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#include "Integrator.hpp" |
2 |
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#include "simError.h" |
3 |
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|
3 |
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#include <cmath> |
4 |
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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 |
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{ |
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|
9 |
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//get properties from SimInfo |
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GenericData* data; |
11 |
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IndexData* index; |
11 |
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ZConsParaData* zConsParaData; |
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DoubleData* sampleTime; |
13 |
+ |
DoubleData* tolerance; |
14 |
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StringData* filename; |
15 |
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|
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|
15 |
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data = info->getProperty("zconsindex"); |
16 |
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if(!data) { |
15 |
> |
double COM[3]; |
16 |
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|
17 |
< |
sprintf( painCave.errMsg, |
18 |
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"ZConstraint error: If you use an ZConstraint\n" |
19 |
< |
" , you must set index of z-constraint molecules.\n"); |
20 |
< |
painCave.isFatal = 1; |
21 |
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simError(); |
23 |
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} |
24 |
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else{ |
25 |
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index = dynamic_cast<IndexData*>(data); |
26 |
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|
27 |
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if(!index){ |
17 |
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//by default, the direction of constraint is z |
18 |
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// 0 --> x |
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// 1 --> y |
20 |
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// 2 --> z |
21 |
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whichDirection = 2; |
22 |
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|
23 |
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sprintf( painCave.errMsg, |
24 |
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"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
26 |
< |
simError(); |
27 |
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|
34 |
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} |
35 |
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else{ |
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|
37 |
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indexOfAllZConsMols = index->getIndexData(); |
38 |
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|
39 |
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//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
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int maxIndex; |
41 |
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int totalNumMol; |
42 |
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|
43 |
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maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
23 |
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//estimate the force constant of harmonical potential |
24 |
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double Kb = 1.986E-3 ; //in kcal/K |
25 |
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|
26 |
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double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
27 |
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zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
28 |
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|
29 |
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#ifndef IS_MPI |
30 |
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totalNumMol = nMols; |
47 |
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#else |
48 |
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totalNumMol = mpiSim->getTotNmol(); |
49 |
< |
#endif |
50 |
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|
51 |
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if(maxIndex > totalNumMol - 1){ |
52 |
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sprintf( painCave.errMsg, |
53 |
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"ZConstraint error: index is out of range\n"); |
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painCave.isFatal = 1; |
55 |
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simError(); |
56 |
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|
57 |
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} |
58 |
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|
59 |
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} |
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|
61 |
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} |
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//retrieve sample time of z-contraint |
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data = info->getProperty(ZCONSTIME_ID); |
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|
63 |
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//retrive sample time of z-contraint |
64 |
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data = info->getProperty("zconstime"); |
65 |
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|
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if(!data) { |
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|
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sprintf( painCave.errMsg, |
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|
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} |
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|
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|
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//retrive output filename of z force |
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data = info->getProperty("zconsfilename"); |
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//retrieve output filename of z force |
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data = info->getProperty(ZCONSFILENAME_ID); |
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if(!data) { |
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|
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|
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|
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} |
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|
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|
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//calculate reference z coordinate for z-constraint molecules |
126 |
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double totalMass_local; |
127 |
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double totalMass; |
128 |
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double totalMZ_local; |
129 |
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double totalMZ; |
130 |
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double massOfUncons_local; |
131 |
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double massOfCurMol; |
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double COM[3]; |
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//retrieve tolerance for z-constraint molecuels |
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data = info->getProperty(ZCONSTOL_ID); |
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|
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totalMass_local = 0; |
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totalMass = 0; |
94 |
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totalMZ_local = 0; |
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totalMZ = 0; |
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massOfUncons_local = 0; |
97 |
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|
140 |
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|
141 |
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for(int i = 0; i < nMols; i++){ |
142 |
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massOfCurMol = molecules[i].getTotalMass(); |
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molecules[i].getCOM(COM); |
144 |
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|
145 |
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totalMass_local += massOfCurMol; |
146 |
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totalMZ_local += massOfCurMol * COM[2]; |
147 |
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|
148 |
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if(isZConstraintMol(&molecules[i]) == -1){ |
149 |
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|
150 |
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massOfUncons_local += massOfCurMol; |
151 |
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} |
152 |
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|
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if(!data) { |
93 |
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|
94 |
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sprintf( painCave.errMsg, |
95 |
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"ZConstraint error: can not get tolerance \n"); |
96 |
> |
painCave.isFatal = 1; |
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simError(); |
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} |
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+ |
else{ |
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|
101 |
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|
102 |
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#ifdef IS_MPI |
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MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
158 |
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MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
159 |
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MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
160 |
< |
#else |
161 |
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totalMass = totalMass_local; |
162 |
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totalMZ = totalMZ_local; |
163 |
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totalMassOfUncons = massOfUncons_local; |
164 |
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#endif |
101 |
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tolerance = dynamic_cast<DoubleData*>(data); |
102 |
> |
|
103 |
> |
if(!tolerance){ |
104 |
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|
105 |
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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 |
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molecules[i].getCOM(COM); |
174 |
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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 |
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} |
111 |
< |
|
111 |
> |
else{ |
112 |
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this->zconsTol = tolerance->getData(); |
113 |
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} |
114 |
> |
|
115 |
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} |
116 |
< |
#else |
117 |
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|
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 |
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|
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 |
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} |
127 |
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else{ |
128 |
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|
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 |
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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 |
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localIndex = i; |
247 |
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break; |
248 |
– |
} |
249 |
– |
|
250 |
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molecules[localIndex].getCOM(COM); |
251 |
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zpos = COM[2]; |
252 |
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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 |
< |
} |
139 |
> |
else{ |
140 |
> |
|
141 |
> |
parameters = zConsParaData->getData(); |
142 |
|
|
143 |
< |
//Brocast the allRefZ to slave nodes; |
144 |
< |
double* allRefZBuf; |
145 |
< |
int nZConsMols; |
269 |
< |
nZConsMols = indexOfAllZConsMols.size(); |
270 |
< |
|
271 |
< |
allRefZBuf = new double[nZConsMols]; |
272 |
< |
|
273 |
