| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#include "ForceFields.hpp" |
| 9 |
#include "SRI.hpp" |
| 10 |
#include "simError.h" |
| 11 |
|
| 12 |
|
| 13 |
DipoleTestFF::DipoleTestFF(){ |
| 14 |
|
| 15 |
#ifdef IS_MPI |
| 16 |
sprintf( painCave.errMsg, |
| 17 |
"DipoleTest ForceField does not currently support mpi" ); |
| 18 |
painCave.isFatal = 1; |
| 19 |
simError(); |
| 20 |
#endif // is_mpi |
| 21 |
|
| 22 |
char fileName[200]; |
| 23 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 24 |
char* ffPath; |
| 25 |
char temp[200]; |
| 26 |
|
| 27 |
// generate the force file name |
| 28 |
|
| 29 |
strcpy( fileName, "DipoleTest.frc" ); |
| 30 |
|
| 31 |
// attempt to open the file in the current directory first. |
| 32 |
|
| 33 |
frcFile = fopen( fileName, "r" ); |
| 34 |
|
| 35 |
if( frcFile == NULL ){ |
| 36 |
|
| 37 |
// next see if the force path enviorment variable is set |
| 38 |
|
| 39 |
ffPath = getenv( ffPath_env ); |
| 40 |
strcpy( temp, ffPath ); |
| 41 |
strcat( temp, "/" ); |
| 42 |
strcat( temp, fileName ); |
| 43 |
strcpy( fileName, temp ); |
| 44 |
|
| 45 |
frcFile = fopen( fileName, "r" ); |
| 46 |
|
| 47 |
if( frcFile == NULL ){ |
| 48 |
|
| 49 |
fprintf( stderr, |
| 50 |
"Error opening the force field parameter file: %s\n" |
| 51 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 52 |
"vairable?\n", |
| 53 |
fileName ); |
| 54 |
exit( 8 ); |
| 55 |
} |
| 56 |
} |
| 57 |
} |
| 58 |
|
| 59 |
DipoleTestFF::~DipoleTestFF(){ |
| 60 |
|
| 61 |
fclose( frcFile ); |
| 62 |
} |
| 63 |
|
| 64 |
void DipoleTestFF::initializeAtoms( void ){ |
| 65 |
|
| 66 |
class LinkedType { |
| 67 |
public: |
| 68 |
LinkedType(){ |
| 69 |
next = NULL; |
| 70 |
name[0] = '\0'; |
| 71 |
} |
| 72 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 73 |
|
| 74 |
LinkedType* find(char* key){ |
| 75 |
if( !strcmp(name, key) ) return this; |
| 76 |
if( next != NULL ) return next->find(key); |
| 77 |
return NULL; |
| 78 |
} |
| 79 |
|
| 80 |
char name[15]; |
| 81 |
int isDipole; |
| 82 |
double mass; |
| 83 |
double epslon; |
| 84 |
double sigma; |
| 85 |
double dipole; |
| 86 |
LinkedType* next; |
| 87 |
}; |
| 88 |
|
| 89 |
LinkedType* headAtomType; |
| 90 |
LinkedType* currentAtomType; |
| 91 |
LinkedType* tempAtomType; |
| 92 |
|
| 93 |
char readLine[500]; |
| 94 |
char* the_token; |
| 95 |
char* eof_test; |
| 96 |
int foundAtom = 0; |
| 97 |
int lineNum = 0; |
| 98 |
int i; |
| 99 |
|
| 100 |
////////////////////////////////////////////////// |
| 101 |
// a quick water fix |
| 102 |
|
| 103 |
double testI[3][3]; |
| 104 |
testI[0][0] = 1.76958347772500; |
| 105 |
testI[0][1] = 0.0; |
| 106 |
testI[0][2] = 0.0; |
| 107 |
|
| 108 |
testI[1][0] = 0.0; |
| 109 |
testI[1][1] = 0.614537057924513; |
| 110 |
testI[1][2] = 0.0; |
| 111 |
|
| 112 |
testI[2][0] = 0.0; |
| 113 |
testI[2][1] = 0.0; |
| 114 |
testI[2][2] = 1.15504641980049; |
| 115 |
|
| 116 |
////////////////////////////////////////////////// |
