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root/group/trunk/SHAPES/forcer.cpp
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Comparing trunk/SHAPES/forcer.cpp (file contents):
Revision 1244 by gezelter, Fri Jun 4 16:21:23 2004 UTC vs.
Revision 1286 by chrisfen, Tue Jun 22 20:38:04 2004 UTC

# Line 4 | Line 4
4   #include <vector>
5   #include "forcerCmd.h"
6   #include "PDBReader.hpp"
7 + #include "RigidBody.hpp"
8 + #include "GridBuilder.hpp"
9  
10   #define MK_STR(s) # s
11   #define STR_DEFINE(t, s) t = MK_STR(s)
# Line 47 | Line 49 | int main(int argc, char* argv[]){
49    vector<Atype*>   vdwAtypes;
50    vector<Atype*>::iterator i;
51    Atype* at;
52 +  RigidBody* rb;
53    vector<VDWAtom*> theAtoms;
54    vector<VDWAtom*>::iterator j;
55    VDWAtom* atom;
56 <
56 >  GridBuilder* gb;
57 >  vector<double> sigmaGrid;
58 >  vector<double> epsGrid;
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    FILE *vdwFile, *structureFile;
70    char* ffPath_env = "VDW_PATH";
71    char* ffPath;
# Line 64 | Line 73 | int main(int argc, char* argv[]){
73    char* foo;
74    char* myType;
75    char* vType;
76 +  char *token;
77 +  const char *file;
78 +  const char *period = ".";
79 +  int k;
80    int lineNum;
81    int nTokens;
82    int FF;
83 +  int bandwidth;
84    short int gotMatch;
85  
86    //parse the command line options
# Line 81 | Line 95 | int main(int argc, char* argv[]){
95      exit(1);
96    }
97  
98 +  file = fileName.c_str();
99 +  strcpy(xyzFile, file);
100 +  token = strtok(xyzFile, period);
101 +  strcpy(xyzFile, token);
102 +  strcat(xyzFile, "ref.xyz");
103 +  ofstream xfiles(xyzFile);
104 +  
105 +  //the bandwidth has a default value (default=16), so it is always given
106 +  bandwidth = args_info.bandwidth_arg;
107 +  
108    if (args_info.charmm_given) {
109      FF=CHARMM;
110      strcpy(vdwFileName, "charmm27.vdw");
# Line 106 | Line 130 | int main(int argc, char* argv[]){
130      strcpy(vdwFileName, "oplsaal.vdw");
131    }
132  
133 +
134 +  printf ("opening %s\n", vdwFileName);
135    vdwFile = fopen( vdwFileName, "r" );
136    
137    if( vdwFile == NULL ){
# Line 122 | Line 148 | int main(int argc, char* argv[]){
148      strcat( temp, vdwFileName );
149      strcpy( vdwFileName, temp );
150      
151 +    printf ("opening %s\n", vdwFileName);
152      vdwFile = fopen( vdwFileName, "r" );
153      
154      if( vdwFile == NULL ){
# Line 132 | Line 159 | int main(int argc, char* argv[]){
159                 vdwFileName );
160        exit(-1);
161      }
162 <    printf( "VDW file %s opened sucessfully.\n", vdwFileName );
163 <    lineNum = 0;
164 <    
162 >  }
163 >  printf( "VDW file %s opened sucessfully.\n", vdwFileName );
164 >  lineNum = 0;
165 >  
166 >  eof_test = fgets( readLine, sizeof(readLine), vdwFile );
167 >  lineNum++;
168 >  
169 >  if( eof_test == NULL ){
170 >    printf("Error in reading Atoms from force file at line %d.\n",
171 >           lineNum );
172 >    exit(-1);
173 >  }
174 >  
175 >  while( eof_test != NULL ){
176 >    // toss comment lines
177 >    if( readLine[0] != '!' && readLine[0] != '#' ){
178 >      
179 >      nTokens = count_tokens(readLine, " ,;\t");
180 >      if (nTokens < 4) {
181 >        printf("Not enough tokens on line %d.\n", lineNum);
182 >        exit(-1);
183 >      }
184 >      
185 >      at = new Atype();
186 >      foo = strtok(readLine, " ,;\t");
187 >      at->setType(foo);
188 >      foo = strtok(NULL, " ,;\t");      
189 >      mass = atof(foo);
190 >      at->setMass(mass);
191 >      foo = strtok(NULL, " ,;\t");
192 >      rpar = atof(foo);
193 >      at->setRpar(rpar);
194 >      foo = strtok(NULL, " ,;\t");
195 >      eps = atof(foo);  
196 >      at->setEps(eps);
197 >      vdwAtypes.push_back(at);        
198 >    }
199      eof_test = fgets( readLine, sizeof(readLine), vdwFile );
200      lineNum++;
201 <    
202 <    if( eof_test == NULL ){
203 <      printf("Error in reading Atoms from force file at line %d.\n",
204 <             lineNum );
144 <      exit(-1);
145 <    }
146 <    
147 <    while( eof_test != NULL ){
148 <      // toss comment lines
149 <      if( readLine[0] != '!' && readLine[0] != '#' ){
150 <      
151 <        nTokens = count_tokens(readLine, " ,;\t");
152 <        if (nTokens < 4) {
153 <          printf("Not enough tokens on line %d.\n", lineNum);
154 <          exit(-1);
155 <        }
156 <              
157 <        at = new Atype();
158 <        foo = strtok(readLine, " ,;\t");
159 <        at->setType(foo);
160 <        foo = strtok(NULL, " ,;\t");      
161 <        mass = atof(foo);
162 <        at->setMass(mass);
163 <        foo = strtok(NULL, " ,;\t");
164 <        rpar = atof(foo);
165 <        at->setRpar(rpar);
166 <        foo = strtok(NULL, " ,;\t");
167 <        eps = atof(foo);  
168 <        at->setEps(eps);
169 <        vdwAtypes.push_back(at);        
170 <      }
171 <      eof_test = fgets( readLine, sizeof(readLine), vdwFile );
172 <      lineNum++;
173 <    }          
174 <    
175 <    fclose( vdwFile );
176 <  }
201 >  }          
202 >  
203 >  fclose( vdwFile );
204 >  
205    printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
206  
207    // Now, open and parse the input file!
# Line 222 | Line 250 | int main(int argc, char* argv[]){
250      }
251    }
252  
253 <  //GridBuilder gb = new GridBuilder();
254 <  //gb->findAxesAndOrigin(theAtoms);
255 <  //gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
256 <
253 >  rb = new RigidBody();
254 >  for( j = theAtoms.begin(); j !=  theAtoms.end(); ++j){
255 >    rb->addAtom(*j);
256 >  }
257  
258 +  rb->calcRefCoords();
259 +  
260 +  //print a reference coordinate xyz file
261 +  xfiles << rb->getNumAtoms() << "\n\n";
262 +  for (k=0; k<rb->getNumAtoms(); k++){
263 +    rb->getAtomRefCoor(xyz3, k);
264 +    xfiles << rb->getAtomType(k) << "\t" <<
265 +              xyz3[0] << "\t" << xyz3[1] << "\t" <<
266 +              xyz3[2] << "\n";
267 +  }
268 +  
269 +  gb = new GridBuilder(rb, bandwidth*2);
270 +
271 +  cout << "Doing GridBuilder calculations...\n";
272 +  gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
273 +  
274 +  //write out the grid files
275   }
276  
277   int count_tokens(char *line, char *delimiters) {

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