1 |
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#include "Integrator.hpp" |
2 |
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#include "simError.h" |
3 |
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#include <math.h> |
4 |
– |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
– |
: T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL), |
6 |
– |
fzOut(NULL), curZconsTime(0), forcePolicy(NULL) |
7 |
– |
{ |
4 |
|
|
5 |
+ |
const double INFINITE_TIME = 10e30; |
6 |
+ |
template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, |
7 |
+ |
ForceFields* the_ff): T(theInfo, the_ff), |
8 |
+ |
fzOut(NULL), |
9 |
+ |
curZconsTime(0), |
10 |
+ |
forcePolicy(NULL), |
11 |
+ |
usingSMD(false), |
12 |
+ |
hasZConsGap(false){ |
13 |
|
//get properties from SimInfo |
14 |
|
GenericData* data; |
15 |
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ZConsParaData* zConsParaData; |
16 |
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DoubleData* sampleTime; |
17 |
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DoubleData* tolerance; |
18 |
+ |
DoubleData* gap; |
19 |
+ |
DoubleData* fixtime; |
20 |
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StringData* policy; |
21 |
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StringData* filename; |
22 |
+ |
IntData* smdFlag; |
23 |
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double COM[3]; |
24 |
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|
25 |
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//by default, the direction of constraint is z |
30 |
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|
31 |
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//estimate the force constant of harmonical potential |
32 |
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double Kb = 1.986E-3 ; //in kcal/K |
26 |
– |
|
27 |
– |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
– |
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
33 |
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|
34 |
+ |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) / |
35 |
+ |
2; |
36 |
+ |
zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox); |
37 |
+ |
|
38 |
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//creat force Subtraction policy |
39 |
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data = info->getProperty(ZCONSFORCEPOLICY_ID); |
40 |
< |
if(!data){ |
41 |
< |
sprintf( painCave.errMsg, |
42 |
< |
"ZConstraint Warning: User does not set force Subtraction policy, " |
43 |
< |
"PolicyByMass is used\n"); |
40 |
> |
if (!data){ |
41 |
> |
sprintf(painCave.errMsg, |
42 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
43 |
> |
"PolicyByMass is used\n"); |
44 |
|
painCave.isFatal = 0; |
45 |
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simError(); |
46 |
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|
47 |
< |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
47 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
48 |
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} |
49 |
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else{ |
50 |
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policy = dynamic_cast<StringData*>(data); |
51 |
< |
|
52 |
< |
if(!policy){ |
53 |
< |
sprintf( painCave.errMsg, |
54 |
< |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
55 |
< |
"PolicyByMass is used\n"); |
51 |
> |
|
52 |
> |
if (!policy){ |
53 |
> |
sprintf(painCave.errMsg, |
54 |
> |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
55 |
> |
"PolicyByMass is used\n"); |
56 |
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painCave.isFatal = 0; |
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simError(); |
58 |
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|
59 |
< |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
59 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
60 |
