| 38 |
|
* University of Notre Dame has been advised of the possibility of |
| 39 |
|
* such damages. |
| 40 |
|
*/ |
| 41 |
< |
|
| 42 |
< |
#include <stdlib.h> |
| 43 |
< |
#include <stdio.h> |
| 44 |
< |
#include <string.h> |
| 41 |
> |
#include <algorithm> |
| 42 |
> |
#include <functional> |
| 43 |
|
#include <iostream> |
| 44 |
< |
|
| 44 |
> |
#include <sstream> |
| 45 |
|
#include "types/MoleculeStamp.hpp" |
| 46 |
+ |
#include "utils/Tuple.hpp" |
| 47 |
+ |
#include "utils/MemoryUtils.hpp" |
| 48 |
+ |
namespace oopse { |
| 49 |
|
|
| 50 |
< |
char MoleculeStamp::errMsg[500]; |
| 50 |
> |
template<class ContainerType> |
| 51 |
> |
bool hasDuplicateElement(const ContainerType& cont) { |
| 52 |
> |
ContainerType tmp = cont; |
| 53 |
> |
std::sort(tmp.begin(), tmp.end()); |
| 54 |
> |
tmp.erase(std::unique(tmp.begin(), tmp.end()), tmp.end()); |
| 55 |
> |
return tmp.size() != cont.size(); |
| 56 |
> |
} |
| 57 |
|
|
| 58 |
< |
MoleculeStamp::MoleculeStamp(){ |
| 59 |
< |
|
| 60 |
< |
n_atoms = 0; |
| 61 |
< |
n_bonds = 0; |
| 62 |
< |
n_bends = 0; |
| 63 |
< |
n_torsions = 0; |
| 64 |
< |
n_rigidbodies = 0; |
| 65 |
< |
n_cutoffgroups = 0; |
| 66 |
< |
n_integrable = 0; |
| 58 |
> |
MoleculeStamp::MoleculeStamp() { |
| 59 |
> |
DefineParameter(Name, "name"); |
| 60 |
> |
|
| 61 |
> |
deprecatedKeywords_.insert("nAtoms"); |
| 62 |
> |
deprecatedKeywords_.insert("nBonds"); |
| 63 |
> |
deprecatedKeywords_.insert("nBends"); |
| 64 |
> |
deprecatedKeywords_.insert("nTorsions"); |
| 65 |
> |
deprecatedKeywords_.insert("nRigidBodies"); |
| 66 |
> |
deprecatedKeywords_.insert("nCutoffGroups"); |
| 67 |
> |
|
| 68 |
> |
} |
| 69 |
|
|
| 70 |
< |
unhandled = NULL; |
| 71 |
< |
atoms = NULL; |
| 72 |
< |
bonds = NULL; |
| 73 |
< |
bends = NULL; |
| 74 |
< |
torsions = NULL; |
| 75 |
< |
rigidBodies = NULL; |
| 76 |
< |
cutoffGroups = NULL; |
| 70 |
> |
MoleculeStamp::~MoleculeStamp() { |
| 71 |
> |
MemoryUtils::deletePointers(atomStamps_); |
| 72 |
> |
MemoryUtils::deletePointers(bondStamps_); |
| 73 |
> |
MemoryUtils::deletePointers(bendStamps_); |
| 74 |
> |
MemoryUtils::deletePointers(torsionStamps_); |
| 75 |
> |
MemoryUtils::deletePointers(rigidBodyStamps_); |
| 76 |
> |
MemoryUtils::deletePointers(cutoffGroupStamps_); |
| 77 |
> |
MemoryUtils::deletePointers(fragmentStamps_); |
| 78 |
> |
} |
| 79 |
|
|
| 80 |
< |
have_name = 0; |
| 81 |
< |
have_atoms = 0; |
| 82 |
< |
have_bonds = 0; |
| 83 |
< |
have_bends = 0; |
| 84 |
< |
have_torsions = 0; |
| 85 |
< |
have_rigidbodies = 0; |
| 86 |
< |
have_cutoffgroups = 0; |
| 80 |
> |
bool MoleculeStamp::addAtomStamp( AtomStamp* atom) { |
| 81 |
> |
bool ret = addIndexSensitiveStamp(atomStamps_, atom); |
| 82 |
> |
if (!ret) { |
| 83 |
> |
std::ostringstream oss; |
| 84 |
> |
oss<< "Error in Molecule " << getName() << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n"; |
| 85 |
> |
throw OOPSEException(oss.str()); |
| 86 |
> |
} |
| 87 |
> |
return ret; |
| 88 |
> |
|
| 89 |
> |
} |
| 90 |
|
|
| 91 |
+ |
bool MoleculeStamp::addBondStamp( BondStamp* bond) { |
| 92 |
+ |
bondStamps_.push_back(bond); |
| 93 |
+ |
return true; |
| 94 |
|
} |
| 95 |
|
|
| 96 |
< |
MoleculeStamp::~MoleculeStamp(){ |
| 97 |
< |
int i; |
| 98 |
< |
|
| 99 |
< |
if( unhandled != NULL) delete unhandled; |
| 83 |
< |
|
| 84 |
< |
if( rigidBodies != NULL ) { |
| 85 |
< |
for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i]; |
| 86 |
< |
} |
| 87 |
< |
delete[] rigidBodies; |
| 96 |
> |
bool MoleculeStamp::addBendStamp( BendStamp* bend) { |
| 97 |
> |
bendStamps_.push_back(bend); |
| 98 |
> |
return true; |
| 99 |
> |
} |
| 100 |
|
|
| 101 |
< |
if( cutoffGroups != NULL ) { |
| 102 |
< |
for( i=0; i<n_cutoffgroups; i++ ) delete cutoffGroups[i]; |
| 103 |
< |
} |
| 104 |
< |
delete[] cutoffGroups; |
| 93 |
< |
|
| 94 |
< |
if( atoms != NULL ){ |
| 95 |
< |
for( i=0; i<n_atoms; i++ ) delete atoms[i]; |
| 96 |
< |
} |
| 97 |
< |
delete[] atoms; |
| 98 |
< |
|
| 99 |
< |
if( bonds != NULL ){ |
| 100 |
< |
for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
| 101 |
< |
} |
| 102 |
< |
delete[] bonds; |
| 103 |
< |
|
| 104 |
< |
if( bends != NULL ){ |
| 105 |
< |
for( i=0; i<n_bends; i++ ) delete bends[i]; |
| 106 |
< |
} |
| 107 |
< |
delete[] bends; |
| 108 |
< |
|
| 109 |
< |
if( torsions != NULL ){ |
| 110 |
< |
for( i=0; i<n_torsions; i++ ) delete torsions[i]; |
| 111 |
< |
} |
| 112 |
< |
delete[] torsions; |
| 113 |
< |
|
| 101 |
> |
bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) { |
| 102 |
> |
torsionStamps_.push_back(torsion); |
| 103 |
> |
return true; |
| 104 |
> |
} |
| 105 |
|
|
| 106 |
< |
|
| 107 |
< |
|
| 106 |
> |
bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) { |
| 107 |
> |
bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody); |
| 108 |
> |
if (!ret) { |
| 109 |