< |
if(worldRank == 0){ |
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 |
< |
for(int i = 0; i < nZConsMols; i++) |
148 |
< |
allRefZBuf[i] = allRefZ[i]; |
149 |
< |
} |
150 |
< |
|
151 |
< |
MPI_Bcast(allRefZBuf, nZConsMols, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD); |
152 |
< |
|
153 |
< |
if(worldRank != 0){ |
154 |
< |
|
155 |
< |
for(int i = 0; i < nZConsMols; i++) |
156 |
< |
allRefZ.push_back(allRefZBuf[i]); |
157 |
< |
} |
158 |
< |
|
159 |
< |
delete[] allRefZBuf; |
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()].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[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
183 |
> |
molecules[i].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 i = 0; i < nMols; i++) |
201 |
> |
if (molecules[i].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
202 |
> |
molecules[i].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 |
265 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
266 |
|
|
267 |
|
#endif |
268 |
< |
|
268 |
> |
|
269 |
> |
//get total number of unconstrained atoms |
270 |
> |
int nUnconsAtoms_local; |
271 |
> |
nUnconsAtoms_local = 0; |
272 |
> |
for(int i = 0; i < unconsMols.size(); i++) |
273 |
> |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
274 |
> |
|
275 |
> |
#ifndef IS_MPI |
276 |
> |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
277 |
> |
#else |
278 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
279 |
> |
#endif |
280 |
> |
|
281 |
> |
checkZConsState(); |
282 |
> |
|
283 |
> |
// |
284 |
|
fzOut = new ZConsWriter(zconsOutput.c_str()); |
285 |
|
|
286 |
|
if(!fzOut){ |
290 |
|
simError(); |
291 |
|
} |
292 |
|
|
342 |
– |
fzOut->writeRefZ(indexOfAllZConsMols, allRefZ); |
293 |
|
} |
294 |
|
|
295 |
|
template<typename T> ZConstraint<T>::~ZConstraint() |
312 |
|
|
313 |
|
zconsMols.clear(); |
314 |
|
massOfZConsMols.clear(); |
315 |
< |
refZ.clear(); |
315 |
> |
zPos.clear(); |
316 |
> |
kz.clear(); |
317 |
|
|
318 |
|
unconsMols.clear(); |
319 |
|
massOfUnconsMols.clear(); |
327 |
|
if(index > -1){ |
328 |
|
|
329 |
|
zconsMols.push_back(&molecules[i]); |
330 |
+ |
zPos.push_back((*parameters)[index].zPos); |
331 |
+ |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
332 |
+ |
|
333 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
334 |
|
|
335 |
|
molecules[i].getCOM(COM); |
382 |
– |
refZ.push_back(allRefZ[index]); |
336 |
|
} |
337 |
|
else |
338 |
|
{ |
394 |
|
index = mol->getGlobalIndex(); |
395 |
|
|
396 |
|
low = 0; |
397 |
< |
high = indexOfAllZConsMols.size() - 1; |
397 |
> |
high = parameters->size() - 1; |
398 |
|
|
399 |
|
//Binary Search (we have sorted the array) |
400 |
|
while(low <= high){ |
401 |
|
mid = (low + high) /2; |
402 |
< |
if (indexOfAllZConsMols[mid] == index) |
402 |
> |
if ((*parameters)[mid].zconsIndex == index) |
403 |
|
return mid; |
404 |
< |
else if (indexOfAllZConsMols[mid] > index ) |
404 |
> |
else if ((*parameters)[mid].zconsIndex > index ) |
405 |
|
high = mid -1; |
406 |
|
else |
407 |
|
low = mid + 1; |
410 |
|
return -1; |
411 |
|
} |
412 |
|
|
413 |
< |
/** Function Name: integrateStep |
414 |
< |
** Parameter: |
415 |
< |
** 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; |
413 |
> |
/** |
414 |
> |
* Description: |
415 |
> |
* Reset the z coordinates |
416 |
|
*/ |
417 |
< |
template<typename T> void ZConstraint<T>::integrateStep( int calcPot, int calcStress ) |
475 |
< |
{ |
476 |
< |
T::integrateStep( calcPot, calcStress ); |
477 |
< |
resetZ(); |
417 |
> |
template<typename T> void ZConstraint<T>::integrate(){ |
418 |
|
|
419 |
< |
double currZConsTime = 0; |
420 |
< |
|
421 |
< |
//write out forces of z constraint |
422 |
< |
if( info->getTime() >= currZConsTime){ |
423 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
424 |
< |
} |
419 |
> |
//zero out the velocities of center of mass of unconstrained molecules |
420 |
> |
//and the velocities of center of mass of every single z-constrained molecueles |
421 |
> |
zeroOutVel(); |
422 |
> |
|
423 |
> |
T::integrate(); |
424 |
> |
|
425 |
|
} |
426 |
+ |
|
427 |
|
|
428 |
< |
/** Function Name: resetZ |
429 |
< |
** Description: |
430 |
< |
** Reset the z coordinates |
428 |
> |
/** |
429 |
> |
* |
430 |
> |
* |
431 |
> |
* |
432 |
> |
* |
433 |
|
*/ |
434 |
|
|
435 |
< |
template<typename T> void ZConstraint<T>::resetZ() |
435 |
> |
|
436 |