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} |
61 |
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else{ |
62 |
< |
if(policy->getData() == "BYNUMBER") |
63 |
< |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
64 |
< |
else if(policy->getData() == "BYMASS") |
65 |
< |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
62 |
> |
if (policy->getData() == "BYNUMBER") |
63 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this); |
64 |
> |
else if (policy->getData() == "BYMASS") |
65 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
66 |
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else{ |
67 |
< |
sprintf( painCave.errMsg, |
68 |
< |
"ZConstraint Warning: unknown force Subtraction policy, " |
69 |
< |
"PolicyByMass is used\n"); |
67 |
> |
sprintf(painCave.errMsg, |
68 |
> |
"ZConstraint Warning: unknown force Subtraction policy, " |
69 |
> |
"PolicyByMass is used\n"); |
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painCave.isFatal = 0; |
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simError(); |
72 |
< |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
73 |
< |
} |
72 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
73 |
> |
} |
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} |
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} |
76 |
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|
77 |
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|
76 |
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|
77 |
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|
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//retrieve sample time of z-contraint |
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data = info->getProperty(ZCONSTIME_ID); |
80 |
< |
|
81 |
< |
if(!data) { |
82 |
< |
|
83 |
< |
sprintf( painCave.errMsg, |
84 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
77 |
< |
" , you must set sample time.\n"); |
80 |
> |
|
81 |
> |
if (!data){ |
82 |
> |
sprintf(painCave.errMsg, |
83 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
84 |
> |
" , you must set sample time.\n"); |
85 |
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painCave.isFatal = 1; |
86 |
< |
simError(); |
86 |
> |
simError(); |
87 |
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} |
88 |
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else{ |
82 |
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|
89 |
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sampleTime = dynamic_cast<DoubleData*>(data); |
84 |
– |
|
85 |
– |
if(!sampleTime){ |
90 |
|
|
91 |
< |
sprintf( painCave.errMsg, |
92 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
91 |
> |
if (!sampleTime){ |
92 |
> |
sprintf(painCave.errMsg, |
93 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
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painCave.isFatal = 1; |
95 |
< |
simError(); |
91 |
< |
|
95 |
> |
simError(); |
96 |
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} |
97 |
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else{ |
98 |
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this->zconsTime = sampleTime->getData(); |
99 |
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} |
96 |
– |
|
100 |
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} |
101 |
< |
|
101 |
> |
|
102 |
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//retrieve output filename of z force |
103 |
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data = info->getProperty(ZCONSFILENAME_ID); |
104 |
< |
if(!data) { |
105 |
< |
|
106 |
< |
|
107 |
< |
sprintf( painCave.errMsg, |
105 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
106 |
< |
" , you must set output filename of z-force.\n"); |
104 |
> |
if (!data){ |
105 |
> |
sprintf(painCave.errMsg, |
106 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
107 |
> |
" , you must set output filename of z-force.\n"); |
108 |
|
painCave.isFatal = 1; |
109 |
< |
simError(); |