> |
std::ostringstream oss; |
| 110 |
> |
oss<< "Error in Molecule " << getName() << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n"; |
| 111 |
> |
throw OOPSEException(oss.str()); |
| 112 |
> |
} |
| 113 |
> |
return ret; |
| 114 |
|
} |
| 115 |
|
|
| 116 |
< |
char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
| 117 |
< |
|
| 118 |
< |
if( !strcmp( lhs, "name" ) ){ |
| 122 |
< |
strcpy( name, rhs ); |
| 123 |
< |
have_name = 1; |
| 124 |
< |
} |
| 125 |
< |
else{ |
| 126 |
< |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 127 |
< |
else unhandled->add( lhs, rhs ); |
| 128 |
< |
have_extras = 1; |
| 129 |
< |
} |
| 130 |
< |
return NULL; |
| 116 |
> |
bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) { |
| 117 |
> |
cutoffGroupStamps_.push_back(cutoffgroup); |
| 118 |
> |
return true; |
| 119 |
|
} |
| 120 |
|
|
| 121 |
< |
char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
| 122 |
< |
int i; |
| 123 |
< |
|
| 136 |
< |
if( !strcmp( lhs, "nAtoms" ) ){ |
| 137 |
< |
n_atoms = (int)rhs; |
| 121 |
> |
bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) { |
| 122 |
> |
return addIndexSensitiveStamp(fragmentStamps_, fragment); |
| 123 |
> |
} |
| 124 |
|
|
| 125 |
< |
if( have_atoms ){ |
| 126 |
< |
sprintf( errMsg, |
| 141 |
< |
"MoleculeStamp error, n_atoms already declared" |
| 142 |
< |
" for molecule: %s\n", |
| 143 |
< |
name); |
| 144 |
< |
return strdup( errMsg ); |
| 145 |
< |
} |
| 146 |
< |
have_atoms = 1; |
| 147 |
< |
atoms = new AtomStamp*[n_atoms]; |
| 148 |
< |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
| 149 |
< |
} |
| 150 |
< |
|
| 151 |
< |
else if( !strcmp( lhs, "nBonds" ) ){ |
| 152 |
< |
n_bonds = (int)rhs; |
| 125 |
> |
void MoleculeStamp::validate() { |
| 126 |
> |
DataHolder::validate(); |
| 127 |
|
|
| 128 |
< |
if( have_bonds ){ |
| 129 |
< |
sprintf( errMsg, |
| 130 |
< |
"MoleculeStamp error, n_bonds already declared for" |
| 131 |
< |
" molecule: %s\n", |
| 132 |
< |
name); |
| 159 |
< |
return strdup( errMsg ); |
| 128 |
> |
atom2Rigidbody.resize(getNAtoms()); |
| 129 |
> |
// negative number means atom is a free atom, does not belong to rigidbody |
| 130 |
> |
//every element in atom2Rigidbody has unique negative number at the very beginning |
| 131 |
> |
for(int i = 0; i < atom2Rigidbody.size(); ++i) { |
| 132 |
> |
atom2Rigidbody[i] = -1 - i; |
| 133 |
|
} |
| 134 |
< |
have_bonds = 1; |
| 135 |
< |
bonds = new BondStamp*[n_bonds]; |
| 136 |
< |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
| 137 |
< |
} |
| 138 |
< |
|
| 139 |
< |
else if( !strcmp( lhs, "nBends" ) ){ |
| 167 |
< |
n_bends = (int)rhs; |
| 168 |
< |
|
| 169 |
< |
if( have_bends ){ |
| 170 |
< |
sprintf( errMsg, |
| 171 |
< |
"MoleculeStamp error, n_bends already declared for" |
| 172 |
< |
" molecule: %s\n", |
| 173 |
< |
name); |
| 174 |
< |
return strdup( errMsg ); |
| 134 |
> |
for (int i = 0; i < getNRigidBodies(); ++i) { |
| 135 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
| 136 |
> |
std::vector<int> members = rbStamp->getMembers(); |
| 137 |
> |
for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) { |
| 138 |
> |
atom2Rigidbody[*j] = i; |
| 139 |
> |
} |
| 140 |
|
} |
| 176 |
– |
have_bends = 1; |
| 177 |
– |
bends = new BendStamp*[n_bends]; |
| 178 |
– |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
| 179 |
– |
} |
| 180 |
– |
|
| 181 |
– |
else if( !strcmp( lhs, "nTorsions" ) ){ |
| 182 |
– |
n_torsions = (int)rhs; |
| 141 |
|
|
| 142 |
< |
if( have_torsions ){ |
| 143 |
< |
sprintf( errMsg, |
| 144 |
< |
"MoleculeStamp error, n_torsions already declared for" |
| 145 |
< |
" molecule: %s\n", |
| 146 |
< |
name ); |
| 147 |
< |
return strdup( errMsg ); |
| 148 |
< |
} |
| 149 |
< |
have_torsions = 1; |
| 192 |
< |
torsions = new TorsionStamp*[n_torsions]; |
| 193 |
< |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
| 194 |
< |
} |
| 195 |
< |
|
| 196 |
< |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
| 197 |
< |
n_rigidbodies = (int)rhs; |
| 198 |
< |
|
| 199 |
< |
if( have_rigidbodies ){ |
| 200 |
< |
sprintf( errMsg, |
| 201 |
< |
"MoleculeStamp error, n_rigidbodies already declared for" |
| 202 |
< |
" molecule: %s\n", |
| 203 |
< |
name ); |
| 204 |
< |
return strdup( errMsg ); |
| 205 |
< |
} |
| 206 |
< |
have_rigidbodies = 1; |
| 207 |
< |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
| 208 |
< |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
| 209 |
< |
} |
| 210 |
< |
|
| 211 |
< |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
| 212 |
< |
n_cutoffgroups = (int)rhs; |
| 142 |
> |
checkAtoms(); |
| 143 |
> |
checkBonds(); |
| 144 |
> |
fillBondInfo(); |
| 145 |
> |
checkBends(); |
| 146 |
> |
checkTorsions(); |
| 147 |
> |
checkRigidBodies(); |
| 148 |
> |
checkCutoffGroups(); |
| 149 |
> |
checkFragments(); |
