1 |
mmeineke |
16 |
#include <iostream> |
2 |
|
|
#include <cstdlib> |
3 |
|
|
#include <cstring> |
4 |
|
|
#include <cstdio> |
5 |
|
|
|
6 |
|
|
#include "SimSetup.hpp" |
7 |
|
|
#include "SimInfo.hpp" |
8 |
|
|
#include "Atom.hpp" |
9 |
|
|
#include "Integrator.hpp" |
10 |
|
|
#include "Thermo.hpp" |
11 |
|
|
#include "ReadWrite.hpp" |
12 |
|
|
|
13 |
|
|
|
14 |
|
|
char* program_name; |
15 |
|
|
using namespace std; |
16 |
|
|
|
17 |
|
|
int main(int argc,char* argv[]){ |
18 |
|
|
|
19 |
|
|
int i, j, k, l; |
20 |
|
|
unsigned int n_atoms, eo, xo; |
21 |
|
|
char* in_name; |
22 |
|
|
SimSetup* startMe; |
23 |
|
|
SimInfo* entry_plug; |
24 |
|
|
Thermo* tStats; |
25 |
|
|
|
26 |
|
|
int lipidNAtoms; |
27 |
|
|
Atom** lipidAtoms; |
28 |
|
|
|
29 |
|
|
int tot_Natoms; |
30 |
|
|
Atom** totAtoms; |
31 |
|
|
|
32 |
|
|
const double water_rho = 0.0334; // number density per cubic angstrom |
33 |
|
|
const double water_vol = 4.0 / water_rho; // volume occupied by 4 waters |
34 |
|
|
const double water_cell = 4.929; // fcc unit cell length |
35 |
|
|
|
36 |
|
|
int n_lipidsX = 5; |
37 |
mmeineke |
27 |
int n_lipidsY = 10; |
38 |
mmeineke |
16 |
int n_lipids = n_lipidsX * n_lipidsY; |
39 |
|
|
|
40 |
|
|
std::cerr << "n_lipids = " << n_lipids << "\n"; |
41 |
|
|
|
42 |
|
|
double water_shell = 10.0; |
43 |
|
|
double water_padding = 2.5; |
44 |
|
|
double lipid_spaceing = 4.0; |
45 |
|
|
|
46 |
|
|
srand48( 1337 ); // initialize the random number generator. |
47 |
|
|
|
48 |
|
|
program_name = argv[0]; /*save the program name in case we need it*/ |
49 |
|
|
if( argc < 3 ){ |
50 |
|
|
cerr<< "Error, input and output bass files are needed to run.\n" |
51 |
|
|
<< program_name << " <input.bass> <output.bass>\n"; |
52 |
|
|
|
53 |
|
|
exit(8); |
54 |
|
|
} |
55 |
|
|
|
56 |
|
|
in_name = argv[1]; |
57 |
|
|
char* out_name = argv[2]; |
58 |
|
|
entry_plug = new SimInfo; |
59 |
|
|
|
60 |
|
|
startMe = new SimSetup; |
61 |
|
|
startMe->setSimInfo( entry_plug ); |
62 |
|
|
startMe->parseFile( in_name ); |
63 |
|
|
startMe->createSim(); |
64 |
|
|
|
65 |
|
|
delete startMe; |
66 |
|
|
|
67 |
|
|
lipidAtoms = entry_plug->atoms; |
68 |
|
|
lipidNAtoms = entry_plug->n_atoms; |
69 |
|
|
|
70 |
|
|
int group_nAtoms = n_lipids * lipidNAtoms; |
71 |
|
|
Atom** group_atoms = new Atom*[group_nAtoms]; |
72 |
|
|
DirectionalAtom* dAtom; |
73 |
|
|
DirectionalAtom* dAtomNew; |
74 |
|
|
|
75 |
|
|
double rotMat[3][3]; |
76 |
|
|
|
77 |
|
|
rotMat[0][0] = 1.0; |
78 |
|
|
rotMat[0][1] = 0.0; |
79 |
|
|
rotMat[0][2] = 0.0; |
80 |
|
|
|
81 |
|
|
rotMat[1][0] = 0.0; |
82 |
|
|
rotMat[1][1] = 1.0; |
83 |
|
|
rotMat[1][2] = 0.0; |
84 |
|
|
|
85 |
|
|
rotMat[2][0] = 0.0; |
86 |
|
|
rotMat[2][1] = 0.0; |
87 |
|
|
rotMat[2][2] = 1.0; |
88 |
|
|
|
89 |
|
|
int index =0; |
90 |
|
|
for(i=0; i<n_lipids; i++ ){ |
91 |
|
|
for(j=0; j<lipidNAtoms; j++){ |
92 |
