1 |
#include <stdlib.h> |
2 |
#include <math.h> |
3 |
#include <vector> |
4 |
|
5 |
#include "simError.h" |
6 |
#include "AllCorr.hpp" |
7 |
|
8 |
|
9 |
AllCorr::AllCorr(){ |
10 |
|
11 |
pairCorrs = NULL; |
12 |
haveFrames = false; |
13 |
pairCorrSet = false; |
14 |
haveLength = false; |
15 |
haveNbins = false; |
16 |
} |
17 |
|
18 |
AllCorr::~AllCorr(){ |
19 |
int i; |
20 |
|
21 |
if( pairCorrs != NULL ){ |
22 |
for(i=0; i<nPairs; i++) |
23 |
delete pairCorrs[i]; |
24 |
delete[] pairCorrs; |
25 |
} |
26 |
} |
27 |
|
28 |
void AllCorr::setMaxLength( double theLength ){ |
29 |
maxLength = theLength; |
30 |
haveLength = true; |
31 |
} |
32 |
|
33 |
void AllCorr::setNbins( int theNbins ){ |
34 |
nBins = theNbins; |
35 |
haveNbins = true; |
36 |
} |
37 |
|
38 |
void AllCorr::setFrames( SimInfo* theInfoArray, int theNframes, |
39 |
DumpReader* theReader ){ |
40 |
int i; |
41 |
|
42 |
|
43 |
infoArray = theInfoArray; |
44 |
nFrames = theNframes; |
45 |
reader = theReader; |
46 |
|
47 |
nAtoms = infoArray[0].n_atoms; |
48 |
|
49 |
|
50 |
// allocate the first frame's atom arrays |
51 |
|
52 |
(infoArray[0].getConfiguration())->createArrays(infoArray[0].n_atoms); |
53 |
for (i = 0; i < infoArray[0].n_atoms; i++) |
54 |
infoArray[0].atoms[i]->setCoords(); |
55 |
|
56 |
// read in the first frame's positions |
57 |
|
58 |
reader->readFrame( &(infoArray[0]), 0 ); |
59 |
|
60 |
if( !haveLength ){ |
61 |
maxLength = infoArray[0].getMaxCutoff(); |
62 |
haveLength = true; |
63 |
} |
64 |
|
65 |
haveFrames = true; |
66 |
} |
67 |
|
68 |
void AllCorr::setPairCorrList( vector <PairCorrList> &theList ){ |
69 |
|
70 |
int i; |
71 |
char pair1[PCL_NAME_LENGTH]; |
72 |
char pair2[PCL_NAME_LENGTH]; |
73 |
|
74 |
if( !haveFrames ){ |
75 |
sprintf( painCave.errMsg, |
76 |
"\n" |
77 |
"AllCorr Error: attempt to create the pair correlations without" |
78 |
" first setting the Frames\n" ); |
79 |
painCave.isFatal = 1; |
80 |
simError(); |
81 |
} |
82 |
|
83 |
if( !haveNbins ){ |
84 |
sprintf( painCave.errMsg, |
85 |
"\n" |
86 |
"AllCorr Error: attempt to create the pair correlations without" |
87 |
" first setting nBins\n" ); |
88 |
painCave.isFatal = 1; |
89 |
simError(); |
90 |
} |
91 |
|
92 |
|
93 |
nPairs = (int)theList.size(); |
94 |
pairCorrs = new PairCorrType*[nPairs]; |
95 |
|
96 |
for(i=0;i<nPairs;i++){ |
97 |
|
98 |
theList[i].getAtom1( pair1 ); |
99 |
theList[i].getAtom2( pair2 ); |
100 |
|
101 |
switch( theList[i].getType() ){ |
102 |
|
103 |
case gofr: |
104 |
pairCorrs[i] = new GofR(pair1, pair2, nAtoms, nBins); |
105 |
break; |
106 |
|
107 |
default: |
108 |
|
109 |
sprintf( painCave.errMsg, |
110 |
"AllCorr Error: Unrecognized pair corr type in " |
111 |
" setPairCorrList()->theList[%d]\n", |
112 |
i ); |
113 |
painCave.isFatal = 1; |
114 |
simError(); |
