| 70 |
|
|
| 71 |
|
char readLine[1024]; |
| 72 |
|
|
| 73 |
< |
string fileName; |
| 74 |
< |
string shapeFileName; |
| 75 |
< |
string tempString; |
| 73 |
> |
std::stringfileName; |
| 74 |
> |
std::stringshapeFileName; |
| 75 |
> |
std::stringtempString; |
| 76 |
|
|
| 77 |
|
char *nameToken; |
| 78 |
|
char *delim = " ,;\t\n"; |
| 82 |
|
int nStrength = 0; |
| 83 |
|
int myATID; |
| 84 |
|
int isError; |
| 85 |
< |
string nameString; |
| 85 |
> |
std::stringnameString; |
| 86 |
|
AtomType* at; |
| 87 |
|
DirectionalAtomType* dat; |
| 88 |
|
ShapeAtomType* st; |
| 89 |
|
|
| 90 |
< |
map<string, AtomType*>::iterator iter; |
| 90 |
> |
std::map<string, AtomType*>::iterator iter; |
| 91 |
|
|
| 92 |
|
// vectors for shape transfer to fortran |
| 93 |
< |
vector<RealSphericalHarmonic*> tempSHVector; |
| 94 |
< |
vector<int> contactL; |
| 95 |
< |
vector<int> contactM; |
| 96 |
< |
vector<int> contactFunc; |
| 97 |
< |
vector<double> contactCoeff; |
| 98 |
< |
vector<int> rangeL; |
| 99 |
< |
vector<int> rangeM; |
| 100 |
< |
vector<int> rangeFunc; |
| 101 |
< |
vector<double> rangeCoeff; |
| 102 |
< |
vector<int> strengthL; |
| 103 |
< |
vector<int> strengthM; |
| 104 |
< |
vector<int> strengthFunc; |
| 105 |
< |
vector<double> strengthCoeff; |
| 93 |
> |
std::vector<RealSphericalHarmonic*> tempSHVector; |
| 94 |
> |
std::vector<int> contactL; |
| 95 |
> |
std::vector<int> contactM; |
| 96 |
> |
std::vector<int> contactFunc; |
| 97 |
> |
std::vector<double> contactCoeff; |
| 98 |
> |
std::vector<int> rangeL; |
| 99 |
> |
std::vector<int> rangeM; |
| 100 |
> |
std::vector<int> rangeFunc; |
| 101 |
> |
std::vector<double> rangeCoeff; |
| 102 |
> |
std::vector<int> strengthL; |
| 103 |
> |
std::vector<int> strengthM; |
| 104 |
> |
std::vector<int> strengthFunc; |
| 105 |
> |
std::vector<double> strengthCoeff; |
| 106 |
|
|
| 107 |
|
// generate the force file name |
| 108 |
|
fileName = "Shapes.frc"; |
| 177 |
|
atomTypeMap.insert(make_pair(nameString, st)); |
| 178 |
|
|
| 179 |
|
} else { |
| 180 |
< |
// atomType map already contained this string (i.e. it was |
| 180 |
> |
// atomType map already contained this std::string(i.e. it was |
| 181 |
|
// declared in a previous block, and we just need to add |
| 182 |
|
// the shape-specific information for this AtomType: |
| 183 |
|
|
| 291 |
|
void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
| 292 |
|
|
| 293 |
|
int i,j,k; |
| 294 |
< |
map<string, AtomType*>::iterator iter; |
| 294 |
> |
std::map<string, AtomType*>::iterator iter; |
| 295 |
|
|
| 296 |
|
// initialize the atoms |
| 297 |
|
DirectionalAtom* dAtom; |
| 302 |
|
double ji[3]; |
| 303 |
|
double inertialMat[3][3]; |
| 304 |
|
Mat3x3d momInt; |
| 305 |
< |
string myTypeString; |
| 305 |
> |
std::stringmyTypeString; |
| 306 |
|
|
| 307 |
|
for( i=0; i<nAtoms; i++ ){ |
| 308 |
|
|
| 400 |
|
int nTokens; |
| 401 |
|
Mat3x3d momInert; |
| 402 |
|
RealSphericalHarmonic* rsh; |
| 403 |
< |
vector<RealSphericalHarmonic*> functionVector; |
| 403 |
> |
std::vector<RealSphericalHarmonic*> functionVector; |
| 404 |
|
ifstrstream shapeFile; |
| 405 |
< |
string tempString; |
| 405 |
> |
std::stringtempString; |
| 406 |
|
|
| 407 |
|
shapeFile.open( shapeFileName.c_str() ); |
| 408 |
|
|