109 |
< |
|
109 |
> |
simError(); |
110 |
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} |
111 |
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else{ |
112 |
– |
|
112 |
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filename = dynamic_cast<StringData*>(data); |
114 |
– |
|
115 |
– |
if(!filename){ |
113 |
|
|
114 |
< |
sprintf( painCave.errMsg, |
115 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
114 |
> |
if (!filename){ |
115 |
> |
sprintf(painCave.errMsg, |
116 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
117 |
|
painCave.isFatal = 1; |
118 |
< |
simError(); |
121 |
< |
|
118 |
> |
simError(); |
119 |
|
} |
120 |
|
else{ |
121 |
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this->zconsOutput = filename->getData(); |
122 |
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} |
126 |
– |
|
123 |
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} |
124 |
|
|
125 |
|
//retrieve tolerance for z-constraint molecuels |
126 |
|
data = info->getProperty(ZCONSTOL_ID); |
127 |
< |
|
128 |
< |
if(!data) { |
129 |
< |
|
134 |
< |
sprintf( painCave.errMsg, |
135 |
< |
"ZConstraint error: can not get tolerance \n"); |
127 |
> |
|
128 |
> |
if (!data){ |
129 |
> |
sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n"); |
130 |
|
painCave.isFatal = 1; |
131 |
< |
simError(); |
131 |
> |
simError(); |
132 |
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} |
133 |
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else{ |
140 |
– |
|
134 |
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tolerance = dynamic_cast<DoubleData*>(data); |
142 |
– |
|
143 |
– |
if(!tolerance){ |
135 |
|
|
136 |
< |
sprintf( painCave.errMsg, |
137 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
136 |
> |
if (!tolerance){ |
137 |
> |
sprintf(painCave.errMsg, |
138 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
139 |
|
painCave.isFatal = 1; |
140 |
< |
simError(); |
149 |
< |
|
140 |
> |
simError(); |
141 |
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} |
142 |
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else{ |
143 |
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this->zconsTol = tolerance->getData(); |
144 |
|
} |
145 |
+ |
} |
146 |
|
|
147 |
+ |
//quick hack here |
148 |
+ |
data = info->getProperty(ZCONSGAP_ID); |
149 |
+ |
|
150 |
+ |
if (data){ |
151 |
+ |
gap = dynamic_cast<DoubleData*>(data); |
152 |
+ |
|
153 |
+ |
if (!gap){ |
154 |
+ |
sprintf(painCave.errMsg, |
155 |
+ |
"ZConstraint error: Can not get property from SimInfo\n"); |
156 |
+ |
painCave.isFatal = 1; |
157 |
+ |
simError(); |
158 |
+ |
} |
159 |
+ |
else{ |
160 |
+ |
this->hasZConsGap = true; |
161 |
+ |
this->zconsGap = gap->getData(); |
162 |
+ |
} |
163 |
|
} |
156 |
– |
|
157 |
– |
//retrieve index of z-constraint molecules |
158 |
– |
data = info->getProperty(ZCONSPARADATA_ID); |
159 |
– |
if(!data) { |
164 |
|
|
165 |
< |
sprintf( painCave.errMsg, |
166 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
167 |
< |
" , you must set index of z-constraint molecules.\n"); |
165 |
> |
|
166 |
> |
|
167 |
> |
data = info->getProperty(ZCONSFIXTIME_ID); |
168 |
> |
|
169 |
> |
if (data){ |
170 |
> |
fixtime = dynamic_cast<DoubleData*>(data); |
171 |
> |
if (!fixtime){ |
172 |
> |
sprintf(painCave.errMsg, |
173 |
> |
"ZConstraint error: Can not get zconsFixTime from SimInfo\n"); |
174 |
> |
painCave.isFatal = 1; |
175 |
> |
simError(); |
176 |
> |
} |
177 |
> |
else{ |
178 |
> |
this->zconsFixTime = fixtime->getData(); |
179 |
> |
} |
180 |
> |
} |
181 |
> |
else if(hasZConsGap){ |
182 |
> |
sprintf(painCave.errMsg, |
183 |
> |
"ZConstraint error: must set fixtime if already set zconsGap\n"); |
184 |
> |
painCave.isFatal = 1; |
185 |
> |
simError(); |
186 |
> |
} |
187 |
> |
|
188 |
> |
|
189 |
> |
|
190 |
> |
data = info->getProperty(ZCONSUSINGSMD_ID); |
191 |
> |
|
192 |
> |
if (data){ |
193 |
> |
smdFlag = dynamic_cast<IntData*>(data); |