| 117 |
|
| 118 |
Atom** the_atoms; |
| 119 |
int nAtoms; |
| 120 |
the_atoms = entry_plug->atoms; |
| 121 |
nAtoms = entry_plug->n_atoms; |
| 122 |
|
| 123 |
// read in the atom types. |
| 124 |
|
| 125 |
rewind( frcFile ); |
| 126 |
headAtomType = new LinkedType; |
| 127 |
currentAtomType = headAtomType; |
| 128 |
|
| 129 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 130 |
lineNum++; |
| 131 |
if( eof_test == NULL ){ |
| 132 |
fprintf( stderr, "Error in reading Atoms from force file.\n" ); |
| 133 |
exit(8); |
| 134 |
} |
| 135 |
|
| 136 |
|
| 137 |
while( !foundAtom ){ |
| 138 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 139 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 140 |
lineNum++; |
| 141 |
} |
| 142 |
if( eof_test == NULL ){ |
| 143 |
fprintf( stderr, |
| 144 |
"Error in reading Atoms from force file at line %d.\n", |
| 145 |
lineNum ); |
| 146 |
exit(8); |
| 147 |
} |
| 148 |
|
| 149 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 150 |
foundAtom = !strcmp( "AtomTypes", the_token ); |
| 151 |
|
| 152 |
if( !foundAtom ){ |
| 153 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 154 |
lineNum++; |
| 155 |
|
| 156 |
if( eof_test == NULL ){ |
| 157 |
fprintf( stderr, |
| 158 |
"Error in reading Atoms from force file at line %d.\n", |
| 159 |
lineNum ); |
| 160 |
exit(8); |
| 161 |
} |
| 162 |
} |
| 163 |
} |
| 164 |
|
| 165 |
// we are now at the AtomTypes section. |
| 166 |
|
| 167 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 168 |
lineNum++; |
| 169 |
|
| 170 |
if( eof_test == NULL ){ |
| 171 |
fprintf( stderr, |
| 172 |
"Error in reading Atoms from force file at line %d.\n", |
| 173 |
lineNum ); |
| 174 |
exit(8); |
| 175 |
} |
| 176 |
|
| 177 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 178 |
|
| 179 |
if( readLine[0] != '!' ){ |
| 180 |
|
| 181 |
the_token = strtok( readLine, " \n\t,;" ); |
| 182 |
if( the_token != NULL ){ |
| 183 |
|
| 184 |
strcpy( currentAtomType->name, the_token ); |
| 185 |
|
| 186 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 187 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 188 |
exit(8); |
| 189 |
} |
| 190 |
|
| 191 |
sscanf( the_token, "%d", ¤tAtomType->isDipole ); |
| 192 |
|
| 193 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 194 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 195 |
exit(8); |
| 196 |
} |
| 197 |
|
| 198 |
sscanf( the_token, "%lf", ¤tAtomType->mass ); |
| 199 |
|
| 200 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 201 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 202 |
exit(8); |
| 203 |
} |
| 204 |
|
| 205 |
sscanf( the_token, "%lf", ¤tAtomType->epslon ); |
| 206 |
|
| 207 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 208 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 209 |
exit(8); |
| 210 |
} |
| 211 |
|
| 212 |
sscanf( the_token, "%lf", ¤tAtomType->sigma ); |
| 213 |
|
| 214 |
if( currentAtomType->isDipole ){ |