|
|
|
93 |
|
|
if( lipidAtoms[j]->isDirectional() ){ |
94 |
|
|
dAtom = (DirectionalAtom *)lipidAtoms[j]; |
95 |
|
|
|
96 |
|
|
dAtomNew = new DirectionalAtom(); |
97 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
98 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
99 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
100 |
|
|
|
101 |
|
|
dAtomNew->setA( rotMat ); |
102 |
|
|
|
103 |
|
|
group_atoms[index] = dAtomNew; |
104 |
|
|
} |
105 |
|
|
else{ |
106 |
|
|
|
107 |
|
|
group_atoms[index] = new GeneralAtom(); |
108 |
|
|
} |
109 |
|
|
|
110 |
|
|
group_atoms[index]->setType( lipidAtoms[j]->getType() ); |
111 |
|
|
|
112 |
|
|
index++; |
113 |
|
|
} |
114 |
|
|
} |
115 |
|
|
|
116 |
|
|
index = 0; |
117 |
|
|
for(i=0; i<n_lipidsX; i++){ |
118 |
|
|
for(j=0; j<n_lipidsY; j++){ |
119 |
|
|
for(l=0; l<lipidNAtoms; l++){ |
120 |
|
|
|
121 |
|
|
group_atoms[index]->setX( lipidAtoms[l]->getX() + |
122 |
|
|
i*lipid_spaceing ); |
123 |
|
|
|
124 |
|
|
group_atoms[index]->setY( lipidAtoms[l]->getY() + |
125 |
|
|
j*lipid_spaceing ); |
126 |
|
|
|
127 |
|
|
group_atoms[index]->setZ( lipidAtoms[l]->getZ() ); |
128 |
|
|
|
129 |
|
|
index++; |
130 |
|
|
} |
131 |
|
|
} |
132 |
|
|
} |
133 |
|
|
|
134 |
|
|
double min_x, min_y, min_z; |
135 |
|
|
double max_x, max_y, max_z; |
136 |
|
|
double test_x, test_y, test_z; |
137 |
|
|
|
138 |
|
|
max_x = min_x = group_atoms[0]->getX(); |
139 |
|
|
max_y = min_y = group_atoms[0]->getY(); |
140 |
|
|
max_z = min_z = group_atoms[0]->getZ(); |
141 |
|
|
|
142 |
|
|
for(i=0; i<group_nAtoms; i++){ |
143 |
|
|
|
144 |
|
|
test_x = group_atoms[i]->getX(); |
145 |
|
|
test_y = group_atoms[i]->getY(); |
146 |
|
|
test_z = group_atoms[i]->getZ(); |
147 |
|
|
|
148 |
|
|
if( test_x < min_x ) min_x = test_x; |
149 |
|
|
if( test_y < min_y ) min_y = test_y; |
150 |
|
|
if( test_z < min_z ) min_z = test_z; |
151 |
|
|
|
152 |
|
|
if( test_x > max_x ) max_x = test_x; |
153 |
|
|
if( test_y > max_y ) max_y = test_y; |
154 |
|
|
if( test_z > max_z ) max_z = test_z; |
155 |
|
|
} |
156 |
|
|
|
157 |
|
|
double box_x = max_x - min_x + 2*water_shell; |
158 |
|
|
double box_y = max_y - min_y + 2*water_shell; |
159 |
|
|
double box_z = max_z - min_z + 2*water_shell; |
160 |
|
|
|
161 |
|
|
int n_cellX = (int)(box_x / water_cell + 0.5 ); |
162 |
|
|
int n_cellY = (int)(box_y / water_cell + 0.5 ); |
163 |
|
|
int n_cellZ = (int)(box_z / water_cell + 0.5 ); |
164 |
|
|
|
165 |
|
|
box_x = water_cell * n_cellX; |
166 |
|
|
box_y = water_cell * n_cellY; |
167 |
|
|
box_z = water_cell * n_cellZ; |
168 |
|
|
|
169 |
|
|
int n_water = n_cellX * n_cellY * n_cellZ * 4; |
170 |
|
|
|
171 |
|
|
double *waterX = new double[n_water]; |
172 |
|
|
double *waterY = new double[n_water]; |
173 |
|
|
double *waterZ = new double[n_water]; |
174 |
|
|
|
175 |
|
|
double cx, cy, cz; |
176 |
|
|
|
177 |
|
|
