1 |
mmeineke |
270 |
#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 |
|
|
} |