ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/SHAPES/shaper.cpp
(Generate patch)

Comparing trunk/SHAPES/shaper.cpp (file contents):
Revision 1295 by gezelter, Thu Jun 24 15:31:52 2004 UTC vs.
Revision 1360 by gezelter, Tue Jul 20 20:02:15 2004 UTC

# Line 63 | Line 63 | int main(int argc, char* argv[]){
63    double mass, rpar, eps;
64    double xyz3[3];
65    double moments[3][3];
66 +  double tolerance;
67    string fileName;  
68    char vdwFileName[2002];
69    char structureFileName[2002];
# Line 93 | Line 94 | int main(int argc, char* argv[]){
94    if (cmdline_parser (argc, argv, &args_info) != 0)
95      exit(1) ;
96  
97 <  if (args_info.input_given){
98 <    fileName = args_info.input_arg;
99 <  }
100 <  else{
97 >
98 >  if (args_info.inputs_num > 0) {
99 >      fileName = args_info.inputs[0];
100 >  } else {
101      std::cerr << "Does not have input file name" << endl;
102      exit(1);
103    }
# Line 109 | Line 110 | int main(int argc, char* argv[]){
110    strcpy(shapeName, token);
111    strcat(xyzFile, "Ref.xyz");
112    strcat(shapeFile, ".shape");
112 –  strcat(shapeName, "_RB_0");
113    ofstream xfiles(xyzFile);
114    
115    //the bandwidth has a default value (default=16), so it is always given
116    bandwidth = args_info.bandwidth_arg;
117    gridwidth = bandwidth*2;
118 <  
118 >
119 >  //the tolerance has a default value (default=0.01), so it is always given
120 >  tolerance = args_info.tolerance_arg;
121 >
122    if (args_info.charmm_given) {
123      FF=CHARMM;
124      strcpy(vdwFileName, "charmm27.vdw");
# Line 220 | Line 223 | int main(int argc, char* argv[]){
223    strcpy(structureFileName, fileName.c_str() );
224  
225    PDBReader* PDBread = new PDBReader();
226 <  PDBread->setPDBfile(structureFileName);
226 >  PDBread->setPDBfileName(structureFileName);
227    theAtoms = PDBread->getAtomList();
228    printf("Found %d atoms\n", theAtoms.size());
229  
# Line 300 | Line 303 | int main(int argc, char* argv[]){
303    printf("Doing SHAPE calculations and outputting results...\n");
304    //do the transforms and write to the shapes file
305    harmonize->doTransforms(sigmaGrid);
306 <  harmonize->printToShapesFile(shapeFile, 0);
306 >  harmonize->printToShapesFile(shapeFile, 0, tolerance);
307    harmonize->doTransforms(sGrid);
308 <  harmonize->printToShapesFile(shapeFile, 1);
308 >  harmonize->printToShapesFile(shapeFile, 1, tolerance);
309    harmonize->doTransforms(epsGrid);
310 <  harmonize->printToShapesFile(shapeFile, 2);
310 >  harmonize->printToShapesFile(shapeFile, 2, tolerance);
311    
312    //clean everything up
313    harmonize->~SphereHarm();  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines