1 |
|
#include "Integrator.hpp" |
2 |
|
#include "simError.h" |
3 |
< |
|
3 |
> |
#include <cmath> |
4 |
|
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
< |
: T(theInfo, the_ff), fz(NULL), indexOfZConsMols(NULL) |
5 |
> |
: T(theInfo, the_ff), fz(NULL), |
6 |
> |
indexOfZConsMols(NULL) |
7 |
|
{ |
8 |
|
|
9 |
|
//get properties from SimInfo |
10 |
|
GenericData* data; |
11 |
< |
IndexData* index; |
11 |
> |
ZConsParaData* zConsParaData; |
12 |
|
DoubleData* sampleTime; |
13 |
+ |
DoubleData* tolerance; |
14 |
|
StringData* filename; |
15 |
< |
|
14 |
< |
|
15 |
< |
data = info->getProperty("zconsindex"); |
16 |
< |
if(!data) { |
15 |
> |
double COM[3]; |
16 |
|
|
17 |
< |
sprintf( painCave.errMsg, |
18 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
19 |
< |
" , you must set index of z-constraint molecules.\n"); |
20 |
< |
painCave.isFatal = 1; |
21 |
< |
simError(); |
23 |
< |
} |
24 |
< |
else{ |
25 |
< |
index = dynamic_cast<IndexData*>(data); |
26 |
< |
|
27 |
< |
if(!index){ |
17 |
> |
//by default, the direction of constraint is z |
18 |
> |
// 0 --> x |
19 |
> |
// 1 --> y |
20 |
> |
// 2 --> z |
21 |
> |
whichDirection = 2; |
22 |
|
|
23 |
< |
sprintf( painCave.errMsg, |
24 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
25 |
< |
painCave.isFatal = 1; |
26 |
< |
simError(); |
27 |
< |
|
34 |
< |
} |
35 |
< |
else{ |
36 |
< |
|
37 |
< |
indexOfAllZConsMols = index->getIndexData(); |
38 |
< |
|
39 |
< |
//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
40 |
< |
int maxIndex; |
41 |
< |
int totalNumMol; |
42 |
< |
|
43 |
< |
maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
23 |
> |
//estimate the force constant of harmonical potential |
24 |
> |
double Kb = 1.986E-3 ; //in kcal/K |
25 |
> |
|
26 |
> |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
27 |
> |
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
28 |
|
|
29 |
< |
#ifndef IS_MPI |
30 |
< |
totalNumMol = nMols; |
47 |
< |
#else |
48 |
< |
totalNumMol = mpiSim->getTotNmol(); |
49 |
< |
#endif |
50 |
< |
|
51 |
< |
if(maxIndex > totalNumMol - 1){ |
52 |
< |
sprintf( painCave.errMsg, |
53 |
< |
"ZConstraint error: index is out of range\n"); |
54 |
< |
painCave.isFatal = 1; |
55 |
< |
simError(); |
56 |
< |
|
57 |
< |
} |
58 |
< |
|
59 |
< |
} |
60 |
< |
|
61 |
< |
} |
29 |
> |
//retrieve sample time of z-contraint |
30 |
> |
data = info->getProperty(ZCONSTIME_ID); |
31 |
|
|
63 |
– |
//retrive sample time of z-contraint |
64 |
– |
data = info->getProperty("zconstime"); |
65 |
– |
|
32 |
|
if(!data) { |
33 |
|
|
34 |
|
sprintf( painCave.errMsg, |
55 |
|
|
56 |
|
} |
57 |
|
|
58 |
< |
|
59 |
< |
//retrive output filename of z force |
94 |
< |
data = info->getProperty("zconsfilename"); |
58 |
> |
//retrieve output filename of z force |
59 |
> |
data = info->getProperty(ZCONSFILENAME_ID); |
60 |
|
if(!data) { |
61 |
|
|
62 |
|
|
86 |
|
|
87 |
|
} |
88 |
|
|
89 |
< |
|
90 |
< |
//calculate reference z coordinate for z-constraint molecules |
126 |
< |
double totalMass_local; |
127 |
< |
double totalMass; |
128 |
< |
double totalMZ_local; |
129 |
< |
double totalMZ; |
130 |
< |
double massOfUncons_local; |
131 |
< |
double massOfCurMol; |
132 |
< |
double COM[3]; |
89 |
> |
//retrieve tolerance for z-constraint molecuels |
90 |
> |
data = info->getProperty(ZCONSTOL_ID); |
91 |
|
|
92 |
< |
totalMass_local = 0; |
93 |
< |
totalMass = 0; |
94 |
< |
totalMZ_local = 0; |
95 |
< |
totalMZ = 0; |
96 |
< |
massOfUncons_local = 0; |
97 |
< |
|
140 |
< |
|
141 |
< |
for(int i = 0; i < nMols; i++){ |
142 |
< |
massOfCurMol = molecules[i].getTotalMass(); |
143 |
< |
molecules[i].getCOM(COM); |
144 |
< |
|
145 |
< |
totalMass_local += massOfCurMol; |
146 |
< |
totalMZ_local += massOfCurMol * COM[2]; |
147 |
< |
|
148 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
149 |
< |
|
150 |
< |
massOfUncons_local += massOfCurMol; |
151 |
< |
} |
152 |
< |
|
92 |
> |
if(!data) { |
93 |
> |
|
94 |
> |
sprintf( painCave.errMsg, |
95 |
> |
"ZConstraint error: can not get tolerance \n"); |
96 |
> |
painCave.isFatal = 1; |
97 |
> |
simError(); |
98 |
|
} |
99 |
+ |
else{ |
100 |
|
|
101 |
< |
|
102 |
< |
#ifdef IS_MPI |
103 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
158 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
159 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
160 |
< |
#else |
161 |
< |
totalMass = totalMass_local; |
162 |
< |
totalMZ = totalMZ_local; |
163 |
< |
totalMassOfUncons = massOfUncons_local; |
164 |
< |
#endif |
101 |
> |
tolerance = dynamic_cast<DoubleData*>(data); |
102 |
> |
|
103 |
> |
if(!tolerance){ |
104 |
|
|
105 |
< |
double zsys; |
106 |
< |
zsys = totalMZ / totalMass; |
107 |
< |
|
108 |
< |
#ifndef IS_MPI |
109 |
< |
for(int i = 0; i < nMols; i++){ |
171 |
< |
|
172 |
< |
if(isZConstraintMol(&molecules[i]) > -1 ){ |
173 |
< |
molecules[i].getCOM(COM); |
174 |
< |
allRefZ.push_back(COM[2] - zsys); |
105 |
> |
sprintf( painCave.errMsg, |
106 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
107 |
> |
painCave.isFatal = 1; |
108 |
> |
simError(); |
109 |
> |
|
110 |
|
} |
111 |
< |
|
111 |
> |
else{ |
112 |
> |
this->zconsTol = tolerance->getData(); |
113 |
> |
} |
114 |
> |
|
115 |
|
} |
116 |
< |
#else |
117 |
< |
|
118 |
< |
int whichNode; |
119 |
< |
enum CommType { RequestMolZPos, EndOfRequest} status; |
120 |
< |
//int status; |
121 |
< |
double zpos; |
122 |
< |
int localIndex; |
123 |
< |
MPI_Status ierr; |
124 |
< |
int tag = 0; |
125 |
< |
|
188 |
< |
if(worldRank == 0){ |
189 |
< |
|
190 |
< |
int globalIndexOfCurMol; |
191 |
< |
int *MolToProcMap; |
192 |
< |
MolToProcMap = mpiSim->getMolToProcMap(); |
193 |
< |
|
194 |
< |
for(int i = 0; i < indexOfAllZConsMols.size(); i++){ |
195 |
< |
|
196 |
< |
whichNode = MolToProcMap[indexOfAllZConsMols[i]]; |
197 |
< |
globalIndexOfCurMol = indexOfAllZConsMols[i]; |
198 |
< |
|
199 |
< |
if(whichNode == 0){ |
200 |
< |
|
201 |
< |
for(int j = 0; j < nMols; j++) |
202 |
< |
if(molecules[j].getGlobalIndex() == globalIndexOfCurMol){ |
203 |
< |
localIndex = j; |
204 |
< |
break; |
205 |
< |
} |
206 |
< |
|
207 |
< |
molecules[localIndex].getCOM(COM); |
208 |
< |
allRefZ.push_back(COM[2] - zsys); |
209 |
< |
|
210 |
< |
} |
211 |
< |
else{ |
212 |
< |
status = RequestMolZPos; |
213 |
< |
MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
214 |
< |
MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
215 |
< |
MPI_Recv(&zpos, 1, MPI_DOUBLE_PRECISION, whichNode, tag, MPI_COMM_WORLD, &ierr); |
216 |
< |
|
217 |
< |
allRefZ.push_back(zpos - zsys); |
218 |
< |
|
219 |
< |
} |
220 |
< |
|
221 |
< |
} //End of Request Loop |
222 |
< |
|
223 |
< |
//Send ending request message to slave nodes |
224 |
< |
status = EndOfRequest; |
225 |
< |
for(int i =1; i < mpiSim->getNumberProcessors(); i++) |
226 |
< |
MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD); |
227 |
< |
|
116 |
> |
|
117 |
> |
//retrieve index of z-constraint molecules |
118 |
> |
data = info->getProperty(ZCONSPARADATA_ID); |
119 |
> |
if(!data) { |
120 |
> |
|
121 |
> |
sprintf( painCave.errMsg, |
122 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
123 |
> |
" , you must set index of z-constraint molecules.\n"); |
124 |
> |
painCave.isFatal = 1; |
125 |
> |
simError(); |
126 |
|
} |
127 |
|
else{ |
128 |
|
|
129 |
< |
int whichMol; |
130 |
< |
bool done = false; |
129 |
> |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
130 |
> |
|
131 |
> |
if(!zConsParaData){ |
132 |
|
|
133 |
< |
while (!done){ |
134 |
< |
|
135 |
< |
MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr); |
133 |
> |
sprintf( painCave.errMsg, |
134 |
> |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
135 |
> |
painCave.isFatal = 1; |
136 |
> |
simError(); |
137 |
|
|
238 |
– |
switch (status){ |
239 |
– |
|
240 |
– |
case RequestMolZPos : |
241 |
– |
|
242 |
– |
MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr); |
243 |
– |
|
244 |
– |
for(int i = 0; i < nMols; i++) |
245 |
– |
if(molecules[i].getGlobalIndex() == whichMol){ |
246 |
– |
localIndex = i; |
247 |
– |
break; |
248 |
– |
} |
249 |
– |
|
250 |
– |
molecules[localIndex].getCOM(COM); |
251 |
– |
zpos = COM[2]; |
252 |
– |
MPI_Send(&zpos, 1, MPI_DOUBLE_PRECISION, 0, tag, MPI_COMM_WORLD); |
253 |
– |
|
254 |
– |
break; |
255 |
– |
|
256 |
– |
case EndOfRequest : |
257 |
– |
|
258 |
– |
done = true; |
259 |
– |
break; |
260 |
– |
} |
261 |
– |
|
138 |
|
} |
139 |
< |
|
140 |
< |
} |
141 |
< |
|
266 |
< |
//Brocast the allRefZ to slave nodes; |
267 |
< |
double* allRefZBuf; |
268 |
< |
int nZConsMols; |
269 |
< |
nZConsMols = indexOfAllZConsMols.size(); |
270 |
< |
|
271 |
< |
allRefZBuf = new double[nZConsMols]; |
272 |
< |
|
273 |
< |
if(worldRank == 0){ |
139 |
> |
else{ |
140 |
> |
|
141 |
> |
parameters = zConsParaData->getData(); |
142 |
|
|
143 |
< |
for(int i = 0; i < nZConsMols; i++) |
144 |
< |
allRefZBuf[i] = allRefZ[i]; |
145 |
< |
} |
146 |
< |
|
147 |
< |
MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD); |
148 |
< |
|
149 |
< |
if(worldRank != 0){ |
150 |
< |
|
151 |
< |
for(int i = 0; i < nZConsMols; i++) |
152 |
< |
allRefZ.push_back(allRefZBuf[i]); |
153 |
< |
} |
154 |
< |
|
155 |
< |
delete[] allRefZBuf; |
143 |
> |
//check the range of zconsIndex |
144 |
> |
//and the minimum value of index is the first one (we already sorted the data) |
145 |
> |
//the maximum value of index is the last one |
146 |
> |
|
147 |
> |
int maxIndex; |
148 |
> |
int minIndex; |
149 |
> |
int totalNumMol; |
150 |
> |
|
151 |
> |
minIndex = (*parameters)[0].zconsIndex; |
152 |
> |
if(minIndex < 0){ |
153 |
> |
sprintf( painCave.errMsg, |
154 |
> |
"ZConstraint error: index is out of range\n"); |
155 |
> |
painCave.isFatal = 1; |
156 |
> |
simError(); |
157 |
> |
} |
158 |
> |
|
159 |
> |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
160 |
> |
|
161 |
> |
#ifndef IS_MPI |
162 |
> |
totalNumMol = nMols; |
163 |
> |
#else |
164 |
> |
totalNumMol = mpiSim->getTotNmol(); |
165 |
> |
#endif |
166 |
> |
|
167 |
> |
if(maxIndex > totalNumMol - 1){ |
168 |
> |
sprintf( painCave.errMsg, |
169 |
> |
"ZConstraint error: index is out of range\n"); |
170 |
> |
painCave.isFatal = 1; |
171 |
> |
simError(); |
172 |
> |
} |
173 |
> |
|
174 |
> |
//if user does not specify the zpos for the zconstraint molecule |
175 |
> |
//its initial z coordinate will be used as default |
176 |
> |
for(int i = 0; i < parameters->size(); i++){ |
177 |
> |
|
178 |
> |
if(!(*parameters)[i].havingZPos){ |
179 |
> |
|
180 |
> |
#ifndef IS_MPI |
181 |
> |
for(int j = 0; j < nMols; j++){ |
182 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
183 |
> |
molecules[j].getCOM(COM); |
184 |
> |
break; |
185 |
> |
} |
186 |
> |
} |
187 |
> |
#else |
188 |
> |
//query which processor current zconstraint molecule belongs to |
189 |
> |
int *MolToProcMap; |
190 |
> |
int whichNode; |
191 |
> |
double initZPos; |
192 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
193 |
> |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
194 |
> |
|
195 |
> |
//broadcast the zpos of current z-contraint molecule |
196 |
> |
//the node which contain this |
197 |
> |
|
198 |
> |
if (worldRank == whichNode ){ |
199 |
> |
|
200 |
> |
for(int j = 0; j < nMols; j++) |
201 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
202 |
> |
molecules[j].getCOM(COM); |
203 |
> |
break; |
204 |
> |
} |
205 |
> |
|
206 |
> |
} |
207 |
> |
|
208 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
209 |
|
#endif |
210 |
+ |
|
211 |
+ |
(*parameters)[i].zPos = COM[whichDirection]; |
212 |
|
|
213 |
< |
|
213 |
> |
sprintf( painCave.errMsg, |
214 |
> |
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
215 |
> |
"initial z coornidate will be used \n"); |
216 |
> |
painCave.isFatal = 0; |
217 |
> |
simError(); |
218 |
> |
|
219 |
> |
} |
220 |
> |
} |
221 |
> |
|
222 |
> |
}//end if (!zConsParaData) |
223 |
> |
}//end if (!data) |
224 |
> |
|
225 |
> |
// |
226 |
|
#ifdef IS_MPI |
227 |
|
update(); |
228 |
|
#else |
229 |
|
int searchResult; |
230 |
< |
|
296 |
< |
refZ = allRefZ; |
297 |
< |
|
230 |
> |
|
231 |
|
for(int i = 0; i < nMols; i++){ |
232 |
|
|
233 |
|
searchResult = isZConstraintMol(&molecules[i]); |
236 |
|
|
237 |
|
zconsMols.push_back(&molecules[i]); |
238 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
239 |
< |
|
239 |
> |
|
240 |
> |
zPos.push_back((*parameters)[searchResult].zPos); |
241 |
> |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
242 |
> |
|
243 |
|
molecules[i].getCOM(COM); |
244 |
|
} |
245 |
|
else |
261 |
|
simError(); |
262 |
|
} |
263 |
|
|
264 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
264 |
> |
//determine the states of z-constraint molecules |
265 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
266 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
267 |
+ |
|
268 |
+ |
zconsMols[i]->getCOM(COM); |
269 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
270 |
+ |
states.push_back(zcsFixed); |
271 |
+ |
else |
272 |
+ |
states.push_back(zcsMoving); |
273 |
+ |
} |
274 |
|
|
275 |
|
#endif |
276 |
+ |
|
277 |
+ |
//get total masss of unconstraint molecules |
278 |
+ |
double totalMassOfUncons_local; |
279 |
+ |
totalMassOfUncons_local = 0; |
280 |
|
|
281 |
+ |
for(int i = 0; i < unconsMols.size(); i++) |
282 |
+ |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
283 |
+ |
|
284 |
+ |
#ifndef IS_MPI |
285 |
+ |
totalMassOfUncons = totalMassOfUncons_local; |
286 |
+ |
#else |
287 |
+ |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
288 |
+ |
#endif |
289 |
+ |
|
290 |
+ |
|
291 |
+ |
//get total number of unconstrained atoms |
292 |
+ |
int nUnconsAtoms_local; |
293 |
+ |
nUnconsAtoms_local = 0; |
294 |
+ |
for(int i = 0; i < unconsMols.size(); i++) |
295 |
+ |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
296 |
+ |
|
297 |
+ |
#ifndef IS_MPI |
298 |
+ |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
299 |
+ |
#else |
300 |
+ |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
301 |
+ |
#endif |
302 |
+ |
|
303 |
+ |
// creat zconsWriter |
304 |
|
fzOut = new ZConsWriter(zconsOutput.c_str()); |
305 |
|
|
306 |
|
if(!fzOut){ |
310 |
|
simError(); |
311 |
|
} |
312 |
|
|
342 |
– |
fzOut->writeRefZ(indexOfAllZConsMols, allRefZ); |
313 |
|
} |
314 |
|
|
315 |
|
template<typename T> ZConstraint<T>::~ZConstraint() |
332 |
|
|
333 |
|
zconsMols.clear(); |
334 |
|
massOfZConsMols.clear(); |
335 |
< |
refZ.clear(); |
335 |
> |
zPos.clear(); |
336 |
> |
kz.clear(); |
337 |
|
|
338 |
|
unconsMols.clear(); |
339 |
|
massOfUnconsMols.clear(); |
347 |
|
if(index > -1){ |
348 |
|
|
349 |
|
zconsMols.push_back(&molecules[i]); |
350 |
+ |
zPos.push_back((*parameters)[index].zPos); |
351 |
+ |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
352 |
+ |
|
353 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
354 |
|
|
355 |
|
molecules[i].getCOM(COM); |
382 |
– |
refZ.push_back(allRefZ[index]); |
356 |
|
} |
357 |
|
else |
358 |
|
{ |
362 |
|
|
363 |
|
} |
364 |
|
} |
365 |
+ |
|
366 |
+ |
//determine the states of z-constraint molecules |
367 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
368 |
+ |
zconsMols[i]->getCOM(COM); |
369 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
370 |
+ |
states.push_back(zcsFixed); |
371 |
+ |
else |
372 |
+ |
states.push_back(zcsMoving); |
373 |
+ |
} |
374 |
+ |
|
375 |
|
|
376 |
|
//The reason to declare fz and indexOfZconsMols as pointer to array is |
377 |
|
// that we want to make the MPI communication simple |
424 |
|
index = mol->getGlobalIndex(); |
425 |
|
|
426 |
|
low = 0; |
427 |
< |
high = indexOfAllZConsMols.size() - 1; |
427 |
> |
high = parameters->size() - 1; |
428 |
|
|
429 |
|
//Binary Search (we have sorted the array) |
430 |
|
while(low <= high){ |
431 |
|
mid = (low + high) /2; |
432 |
< |
if (indexOfAllZConsMols[mid] == index) |
432 |
> |
if ((*parameters)[mid].zconsIndex == index) |
433 |
|
return mid; |
434 |
< |
else if (indexOfAllZConsMols[mid] > index ) |
434 |
> |
else if ((*parameters)[mid].zconsIndex > index ) |
435 |
|
high = mid -1; |
436 |
|
else |
437 |
|
low = mid + 1; |
440 |
|
return -1; |
441 |
|
} |
442 |
|
|
443 |
< |
/** Function Name: integrateStep |
461 |
< |
** Parameter: |
462 |
< |
** int calcPot; |
463 |
< |
** int calcStress; |
464 |
< |
** Description: |
465 |
< |
** Advance One Step. |
466 |
< |
** Memo: |
467 |
< |
** The best way to implement z-constraint is to override integrateStep |
468 |
< |
** Overriding constrainB is not a good choice, since in integrateStep, |
469 |
< |
** constrainB is invoked by below line, |
470 |
< |
** if(nConstrained) constrainB(); |
471 |
< |
** For instance, we would like to apply z-constraint without bond contrain, |
472 |
< |
** In that case, if we override constrainB, Z-constrain method will never be executed; |
473 |
< |
*/ |
474 |
< |
template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress ) |
475 |
< |
{ |
476 |
< |
T::integrateStep( calcPot, calcStress ); |
477 |
< |
resetZ(); |
443 |
> |
template<typename T> void ZConstraint<T>::integrate(){ |
444 |
|
|
445 |
< |
double currZConsTime = 0; |
446 |
< |
|
447 |
< |
//write out forces of z constraint |
448 |
< |
if( info->getTime() >= currZConsTime){ |
449 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
450 |
< |
} |
445 |
> |
//zero out the velocities of center of mass of unconstrained molecules |
446 |
> |
//and the velocities of center of mass of every single z-constrained molecueles |
447 |
> |
zeroOutVel(); |
448 |
> |
|
449 |
> |
T::integrate(); |
450 |
> |
|
451 |
|
} |
452 |
+ |
|
453 |
|
|
454 |
< |
/** Function Name: resetZ |
455 |
< |
** Description: |
456 |
< |
** Reset the z coordinates |
457 |
< |
*/ |
454 |
> |
/** |
455 |
> |
* |
456 |
> |