115 |
break; |
116 |
} |
117 |
} |
118 |
|
119 |
pairCorrSet = true; |
120 |
} |
121 |
|
122 |
void AllCorr::initCorrelations( char* theOutPrefix, bool theIsSeparateOut, |
123 |
bool theHavePairCorrs, |
124 |
bool theHaveStaticCorrs ){ |
125 |
int i; |
126 |
atomName* theNames = new atomName[nAtoms]; |
127 |
|
128 |
havePairCorrs = theHavePairCorrs; |
129 |
haveStaticCorrs = theHaveStaticCorrs; |
130 |
|
131 |
if( havePairCorrs){ |
132 |
|
133 |
if(!pairCorrSet){ |
134 |
sprintf( painCave.errMsg, |
135 |
"AllCorr error: Attempt to initialize pair correlations " |
136 |
" without first setting the pair correlation list.\n" ); |
137 |
painCave.isFatal = 1; |
138 |
simError(); |
139 |
} |
140 |
|
141 |
for(i=0;i<nAtoms;i++){ |
142 |
|
143 |
strcpy(theNames[i].name, infoArray[0].atoms[i]->getType() ); |
144 |
} |
145 |
|
146 |
for(i=0;i<nPairs;i++){ |
147 |
pairCorrs[i]->initCorr(maxLength, theNames ); |
148 |
} |
149 |
} |
150 |
|
151 |
if( haveStaticCorrs ){ |
152 |
|
153 |
// empty for now |
154 |
} |
155 |
|
156 |
strcpy(outPrefix, theOutPrefix); |
157 |
isSeparateOut = theIsSeparateOut; |
158 |
} |
159 |
|
160 |
|
161 |
void AllCorr::calcCorrelations(){ |
162 |
|
163 |
SimInfo* currInfo; |
164 |
int i,j,k,l; |
165 |
double rij[3], rDist, uHatI[3], uHatJ[3]; |
166 |
double* grndOut = NULL; |
167 |
double dSqr, ri[3], rj[3]; |
168 |
DirectionalAtom* dAtom; |
169 |
double frameVolume; |
170 |
|
171 |
|
172 |
for(k=0; k<nFrames; k++){ |
173 |
|
174 |
currInfo = &(infoArray[k]); |
175 |
|
176 |
// skip the first frame, as it is already initialized |
177 |
if( k != 0 ){ |
178 |
|
179 |
// allocate the frame's atom arrays |
180 |
|
181 |
(currInfo->getConfiguration())->createArrays(currInfo->n_atoms); |
182 |
for (i = 0; i < currInfo->n_atoms; i++) |
183 |
currInfo->atoms[i]->setCoords(); |
184 |
|
185 |
// read in the frame's positions |
186 |
|
187 |
reader->readFrame( &(infoArray[k]), 0 ); |
188 |
} |
189 |
|
190 |
frameVolume = currInfo->boxVol; |
191 |
this->setFrameVolume( frameVolume ); |
192 |
|
193 |
if(havePairCorrs){ |
194 |
|
195 |
// do the pair loop |
196 |
|
197 |
for(i=0;i<(nAtoms-1);i++){ |
198 |
|
199 |
if( this->matchI(i) ){ |
200 |
|
201 |
for(j=i+1;j<nAtoms;j++){ |
202 |
|
203 |
if( this->matchJ(j) ){ |
204 |
|
205 |
// calc rdist and rij; |
206 |
|
207 |
currInfo->atoms[i]->getPos( ri ); |
208 |
|
209 |
currInfo->atoms[j]->getPos( rj ); |
210 |
|
211 |
for(l=0;l<3;l++) |
212 |
rij[l] = rj[l] - ri[l]; |
213 |
|
214 |
currInfo->wrapVector( rij ); |
215 |
|
216 |
dSqr=0; |
217 |
for(l=0;l<3;l++) |
218 |
dSqr += rij[l] * rij[l]; |
219 |
|
220 |
rDist = sqrt( dSqr ); |
221 |
|
222 |
if( currInfo->atoms[i]->isDirectional() ){ |
223 |
|
224 |
dAtom = (DirectionalAtom*)currInfo->atoms[i]; |
225 |
dAtom->getU( uHatI ); |
226 |
|
227 |
