1 |
mmeineke |
504 |
#include <iostream> |
2 |
|
|
|
3 |
mmeineke |
498 |
#include <cstdlib> |
4 |
|
|
#include <cstring> |
5 |
|
|
#include <cmath> |
6 |
|
|
|
7 |
|
|
#include "simError.h" |
8 |
|
|
#include "SimInfo.hpp" |
9 |
|
|
#include "ReadWrite.hpp" |
10 |
|
|
|
11 |
mmeineke |
501 |
#include "MoLocator.hpp" |
12 |
mmeineke |
498 |
#include "sysBuild.hpp" |
13 |
|
|
#include "bilayerSys.hpp" |
14 |
|
|
|
15 |
|
|
|
16 |
mmeineke |
501 |
int buildRandomBilayer( void ); |
17 |
mmeineke |
498 |
|
18 |
mmeineke |
501 |
void getRandomRot( double rot[3][3] ); |
19 |
mmeineke |
498 |
|
20 |
mmeineke |
501 |
int buildBilayer( int isRandom ){ |
21 |
mmeineke |
498 |
|
22 |
mmeineke |
501 |
if( isRandom ){ |
23 |
|
|
return buildRandomBilayer(); |
24 |
mmeineke |
498 |
} |
25 |
|
|
else{ |
26 |
|
|
sprintf( painCave.errMsg, |
27 |
|
|
"Cannot currently create a non-random bilayer.\n" ); |
28 |
|
|
painCave.isFatal = 1; |
29 |
|
|
simError(); |
30 |
mmeineke |
501 |
return 0; |
31 |
mmeineke |
498 |
} |
32 |
|
|
} |
33 |
|
|
|
34 |
|
|
|
35 |
|
|
|
36 |
mmeineke |
501 |
int buildRandomBilayer( void ){ |
37 |
mmeineke |
498 |
|
38 |
mmeineke |
501 |
int i,j,k; |
39 |
mmeineke |
502 |
int nAtoms, atomIndex, molIndex, molID; |
40 |
mmeineke |
501 |
int* molSeq; |
41 |
|
|
int* molMap; |
42 |
mmeineke |
504 |
int* molStart; |
43 |
mmeineke |
501 |
int* cardDeck; |
44 |
|
|
int deckSize; |
45 |
|
|
int rSite, rCard; |
46 |
|
|
double cell; |
47 |
|
|
int nCells, nSites, siteIndex; |
48 |
|
|
double rot[3][3]; |
49 |
|
|
double pos[3]; |
50 |
|
|
|
51 |
|
|
Atom** atoms; |
52 |
mmeineke |
498 |
SimInfo* simnfo; |
53 |
mmeineke |
501 |
DumpWriter* writer; |
54 |
|
|
MoLocator** locate; |
55 |
|
|
|
56 |
|
|
// initialize functions and variables |
57 |
mmeineke |
498 |
|
58 |
mmeineke |
501 |
srand48( RAND_SEED ); |
59 |
|
|
molSeq = NULL; |
60 |
mmeineke |
504 |
molStart = NULL; |
61 |
mmeineke |
501 |
molMap = NULL; |
62 |
|
|
cardDeck = NULL; |
63 |
|
|
atoms = NULL; |
64 |
|
|
locate = NULL; |
65 |
|
|
simnfo = NULL; |
66 |
|
|
writer = NULL; |
67 |
|
|
|
68 |
|
|
// calculate the number of cells in the fcc box |
69 |
|
|
|
70 |
|
|
nCells = 0; |
71 |
|
|
nSites = 0; |
72 |
|
|
while( nSites < bsInfo.totNmol ){ |
73 |
|
|
nCells++; |
74 |
mmeineke |
502 |
nSites = 4.0 * pow( (double)nCells, 3.0 ); |
75 |
mmeineke |
501 |
} |
76 |
|
|
|
77 |
|
|
|
78 |
|
|
// create the molMap and cardDeck arrays |
79 |
mmeineke |
498 |
|
80 |
mmeineke |
501 |
molMap = new int[nSites]; |
81 |
|
|
cardDeck = new int[nSites]; |
82 |
mmeineke |
498 |
|
83 |
mmeineke |
501 |
for(i=0; i<nSites; i++){ |
84 |
|
|
molMap[i] = -1; |
85 |
|
|
cardDeck[i] = i; |
86 |
|
|
} |
87 |
|
|
|
88 |
|
|
// randomly place the molecules on the sites |
89 |
mmeineke |
498 |
|
90 |
mmeineke |
501 |
deckSize = nSites; |
91 |
|
|
for(i=0; i<bsInfo.totNmol; i++){ |
92 |
|
|
rCard = (int)( deckSize * drand48() ); |
93 |
|
|
rSite = cardDeck[rCard]; |
94 |
|
|
molMap[rSite] = i; |
95 |
|
|
|
96 |
|
|
// book keep the card deck; |
97 |
|
|
|
98 |
|
|
deckSize--; |
99 |
|
|