| 150 |
|
|
| 151 |
< |
if( have_cutoffgroups ){ |
| 152 |
< |
sprintf( errMsg, |
| 153 |
< |
"MoleculeStamp error, n_cutoffgroups already declared for" |
| 154 |
< |
" molecule: %s\n", |
| 218 |
< |
name ); |
| 219 |
< |
return strdup( errMsg ); |
| 151 |
> |
int nrigidAtoms = 0; |
| 152 |
> |
for (int i = 0; i < getNRigidBodies(); ++i) { |
| 153 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
| 154 |
> |
nrigidAtoms += rbStamp->getNMembers(); |
| 155 |
|
} |
| 156 |
< |
have_cutoffgroups = 1; |
| 222 |
< |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
| 223 |
< |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
| 224 |
< |
} |
| 225 |
< |
|
| 226 |
< |
else{ |
| 227 |
< |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 228 |
< |
else unhandled->add( lhs, rhs ); |
| 229 |
< |
have_extras = 1; |
| 230 |
< |
} |
| 231 |
< |
return NULL; |
| 232 |
< |
} |
| 156 |
> |
nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms; |
| 157 |
|
|
| 158 |
< |
char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
| 235 |
< |
int i; |
| 236 |
< |
|
| 237 |
< |
if( !strcmp( lhs, "nAtoms" ) ){ |
| 238 |
< |
n_atoms = rhs; |
| 239 |
< |
|
| 240 |
< |
if( have_atoms ){ |
| 241 |
< |
sprintf( errMsg, |
| 242 |
< |
"MoleculeStamp error, n_atoms already declared for" |
| 243 |
< |
" molecule: %s\n", |
| 244 |
< |
name); |
| 245 |
< |
return strdup( errMsg ); |
| 246 |
< |
} |
| 247 |
< |
have_atoms = 1; |
| 248 |
< |
atoms = new AtomStamp*[n_atoms]; |
| 249 |
< |
for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
| 250 |
< |
} |
| 251 |
< |
|
| 252 |
< |
else if( !strcmp( lhs, "nBonds" ) ){ |
| 253 |
< |
n_bonds = rhs; |
| 158 |
> |
} |
| 159 |
|
|
| 160 |
< |
if( have_bonds ){ |
| 161 |
< |
sprintf( errMsg, |
| 162 |
< |
"MoleculeStamp error, n_bonds already declared for" |
| 163 |
< |
" molecule: %s\n", |
| 164 |
< |
name); |
| 165 |
< |
return strdup( errMsg ); |
| 160 |
> |
void MoleculeStamp::checkAtoms() { |
| 161 |
> |
std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL)); |
| 162 |
> |
if (ai != atomStamps_.end()) { |
| 163 |
> |
std::ostringstream oss; |
| 164 |
> |
oss << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n"; |
| 165 |
> |
throw OOPSEException(oss.str()); |
| 166 |
|
} |
| 262 |
– |
have_bonds = 1; |
| 263 |
– |
bonds = new BondStamp*[n_bonds]; |
| 264 |
– |
for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
| 265 |
– |
} |
| 266 |
– |
|
| 267 |
– |
else if( !strcmp( lhs, "nBends" ) ){ |
| 268 |
– |
n_bends = rhs; |
| 167 |
|
|
| 168 |
< |
if( have_bends ){ |
| 271 |
< |
sprintf( errMsg, |
| 272 |
< |
"MoleculeStamp error, n_bends already declared for" |
| 273 |
< |
" molecule: %s\n", |
| 274 |
< |
name ); |
| 275 |
< |
return strdup( errMsg ); |
| 276 |
< |
} |
| 277 |
< |
have_bends = 1; |
| 278 |
< |
bends = new BendStamp*[n_bends]; |
| 279 |
< |
for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
| 280 |
< |
} |
| 281 |
< |
|
| 282 |
< |
else if( !strcmp( lhs, "nTorsions" ) ){ |
| 283 |
< |
n_torsions = rhs; |
| 168 |
> |
} |
| 169 |
|
|
| 170 |
< |
if( have_torsions ){ |
| 171 |
< |
sprintf( errMsg, |
| 172 |
< |
"MoleculeStamp error, n_torsions already declared for" |
| 173 |
< |
" molecule: %s\n", |
| 174 |
< |
name); |
| 175 |
< |
return strdup( errMsg ); |
| 170 |
> |
void MoleculeStamp::checkBonds() { |
| 171 |
> |
std::ostringstream oss; |
| 172 |
> |
//make sure index is not out of range |
| 173 |
> |
int natoms = getNAtoms(); |
| 174 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
| 175 |
> |
BondStamp* bondStamp = getBondStamp(i); |
| 176 |
> |
if (bondStamp->getA() > natoms-1 || bondStamp->getA() < 0 || bondStamp->getB() > natoms-1 || bondStamp->getB() < 0 || bondStamp->getA() == bondStamp->getB()) { |
| 177 |
> |
|
| 178 |
> |
oss << "Error in Molecule " << getName() << ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n"; |
| 179 |
> |
throw OOPSEException(oss.str()); |
| 180 |
> |
} |
| 181 |
|
} |
| 182 |
< |
have_torsions = 1; |
| 183 |
< |
torsions = new TorsionStamp*[n_torsions]; |
| 184 |
< |
for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
| 185 |
< |
} |
| 186 |
< |
|
| 187 |
< |
else if( !strcmp( lhs, "nRigidBodies" ) ){ |
| 188 |
< |
n_rigidbodies = rhs; |
| 189 |
< |
|
| 190 |
< |
if( have_rigidbodies ){ |
| 191 |
< |
sprintf( errMsg, |
| 192 |
< |
"MoleculeStamp error, n_rigidbodies already declared for" |
| 193 |
< |
" molecule: %s\n", |
| 194 |
< |
name); |
| 195 |
< |
return strdup( errMsg ); |
| 182 |
> |
|
| 183 |
> |
//make sure bonds are unique |
| 184 |
> |
std::set<std::pair<int, int> > allBonds; |
| 185 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
| 186 |
> |
BondStamp* bondStamp= getBondStamp(i); |
| 187 |
> |
std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB()); |
| 188 |
> |