194 |
> |
|
195 |
> |
if (!smdFlag){ |
196 |
> |
sprintf(painCave.errMsg, |
197 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
198 |
> |
painCave.isFatal = 1; |
199 |
> |
simError(); |
200 |
> |
} |
201 |
> |
else{ |
202 |
> |
this->usingSMD= smdFlag->getData() ? true : false; |
203 |
> |
} |
204 |
> |
|
205 |
> |
} |
206 |
> |
|
207 |
> |
|
208 |
> |
|
209 |
> |
//retrieve index of z-constraint molecules |
210 |
> |
data = info->getProperty(ZCONSPARADATA_ID); |
211 |
> |
if (!data){ |
212 |
> |
sprintf(painCave.errMsg, |
213 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
214 |
> |
" , you must set index of z-constraint molecules.\n"); |
215 |
|
painCave.isFatal = 1; |
216 |
< |
simError(); |
216 |
> |
simError(); |
217 |
|
} |
218 |
|
else{ |
168 |
– |
|
219 |
|
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
170 |
– |
|
171 |
– |
if(!zConsParaData){ |
220 |
|
|
221 |
< |
sprintf( painCave.errMsg, |
222 |
< |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
221 |
> |
if (!zConsParaData){ |
222 |
> |
sprintf(painCave.errMsg, |
223 |
> |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
224 |
|
painCave.isFatal = 1; |
225 |
< |
simError(); |
177 |
< |
|
225 |
> |
simError(); |
226 |
|
} |
227 |
|
else{ |
180 |
– |
|
228 |
|
parameters = zConsParaData->getData(); |
229 |
|
|
230 |
|
//check the range of zconsIndex |
236 |
|
int totalNumMol; |
237 |
|
|
238 |
|
minIndex = (*parameters)[0].zconsIndex; |
239 |
< |
if(minIndex < 0){ |
240 |
< |
sprintf( painCave.errMsg, |
194 |
< |
"ZConstraint error: index is out of range\n"); |
239 |
> |
if (minIndex < 0){ |
240 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
241 |
|
painCave.isFatal = 1; |
242 |
< |
simError(); |
243 |
< |
} |
242 |
> |
simError(); |
243 |
> |
} |
244 |
|
|
245 |
|
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
246 |
|
|
247 |
|
#ifndef IS_MPI |
248 |
|
totalNumMol = nMols; |
249 |
|
#else |
250 |
< |
totalNumMol = mpiSim->getTotNmol(); |
250 |
> |
totalNumMol = mpiSim->getNMolGlobal(); |
251 |
|
#endif |
252 |
< |
|
253 |
< |
if(maxIndex > totalNumMol - 1){ |
254 |
< |
sprintf( painCave.errMsg, |
209 |
< |
"ZConstraint error: index is out of range\n"); |
252 |
> |
|
253 |
> |
if (maxIndex > totalNumMol - 1){ |
254 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
255 |
|
painCave.isFatal = 1; |
256 |
< |
simError(); |
256 |
> |
simError(); |
257 |
|
} |
258 |
|
|
259 |
|
//if user does not specify the zpos for the zconstraint molecule |
260 |
|
//its initial z coordinate will be used as default |
261 |
< |
for(int i = 0; i < (int)(parameters->size()); i++){ |
262 |
< |
|
218 |
< |
if(!(*parameters)[i].havingZPos){ |
261 |
> |
for (int i = 0; i < (int) (parameters->size()); i++){ |
262 |
> |
if (!(*parameters)[i].havingZPos){ |
263 |
|
#ifndef IS_MPI |
264 |
< |
for(int j = 0; j < nMols; j++){ |
264 |
> |
for (int j = 0; j < nMols; j++){ |
265 |
|
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
266 |
|
molecules[j].getCOM(COM); |
267 |
< |
break; |
267 |
> |
break; |
268 |
|
} |
269 |
|
} |
270 |
|
#else |
271 |
< |
//query which processor current zconstraint molecule belongs to |
272 |
< |
int *MolToProcMap; |
271 |
> |
//query which processor current zconstraint molecule belongs to |
272 |
> |
int* MolToProcMap; |
273 |
|
int whichNode; |
274 |
< |
|
274 |
> |
|
275 |
|
MolToProcMap = mpiSim->getMolToProcMap(); |
276 |
|
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
277 |
< |
|
277 |
> |
|
278 |
|
//broadcast the zpos of current z-contraint molecule |
279 |
|
//the node which contain this |
280 |
< |
|
281 |
< |
if (worldRank == whichNode ){ |
282 |
< |
|
239 |
< |
for(int j = 0; j < nMols; j++) |
280 |
> |
|
281 |
> |
if (worldRank == whichNode){ |
282 |
> |
for (int j = 0; j < nMols; j++) |
283 |
|
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
284 |
|
molecules[j].getCOM(COM); |
285 |
< |
break; |
285 |
> |
break; |
286 |
|
} |
244 |
