invalid" <<
std::endl;
throw OpenMDException(oss.str());
}
}
void addSatellite(int sat) {
if (satellites_.size() > 3) {
std::ostringstream oss;
oss << "Too many satellites in inversion to add another!" << std::endl;
throw OpenMDException(oss.str());
} else {
satellites_.push_back(sat);
}
}
virtual void validate() {
ParamMap::iterator i;
for (i = parameters_.begin(); i != parameters_.end(); ++i) {
if (!i->second->isOptional() && i->second->empty()) {
std::stringstream ss;
ss << i->second->getKeyword() << " must be set.\n";
throw OpenMDException(ss.str());
}
}
}
void assign(const std::string& keyword, T val) {
ParamMap::iterator i =parameters_.find(keyword);
if (i != parameters_.end()) {
bool result = i->second->setData(val);
if (!result ) {
std::stringstream ss;
ss << "Error in parsing " << keyword << ": expected " <<
i->second->getParamType() << " but got " << val << "\n";
throw OpenMDException(ss.str());
}
} else if (deprecatedKeywords_.find(keyword) !=
deprecatedKeywords_.end()){
std::cout << keyword <<
" has been deprecated in OpenMD. Please update your .md file.\n";
} else {
std::stringstream ss;
ss << keyword << " is not a recognized keyword.\n";
throw OpenMDException(ss.str());
}
}
void setSatellites(const std::vector<int> &sats) {
if (sats.size() == 3) {
satellites_.push_back(sats.at(0));
satellites_.push_back(sats.at(1));
satellites_.push_back(sats.at(2));
} else {
std::ostringstream oss;
oss << "Incorrect number of satellites to add to inversion!" << std::endl;
throw OpenMDException(oss.str());
}
}
TorsionType* TorsionTypeParser::parseLine(const std::string& line) {
StringTokenizer tokenizer(line);
TorsionType* torsionType = NULL;
int nTokens = tokenizer.countTokens();
if (nTokens < 1) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
}
TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken());
nTokens -= 1;
switch(tt) {
case ttGhostTorsion:
if (nTokens < 4) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
RealType k3 = tokenizer.nextTokenAsDouble();
RealType k2 = tokenizer.nextTokenAsDouble();
RealType k1 = tokenizer.nextTokenAsDouble();
RealType k0 = tokenizer.nextTokenAsDouble();
if (trans180_)
torsionType = new CubicTorsionType( k3, k2, k1, k0);
else
torsionType = new CubicTorsionType(-k3, k2, -k1, k0);
}
break;
case ttCubic :
if (nTokens < 4) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
RealType k3 = tokenizer.nextTokenAsDouble();
RealType k2 = tokenizer.nextTokenAsDouble();
RealType k1 = tokenizer.nextTokenAsDouble();
RealType k0 = tokenizer.nextTokenAsDouble();
if (trans180_)
torsionType = new CubicTorsionType( k3, k2, k1, k0);
else
torsionType = new CubicTorsionType(-k3, k2, -k1, k0);
}
break;
case ttQuartic:
if (nTokens < 5) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
RealType k4 = tokenizer.nextTokenAsDouble();
RealType k3 = tokenizer.nextTokenAsDouble();
RealType k2 = tokenizer.nextTokenAsDouble();
RealType k1 = tokenizer.nextTokenAsDouble();
RealType k0 = tokenizer.nextTokenAsDouble();
if (trans180_)
torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0);
else
torsionType = new QuarticTorsionType( k4, -k3, k2, -k1, k0);
}
break;
case ttPolynomial:
if (nTokens < 2 || nTokens % 2 != 0) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
int nPairs = nTokens / 2;
int power;
RealType coefficient;
torsionType = new PolynomialTorsionType();
PolynomialTorsionType* ptt = dynamic_cast<PolynomialTorsionType*>(torsionType);
for (int i = 0; i < nPairs; ++i) {
power = tokenizer.nextTokenAsInt();
bool isOdd = power % 2 == 0 ? false : true;
coefficient = tokenizer.nextTokenAsDouble();
if (!trans180_ && isOdd)
coefficient = -coefficient;
ptt->setCoefficient(power, coefficient);
}
}
break;
case ttCharmm:
if (nTokens < 3 || nTokens % 3 != 0) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
int nSets = nTokens / 3;
std::vector<CharmmTorsionParameter> parameters;
for (int i = 0; i < nSets; ++i) {
CharmmTorsionParameter currParam;
currParam.kchi = tokenizer.nextTokenAsDouble();
currParam.n = tokenizer.nextTokenAsInt();
currParam.delta = tokenizer.nextTokenAsDouble() / 180.0 * NumericConstant::PI; //convert to rad
bool isOdd = currParam.n % 2 == 0 ? false : true;
if (!trans180_) {
currParam.delta = NumericConstant::PI - currParam.delta;
if (isOdd) currParam.kchi = -currParam.kchi;
}
parameters.push_back(currParam);
}
torsionType = new CharmmTorsionType(parameters);
}
break;
case ttOpls:
if (nTokens < 3) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
RealType v1 = tokenizer.nextTokenAsDouble();
RealType v2 = tokenizer.nextTokenAsDouble();
RealType v3 = tokenizer.nextTokenAsDouble();
torsionType = new OplsTorsionType(v1, v2, v3, trans180_);
}
break;
case ttTrappe:
if (nTokens < 4) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
RealType c0 = tokenizer.nextTokenAsDouble();
RealType c1 = tokenizer.nextTokenAsDouble();
RealType c2 = tokenizer.nextTokenAsDouble();
RealType c3 = tokenizer.nextTokenAsDouble();
torsionType = new TrappeTorsionType(c0, c1, c2, c3, trans180_);
}
break;
case ttHarmonic:
if (nTokens < 2) {
throw OpenMDException("TorsionTypeParser: Not enough tokens");
} else {
// Most torsions don't have specific angle information since
// they are cosine polynomials. This one is different,
// however. To match our other force field files
// (particularly for bends):
//
// phi0 should be read in degrees
// d0 should be read in kcal / mol / degrees^2
RealType degreesPerRadian = 180.0 / NumericConstant::PI;
// convert to radians
RealType phi0 = tokenizer.nextTokenAsDouble() / degreesPerRadian;
// convert to kcal / mol / radians^2
RealType d0 = tokenizer.nextTokenAsDouble() * pow(degreesPerRadian,2);
if (!trans180_)
phi0 = NumericConstant::PI - phi0;
torsionType = new HarmonicTorsionType(d0, phi0);
}
break;
case ttUnknown :
default:
throw OpenMDException("TorsionTypeParser: Unknown Torsion Type");
}
return torsionType;
}