//make sure bondTuple.first is always less than or equal to bondTuple.third |
| 189 |
> |
if (bondPair.first > bondPair.second) { |
| 190 |
> |
std::swap(bondPair.first, bondPair.second); |
| 191 |
> |
} |
| 192 |
> |
|
| 193 |
> |
std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair); |
| 194 |
> |
if ( iter != allBonds.end()) { |
| 195 |
> |
|
| 196 |
> |
oss << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ") appears multiple times\n"; |
| 197 |
> |
throw OOPSEException(oss.str()); |
| 198 |
> |
} else { |
| 199 |
> |
allBonds.insert(bondPair); |
| 200 |
> |
} |
| 201 |
|
} |
| 202 |
< |
have_rigidbodies = 1; |
| 203 |
< |
rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
| 204 |
< |
for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
| 205 |
< |
} |
| 206 |
< |
else if( !strcmp( lhs, "nCutoffGroups" ) ){ |
| 207 |
< |
n_cutoffgroups = rhs; |
| 208 |
< |
|
| 209 |
< |
if( have_cutoffgroups ){ |
| 210 |
< |
sprintf( errMsg, |
| 316 |
< |
"MoleculeStamp error, n_cutoffgroups already declared for" |
| 317 |
< |
" molecule: %s\n", |
| 318 |
< |
name); |
| 319 |
< |
return strdup( errMsg ); |
| 202 |
> |
|
| 203 |
> |
//make sure atoms belong to same rigidbody do not bond to each other |
| 204 |
> |
for(int i = 0; i < getNBonds(); ++i) { |
| 205 |
> |
BondStamp* bondStamp = getBondStamp(i); |
| 206 |
> |
if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) { |
| 207 |
> |
|
| 208 |
> |
oss << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n"; |
| 209 |
> |
throw OOPSEException(oss.str()); |
| 210 |
> |
} |
| 211 |
|
} |
| 212 |
< |
have_cutoffgroups = 1; |
| 322 |
< |
cutoffGroups = new CutoffGroupStamp*[n_cutoffgroups]; |
| 323 |
< |
for( i=0; i<n_cutoffgroups; i++ ) cutoffGroups[i] = NULL; |
| 324 |
< |
} |
| 325 |
< |
else{ |
| 326 |
< |
if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
| 327 |
< |
else unhandled->add( lhs, rhs ); |
| 328 |
< |
have_extras = 1; |
| 329 |
< |
} |
| 330 |
< |
return NULL; |
| 212 |
> |
|
| 213 |
|
} |
| 214 |
|
|
| 215 |
< |
char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
| 216 |
< |
|
| 217 |
< |
if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
| 218 |
< |
else { |
| 219 |
< |
if( have_atoms ){ |
| 220 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
| 221 |
< |
atomIndex ); |
| 340 |
< |
return strdup( errMsg ); |
| 341 |
< |
} |
| 342 |
< |
else return strdup("MoleculeStamp error, nAtoms not given before" |
| 343 |
< |
" first atom declaration." ); |
| 344 |
< |
} |
| 215 |
> |
void MoleculeStamp::checkBends() { |
| 216 |
> |
std::ostringstream oss; |
| 217 |
> |
for(int i = 0; i < getNBends(); ++i) { |
| 218 |
> |
BendStamp* bendStamp = getBendStamp(i); |
| 219 |
> |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
| 220 |
> |
std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 221 |
> |
std::vector<int>::iterator k =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::less<int>(), 0)); |
| 222 |
|
|
| 223 |
< |
return NULL; |
| 224 |
< |
} |
| 225 |
< |
|
| 226 |
< |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
| 227 |
< |
int rigidBodyIndex ){ |
| 228 |
< |
|
| 229 |
< |
if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
| 230 |
< |
rigidBodies[rigidBodyIndex] = the_rigidbody; |
| 231 |
< |
else { |
| 232 |
< |
if( have_rigidbodies ){ |
| 233 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
| 234 |
< |
rigidBodyIndex ); |
| 235 |
< |
return strdup( errMsg ); |
| 223 |
> |
if (j != bendAtoms.end() || k != bendAtoms.end()) { |
| 224 |
> |
|
| 225 |
> |
oss << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << " have invalid indices\n"; |
| 226 |
> |
throw OOPSEException(oss.str()); |
| 227 |
> |
} |
| 228 |
> |
|
| 229 |
> |
if (hasDuplicateElement(bendAtoms)) { |
| 230 |
> |
oss << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << " have duplicated indices\n"; |
| 231 |
> |
throw OOPSEException(oss.str()); |
| 232 |
> |
} |
| 233 |
> |
|
| 234 |
> |
if (bendAtoms.size() == 2 ) { |
| 235 |
> |
if (!bendStamp->haveGhostVectorSource()) { |
| 236 |
> |
|
| 237 |
> |
oss << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n"; |
| 238 |
> |
throw OOPSEException(oss.str()); |
| 239 |
> |
}else{ |
| 240 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
| 241 |
> |
if (ghostIndex < getNAtoms()) { |
| 242 |
> |
if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) { |
| 243 |
> |
|
| 244 |
> |
oss << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; |
| 245 |
> |
throw OOPSEException(oss.str()); |
| 246 |
> |
} |
| 247 |
> |
if (!getAtomStamp(ghostIndex)->haveOrientation()) { |
| 248 |
> |
|
| 249 |
> |
oss << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; |
| 250 |
> |
throw OOPSEException(oss.str()); |
| 251 |
> |
} |
| 252 |
> |
}else { |
| 253 |
> |
oss << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n"; |