– |
|
287 |
|
} |
288 |
|
|
289 |
< |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, MPI_COMM_WORLD); |
289 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, |
290 |
> |
MPI_COMM_WORLD); |
291 |
|
#endif |
292 |
< |
|
292 |
> |
|
293 |
|
(*parameters)[i].zPos = COM[whichDirection]; |
294 |
|
|
295 |
< |
sprintf( painCave.errMsg, |
296 |
< |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
297 |
< |
"initial z coornidate will be used \n"); |
298 |
< |
painCave.isFatal = 0; |
299 |
< |
simError(); |
300 |
< |
|
258 |
< |
} |
295 |
> |
sprintf(painCave.errMsg, |
296 |
> |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
297 |
> |
"initial z coornidate will be used \n"); |
298 |
> |
painCave.isFatal = 0; |
299 |
> |
simError(); |
300 |
> |
} |
301 |
|
} |
260 |
– |
|
302 |
|
}//end if (!zConsParaData) |
303 |
+ |
|
304 |
|
}//end if (!data) |
305 |
< |
|
306 |
< |
// |
305 |
> |
|
306 |
> |
// |
307 |
|
#ifdef IS_MPI |
308 |
|
update(); |
309 |
|
#else |
310 |
|
int searchResult; |
311 |
< |
|
312 |
< |
for(int i = 0; i < nMols; i++){ |
271 |
< |
|
311 |
> |
|
312 |
> |
for (int i = 0; i < nMols; i++){ |
313 |
|
searchResult = isZConstraintMol(&molecules[i]); |
314 |
< |
|
315 |
< |
if(searchResult > -1){ |
275 |
< |
|
314 |
> |
|
315 |
> |
if (searchResult > -1){ |
316 |
|
zconsMols.push_back(&molecules[i]); |
317 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
318 |
|
|
319 |
|
zPos.push_back((*parameters)[searchResult].zPos); |
280 |
– |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
– |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 |
– |
|
320 |
|
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
321 |
< |
molecules[i].getCOM(COM); |
321 |
> |
|
322 |
> |
if(usingSMD) |
323 |
> |
cantVel.push_back((*parameters)[searchResult].cantVel); |
324 |
> |
|
325 |
|
} |
326 |
< |
else |
287 |
< |
{ |
288 |
< |
|
326 |
> |
else{ |
327 |
|
unconsMols.push_back(&molecules[i]); |
328 |
|
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
291 |
– |
|
329 |
|
} |
330 |
|
} |
331 |
|
|
332 |
< |
fz = new double[zconsMols.size()]; |
333 |
< |
curZPos = new double[zconsMols.size()]; |
334 |
< |
indexOfZConsMols = new int [zconsMols.size()]; |
332 |
> |
fz.resize(zconsMols.size()); |
333 |
> |
curZPos.resize(zconsMols.size()); |
334 |
> |
indexOfZConsMols.resize(zconsMols.size()); |
335 |
|
|
299 |
– |
if(!fz || !curZPos || !indexOfZConsMols){ |
300 |
– |
sprintf( painCave.errMsg, |
301 |
– |
"Memory allocation failure in class Zconstraint\n"); |
302 |
– |
painCave.isFatal = 1; |
303 |
– |
simError(); |
304 |
– |
} |
305 |
– |
|
336 |
|
//determine the states of z-constraint molecules |
337 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
337 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
338 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
339 |
|
|
340 |
|
zconsMols[i]->getCOM(COM); |
341 |
< |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
341 |
> |
|
342 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
343 |
|
states.push_back(zcsFixed); |
344 |
< |
else |
344 |
> |
|
345 |
> |
if (hasZConsGap) |
346 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
347 |
> |
} |
348 |
> |
else{ |
349 |
|
states.push_back(zcsMoving); |
350 |
+ |
|
351 |
+ |
if (hasZConsGap) |
352 |
+ |
endFixTime.push_back(INFINITE_TIME); |
353 |
+ |
} |
354 |
+ |
|
355 |
+ |
if(usingSMD) |
356 |
+ |
cantPos.push_back(COM[whichDirection]); |
357 |
|
} |
358 |
< |
|
358 |
> |
|
359 |
> |
if(usingSMD) |
360 |
> |
prevCantPos = cantPos; |
361 |
|
#endif |
362 |
|
|
363 |
+ |
|
364 |
|
//get total masss of unconstraint molecules |
365 |
|
double totalMassOfUncons_local; |
366 |
|
totalMassOfUncons_local = 0; |
367 |
< |
|
368 |
< |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
367 |
> |
|
368 |
> |
for (size_t i = 0; i < unconsMols.size(); i++) |
369 |
|
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
370 |
< |
|
370 |
> |
|
371 |