cardDeck[rCard] = cardDeck[deckSize]; |
100 |
|
|
} |
101 |
mmeineke |
498 |
|
102 |
|
|
|
103 |
mmeineke |
501 |
// create the MoLocator and Atom arrays |
104 |
|
|
|
105 |
|
|
nAtoms = 0; |
106 |
|
|
molIndex = 0; |
107 |
|
|
locate = new MoLocator*[bsInfo.nComponents]; |
108 |
|
|
molSeq = new int[bsInfo.totNmol]; |
109 |
mmeineke |
504 |
molStart = new int[bsInfo.totNmol]; |
110 |
mmeineke |
501 |
for(i=0; i<bsInfo.nComponents; i++){ |
111 |
|
|
locate[i] = new MoLocator( bsInfo.compStamps[i] ); |
112 |
|
|
for(j=0; j<bsInfo.componentsNmol[i]; j++){ |
113 |
|
|
molSeq[molIndex] = i; |
114 |
mmeineke |
504 |
molStart[molIndex] = nAtoms; |
115 |
mmeineke |
501 |
molIndex++; |
116 |
mmeineke |
502 |
nAtoms += bsInfo.compStamps[i]->getNAtoms(); |
117 |
mmeineke |
501 |
} |
118 |
|
|
} |
119 |
|
|
|
120 |
|
|
Atom::createArrays( nAtoms ); |
121 |
|
|
atoms = new Atom*[nAtoms]; |
122 |
|
|
|
123 |
|
|
|
124 |
|
|
// place the molecules at each FCC site |
125 |
|
|
|
126 |
|
|
cell = 5.0; |
127 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
128 |
|
|
if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength(); |
129 |
|
|
} |
130 |
mmeineke |
502 |
cell *= M_SQRT2; |
131 |
mmeineke |
498 |
|
132 |
mmeineke |
501 |
siteIndex = 0; |
133 |
|
|
for(i=0; i<nCells; i++){ |
134 |
|
|
for(j=0; j<nCells; j++){ |
135 |
|
|
for(k=0; k<nCells; k++){ |
136 |
|
|
|
137 |
|
|
if( molMap[siteIndex] >= 0 ){ |
138 |
|
|
pos[0] = i * cell; |
139 |
|
|
pos[1] = j * cell; |
140 |
|
|
pos[2] = k * cell; |
141 |
|
|
|
142 |
|
|
getRandomRot( rot ); |
143 |
|
|
molID = molSeq[molMap[siteIndex]]; |
144 |
mmeineke |
504 |
atomIndex = molStart[ molMap[siteIndex] ]; |
145 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
146 |
mmeineke |
501 |
} |
147 |
|
|
siteIndex++; |
148 |
mmeineke |
498 |
|
149 |
mmeineke |
501 |
if( molMap[siteIndex] >= 0 ){ |
150 |
|
|
pos[0] = i * cell + (0.5 * cell); |
151 |
|
|
pos[1] = j * cell; |
152 |
|
|
pos[2] = k * cell + (0.5 * cell); |
153 |
mmeineke |
504 |
|
154 |
mmeineke |
501 |
getRandomRot( rot ); |
155 |
|
|
molID = molSeq[molMap[siteIndex]]; |
156 |
mmeineke |
504 |
atomIndex = molStart[ molMap[siteIndex] ]; |
157 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
158 |
mmeineke |
501 |
} |
159 |
|
|
siteIndex++; |
160 |
mmeineke |
498 |
|
161 |
mmeineke |
501 |
if( molMap[siteIndex] >= 0 ){ |
162 |
|
|
pos[0] = i * cell + (0.5 * cell); |
163 |
|
|
pos[1] = j * cell + (0.5 * cell); |
164 |
|
|
pos[2] = k * cell; |
165 |
|
|
|
166 |
|
|
getRandomRot( rot ); |
167 |
|
|
molID = molSeq[molMap[siteIndex]]; |
168 |
mmeineke |
504 |
atomIndex = molStart[ molMap[siteIndex] ]; |
169 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
170 |
mmeineke |
501 |
} |
171 |
|
|
siteIndex++; |
172 |
mmeineke |
498 |
|
173 |
mmeineke |
501 |
if( molMap[siteIndex] >= 0 ){ |
174 |
|
|
pos[0] = i * cell; |
175 |
|
|
pos[1] = j * cell + (0.5 * cell); |
176 |
|
|
pos[2] = k * cell + (0.5 * cell); |
177 |
mmeineke |
504 |
|
178 |
mmeineke |
501 |
getRandomRot( rot ); |
179 |
|
|
molID = molSeq[molMap[siteIndex]]; |
180 |
mmeineke |