| 254 |
> |
throw OOPSEException(oss.str()); |
| 255 |
> |
} |
| 256 |
> |
} |
| 257 |
> |
} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) { |
| 258 |
> |
oss << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; |
| 259 |
> |
throw OOPSEException(oss.str()); |
| 260 |
> |
} |
| 261 |
|
} |
| 360 |
– |
else return strdup("MoleculeStamp error, nRigidBodies not given before" |
| 361 |
– |
" first rigidBody declaration." ); |
| 362 |
– |
} |
| 363 |
– |
|
| 364 |
– |
return NULL; |
| 365 |
– |
} |
| 262 |
|
|
| 263 |
< |
char* MoleculeStamp::addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, |
| 264 |
< |
int cutoffGroupIndex ){ |
| 265 |
< |
|
| 266 |
< |
if( have_cutoffgroups && cutoffGroupIndex < n_cutoffgroups ) |
| 267 |
< |
cutoffGroups[cutoffGroupIndex] = the_cutoffgroup; |
| 268 |
< |
else { |
| 269 |
< |
if( have_cutoffgroups ){ |
| 270 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nCutoffGroups range", |
| 271 |
< |
cutoffGroupIndex ); |
| 272 |
< |
return strdup( errMsg ); |
| 263 |
> |
for(int i = 0; i < getNBends(); ++i) { |
| 264 |
> |
BendStamp* bendStamp = getBendStamp(i); |
| 265 |
> |
std::vector<int> bendAtoms = bendStamp->getMembers(); |
| 266 |
> |
std::vector<int> rigidSet(getNRigidBodies(), 0); |
| 267 |
> |
std::vector<int>::iterator j; |
| 268 |
> |
for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) { |
| 269 |
> |
int rigidbodyIndex = atom2Rigidbody[*j]; |
| 270 |
> |
if (rigidbodyIndex >= 0) { |
| 271 |
> |
++rigidSet[rigidbodyIndex]; |
| 272 |
> |
if (rigidSet[rigidbodyIndex] > 1) { |
| 273 |
> |
oss << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n"; |
| 274 |
> |
throw OOPSEException(oss.str()); |
| 275 |
> |
} |
| 276 |
> |
} |
| 277 |
> |
} |
| 278 |
> |
} |
| 279 |
> |
|
| 280 |
> |
|
| 281 |
> |
std::set<IntTuple3> allBends; |
| 282 |
> |
std::set<IntTuple3>::iterator iter; |
| 283 |
> |
for(int i = 0; i < getNBends(); ++i) { |
| 284 |
> |
BendStamp* bendStamp= getBendStamp(i); |
| 285 |
> |
std::vector<int> bend = bendStamp->getMembers(); |
| 286 |
> |
if (bend.size() == 2) { |
| 287 |
> |
// in case we have two ghost bend. For example, |
| 288 |
> |
// bend { |
| 289 |
> |
// members (0, 1); |
| 290 |
> |
// ghostVectorSource = 0; |
| 291 |
> |
// } |
| 292 |
> |
// and |
| 293 |
> |
// bend { |
| 294 |
> |
// members (0, 1); |
| 295 |
> |
// ghostVectorSource = 0; |
| 296 |
> |
// } |
| 297 |
> |
// In order to distinguish them. we expand them to Tuple3. |
| 298 |
> |
// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1) |
| 299 |
> |
int ghostIndex = bendStamp->getGhostVectorSource(); |
| 300 |
> |
std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex); |
| 301 |
> |
if (j != bend.end()) { |
| 302 |
> |
bend.insert(j, ghostIndex); |
| 303 |
> |
} |
| 304 |
> |
} |
| 305 |
> |
|
| 306 |
> |
IntTuple3 bendTuple(bend[0], bend[1], bend[2]); |
| 307 |
> |
//make sure bendTuple.first is always less than or equal to bendTuple.third |
| 308 |
> |
if (bendTuple.first > bendTuple.third) { |
| 309 |
> |
std::swap(bendTuple.first, bendTuple.third); |
| 310 |
> |
} |
| 311 |
> |
|
| 312 |
> |
iter = allBends.find(bendTuple); |
| 313 |
> |
if ( iter != allBends.end()) { |
| 314 |
> |
oss << "Error in Molecule " << getName() << ": " << "Bend" << containerToString(bend)<< " appears multiple times\n"; |
| 315 |
> |
throw OOPSEException(oss.str()); |
| 316 |
> |
} else { |
| 317 |
> |
allBends.insert(bendTuple); |
| 318 |
> |
} |
| 319 |
|
} |
| 378 |
– |
else return strdup("MoleculeStamp error, nCutoffGroups not given before" |
| 379 |
– |
" first CutoffGroup declaration." ); |
| 380 |
– |
} |
| 381 |
– |
|
| 382 |
– |
return NULL; |
| 383 |
– |
} |
| 320 |
|
|
| 321 |
< |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
| 322 |
< |
|
| 323 |
< |
|
| 324 |
< |
if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
| 389 |
< |
else{ |
| 390 |
< |
if( have_bonds ){ |
| 391 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
| 392 |
< |
bondIndex ); |
| 393 |
< |
return strdup( errMsg ); |
| 394 |
< |
} |
| 395 |
< |
else return strdup("MoleculeStamp error, nBonds not given before" |
| 396 |
< |
"first bond declaration." ); |
| 397 |
< |
} |
| 321 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
| 322 |
> |
BondStamp* bondStamp = getBondStamp(i); |
| 323 |
> |
int a = bondStamp->getA(); |
| 324 |
> |
int b = bondStamp->getB(); |
| 325 |
|
|
| 326 |
< |
return NULL; |
| 327 |
< |
} |
| 326 |
> |
AtomStamp* atomA = getAtomStamp(a); |
| 327 |
> |
AtomStamp* atomB = getAtomStamp(b); |
| 328 |
|
|
| 329 |
< |
char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
| 330 |
< |
|
| 331 |
< |
|
| 332 |
< |
if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
| 333 |
< |
else{ |
| 334 |
< |
if( have_bends ){ |
| 335 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