> |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
437 |
> |
|
438 |
> |
T::calcForce(calcPot, calcStress); |
439 |
> |
|
440 |
> |
if (checkZConsState()) |
441 |
> |
zeroOutVel(); |
442 |
> |
|
443 |
> |
//do zconstraint force; |
444 |
> |
if (haveFixedZMols()) |
445 |
> |
this->doZconstraintForce(); |
446 |
> |
|
447 |
> |
//use harmonical poteintial to move the molecules to the specified positions |
448 |
> |
if (haveMovingZMols()) |
449 |
> |
//this->doHarmonic(); |
450 |
> |
|
451 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
452 |
> |
|
453 |
> |
} |
454 |
> |
|
455 |
> |
template<typename T> double ZConstraint<T>::calcZSys() |
456 |
|
{ |
457 |
< |
double deltaZ; |
458 |
< |
double mzOfZCons; //total sum of m*z of z-constrain molecules |
459 |
< |
double mzOfUncons; //total sum of m*z of unconstrain molecuels; |
460 |
< |
double totalMZOfZCons; |
461 |
< |
double totalMZOfUncons; |
457 |
> |
//calculate reference z coordinate for z-constraint molecules |
458 |
> |
double totalMass_local; |
459 |
> |
double totalMass; |
460 |
> |
double totalMZ_local; |
461 |
> |
double totalMZ; |
462 |
> |
double massOfUncons_local; |
463 |
> |
double massOfCurMol; |
464 |
|
double COM[3]; |
465 |
+ |
|
466 |
+ |
totalMass_local = 0; |
467 |
+ |
totalMass = 0; |
468 |
+ |
totalMZ_local = 0; |
469 |
+ |
totalMZ = 0; |
470 |
+ |
massOfUncons_local = 0; |
471 |
+ |
|
472 |
+ |
|
473 |
+ |
for(int i = 0; i < nMols; i++){ |
474 |
+ |
massOfCurMol = molecules[i].getTotalMass(); |
475 |
+ |
molecules[i].getCOM(COM); |
476 |
+ |
|
477 |
+ |
totalMass_local += massOfCurMol; |
478 |
+ |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
479 |
+ |
|
480 |
+ |
if(isZConstraintMol(&molecules[i]) == -1){ |
481 |
+ |
|
482 |
+ |
massOfUncons_local += massOfCurMol; |
483 |
+ |
} |
484 |
+ |
|
485 |
+ |
} |
486 |
+ |
|
487 |
+ |
|
488 |
+ |
#ifdef IS_MPI |
489 |
+ |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
490 |
+ |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
491 |
+ |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
492 |
+ |
#else |
493 |
+ |
totalMass = totalMass_local; |
494 |
+ |
totalMZ = totalMZ_local; |
495 |
+ |
totalMassOfUncons = massOfUncons_local; |
496 |
+ |
#endif |
497 |
+ |
|
498 |
|
double zsys; |
499 |
< |
Atom** zconsAtoms; |
499 |
> |
zsys = totalMZ / totalMass; |
500 |
|
|
501 |
< |
mzOfZCons = 0; |
502 |
< |
mzOfUncons = 0; |
501 |
> |
return zsys; |
502 |
> |
} |
503 |
> |
|
504 |
> |
/** |
505 |
> |
* |
506 |
> |
*/ |
507 |
> |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
508 |
> |
|
509 |
> |
T::thermalize(); |
510 |
> |
zeroOutVel(); |
511 |
> |
} |
512 |
> |
|
513 |
> |
/** |
514 |
> |
* |
515 |
> |
* |
516 |
> |
* |
517 |
> |
*/ |
518 |
> |
|
519 |
> |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
520 |
> |
|
521 |
> |
Atom** fixedZAtoms; |
522 |
> |
double COMvel[3]; |
523 |
> |
double vel[3]; |
524 |
|
|
525 |
+ |
//zero out the velocities of center of mass of fixed z-constrained molecules |
526 |
+ |
|
527 |
|
for(int i = 0; i < zconsMols.size(); i++){ |
528 |
< |
mzOfZCons += massOfZConsMols[i] * refZ[i]; |
528 |
> |
|
529 |
> |
if (states[i] == zcsFixed){ |
530 |
> |
|
531 |
> |
zconsMols[i]->getCOMvel(COMvel); |
532 |
> |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
533 |
> |
|
534 |
> |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
535 |
> |
fixedZAtoms[j]->getVel(vel); |
536 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
537 |
> |
fixedZAtoms[j]->setVel(vel); |
538 |
> |
} |
539 |
> |
|
540 |
> |
} |
541 |
> |
|
542 |
|
} |
543 |
+ |
|
544 |
+ |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
545 |
+ |
double MVzOfMovingMols_local; |
546 |
+ |
double MVzOfMovingMols; |
547 |
+ |
double totalMassOfMovingZMols_local; |
548 |
+ |
double totalMassOfMovingZMols; |
549 |
+ |
|
550 |
+ |
MVzOfMovingMols_local = 0; |
551 |
+ |
totalMassOfMovingZMols_local = 0; |
552 |
|
|
553 |
< |
#ifdef IS_MPI |
554 |
< |
MPI_Allreduce(&mzOfZCons, &totalMZOfZCons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
553 |
> |
for(int i =0; i < unconsMols.size(); i++){ |
554 |
> |
unconsMols[i]->getCOMvel(COMvel); |
555 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
556 |
> |
} |
557 |
> |
|
558 |
> |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
559 |
> |
|
560 |
> |
if (states[i] == zcsMoving){ |
561 |
> |