cx = 0.0; |
178 |
|
|
cy = 0.0; |
179 |
|
|
cz = 0.0; |
180 |
|
|
for(i=0; i<group_nAtoms; i++){ |
181 |
|
|
cx += group_atoms[i]->getX(); |
182 |
|
|
cy += group_atoms[i]->getY(); |
183 |
|
|
cz += group_atoms[i]->getZ(); |
184 |
|
|
} |
185 |
|
|
cx /= group_nAtoms; |
186 |
|
|
cy /= group_nAtoms; |
187 |
|
|
cz /= group_nAtoms; |
188 |
|
|
|
189 |
|
|
double x0 = cx - ( box_x * 0.5 ); |
190 |
|
|
double y0 = cy - ( box_y * 0.5 ); |
191 |
|
|
double z0 = cz - ( box_z * 0.5 ); |
192 |
|
|
|
193 |
|
|
index = 0; |
194 |
|
|
for( i=0; i < n_cellX; i++ ){ |
195 |
|
|
for( j=0; j < n_cellY; j++ ){ |
196 |
|
|
for( k=0; k < n_cellZ; k++ ){ |
197 |
|
|
|
198 |
|
|
waterX[index] = i * water_cell + x0; |
199 |
|
|
waterY[index] = j * water_cell + y0; |
200 |
|
|
waterZ[index] = k * water_cell + z0; |
201 |
|
|
index++; |
202 |
|
|
|
203 |
|
|
waterX[index] = i * water_cell + 0.5 * water_cell + x0; |
204 |
|
|
waterY[index] = j * water_cell + 0.5 * water_cell + y0; |
205 |
|
|
waterZ[index] = k * water_cell + z0; |
206 |
|
|
index++; |
207 |
|
|
|
208 |
|
|
waterX[index] = i * water_cell + x0; |
209 |
|
|
waterY[index] = j * water_cell + 0.5 * water_cell + y0; |
210 |
|
|
waterZ[index] = k * water_cell + 0.5 * water_cell + z0; |
211 |
|
|
index++; |
212 |
|
|
|
213 |
|
|
waterX[index] = i * water_cell + 0.5 * water_cell + x0; |
214 |
|
|
waterY[index] = j * water_cell + y0; |
215 |
|
|
waterZ[index] = k * water_cell + 0.5 * water_cell + z0; |
216 |
|
|
index++; |
217 |
|
|
} |
218 |
|
|
} |
219 |
|
|
} |
220 |
|
|
|
221 |
|
|
int *isActive = new int[n_water]; |
222 |
|
|
for(i=0; i<n_water; i++) isActive[i] = 1; |
223 |
|
|
|
224 |
|
|
int n_active = n_water; |
225 |
|
|
double dx, dy, dz; |
226 |
|
|
double dx2, dy2, dz2, dSqr; |
227 |
|
|
double rCutSqr = water_padding * water_padding; |
228 |
|
|
|
229 |
|
|
for(i=0; ( (i<n_water) && isActive[i] ); i++){ |
230 |
|
|
for(j=0; ( (j<group_nAtoms) && isActive[i] ); j++){ |
231 |
|
|
|
232 |
|
|
dx = waterX[i] - group_atoms[j]->getX(); |
233 |
|
|
dy = waterY[i] - group_atoms[j]->getY(); |
234 |
|
|
dz = waterZ[i] - group_atoms[j]->getZ(); |
235 |
|
|
|
236 |
|
|
dx2 = dx * dx; |
237 |
|
|
dy2 = dy * dy; |
238 |
|
|
dz2 = dz * dz; |
239 |
|
|
|
240 |
|
|
dSqr = dx2 + dy2 + dz2; |
241 |
|
|
if( dSqr < rCutSqr ){ |
242 |
|
|
isActive[i] = 0; |
243 |
|
|
n_active--; |
244 |
|
|
} |
245 |
|
|
} |
246 |
|
|
} |
247 |
|
|
|
248 |
|
|
std::cerr << "final n_waters = " << n_active << "\n"; |
249 |
|
|
|
250 |
|
|
int new_nAtoms = group_nAtoms + n_active; |
251 |
|
|
Atom** new_atoms = new Atom*[new_nAtoms]; |
252 |
|
|
|
253 |
|
|
index = 0; |
254 |
|
|
for(i=0; i<group_nAtoms; i++ ){ |
255 |
|
|
|
256 |
|
|
if( group_atoms[i]->isDirectional() ){ |
257 |
|
|
dAtom = (DirectionalAtom *)group_atoms[i]; |
258 |
|
|
|
259 |
|
|
dAtomNew = new DirectionalAtom(); |
260 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