* |
457 |
> |
* |
458 |
> |
* |
459 |
> |
*/ |
460 |
> |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
461 |
> |
double zsys; |
462 |
|
|
463 |
< |
template<typename T> void ZConstraint<T>::resetZ() |
463 |
> |
T::calcForce(calcPot, calcStress); |
464 |
> |
|
465 |
> |
if (checkZConsState()) |
466 |
> |
zeroOutVel(); |
467 |
> |
|
468 |
> |
zsys = calcZSys(); |
469 |
> |
cout << "---------------------------------------------------------------------" <<endl; |
470 |
> |
cout << "current time: " << info->getTime() << endl; |
471 |
> |
cout << "center of mass at z: " << zsys << endl; |
472 |
> |
//cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
473 |
> |
cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
474 |
> |
|
475 |
> |
//cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
476 |
> |
|
477 |
> |
//do zconstraint force; |
478 |
> |
if (haveFixedZMols()) |
479 |
> |
this->doZconstraintForce(); |
480 |
> |
|
481 |
> |
//use harmonical poteintial to move the molecules to the specified positions |
482 |
> |
if (haveMovingZMols()) |
483 |
> |
this->doHarmonic(); |
484 |
> |
|
485 |
> |
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
486 |
> |
|
487 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
488 |
> |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
489 |
> |
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
490 |
> |
} |
491 |
> |
|
492 |
> |
template<typename T> double ZConstraint<T>::calcZSys() |
493 |
|
{ |
494 |
< |
double deltaZ; |
495 |
< |
double mzOfZCons; //total sum of m*z of z-constrain molecules |
496 |
< |
double mzOfUncons; //total sum of m*z of unconstrain molecuels; |
497 |
< |
double totalMZOfZCons; |
498 |
< |
double totalMZOfUncons; |
494 |
> |
//calculate reference z coordinate for z-constraint molecules |
495 |
> |
double totalMass_local; |
496 |
> |
double totalMass; |
497 |
> |
double totalMZ_local; |
498 |
> |
double totalMZ; |
499 |
> |
double massOfCurMol; |
500 |
|
double COM[3]; |
501 |
+ |
|
502 |
+ |
totalMass_local = 0; |
503 |
+ |
totalMZ_local = 0; |
504 |
+ |
|
505 |
+ |
for(int i = 0; i < nMols; i++){ |
506 |
+ |
massOfCurMol = molecules[i].getTotalMass(); |
507 |
+ |
molecules[i].getCOM(COM); |
508 |
+ |
|
509 |
+ |
totalMass_local += massOfCurMol; |
510 |
+ |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
511 |
+ |
|
512 |
+ |
} |
513 |
+ |
|
514 |
+ |
|
515 |
+ |
#ifdef IS_MPI |
516 |
+ |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
517 |
+ |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
518 |
+ |
#else |
519 |
+ |
totalMass = totalMass_local; |
520 |
+ |
totalMZ = totalMZ_local; |
521 |
+ |
#endif |
522 |
+ |
|
523 |
|
double zsys; |
524 |
< |
Atom** zconsAtoms; |
524 |
> |
zsys = totalMZ / totalMass; |
525 |
|
|
526 |
< |
mzOfZCons = 0; |
527 |
< |
mzOfUncons = 0; |
526 |
> |
return zsys; |
527 |
> |
} |
528 |
> |
|
529 |
> |
/** |
530 |
> |
* |
531 |
> |
*/ |
532 |
> |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
533 |
> |
|
534 |
> |
T::thermalize(); |
535 |
> |
zeroOutVel(); |
536 |
> |
} |
537 |
> |
|
538 |
> |
/** |
539 |
> |
* |
540 |
> |
* |
541 |
> |
* |
542 |
> |
*/ |
543 |
> |
|
544 |
> |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
545 |
> |
|
546 |
> |
Atom** fixedZAtoms; |
547 |
> |
double COMvel[3]; |
548 |
> |
double vel[3]; |
549 |
> |
|
550 |
> |
//zero out the velocities of center of mass of fixed z-constrained molecules |
551 |
|
|
552 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
553 |
< |
mzOfZCons += massOfZConsMols[i] * refZ[i]; |
553 |
> |
|
554 |
> |
if (states[i] == zcsFixed){ |
555 |
> |
|
556 |
> |
zconsMols[i]->getCOMvel(COMvel); |
557 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
558 |
> |
|
559 |
> |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
560 |
> |
|
561 |
> |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
562 |
> |
fixedZAtoms[j]->getVel(vel); |
563 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
564 |
> |
fixedZAtoms[j]->setVel(vel); |
565 |
> |
} |
566 |
> |
|
567 |
> |
zconsMols[i]->getCOMvel(COMvel); |
568 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
569 |
> |
} |
570 |
> |
|
571 |
|
} |
572 |
|
|
573 |
< |
#ifdef IS_MPI |
574 |
< |
MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
573 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
574 |
> |
cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl; |
575 |
> |
|
576 |