| 336 |
< |
bendIndex ); |
| 337 |
< |
return strdup( errMsg ); |
| 338 |
< |
} |
| 339 |
< |
else return strdup("MoleculeStamp error, nBends not given before" |
| 413 |
< |
"first bend declaration." ); |
| 414 |
< |
} |
| 329 |
> |
//find bend c--a--b |
| 330 |
> |
AtomStamp::AtomIter ai; |
| 331 |
> |
for(int c= atomA->getFirstBondedAtom(ai);c != -1;c = atomA->getNextBondedAtom(ai)) |
| 332 |
> |
{ |
| 333 |
> |
if(b == c) |
| 334 |
> |
continue; |
| 335 |
> |
|
| 336 |
> |
IntTuple3 newBend(c, a, b); |
| 337 |
> |
if (newBend.first > newBend.third) { |
| 338 |
> |
std::swap(newBend.first, newBend.third); |
| 339 |
> |
} |
| 340 |
|
|
| 341 |
< |
return NULL; |
| 342 |
< |
} |
| 341 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
| 342 |
> |
allBends.insert(newBend); |
| 343 |
> |
BendStamp * newBendStamp = new BendStamp(); |
| 344 |
> |
newBendStamp->setMembers(newBend); |
| 345 |
> |
addBendStamp(newBendStamp); |
| 346 |
> |
} |
| 347 |
> |
} |
| 348 |
|
|
| 349 |
< |
char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
| 350 |
< |
|
| 351 |
< |
|
| 352 |
< |
if( have_torsions && torsionIndex < n_torsions ) |
| 353 |
< |
torsions[torsionIndex] = the_torsion; |
| 354 |
< |
else{ |
| 355 |
< |
if( have_torsions ){ |
| 356 |
< |
sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
| 357 |
< |
torsionIndex ); |
| 358 |
< |
return strdup( errMsg ); |
| 349 |
> |
//find bend a--b--c |
| 350 |
> |
for(int c= atomB->getFirstBondedAtom(ai);c != -1;c = atomB->getNextBondedAtom(ai)) |
| 351 |
> |
{ |
| 352 |
> |
if(a == c) |
| 353 |
> |
continue; |
| 354 |
> |
|
| 355 |
> |
IntTuple3 newBend( a, b, c); |
| 356 |
> |
if (newBend.first > newBend.third) { |
| 357 |
> |
std::swap(newBend.first, newBend.third); |
| 358 |
> |
} |
| 359 |
> |
if (allBends.find(newBend) == allBends.end() ) { |
| 360 |
> |
allBends.insert(newBend); |
| 361 |
> |
BendStamp * newBendStamp = new BendStamp(); |
| 362 |
> |
newBendStamp->setMembers(newBend); |
| 363 |
> |
addBendStamp(newBendStamp); |
| 364 |
> |
} |
| 365 |
> |
} |
| 366 |
|
} |
| 430 |
– |
else return strdup("MoleculeStamp error, nTorsions not given before" |
| 431 |
– |
"first torsion declaration." ); |
| 432 |
– |
} |
| 367 |
|
|
| 434 |
– |
return NULL; |
| 368 |
|
} |
| 369 |
|
|
| 370 |
< |
char* MoleculeStamp::checkMe( void ){ |
| 371 |
< |
|
| 372 |
< |
int i; |
| 373 |
< |
short int no_atom, no_rigidbody, no_cutoffgroup; |
| 370 |
> |
void MoleculeStamp::checkTorsions() { |
| 371 |
> |
std::ostringstream oss; |
| 372 |
> |
for(int i = 0; i < getNTorsions(); ++i) { |
| 373 |
> |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
| 374 |
> |
std::vector<int> torsionAtoms = torsionStamp ->getMembers(); |
| 375 |
> |
std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 376 |
> |
std::vector<int>::iterator k =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::less<int>(), 0)); |
| 377 |
|
|
| 378 |
< |
if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
| 379 |
< |
" was not given.\n" ); |
| 380 |
< |
|
| 381 |
< |
if( !have_atoms ){ |
| 382 |
< |
return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
| 383 |
< |
} |
| 384 |
< |
|
| 385 |
< |
no_rigidbody = 0; |
| 386 |
< |
for( i=0; i<n_rigidbodies; i++ ){ |
| 387 |
< |
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
| 388 |
< |
} |
| 389 |
< |
|
| 390 |
< |
if( no_rigidbody ){ |
| 391 |
< |
sprintf( errMsg, |
| 392 |
< |
"MoleculeStamp error. Not all of the RigidBodies were" |
| 393 |
< |
" declared in molecule \"%s\".\n", name ); |
| 394 |
< |
return strdup( errMsg ); |
| 395 |
< |
} |
| 396 |
< |
|
| 397 |
< |
no_cutoffgroup = 0; |
| 398 |
< |
for( i=0; i<n_cutoffgroups; i++ ){ |
| 399 |
< |
if( cutoffGroups[i] == NULL ) no_cutoffgroup = 1; |
| 400 |
< |
} |
| 378 |
> |
if (j != torsionAtoms.end() || k != torsionAtoms.end()) { |
| 379 |
> |
oss << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n"; |
| 380 |
> |
throw OOPSEException(oss.str()); |
| 381 |
> |
} |
| 382 |
> |
if (hasDuplicateElement(torsionAtoms)) { |
| 383 |
> |
oss << "Error in Molecule " << getName() << " : atoms of torsion" << containerToString(torsionAtoms) << " have duplicated indices\n"; |
| 384 |
> |
throw OOPSEException(oss.str()); |
| 385 |
> |
} |
| 386 |
> |
} |
| 387 |
> |
|
| 388 |
> |
for(int i = 0; i < getNTorsions(); ++i) { |
| 389 |
> |
TorsionStamp* torsionStamp = getTorsionStamp(i); |
| 390 |
> |
std::vector<int> torsionAtoms = torsionStamp->getMembers(); |
| 391 |
> |
std::vector<int> rigidSet(getNRigidBodies(), 0); |
| 392 |
> |
std::vector<int>::iterator j; |
| 393 |
> |
for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) { |
| 394 |
> |
int rigidbodyIndex = atom2Rigidbody[*j]; |
| 395 |
> |
if (rigidbodyIndex >= 0) { |
| 396 |
> |
++rigidSet[rigidbodyIndex]; |
| 397 |
> |