261 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
262 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
263 |
|
|
|
264 |
|
|
dAtomNew->setA( rotMat ); |
265 |
|
|
|
266 |
|
|
new_atoms[index] = dAtomNew; |
267 |
|
|
} |
268 |
|
|
else{ |
269 |
|
|
|
270 |
|
|
new_atoms[index] = new GeneralAtom(); |
271 |
|
|
} |
272 |
|
|
|
273 |
|
|
new_atoms[index]->setType( group_atoms[i]->getType() ); |
274 |
|
|
|
275 |
|
|
new_atoms[index]->setX( group_atoms[i]->getX() ); |
276 |
|
|
new_atoms[index]->setY( group_atoms[i]->getY() ); |
277 |
|
|
new_atoms[index]->setZ( group_atoms[i]->getZ() ); |
278 |
|
|
|
279 |
|
|
new_atoms[index]->set_vx( 0.0 ); |
280 |
|
|
new_atoms[index]->set_vy( 0.0 ); |
281 |
|
|
new_atoms[index]->set_vz( 0.0 ); |
282 |
|
|
|
283 |
|
|
index++; |
284 |
|
|
} |
285 |
|
|
|
286 |
|
|
|
287 |
|
|
|
288 |
|
|
|
289 |
|
|
for(i=0; i<n_water; i++){ |
290 |
|
|
if(isActive[i]){ |
291 |
|
|
|
292 |
|
|
new_atoms[index] = new DirectionalAtom(); |
293 |
|
|
new_atoms[index]->setType( "SSD" ); |
294 |
|
|
|
295 |
|
|
new_atoms[index]->setX( waterX[i] ); |
296 |
|
|
new_atoms[index]->setY( waterY[i] ); |
297 |
|
|
new_atoms[index]->setZ( waterZ[i] ); |
298 |
|
|
|
299 |
|
|
new_atoms[index]->set_vx( 0.0 ); |
300 |
|
|
new_atoms[index]->set_vy( 0.0 ); |
301 |
|
|
new_atoms[index]->set_vz( 0.0 ); |
302 |
|
|
|
303 |
|
|
dAtom = (DirectionalAtom *) new_atoms[index]; |
304 |
|
|
|
305 |
|
|
dAtom->setSUx( 0.0 ); |
306 |
|
|
dAtom->setSUy( 0.0 ); |
307 |
|
|
dAtom->setSUz( 1.0 ); |
308 |
|
|
|
309 |
|
|
dAtom->setA( rotMat ); |
310 |
|
|
|
311 |
|
|
index++; |
312 |
|
|
} |
313 |
|
|
} |
314 |
|
|
|
315 |
|
|
entry_plug->n_atoms = new_nAtoms; |
316 |
|
|
entry_plug->atoms = new_atoms; |
317 |
|
|
|
318 |
|
|
entry_plug->box_x = box_x; |
319 |
|
|
entry_plug->box_y = box_y; |
320 |
|
|
entry_plug->box_z = box_z; |
321 |
|
|
|
322 |
|
|
DumpWriter* xyz_out = new DumpWriter( entry_plug ); |
323 |
|
|
xyz_out->writeFinal(); |
324 |
|
|
delete xyz_out; |
325 |
|
|
|
326 |
|
|
FILE* out_file; |
327 |
|
|
|
328 |
|
|
out_file = fopen( out_name, "w" ); |
329 |
|
|
|
330 |
|
|
fprintf(out_file, |
331 |
|
|
"#include \"water.mdl\"\n" |
332 |
|
|
"#include \"lipid.mdl\"\n" |
333 |
|
|
"\n" |
334 |
|
|
"nComponents = 2;\n" |
335 |
|
|
"component{\n" |
336 |
|
|
" type = \"theLipid\";\n" |
337 |
|
|
" nMol = %d;\n" |
338 |
|
|
"}\n" |
339 |
|
|
"\n" |
340 |
|
|
"component{\n" |
341 |
|
|
" type = \"SSD_water\";\n" |
342 |
|
|
" nMol = %d;\n" |
343 |
|
|
"}\n" |
344 |
|
|
"\n" |
345 |
|
|
"initialConfig = \"%s\";\n" |
346 |
|
|
"\n" |
347 |
|
|
"boxX = %lf;\n" |
348 |
|
|
"boxY = %lf;\n" |
349 |
|
|
"boxZ = %lf;\n", |
350 |
|
|
n_lipids, n_active, entry_plug->finalName, |
351 |
|
|
box_x, box_y, box_z ); |
352 |
|
|
|
353 |
|
|
fclose( out_file ); |
354 |
|
|
|
355 |
|
|
return 0; |
356 |
|
|
} |