> |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
577 |
> |
double MVzOfMovingMols_local; |
578 |
> |
double MVzOfMovingMols; |
579 |
> |
double totalMassOfMovingZMols_local; |
580 |
> |
double totalMassOfMovingZMols; |
581 |
> |
|
582 |
> |
MVzOfMovingMols_local = 0; |
583 |
> |
totalMassOfMovingZMols_local = 0; |
584 |
> |
|
585 |
> |
for(int i =0; i < unconsMols.size(); i++){ |
586 |
> |
unconsMols[i]->getCOMvel(COMvel); |
587 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
588 |
> |
} |
589 |
> |
|
590 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
591 |
> |
if (states[i] == zcsMoving){ |
592 |
> |
zconsMols[i]->getCOMvel(COMvel); |
593 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
594 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
595 |
> |
} |
596 |
> |
|
597 |
> |
} |
598 |
> |
|
599 |
> |
#ifndef IS_MPI |
600 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
601 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
602 |
|
#else |
603 |
< |
totalMZOfZCons = mzOfZCons; |
603 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
604 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
605 |
|
#endif |
606 |
|
|
607 |
+ |
double vzOfMovingMols; |
608 |
+ |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
609 |
+ |
|
610 |
+ |
//modify the velocites of unconstrained molecules |
611 |
+ |
Atom** unconsAtoms; |
612 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
517 |
– |
unconsMols[i]->getCOM(COM); |
518 |
– |
mzOfUncons += massOfUnconsMols[i] * COM[2]; |
519 |
– |
} |
613 |
|
|
614 |
< |
#ifdef IS_MPI |
615 |
< |
MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
616 |
< |
#else |
617 |
< |
totalMZOfUncons = mzOfUncons; |
618 |
< |
#endif |
614 |
> |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
615 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
616 |
> |
unconsAtoms[j]->getVel(vel); |
617 |
> |
vel[whichDirection] -= vzOfMovingMols; |
618 |
> |
unconsAtoms[j]->setVel(vel); |
619 |
> |
} |
620 |
|
|
621 |
< |
zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons; |
621 |
> |
} |
622 |
|
|
623 |
< |
cout << "current time: " << info->getTime() <<endl; |
624 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
623 |
> |
//modify the velocities of moving z-constrained molecuels |
624 |
> |
Atom** movingZAtoms; |
625 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
626 |
> |
|
627 |
> |
if (states[i] ==zcsMoving){ |
628 |
|
|
629 |
< |
zconsMols[i]->getCOM(COM); |
629 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
630 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
631 |
> |
movingZAtoms[j]->getVel(vel); |
632 |
> |
vel[whichDirection] -= vzOfMovingMols; |
633 |
> |
movingZAtoms[j]->setVel(vel); |
634 |
> |
} |
635 |
> |
|
636 |
> |
} |
637 |
> |
|
638 |
> |
} |
639 |
> |
|
640 |
> |
cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl; |
641 |
> |
|
642 |
> |
} |
643 |
> |
|
644 |
> |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
645 |
> |
|
646 |
> |
Atom** zconsAtoms; |
647 |
> |
double totalFZ; |
648 |
> |
double totalFZ_local; |
649 |
> |
double COMvel[3]; |
650 |
> |
double COM[3]; |
651 |
> |
double force[3]; |
652 |
> |
|
653 |
> |
|
654 |
> |
|
655 |
> |
//constrain the molecules which do not reach the specified positions |
656 |
|
|
657 |
< |
cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t"; |
658 |
< |
deltaZ = zsys + refZ[i] - COM[2]; |
659 |
< |
cout << "\tdistance: " << COM[2] +deltaZ - zsys; |
660 |
< |
//update z coordinate |
661 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
662 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
663 |
< |
zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ); |
664 |
< |
} |
657 |
> |
//Zero Out the force of z-contrained molecules |
658 |
> |
totalFZ_local = 0; |
659 |
> |
|
660 |
> |
//calculate the total z-contrained force of fixed z-contrained molecules |
661 |
> |
cout << "Fixed Molecules" << endl; |
662 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
663 |
> |
|
664 |
> |
if (states[i] == zcsFixed){ |
665 |
> |
|
666 |
> |
zconsMols[i]->getCOM(COM); |
667 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
668 |
> |
|
669 |
> |
fz[i] = 0; |
670 |
> |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
671 |
> |
zconsAtoms[j]->getFrc(force); |
672 |
> |
fz[i] += force[whichDirection]; |
673 |
> |
} |
674 |
> |
totalFZ_local += fz[i]; |
675 |
> |
|
676 |
> |
cout << "index: " << indexOfZConsMols[i] |