|
#ifndef IS_MPI |
372 |
|
totalMassOfUncons = totalMassOfUncons_local; |
373 |
|
#else |
374 |
< |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
375 |
< |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
374 |
> |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, |
375 |
> |
MPI_SUM, MPI_COMM_WORLD); |
376 |
|
#endif |
377 |
|
|
378 |
|
//get total number of unconstrained atoms |
379 |
|
int nUnconsAtoms_local; |
380 |
|
nUnconsAtoms_local = 0; |
381 |
< |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
381 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++) |
382 |
|
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
383 |
< |
|
383 |
> |
|
384 |
|
#ifndef IS_MPI |
385 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
386 |
|
#else |
387 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
388 |
< |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
387 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM, |
388 |
> |
MPI_COMM_WORLD); |
389 |
|
#endif |
390 |
|
|
391 |
|
forcePolicy->update(); |
392 |
|
} |
393 |
|
|
394 |
< |
template<typename T> ZConstraint<T>::~ZConstraint() |
350 |
< |
{ |
351 |
< |
if(fz) |
352 |
< |
delete[] fz; |
394 |
> |
template<typename T> ZConstraint<T>::~ZConstraint(){ |
395 |
|
|
396 |
< |
if(curZPos) |
355 |
< |
delete[] curZPos; |
356 |
< |
|
357 |
< |
if(indexOfZConsMols) |
358 |
< |
delete[] indexOfZConsMols; |
359 |
< |
|
360 |
< |
if(fzOut) |
396 |
> |
if (fzOut){ |
397 |
|
delete fzOut; |
398 |
< |
|
399 |
< |
if(forcePolicy) |
398 |
> |
} |
399 |
> |
|
400 |
> |
if (forcePolicy){ |
401 |
|
delete forcePolicy; |
402 |
+ |
} |
403 |
|
} |
404 |
|
|
405 |
|
|
408 |
|
*/ |
409 |
|
|
410 |
|
#ifdef IS_MPI |
411 |
< |
template<typename T> void ZConstraint<T>::update() |
374 |
< |
{ |
411 |
> |
template<typename T> void ZConstraint<T>::update(){ |
412 |
|
double COM[3]; |
413 |
|
int index; |
414 |
< |
|
414 |
> |
|
415 |
|
zconsMols.clear(); |
416 |
|
massOfZConsMols.clear(); |
417 |
|
zPos.clear(); |
418 |
|
kz.clear(); |
419 |
< |
|
419 |
> |
cantPos.clear(); |
420 |
> |
cantVel.clear(); |
421 |
> |
|
422 |
|
unconsMols.clear(); |
423 |
|
massOfUnconsMols.clear(); |
385 |
– |
|
424 |
|
|
425 |
+ |
|
426 |
|
//creat zconsMol and unconsMol lists |
427 |
< |
for(int i = 0; i < nMols; i++){ |
389 |
< |
|
427 |
> |
for (int i = 0; i < nMols; i++){ |
428 |
|
index = isZConstraintMol(&molecules[i]); |
429 |
< |
|
430 |
< |
if(index > -1){ |
393 |
< |
|
429 |
> |
|
430 |
> |
if (index > -1){ |
431 |
|
zconsMols.push_back(&molecules[i]); |
432 |
|
zPos.push_back((*parameters)[index].zPos); |
433 |
|
kz.push_back((*parameters)[index].kRatio * zForceConst); |
434 |
< |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
435 |
< |
|
436 |
< |
molecules[i].getCOM(COM); |
434 |
> |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
435 |
> |
|
436 |
> |
if(usingSMD) |
437 |
> |
cantVel.push_back((*parameters)[index].cantVel); |
438 |
> |
|
439 |
|
} |
440 |
< |
else |
402 |
< |
{ |
403 |
< |
|
440 |
> |
else{ |
441 |
|
unconsMols.push_back(&molecules[i]); |
442 |
|
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
406 |
– |
|
443 |
|
} |
444 |
|
} |
445 |
|
|
446 |
< |
//determine the states of z-constraint molecules |
447 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
448 |
< |
zconsMols[i]->getCOM(COM); |
449 |
< |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
450 |
< |
states.push_back(zcsFixed); |
451 |
< |
else |
416 |
< |
states.push_back(zcsMoving); |
446 |
> |
fz.resize(zconsMols.size()); |
447 |
> |
curZPos.resize(zconsMols.size()); |
448 |
> |
indexOfZConsMols.resize(zconsMols.size()); |
449 |
> |
|
450 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
451 |
> |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
452 |
|
} |
453 |
+ |
|
454 |
+ |
//determine the states of z-constraint molecules |
455 |
+ |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
456 |
|
|