| 215 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 216 |
fprintf( stderr, "Error parseing AtomTypes: line %d\n", lineNum ); |
| 217 |
exit(8); |
| 218 |
} |
| 219 |
|
| 220 |
sscanf( the_token, "%lf", ¤tAtomType->dipole ); |
| 221 |
} |
| 222 |
} |
| 223 |
} |
| 224 |
|
| 225 |
tempAtomType = new LinkedType; |
| 226 |
currentAtomType->next = tempAtomType; |
| 227 |
currentAtomType = tempAtomType; |
| 228 |
|
| 229 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 230 |
lineNum++; |
| 231 |
} |
| 232 |
|
| 233 |
|
| 234 |
// initialize the atoms |
| 235 |
|
| 236 |
DirectionalAtom* dAtom; |
| 237 |
|
| 238 |
for( i=0; i<nAtoms; i++ ){ |
| 239 |
|
| 240 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 241 |
if( currentAtomType == NULL ){ |
| 242 |
fprintf( stderr, "AtomType error, %s not found in force file.\n", |
| 243 |
the_atoms[i]->getType() ); |
| 244 |
exit(8); |
| 245 |
} |
| 246 |
|
| 247 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 248 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 249 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 250 |
the_atoms[i]->setLJ(); |
| 251 |
|
| 252 |
if( currentAtomType->isDipole ){ |
| 253 |
if( the_atoms[i]->isDirectional() ){ |
| 254 |
dAtom = (DirectionalAtom *) the_atoms[i]; |
| 255 |
dAtom->setMu( currentAtomType->dipole ); |
| 256 |
dAtom->setHasDipole( 1 ); |
| 257 |
dAtom->setSSD( 1 ); |
| 258 |
dAtom->setJx( 0.0 ); |
| 259 |
dAtom->setJy( 0.0 ); |
| 260 |
dAtom->setJz( 0.0 ); |
| 261 |
|
| 262 |
dAtom->setI( testI ); |
| 263 |
|
| 264 |
entry_plug->n_dipoles++; |
| 265 |
} |
| 266 |
else{ |
| 267 |
std::cerr |
| 268 |
<< "DipoleTestFF error: Atom \"" |
| 269 |
<< currentAtomType->name << "\" is a dipole, yet no standard" |
| 270 |
<< " orientation was specifed in the BASS file.\n"; |
| 271 |
exit(8); |
| 272 |
} |
| 273 |
} |
| 274 |
else{ |
| 275 |
if( the_atoms[i]->isDirectional() ){ |
| 276 |
std::cerr |
| 277 |
<< "DipoleTestFF error: Atom \"" |
| 278 |
<< currentAtomType->name << "\" was given a standard orientation" |
| 279 |
<< " in the BASS file, yet it is not a dipole.\n"; |
| 280 |
exit(8); |
| 281 |
} |
| 282 |
} |
| 283 |
} |
| 284 |
|
| 285 |
|
| 286 |
// clean up the memory |
| 287 |
|
| 288 |
delete headAtomType; |
| 289 |
} |
| 290 |
|
| 291 |
void DipoleTestFF::initializeBonds( bond_pair* the_bonds ){ |
| 292 |
|
| 293 |
if( entry_plug->n_bonds ){ |
| 294 |
std::cerr << "DipoleTest does not support bonds!\n"; |
| 295 |
exit(8); |
| 296 |
} |
| 297 |
} |
| 298 |
|
| 299 |
void DipoleTestFF::initializeBends( bend_set* the_bends ){ |
| 300 |
|
| 301 |
if( entry_plug->n_bends ){ |
| 302 |
std::cerr << "DipoleTest does not support bends!\n"; |
| 303 |
exit(8); |
| 304 |
} |
| 305 |
} |
| 306 |
|
| 307 |
void DipoleTestFF::initializeTorsions( torsion_set* the_torsions ){ |
| 308 |
|
| 309 |
if( entry_plug->n_torsions ){ |
| 310 |
std::cerr << "DipoleTest does not support torsions!\n"; |
| 311 |
exit(8); |
| 312 |
} |
| 313 |
} |
