| 69 |
|
int lineNum; |
| 70 |
|
int nTokens; |
| 71 |
|
int FF; |
| 72 |
+ |
int bandwidth; |
| 73 |
|
short int gotMatch; |
| 74 |
|
|
| 75 |
|
//parse the command line options |
| 84 |
|
exit(1); |
| 85 |
|
} |
| 86 |
|
|
| 87 |
+ |
//the bandwidth has a default value (default=8), so it is always given |
| 88 |
+ |
bandwidth = args_info.bandwidth_arg; |
| 89 |
+ |
|
| 90 |
|
if (args_info.charmm_given) { |
| 91 |
|
FF=CHARMM; |
| 92 |
|
strcpy(vdwFileName, "charmm27.vdw"); |
| 112 |
|
strcpy(vdwFileName, "oplsaal.vdw"); |
| 113 |
|
} |
| 114 |
|
|
| 115 |
+ |
|
| 116 |
+ |
printf ("opening %s\n", vdwFileName); |
| 117 |
|
vdwFile = fopen( vdwFileName, "r" ); |
| 118 |
|
|
| 119 |
|
if( vdwFile == NULL ){ |
| 130 |
|
strcat( temp, vdwFileName ); |
| 131 |
|
strcpy( vdwFileName, temp ); |
| 132 |
|
|
| 133 |
+ |
printf ("opening %s\n", vdwFileName); |
| 134 |
|
vdwFile = fopen( vdwFileName, "r" ); |
| 135 |
|
|
| 136 |
|
if( vdwFile == NULL ){ |
| 141 |
|
vdwFileName ); |
| 142 |
|
exit(-1); |
| 143 |
|
} |
| 144 |
< |
printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
| 145 |
< |
lineNum = 0; |
| 146 |
< |
|
| 144 |
> |
} |
| 145 |
> |
printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
| 146 |
> |
lineNum = 0; |
| 147 |
> |
|
| 148 |
> |
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 149 |
> |
lineNum++; |
| 150 |
> |
|
| 151 |
> |
if( eof_test == NULL ){ |
| 152 |
> |
printf("Error in reading Atoms from force file at line %d.\n", |
| 153 |
> |
lineNum ); |
| 154 |
> |
exit(-1); |
| 155 |
> |
} |
| 156 |
> |
|
| 157 |
> |
while( eof_test != NULL ){ |
| 158 |
> |
// toss comment lines |
| 159 |
> |
if( readLine[0] != '!' && readLine[0] != '#' ){ |
| 160 |
> |
|
| 161 |
> |
nTokens = count_tokens(readLine, " ,;\t"); |
| 162 |
> |
if (nTokens < 4) { |
| 163 |
> |
printf("Not enough tokens on line %d.\n", lineNum); |
| 164 |
> |
exit(-1); |
| 165 |
> |
} |
| 166 |
> |
|
| 167 |
> |
at = new Atype(); |
| 168 |
> |
foo = strtok(readLine, " ,;\t"); |
| 169 |
> |
at->setType(foo); |
| 170 |
> |
foo = strtok(NULL, " ,;\t"); |
| 171 |
> |
mass = atof(foo); |
| 172 |
> |
at->setMass(mass); |
| 173 |
> |
foo = strtok(NULL, " ,;\t"); |
| 174 |
> |
rpar = atof(foo); |
| 175 |
> |
at->setRpar(rpar); |
| 176 |
> |
foo = strtok(NULL, " ,;\t"); |
| 177 |
> |
eps = atof(foo); |
| 178 |
> |
at->setEps(eps); |
| 179 |
> |
vdwAtypes.push_back(at); |
| 180 |
> |
} |
| 181 |
|
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 182 |
|
lineNum++; |
| 183 |
< |
|
| 184 |
< |
if( eof_test == NULL ){ |
| 185 |
< |
printf("Error in reading Atoms from force file at line %d.\n", |
| 186 |
< |
lineNum ); |
| 146 |
< |
exit(-1); |
| 147 |
< |
} |
| 148 |
< |
|
| 149 |
< |
while( eof_test != NULL ){ |
| 150 |
< |
// toss comment lines |
| 151 |
< |
if( readLine[0] != '!' && readLine[0] != '#' ){ |
| 152 |
< |
|
| 153 |
< |
nTokens = count_tokens(readLine, " ,;\t"); |
| 154 |
< |
if (nTokens < 4) { |
| 155 |
< |
printf("Not enough tokens on line %d.\n", lineNum); |
| 156 |
< |
exit(-1); |
| 157 |
< |
} |
| 158 |
< |
|
| 159 |
< |
at = new Atype(); |
| 160 |
< |
foo = strtok(readLine, " ,;\t"); |
| 161 |
< |
at->setType(foo); |
| 162 |
< |
foo = strtok(NULL, " ,;\t"); |
| 163 |
< |
mass = atof(foo); |
| 164 |
< |
at->setMass(mass); |
| 165 |
< |
foo = strtok(NULL, " ,;\t"); |
| 166 |
< |
rpar = atof(foo); |
| 167 |
< |
at->setRpar(rpar); |
| 168 |
< |
foo = strtok(NULL, " ,;\t"); |
| 169 |
< |
eps = atof(foo); |
| 170 |
< |
at->setEps(eps); |
| 171 |
< |
vdwAtypes.push_back(at); |
| 172 |
< |
} |
| 173 |
< |
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 174 |
< |
lineNum++; |
| 175 |
< |
} |
| 176 |
< |
|
| 177 |
< |
fclose( vdwFile ); |
| 178 |
< |
} |
| 183 |
> |
} |
| 184 |
> |
|
| 185 |
> |
fclose( vdwFile ); |
| 186 |
> |
|
| 187 |
|
printf("%d Atom Types read from VDW file\n", vdwAtypes.size()); |
| 188 |
|
|
| 189 |
|
// Now, open and parse the input file! |
| 234 |
|
|
| 235 |
|
rb = new RigidBody(); |
| 236 |
|
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 237 |
< |
rb->addAtom(*j); |
| 237 |
> |
rb->addAtom(*j); |
| 238 |
|
} |
| 239 |
+ |
|
| 240 |
+ |
//GridBuilder gb = new GridBuilder(rb); |
| 241 |
|
|
| 232 |
– |
//GridBuilder gb = new GridBuilder(); |
| 233 |
– |
//gb->findAxesAndOrigin(theAtoms); |
| 242 |
|
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 235 |
– |
|
| 243 |
|
|
| 244 |
+ |
|
| 245 |
|
} |
| 246 |
|
|
| 247 |
|
int count_tokens(char *line, char *delimiters) { |