677 |
> |
<<"\tcurrent zpos: " << COM[whichDirection] |
678 |
> |
<< "\tcurrent fz: " <<fz[i] << endl; |
679 |
> |
|
680 |
> |
} |
681 |
> |
|
682 |
> |
} |
683 |
> |
|
684 |
> |
// apply negative to fixed z-constrained molecues; |
685 |
> |
force[0]= 0; |
686 |
> |
force[1]= 0; |
687 |
> |
force[2]= 0; |
688 |
> |
|
689 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
690 |
> |
|
691 |
> |
if (states[i] == zcsFixed){ |
692 |
> |
|
693 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
694 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
695 |
|
|
696 |
< |
//calculate z constrain force |
697 |
< |
fz[i] = massOfZConsMols[i]* deltaZ / dt2; |
698 |
< |
|
699 |
< |
cout << "\tforce: " << fz[i] << endl; |
696 |
> |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
697 |
> |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
698 |
> |
zconsAtoms[j]->addFrc(force); |
699 |
> |
} |
700 |
> |
|
701 |
> |
} |
702 |
> |
|
703 |
> |
} |
704 |
> |
|
705 |
> |
cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
706 |
> |
<< "total force is " << calcTotalForce() << endl; |
707 |
> |
//calculate the number of atoms of moving z-constrained molecules |
708 |
> |
int nMovingZAtoms_local; |
709 |
> |
int nMovingZAtoms; |
710 |
> |
|
711 |
> |
nMovingZAtoms_local = 0; |
712 |
> |
for(int i = 0; i < zconsMols.size(); i++) |
713 |
> |
if(states[i] == zcsMoving) |
714 |
> |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
715 |
> |
|
716 |
> |
#ifdef IS_MPI |
717 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
718 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
719 |
> |
#else |
720 |
> |
totalFZ = totalFZ_local; |
721 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
722 |
> |
#endif |
723 |
> |
|
724 |
> |
force[0]= 0; |
725 |
> |
force[1]= 0; |
726 |
> |
force[2]= 0; |
727 |
> |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
728 |
> |
|
729 |
> |
//modify the forces of unconstrained molecules |
730 |
> |
int accessCount = 0; |
731 |
> |
for(int i = 0; i < unconsMols.size(); i++){ |
732 |
> |
|
733 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
734 |
> |
|
735 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
736 |
> |
unconsAtoms[j]->addFrc(force); |
737 |
> |
|
738 |
> |
} |
739 |
> |
|
740 |
> |
//modify the forces of moving z-constrained molecules |
741 |
> |
for(int i = 0; i < zconsMols.size(); i++) { |
742 |
> |
if (states[i] == zcsMoving){ |
743 |
> |
|
744 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
745 |
> |
|
746 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
747 |
> |
movingZAtoms[j]->addFrc(force); |
748 |
> |
} |
749 |
|
} |
750 |
+ |
|
751 |
+ |
cout << "after substracting z-constraint force from moving molecuels " |
752 |
+ |
<< "total force is " << calcTotalForce() << endl; |
753 |
|
|
754 |
+ |
} |
755 |
+ |
|
756 |
+ |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
757 |
+ |
double COM[3]; |
758 |
+ |
double diff; |
759 |
+ |
|
760 |
+ |
bool changed; |
761 |
+ |
|
762 |
+ |
changed = false; |
763 |
+ |
|
764 |
+ |
for(int i =0; i < zconsMols.size(); i++){ |
765 |
+ |
|
766 |
+ |
zconsMols[i]->getCOM(COM); |
767 |
+ |
diff = fabs(COM[whichDirection] - zPos[i]); |
768 |
+ |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
769 |
+ |
states[i] = zcsFixed; |
770 |
+ |
changed = true; |
771 |
+ |
} |
772 |
+ |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
773 |
+ |
states[i] = zcsMoving; |
774 |
+ |
changed = true; |
775 |
+ |
} |
776 |
+ |
|
777 |
+ |
} |
778 |
+ |
|
779 |
+ |
return changed; |
780 |
+ |
} |
781 |
+ |
|
782 |
+ |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
783 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
784 |
+ |
if (states[i] == zcsFixed) |
785 |
+ |
return true; |
786 |
+ |
|
787 |
+ |
return false; |
788 |
+ |
} |
789 |
+ |
|
790 |
+ |
|
791 |
+ |
/** |
792 |
+ |
* |
793 |
+ |
*/ |
794 |
+ |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
795 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
796 |
+ |
if (states[i] == zcsMoving) |
797 |
+ |
return true; |
798 |
+ |
|
799 |
+ |
return false; |
800 |
+ |
|
801 |
+ |
} |
802 |
+ |
|
803 |
+ |
/** |
804 |
+ |
* |
805 |
+ |
* |
806 |
+ |
*/ |
807 |
+ |
|
808 |
+ |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
809 |
+ |
double force[3]; |
810 |
+ |
double harmonicU; |
811 |
+ |
double harmonicF; |
812 |
+ |
double COM[3]; |
813 |
+ |
double diff; |