if( currInfo->atoms[j]->isDirectional() ){ |
228 |
|
229 |
dAtom = (DirectionalAtom*)currInfo->atoms[j]; |
230 |
dAtom->getU( uHatJ ); |
231 |
|
232 |
this->pairCorrelate( rij, rDist, uHatI, uHatJ ); |
233 |
} |
234 |
else{ |
235 |
|
236 |
this->pairCorrelate( rij, rDist, uHatI, grndOut ); |
237 |
} |
238 |
} |
239 |
else if( currInfo->atoms[j]->isDirectional() ){ |
240 |
|
241 |
dAtom = (DirectionalAtom*)currInfo->atoms[j]; |
242 |
dAtom->getU( uHatJ ); |
243 |
|
244 |
this->pairCorrelate( rij, rDist, grndOut, uHatJ ); |
245 |
} |
246 |
else{ |
247 |
this->pairCorrelate( rij, rDist, grndOut, grndOut ); |
248 |
} |
249 |
} |
250 |
} |
251 |
} |
252 |
} |
253 |
} |
254 |
|
255 |
if( haveStaticCorrs ){ |
256 |
|
257 |
// empty for now |
258 |
|
259 |
} |
260 |
|
261 |
// accumulate the averages for this frame |
262 |
|
263 |
this->accumulateFrame(); |
264 |
|
265 |
// de-allocate the frame |
266 |
|
267 |
(currInfo->getConfiguration())->destroyArrays(); |
268 |
} |
269 |
|
270 |
this->writeCorrs(); |
271 |
} |
272 |
|
273 |
bool AllCorr::matchI(int i){ |
274 |
|
275 |
int k; |
276 |
bool result; |
277 |
|
278 |
result = false; |
279 |
|
280 |
for(k=0;k<nPairs;k++) |
281 |
result = (result || pairCorrs[k]->matchI(i) ); |
282 |
|
283 |
return result; |
284 |
} |
285 |
|
286 |
bool AllCorr::matchJ(int j){ |
287 |
|
288 |
int k; |
289 |
bool result; |
290 |
|
291 |
result = false; |
292 |
|
293 |
for(k=0;k<nPairs;k++) |
294 |
result = (result || pairCorrs[k]->matchJ(j) ); |
295 |
|
296 |
return result; |
297 |
} |
298 |
|
299 |
void AllCorr::pairCorrelate( double Rij[3], double dist, |
300 |
double uHatI[3], double uHatJ[3] ){ |
301 |
|
302 |
int i; |
303 |
|
304 |
for(i=0;i<nPairs;i++) |
305 |
pairCorrs[i]->correlate( Rij, dist, uHatI, uHatJ ); |
306 |
} |
307 |
|
308 |
void AllCorr::setFrameVolume( double theVolume ){ |
309 |
|
310 |
int i; |
311 |
|
312 |
if( havePairCorrs ){ |
313 |
|
314 |
for(i=0;i<nPairs;i++) |
315 |
pairCorrs[i]->setFrameVolume( theVolume ); |
316 |
} |
317 |
|
318 |
if( haveStaticCorrs ){ |
319 |
|
320 |
// empty for now |
321 |
} |
322 |
} |
323 |
|
324 |
void AllCorr::accumulateFrame( void ){ |
325 |
|
326 |
int i; |
327 |
|
328 |
if( havePairCorrs ){ |
329 |
|
330 |
for(i=0;i<nPairs;i++) |
331 |
pairCorrs[i]->accumulateFrame(); |
332 |
} |
333 |
|
334 |
if( haveStaticCorrs ){ |
335 |
|
336 |
// empty for now |
337 |
} |
338 |
} |
339 |
|
340 |
void AllCorr::writeCorrs( void ){ |
341 |
int i; |
342 |
|
343 |
if( isSeparateOut ){ |
344 |
|
345 |
if( havePairCorrs ){ |
346 |
|
347 |
for(i=0;i<nPairs;i++) |
348 |
pairCorrs[i]->writeCorr( outPrefix ); |
349 |
} |
350 |
|
351 |
if( haveStaticCorrs ){ |
352 |
|
353 |
// empty for now |
354 |
} |
355 |
|
356 |
} |
357 |
else{ |
358 |
|
359 |
// empty for now |
360 |
} |
361 |
|
362 |
} |