504 |
atomIndex = molStart[ molMap[siteIndex] ]; |
181 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
182 |
mmeineke |
501 |
} |
183 |
|
|
siteIndex++; |
184 |
|
|
} |
185 |
|
|
} |
186 |
|
|
} |
187 |
mmeineke |
498 |
|
188 |
mmeineke |
501 |
// set up the SimInfo object |
189 |
|
|
|
190 |
|
|
bsInfo.boxX = nCells * cell; |
191 |
|
|
bsInfo.boxY = nCells * cell; |
192 |
|
|
bsInfo.boxZ = nCells * cell; |
193 |
|
|
|
194 |
|
|
simnfo = new SimInfo(); |
195 |
mmeineke |
502 |
simnfo->n_atoms = nAtoms; |
196 |
|
|
simnfo->box_x = bsInfo.boxX; |
197 |
|
|
simnfo->box_y = bsInfo.boxY; |
198 |
|
|
simnfo->box_z = bsInfo.boxZ; |
199 |
mmeineke |
501 |
|
200 |
mmeineke |
504 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
201 |
mmeineke |
502 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
202 |
mmeineke |
504 |
|
203 |
mmeineke |
502 |
simnfo->atoms = atoms; |
204 |
mmeineke |
501 |
|
205 |
|
|
// set up the writer and write out |
206 |
|
|
|
207 |
mmeineke |
502 |
writer = new DumpWriter( simnfo ); |
208 |
mmeineke |
501 |
writer->writeFinal(); |
209 |
mmeineke |
498 |
|
210 |
mmeineke |
501 |
// clean up the memory |
211 |
|
|
|
212 |
|
|
if( molMap != NULL ) delete[] molMap; |
213 |
|
|
if( cardDeck != NULL ) delete[] cardDeck; |
214 |
|
|
if( locate != NULL ){ |
215 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
216 |
|
|
delete locate[i]; |
217 |
mmeineke |
498 |
} |
218 |
mmeineke |
501 |
delete[] locate; |
219 |
|
|
} |
220 |
|
|
if( atoms != NULL ){ |
221 |
|
|
for(i=0; i<nAtoms; i++){ |
222 |
|
|
delete atoms[i]; |
223 |
mmeineke |
498 |
} |
224 |
mmeineke |
501 |
Atom::destroyArrays(); |
225 |
|
|
delete[] atoms; |
226 |
|
|
} |
227 |
|
|
if( molSeq != NULL ) delete[] molSeq; |
228 |
|
|
if( simnfo != NULL ) delete simnfo; |
229 |
|
|
if( writer != NULL ) delete writer; |
230 |
mmeineke |
498 |
|
231 |
mmeineke |
501 |
return 1; |
232 |
|
|
} |
233 |
mmeineke |
498 |
|
234 |
|
|
|
235 |
mmeineke |
501 |
void getRandomRot( double rot[3][3] ){ |
236 |
mmeineke |
498 |
|
237 |
mmeineke |
501 |
double theta, phi, psi; |
238 |
|
|
double cosTheta; |
239 |
mmeineke |
498 |
|
240 |
mmeineke |
501 |
// select random phi, psi, and cosTheta |
241 |
mmeineke |
498 |
|
242 |
mmeineke |
501 |
phi = 2.0 * M_PI * drand48(); |
243 |
|
|
psi = 2.0 * M_PI * drand48(); |
244 |
|
|
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
245 |
mmeineke |
498 |
|
246 |
mmeineke |
501 |
theta = acos( cosTheta ); |
247 |
mmeineke |
498 |
|
248 |
mmeineke |
501 |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
249 |
|
|
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
250 |
mmeineke |
502 |
rot[0][2] = sin(theta) * sin(psi); |
251 |
mmeineke |
501 |
|
252 |
|
|
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
253 |
|
|
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
254 |
|
|
rot[1][2] = sin(theta) * cos(psi); |
255 |
|
|
|
256 |
|
|
rot[2][0] = sin(phi) * sin(theta); |
257 |
|
|
rot[2][1] = -cos(phi) * sin(theta); |
258 |
|
|
rot[2][2] = cos(theta); |
259 |
mmeineke |
498 |
} |
260 |
mmeineke |
501 |
|