if (rigidSet[rigidbodyIndex] > 1) { |
| 398 |
> |
oss << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n"; |
| 399 |
> |
throw OOPSEException(oss.str()); |
| 400 |
> |
} |
| 401 |
> |
} |
| 402 |
> |
} |
| 403 |
> |
} |
| 404 |
|
|
| 405 |
< |
if( no_cutoffgroup ){ |
| 406 |
< |
sprintf( errMsg, |
| 407 |
< |
"MoleculeStamp error. Not all of the CutoffGroups were" |
| 408 |
< |
" declared in molecule \"%s\".\n", name ); |
| 409 |
< |
return strdup( errMsg ); |
| 410 |
< |
} |
| 411 |
< |
|
| 412 |
< |
no_atom = 0; |
| 413 |
< |
for( i=0; i<n_atoms; i++ ){ |
| 414 |
< |
if( atoms[i] == NULL ) no_atom = 1; |
| 415 |
< |
} |
| 405 |
> |
std::set<IntTuple4> allTorsions; |
| 406 |
> |
std::set<IntTuple4>::iterator iter; |
| 407 |
> |
for(int i = 0; i < getNTorsions(); ++i) { |
| 408 |
> |
TorsionStamp* torsionStamp= getTorsionStamp(i); |
| 409 |
> |
std::vector<int> torsion = torsionStamp->getMembers(); |
| 410 |
> |
if (torsion.size() == 3) { |
| 411 |
> |
int ghostIndex = torsionStamp->getGhostVectorSource(); |
| 412 |
> |
std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex); |
| 413 |
> |
if (j != torsion.end()) { |
| 414 |
> |
torsion.insert(j, ghostIndex); |
| 415 |
> |
} |
| 416 |
> |
} |
| 417 |
|
|
| 418 |
< |
if( no_atom ){ |
| 419 |
< |
sprintf( errMsg, |
| 420 |
< |
"MoleculeStamp error. Not all of the atoms were" |
| 421 |
< |
" declared in molecule \"%s\".\n", name ); |
| 422 |
< |
return strdup( errMsg ); |
| 483 |
< |
} |
| 418 |
> |
IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]); |
| 419 |
> |
if (torsionTuple.first > torsionTuple.fourth) { |
| 420 |
> |
std::swap(torsionTuple.first, torsionTuple.fourth); |
| 421 |
> |
std::swap(torsionTuple.second, torsionTuple.third); |
| 422 |
> |
} |
| 423 |
|
|
| 424 |
< |
n_integrable = n_atoms; |
| 425 |
< |
for (i = 0; i < n_rigidbodies; i++) |
| 426 |
< |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
| 427 |
< |
|
| 428 |
< |
if (n_integrable <= 0 || n_integrable > n_atoms) { |
| 429 |
< |
sprintf( errMsg, |
| 430 |
< |
"MoleculeStamp error. n_integrable is either <= 0 or" |
| 431 |
< |
" greater than n_atoms in molecule \"%s\".\n", name ); |
| 493 |
< |
return strdup( errMsg ); |
| 494 |
< |
} |
| 424 |
> |
iter = allTorsions.find(torsionTuple); |
| 425 |
> |
if ( iter == allTorsions.end()) { |
| 426 |
> |
allTorsions.insert(torsionTuple); |
| 427 |
> |
} else { |
| 428 |
> |
oss << "Error in Molecule " << getName() << ": " << "Torsion" << containerToString(torsion)<< " appears multiple times\n"; |
| 429 |
> |
throw OOPSEException(oss.str()); |
| 430 |
> |
} |
| 431 |
> |
} |
| 432 |
|
|
| 433 |
< |
return NULL; |
| 434 |
< |
} |
| 433 |
> |
for (int i = 0; i < getNBonds(); ++i) { |
| 434 |
> |
BondStamp* bondStamp = getBondStamp(i); |
| 435 |
> |
int b = bondStamp->getA(); |
| 436 |
> |
int c = bondStamp->getB(); |
| 437 |
|
|
| 438 |
+ |
AtomStamp* atomB = getAtomStamp(b); |
| 439 |
+ |
AtomStamp* atomC = getAtomStamp(c); |
| 440 |
|
|
| 441 |
+ |
AtomStamp::AtomIter ai2; |
| 442 |
+ |
AtomStamp::AtomIter ai3; |
| 443 |
+ |
|
| 444 |
+ |
for(int a = atomB->getFirstBondedAtom(ai2);a != -1;a = atomB->getNextBondedAtom(ai2)) |
| 445 |
+ |
{ |
| 446 |
+ |
if(a == c) |
| 447 |
+ |
continue; |
| 448 |
+ |
|
| 449 |
+ |
for(int d = atomC->getFirstBondedAtom(ai3);d != -1;d = atomC->getNextBondedAtom(ai3)) |
| 450 |
+ |
{ |
| 451 |
+ |
if(d == b) |
| 452 |
+ |
continue; |
| 453 |
+ |
|
| 454 |
+ |
IntTuple4 newTorsion(a, b, c, d); |
| 455 |
+ |
//make sure the first element is always less than or equal to the fourth element in IntTuple4 |
| 456 |
+ |
if (newTorsion.first > newTorsion.fourth) { |
| 457 |
+ |
std::swap(newTorsion.first, newTorsion.fourth); |
| 458 |
+ |
std::swap(newTorsion.second, newTorsion.third); |
| 459 |
+ |
} |
| 460 |
+ |
if (allTorsions.find(newTorsion) == allTorsions.end() ) { |
| 461 |
+ |
allTorsions.insert(newTorsion); |
| 462 |
+ |
TorsionStamp * newTorsionStamp = new TorsionStamp(); |
| 463 |
+ |
newTorsionStamp->setMembers(newTorsion); |
| 464 |
+ |
addTorsionStamp(newTorsionStamp); |
| 465 |
+ |
} |
| 466 |
+ |
} |
| 467 |
+ |
} |
| 468 |
+ |
} |
| 469 |
+ |
|
| 470 |
+ |
} |
| 471 |
+ |
|
| 472 |
+ |
void MoleculeStamp::checkRigidBodies() { |
| 473 |
+ |
std::ostringstream oss; |
| 474 |
+ |
std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL)); |
| 475 |
+ |
if (ri != rigidBodyStamps_.end()) { |
| 476 |
+ |
oss << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n"; |
| 477 |
+ |
throw OOPSEException(oss.str()); |
| 478 |
+ |
} |
| 479 |
+ |
|
| 480 |
+ |
for (int i = 0; i < getNRigidBodies(); ++i) { |
| 481 |
+ |
RigidBodyStamp* rbStamp = getRigidBodyStamp(i); |
| 482 |
+ |
std::vector<int> rigidAtoms = rbStamp ->getMembers(); |
| 483 |
+ |
std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 484 |
+ |
if (j != rigidAtoms.end()) { |