zconsMols[i]->getCOMvel(COMvel); |
562 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
563 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
564 |
> |
} |
565 |
> |
|
566 |
> |
} |
567 |
> |
|
568 |
> |
#ifndef IS_MPI |
569 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
570 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
571 |
|
#else |
572 |
< |
totalMZOfZCons = mzOfZCons; |
572 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
573 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
574 |
|
#endif |
575 |
|
|
576 |
+ |
double vzOfMovingMols; |
577 |
+ |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
578 |
+ |
|
579 |
+ |
//modify the velocites of unconstrained molecules |
580 |
+ |
Atom** unconsAtoms; |
581 |
|
for(int i = 0; i < unconsMols.size(); i++){ |
517 |
– |
unconsMols[i]->getCOM(COM); |
518 |
– |
mzOfUncons += massOfUnconsMols[i] * COM[2]; |
519 |
– |
} |
582 |
|
|
583 |
< |
#ifdef IS_MPI |
584 |
< |
MPI_Allreduce(&mzOfUncons, &totalMZOfUncons, 1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
585 |
< |
#else |
586 |
< |
totalMZOfUncons = mzOfUncons; |
587 |
< |
#endif |
583 |
> |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
584 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
585 |
> |
unconsAtoms[j]->getVel(vel); |
586 |
> |
vel[whichDirection] -= vzOfMovingMols; |
587 |
> |
unconsAtoms[j]->setVel(vel); |
588 |
> |
} |
589 |
|
|
590 |
< |
zsys = (totalMZOfZCons + totalMZOfUncons) /totalMassOfUncons; |
590 |
> |
} |
591 |
|
|
592 |
< |
cout << "current time: " << info->getTime() <<endl; |
593 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
592 |
> |
//modify the velocities of moving z-constrained molecuels |
593 |
> |
Atom** movingZAtoms; |
594 |
> |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
595 |
> |
|
596 |
> |
if (states[i] ==zcsMoving){ |
597 |
|
|
598 |
< |
zconsMols[i]->getCOM(COM); |
598 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
599 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
600 |
> |
movingZAtoms[j]->getVel(vel); |
601 |
> |
vel[whichDirection] -= vzOfMovingMols; |
602 |
> |
movingZAtoms[j]->setVel(vel); |
603 |
> |
} |
604 |
> |
|
605 |
> |
} |
606 |
> |
|
607 |
> |
} |
608 |
> |
|
609 |
> |
} |
610 |
> |
|
611 |
> |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
612 |
> |
|
613 |
> |
Atom** zconsAtoms; |
614 |
> |
double totalFZ; |
615 |
> |
double totalFZ_local; |
616 |
> |
double COMvel[3]; |
617 |
> |
double COM[3]; |
618 |
> |
double force[3]; |
619 |
> |
double zsys; |
620 |
> |
|
621 |
> |
int nMovingZMols_local; |
622 |
> |
int nMovingZMols; |
623 |
> |
|
624 |
> |
//constrain the molecules which do not reach the specified positions |
625 |
> |
|
626 |
> |
zsys = calcZSys(); |
627 |
> |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
628 |
|
|
629 |
< |
cout << "global index: " << zconsMols[i]->getGlobalIndex() << "\tZ: " << COM[2] << "\t"; |
630 |
< |
deltaZ = zsys + refZ[i] - COM[2]; |
631 |
< |
cout << "\tdistance: " << COM[2] +deltaZ - zsys; |
632 |
< |
//update z coordinate |
633 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
634 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
635 |
< |
zconsAtoms[j]->setZ(zconsAtoms[j]->getZ() + deltaZ); |
636 |
< |
} |
629 |
> |
//Zero Out the force of z-contrained molecules |
630 |
> |
totalFZ_local = 0; |
631 |
> |
|
632 |
> |
//calculate the total z-contrained force of fixed z-contrained molecules |
633 |
> |
cout << "Fixed Molecules" << endl; |
634 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
635 |
> |
|
636 |
> |
if (states[i] == zcsFixed){ |
637 |
> |
|
638 |
> |
zconsMols[i]->getCOM(COM); |
639 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
640 |
> |
|
641 |
> |
fz[i] = 0; |
642 |
> |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
643 |
> |
zconsAtoms[j]->getFrc(force); |
644 |
> |
fz[i] += force[whichDirection]; |
645 |
> |
} |
646 |
> |
totalFZ_local += fz[i]; |
647 |
> |
|
648 |
> |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
649 |
> |
|
650 |
> |
} |
651 |
> |
|
652 |
> |
} |
653 |
> |
|
654 |
> |
//calculate the number of atoms of moving z-constrained molecules |
655 |
> |
nMovingZMols_local = 0; |
656 |
> |
for(int i = 0; zconsMols.size(); i++){ |
657 |
> |
if(states[i] == zcsMoving) |
658 |
> |
nMovingZMols_local += massOfZConsMols[i]; |
659 |
> |
} |
660 |
> |
#ifdef IS_MPI |
