| 59 |
|
vector<double> sGrid; |
| 60 |
|
|
| 61 |
|
double mass, rpar, eps; |
| 62 |
+ |
double xyz3[3]; |
| 63 |
|
string fileName; |
| 64 |
|
char vdwFileName[2002]; |
| 65 |
|
char structureFileName[2002]; |
| 66 |
|
char temp[200]; |
| 67 |
|
char readLine[500]; |
| 68 |
+ |
char xyzFile[200]; |
| 69 |
+ |
char shapeFile[200]; |
| 70 |
|
FILE *vdwFile, *structureFile; |
| 71 |
|
char* ffPath_env = "VDW_PATH"; |
| 72 |
|
char* ffPath; |
| 74 |
|
char* foo; |
| 75 |
|
char* myType; |
| 76 |
|
char* vType; |
| 77 |
+ |
char *token; |
| 78 |
+ |
const char *file; |
| 79 |
+ |
const char *period = "."; |
| 80 |
+ |
int k; |
| 81 |
|
int lineNum; |
| 82 |
|
int nTokens; |
| 83 |
|
int FF; |
| 84 |
|
int bandwidth; |
| 85 |
+ |
int gridwidth; |
| 86 |
|
short int gotMatch; |
| 87 |
|
|
| 88 |
|
//parse the command line options |
| 97 |
|
exit(1); |
| 98 |
|
} |
| 99 |
|
|
| 100 |
< |
//the bandwidth has a default value (default=8), so it is always given |
| 100 |
> |
file = fileName.c_str(); |
| 101 |
> |
strcpy(xyzFile, file); |
| 102 |
> |
token = strtok(xyzFile, period); |
| 103 |
> |
strcpy(xyzFile, token); |
| 104 |
> |
strcpy(shapeFile, token); |
| 105 |
> |
strcat(xyzFile, "Ref.xyz"); |
| 106 |
> |
strcat(shapeFile, ".shape"); |
| 107 |
> |
ofstream xfiles(xyzFile); |
| 108 |
> |
|
| 109 |
> |
//the bandwidth has a default value (default=16), so it is always given |
| 110 |
|
bandwidth = args_info.bandwidth_arg; |
| 111 |
+ |
gridwidth = bandwidth*2; |
| 112 |
|
|
| 113 |
|
if (args_info.charmm_given) { |
| 114 |
|
FF=CHARMM; |
| 259 |
|
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 260 |
|
rb->addAtom(*j); |
| 261 |
|
} |
| 262 |
< |
|
| 262 |
> |
|
| 263 |
|
rb->calcRefCoords(); |
| 264 |
|
|
| 265 |
< |
gb = new GridBuilder(rb, bandwidth); |
| 265 |
> |
//print a reference coordinate xyz file |
| 266 |
> |
xfiles << rb->getNumAtoms() << "\n\n"; |
| 267 |
> |
for (k=0; k<rb->getNumAtoms(); k++){ |
| 268 |
> |
rb->getAtomRefCoor(xyz3, k); |
| 269 |
> |
xfiles << rb->getAtomBase(k) << "\t" << |
| 270 |
> |
xyz3[0] << "\t" << xyz3[1] << "\t" << |
| 271 |
> |
xyz3[2] << "\n"; |
| 272 |
> |
} |
| 273 |
> |
|
| 274 |
> |
gb = new GridBuilder(rb, gridwidth); |
| 275 |
|
|
| 276 |
+ |
cout << "Doing GridBuilder calculations...\n"; |
| 277 |
|
gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 278 |
+ |
|
| 279 |
+ |
gb->printGridFiles(); |
| 280 |
+ |
|
| 281 |
+ |
//load the grid element values to the main grid vectors |
| 282 |
+ |
for (k=0; k<gridwidth*gridwidth; k++){ |
| 283 |
+ |
sigmaGrid.push_back(gb->passSig(k)); |
| 284 |
+ |
sGrid.push_back(gb->passS(k)); |
| 285 |
+ |
epsGrid.push_back(gb->passEps(k)); |
| 286 |
+ |
} |
| 287 |
|
|
| 288 |
< |
|
| 288 |
> |
|
| 289 |
> |
|
| 290 |
|
} |
| 291 |
|
|
| 292 |
|
int count_tokens(char *line, char *delimiters) { |