| 485 |
+ |
oss << "Error in Molecule " << getName(); |
| 486 |
+ |
throw OOPSEException(oss.str()); |
| 487 |
+ |
} |
| 488 |
+ |
|
| 489 |
+ |
} |
| 490 |
+ |
} |
| 491 |
+ |
|
| 492 |
+ |
void MoleculeStamp::checkCutoffGroups() { |
| 493 |
+ |
for(int i = 0; i < getNCutoffGroups(); ++i) { |
| 494 |
+ |
CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i); |
| 495 |
+ |
std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers(); |
| 496 |
+ |
std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1)); |
| 497 |
+ |
if (j != cutoffGroupAtoms.end()) { |
| 498 |
+ |
std::ostringstream oss; |
| 499 |
+ |
oss << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; |
| 500 |
+ |
throw OOPSEException(oss.str()); |
| 501 |
+ |
} |
| 502 |
+ |
} |
| 503 |
+ |
} |
| 504 |
+ |
|
| 505 |
+ |
void MoleculeStamp::checkFragments() { |
| 506 |
+ |
|
| 507 |
+ |
std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL)); |
| 508 |
+ |
if (fi != fragmentStamps_.end()) { |
| 509 |
+ |
std::ostringstream oss; |
| 510 |
+ |
oss << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n"; |
| 511 |
+ |
throw OOPSEException(oss.str()); |
| 512 |
+ |
} |
| 513 |
+ |
|
| 514 |
+ |
} |
| 515 |
+ |
|
| 516 |
+ |
void MoleculeStamp::fillBondInfo() { |
| 517 |
+ |
|
| 518 |
+ |
for (int i = 0; i < getNBonds(); ++i) { |
| 519 |
+ |
BondStamp* bondStamp = getBondStamp(i); |
| 520 |
+ |
int a = bondStamp->getA(); |
| 521 |
+ |
int b = bondStamp->getB(); |
| 522 |
+ |
AtomStamp* atomA = getAtomStamp(a); |
| 523 |
+ |
AtomStamp* atomB = getAtomStamp(b); |
| 524 |
+ |
atomA->addBond(i); |
| 525 |
+ |
atomA->addBondedAtom(b); |
| 526 |
+ |
atomB->addBond(i); |
| 527 |
+ |
atomB->addBondedAtom(a); |
| 528 |
+ |
|
| 529 |
+ |
} |
| 530 |
+ |
} |
| 531 |
+ |
|
| 532 |
+ |
|
| 533 |
+ |
|
| 534 |
|
//Function Name: isBondInSameRigidBody |
| 535 |
|
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false |
| 536 |
|
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){ |
| 554 |
|
// Function Name: isAtomInRigidBody |
| 555 |
|
//return false if atom does not belong to a rigid body, otherwise return true |
| 556 |
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){ |
| 557 |
< |
int whichRigidBody; |
| 524 |
< |
int consAtomIndex; |
| 525 |
< |
|
| 526 |
< |
return isAtomInRigidBody(atomIndex, whichRigidBody, consAtomIndex); |
| 557 |
> |
return atom2Rigidbody[atomIndex] >=0 ; |
| 558 |
|
|
| 559 |
|
} |
| 560 |
|
|
| 565 |
|
//whichRigidBody: the index of rigidbody in component |
| 566 |
|
//consAtomIndex: the position of joint atom apears in rigidbody's definition |
| 567 |
|
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){ |
| 537 |
– |
RigidBodyStamp* rbStamp; |
| 538 |
– |
int numRb; |
| 539 |
– |
int numAtom; |
| 568 |
|
|
| 569 |
+ |
|
| 570 |
+ |
|
| 571 |
|
whichRigidBody = -1; |
| 572 |
|
consAtomIndex = -1; |
| 573 |
|
|
| 574 |
< |
numRb = this->getNRigidBodies(); |
| 575 |
< |
|
| 576 |
< |
for(int i = 0 ; i < numRb; i++){ |
| 577 |
< |
rbStamp = this->getRigidBody(i); |
| 578 |
< |
numAtom = rbStamp->getNMembers(); |
| 579 |
< |
for(int j = 0; j < numAtom; j++) |
| 550 |
< |
if (rbStamp->getMember(j) == atomIndex){ |
| 551 |
< |
whichRigidBody = i; |
| 574 |
> |
if (atom2Rigidbody[atomIndex] >=0) { |
| 575 |
> |
whichRigidBody = atom2Rigidbody[atomIndex]; |
| 576 |
> |
RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody); |
| 577 |
> |
int numAtom = rbStamp->getNMembers(); |
| 578 |
> |
for(int j = 0; j < numAtom; j++) { |
| 579 |
> |
if (rbStamp->getMemberAt(j) == atomIndex){ |
| 580 |
|
consAtomIndex = j; |
| 581 |
|
return true; |
| 582 |
|
} |
| 583 |
+ |
} |
| 584 |
|
} |
| 585 |
|
|
| 586 |
|
return false; |
| 599 |
|
int atomIndex2; |
| 600 |
|
std::vector<std::pair<int, int> > jointAtomIndexPair; |
| 601 |
|
|
| 602 |
< |
rbStamp1 = this->getRigidBody(rb1); |
| 602 |
> |
rbStamp1 = this->getRigidBodyStamp(rb1); |
| 603 |
|
natomInRb1 =rbStamp1->getNMembers(); |
| 604 |
|
|
| 605 |
< |
rbStamp2 = this->getRigidBody(rb2); |
| 605 |
> |
rbStamp2 = this->getRigidBodyStamp(rb2); |
| 606 |
|
natomInRb2 =rbStamp2->getNMembers(); |
| 607 |
|
|
| 608 |
|
for(int i = 0; i < natomInRb1; i++){ |
| 609 |
< |
atomIndex1 = rbStamp1->getMember(i); |
| 609 |
> |
atomIndex1 = rbStamp1->getMemberAt(i); |
| 610 |
|
|
| 611 |
|
for(int j= 0; j < natomInRb1; j++){ |
| 612 |
< |
atomIndex2 = rbStamp2->getMember(j); |
| 612 |
> |
atomIndex2 = rbStamp2->getMemberAt(j); |
| 613 |
|
|
| 614 |
|
if(atomIndex1 == atomIndex2){ |
| 615 |
|
jointAtomIndexPair.push_back(std::make_pair(i, j)); |
| 616 |
|
break; |
| 617 |
|
} |
| 618 |
|
|
| 619 |
< |
}//end for(j =0) |
| 619 |
> |
} |
| 620 |
|
|
| 621 |
< |
}//end for (i = 0) |
| 621 |
> |
} |
| 622 |
|
|
| 623 |
|
return jointAtomIndexPair; |
| 624 |
|
} |
| 625 |
+ |
|
| 626 |
+ |
} |