661 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
662 |
> |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
663 |
> |
#else |
664 |
> |
totalFZ = totalFZ_local; |
665 |
> |
nMovingZMols = nMovingZMols_local; |
666 |
> |
#endif |
667 |
> |
|
668 |
> |
force[0]= 0; |
669 |
> |
force[1]= 0; |
670 |
> |
force[2]= 0; |
671 |
> |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
672 |
> |
|
673 |
> |
//modify the velocites of unconstrained molecules |
674 |
> |
for(int i = 0; i < unconsMols.size(); i++){ |
675 |
> |
|
676 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
677 |
> |
|
678 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
679 |
> |
unconsAtoms[j]->addFrc(force); |
680 |
> |
|
681 |
> |
} |
682 |
> |
|
683 |
> |
//modify the velocities of moving z-constrained molecules |
684 |
> |
for(int i = 0; i < zconsMols.size(); i++) { |
685 |
> |
if (states[i] == zcsMoving){ |
686 |
> |
|
687 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
688 |
> |
|
689 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
690 |
> |
movingZAtoms[j]->addFrc(force); |
691 |
> |
} |
692 |
> |
} |
693 |
> |
|
694 |
> |
// apply negative to fixed z-constrained molecues; |
695 |
> |
force[0]= 0; |
696 |
> |
force[1]= 0; |
697 |
> |
force[2]= 0; |
698 |
> |
|
699 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
700 |
> |
|
701 |
> |
if (states[i] == zcsFixed){ |
702 |
> |
|
703 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
704 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
705 |
|
|
706 |
< |
//calculate z constrain force |
707 |
< |
fz[i] = massOfZConsMols[i]* deltaZ / dt2; |
708 |
< |
|
709 |
< |
cout << "\tforce: " << fz[i] << endl; |
706 |
> |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
707 |
> |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
708 |
> |
zconsAtoms[j]->addFrc(force); |
709 |
> |
} |
710 |
> |
|
711 |
> |
} |
712 |
> |
|
713 |
> |
} |
714 |
> |
|
715 |
> |
} |
716 |
> |
|
717 |
> |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
718 |
> |
double COM[3]; |
719 |
> |
double diff; |
720 |
> |
|
721 |
> |
bool changed; |
722 |
> |
|
723 |
> |
changed = false; |
724 |
> |
|
725 |
> |
for(int i =0; i < zconsMols.size(); i++){ |
726 |
> |
|
727 |
> |
zconsMols[i]->getCOM(COM); |
728 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
729 |
> |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
730 |
> |
states[i] = zcsFixed; |
731 |
> |
changed = true; |
732 |
> |
} |
733 |
> |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
734 |
> |
states[i] = zcsMoving; |
735 |
> |
changed = true; |
736 |
> |
} |
737 |
> |
|
738 |
|
} |
739 |
|
|
740 |
< |
|
740 |
> |
return changed; |
741 |
|
} |
742 |
+ |
|
743 |
+ |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
744 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
745 |
+ |
if (states[i] == zcsFixed) |
746 |
+ |
return true; |
747 |
+ |
|
748 |
+ |
return false; |
749 |
+ |
} |
750 |
+ |
|
751 |
+ |
|
752 |
+ |
/** |
753 |
+ |
* |
754 |
+ |
*/ |
755 |
+ |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
756 |
+ |
for(int i = 0; i < zconsMols.size(); i++) |
757 |
+ |
if (states[i] == zcsMoving) |
758 |
+ |
return true; |
759 |
+ |
|
760 |
+ |
return false; |
761 |
+ |
|
762 |
+ |
} |
763 |
+ |
|
764 |
+ |
/** |
765 |
+ |
* |
766 |
+ |
* |
767 |
+ |
*/ |
768 |
+ |
|
769 |
+ |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
770 |
+ |
double force[3]; |
771 |
+ |
double harmonicU; |
772 |
+ |
double COM[3]; |
773 |
+ |
double diff; |
774 |
+ |
|
775 |
+ |
force[0] = 0; |
776 |
+ |
force[1] = 0; |
777 |
+ |
force[2] = 0; |
778 |
+ |
|
779 |
+ |
cout << "Moving Molecules" << endl; |
780 |
+ |
for(int i = 0; i < zconsMols.size(); i++) { |
781 |
+ |
|
782 |
+ |
if (states[i] == zcsMoving){ |
783 |
+ |
zconsMols[i]->getCOM(COM): |
784 |
+ |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
785 |
+ |
|
786 |
+ |
diff = COM[whichDirection] -zPos[i]; |
787 |
+ |
|
788 |
+ |
harmonicU = 0.5 * kz[i] * diff * diff; |
789 |
+ |
info->ltPot += harmonicU; |
790 |
+ |
|
791 |
+ |
force[whichDirection] = - kz[i] * diff / zconsMols[i]->getNAtoms(); |
792 |
+ |
|
793 |
+ |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
794 |
+ |
|
795 |
+ |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
796 |
+ |
movingZAtoms[j]->addFrc(force); |
797 |
+ |
} |
798 |
+ |
|
799 |
+ |
} |
800 |
+ |
|
801 |
+ |
} |