814 |
+ |
double totalFZ; |
815 |
+ |
|
816 |
+ |
force[0] = 0; |
817 |
+ |
force[1] = 0; |
818 |
+ |
force[2] = 0; |
819 |
+ |
|
820 |
+ |
totalFZ = 0; |
821 |
+ |
|
822 |
+ |
cout << "Moving Molecules" << endl; |
823 |
+ |
for(int i = 0; i < zconsMols.size(); i++) { |
824 |
+ |
|
825 |
+ |
if (states[i] == zcsMoving){ |
826 |
+ |
zconsMols[i]->getCOM(COM); |
827 |
+ |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
828 |
+ |
|
829 |
+ |
diff = COM[whichDirection] -zPos[i]; |
830 |
+ |
|
831 |
+ |
harmonicU = 0.5 * kz[i] * diff * diff; |
832 |
+ |
info->lrPot += harmonicU; |
833 |
+ |
|
834 |
+ |
harmonicF = - kz[i] * diff; |
835 |
+ |
totalFZ += harmonicF; |
836 |
+ |
|
837 |
+ |
// |
838 |
+ |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
839 |
+ |
|
840 |
+ |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
841 |
+ |
|
842 |
+ |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
843 |
+ |
movingZAtoms[j]->addFrc(force); |
844 |
+ |
} |
845 |
+ |
|
846 |
+ |
} |
847 |
+ |
|
848 |
+ |
force[0]= 0; |
849 |
+ |
force[1]= 0; |
850 |
+ |
force[2]= 0; |
851 |
+ |
force[whichDirection] = -totalFZ /totNumOfUnconsAtoms; |
852 |
+ |
|
853 |
+ |
//modify the forces of unconstrained molecules |
854 |
+ |
for(int i = 0; i < unconsMols.size(); i++){ |
855 |
+ |
|
856 |
+ |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
857 |
+ |
|
858 |
+ |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
859 |
+ |
unconsAtoms[j]->addFrc(force); |
860 |
+ |
} |
861 |
+ |
|
862 |
+ |
} |
863 |
+ |
|
864 |
+ |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
865 |
+ |
{ |
866 |
+ |
double MVzOfMovingMols_local; |
867 |
+ |
double MVzOfMovingMols; |
868 |
+ |
double totalMassOfMovingZMols_local; |
869 |
+ |
double totalMassOfMovingZMols; |
870 |
+ |
double COMvel[3]; |
871 |
|
|
872 |
+ |
MVzOfMovingMols_local = 0; |
873 |
+ |
totalMassOfMovingZMols_local = 0; |
874 |
+ |
|
875 |
+ |
for(int i =0; i < unconsMols.size(); i++){ |
876 |
+ |
unconsMols[i]->getCOMvel(COMvel); |
877 |
+ |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
878 |
+ |
} |
879 |
+ |
|
880 |
+ |
for(int i = 0; i < zconsMols.size(); i++){ |
881 |
+ |
|
882 |
+ |
if (states[i] == zcsMoving){ |
883 |
+ |
zconsMols[i]->getCOMvel(COMvel); |
884 |
+ |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
885 |
+ |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
886 |
+ |
} |
887 |
+ |
|
888 |
+ |
} |
889 |
+ |
|
890 |
+ |
#ifndef IS_MPI |
891 |
+ |
MVzOfMovingMols = MVzOfMovingMols_local; |
892 |
+ |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
893 |
+ |
#else |
894 |
+ |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
895 |
+ |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
896 |
+ |
#endif |
897 |
+ |
|
898 |
+ |
double vzOfMovingMols; |
899 |
+ |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
900 |
+ |
|
901 |
+ |
return vzOfMovingMols; |
902 |
|
} |
903 |
+ |
|
904 |
+ |
|
905 |
+ |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
906 |
+ |
{ |
907 |
+ |
double COMvel[3]; |
908 |
+ |
double tempMVz = 0; |
909 |
+ |
|
910 |
+ |
for(int i =0 ; i < nMols; i++){ |
911 |
+ |
molecules[i].getCOMvel(COMvel); |
912 |
+ |
tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection]; |
913 |
+ |
} |
914 |
+ |
|
915 |
+ |
double massOfZCons_local; |
916 |
+ |
double massOfZCons; |
917 |
+ |
|
918 |
+ |
massOfZCons_local = 0; |
919 |
+ |
|
920 |
+ |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
921 |
+ |
massOfZCons_local += massOfZConsMols[i]; |
922 |
+ |
} |
923 |
+ |
#ifndef IS_MPI |
924 |
+ |
massOfZCons = massOfZCons_local; |
925 |
+ |
#else |
926 |
+ |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
927 |
+ |
#endif |
928 |
+ |
|
929 |
+ |
return tempMVz /(totalMassOfUncons + massOfZCons); |
930 |
+ |
} |
931 |
+ |
|
932 |
+ |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
933 |
+ |
|
934 |
+ |
double force[3]; |
935 |
+ |
double totalForce_local; |
936 |
+ |
double totalForce; |
937 |
+ |
|
938 |
+ |
totalForce_local = 0; |
939 |
+ |
|
940 |
+ |
for(int i = 0; i < nAtoms; i++){ |
941 |
+ |
atoms[i]->getFrc(force); |
942 |
+ |
totalForce_local += force[whichDirection]; |
943 |
+ |
} |
944 |
+ |
|
945 |
+ |
#ifndef IS_MPI |
946 |
+ |
totalForce = totalForce_local; |
947 |
+ |
#else |
948 |
+ |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
949 |
+ |
#endif |
950 |
+ |
|
951 |
+ |
return totalForce; |
952 |
+ |
|
953 |
+ |
} |