457 |
+ |
zconsMols[i]->getCOM(COM); |
458 |
|
|
459 |
< |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
460 |
< |
// that we want to make the MPI communication simple |
461 |
< |
if(fz) |
462 |
< |
delete[] fz; |
463 |
< |
|
425 |
< |
if(curZPos) |
426 |
< |
delete[] curZPos; |
427 |
< |
|
428 |
< |
if(indexOfZConsMols) |
429 |
< |
delete[] indexOfZConsMols; |
430 |
< |
|
431 |
< |
if (zconsMols.size() > 0){ |
432 |
< |
fz = new double[zconsMols.size()]; |
433 |
< |
curZPos = new double[zconsMols.size()]; |
434 |
< |
indexOfZConsMols = new int[zconsMols.size()]; |
435 |
< |
|
436 |
< |
if(!fz || !curZPos || !indexOfZConsMols){ |
437 |
< |
sprintf( painCave.errMsg, |
438 |
< |
"Memory allocation failure in class Zconstraint\n"); |
439 |
< |
painCave.isFatal = 1; |
440 |
< |
simError(); |
459 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
460 |
> |
states.push_back(zcsFixed); |
461 |
> |
|
462 |
> |
if (hasZConsGap) |
463 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
464 |
|
} |
465 |
< |
|
466 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
467 |
< |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
465 |
> |
else{ |
466 |
> |
states.push_back(zcsMoving); |
467 |
> |
|
468 |
> |
if (hasZConsGap) |
469 |
> |
endFixTime.push_back(INFINITE_TIME); |
470 |
|
} |
471 |
|
|
472 |
< |
} |
473 |
< |
else{ |
474 |
< |
fz = NULL; |
475 |
< |
curZPos = NULL; |
476 |
< |
indexOfZConsMols = NULL; |
477 |
< |
} |
478 |
< |
|
472 |
> |
if(usingSMD) |
473 |
> |
cantPos.push_back(COM[whichDirection]); |
474 |
> |
} |
475 |
> |
|
476 |
> |
if(usingSMD) |
477 |
> |
prevCantPos = cantPos; |
478 |
> |
|
479 |
|
// |
480 |
|
forcePolicy->update(); |
456 |
– |
|
481 |
|
} |
482 |
|
|
483 |
|
#endif |
491 |
|
* other non-negative values, its index in indexOfAllZConsMols vector |
492 |
|
*/ |
493 |
|
|
494 |
< |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
471 |
< |
{ |
494 |
> |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){ |
495 |
|
int index; |
496 |
|
int low; |
497 |
|
int high; |
498 |
|
int mid; |
499 |
|
|
500 |
|
index = mol->getGlobalIndex(); |
501 |
< |
|
501 |
> |
|
502 |
|
low = 0; |
503 |
|
high = parameters->size() - 1; |
504 |
< |
|
504 |
> |
|
505 |
|
//Binary Search (we have sorted the array) |
506 |
< |
while(low <= high){ |
507 |
< |
mid = (low + high) /2; |
506 |
> |
while (low <= high){ |
507 |
> |
mid = (low + high) / 2; |
508 |
|
if ((*parameters)[mid].zconsIndex == index) |
509 |
|
return mid; |
510 |
< |
else if ((*parameters)[mid].zconsIndex > index ) |
511 |
< |
high = mid -1; |
512 |
< |
else |
513 |
< |
low = mid + 1; |
510 |
> |
else if ((*parameters)[mid].zconsIndex > index) |
511 |
> |
high = mid - 1; |
512 |
> |
else |
513 |
> |
low = mid + 1; |
514 |
|
} |
515 |
< |
|
515 |
> |
|
516 |
|
return -1; |
517 |
|
} |
518 |
|
|
519 |
|
template<typename T> void ZConstraint<T>::integrate(){ |
497 |
– |
|
520 |
|
// creat zconsWriter |
521 |
|
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
522 |
< |
|
523 |
< |
if(!fzOut){ |
524 |
< |
sprintf( painCave.errMsg, |
503 |
< |
"Memory allocation failure in class Zconstraint\n"); |
522 |
> |
|
523 |
> |
if (!fzOut){ |
524 |
> |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
525 |
|
painCave.isFatal = 1; |
526 |
|
simError(); |
527 |
|
} |
528 |
< |
|
528 |
> |
|
529 |
|
//zero out the velocities of center of mass of unconstrained molecules |
530 |
|
//and the velocities of center of mass of every single z-constrained molecueles |
531 |
|
zeroOutVel(); |
532 |
|
|
533 |
|
curZconsTime = zconsTime + info->getTime(); |
513 |
– |
|
514 |
– |
T::integrate(); |
534 |
|
|
535 |
+ |
T::integrate(); |
536 |
|
} |
517 |
– |
|
537 |
|
|
538 |
+ |
|
539 |
|
/** |
540 |
|
* |
541 |
|
* |
550 |
|
|
551 |
|
T::calcForce(calcPot, calcStress); |
552 |
|
|
553 |
< |
if (checkZConsState()){ |
553 |
> |
|
554 |
> |
if (hasZConsGap){ |
555 |
> |
updateZPos(); |
556 |
> |
} |
557 |
> |
|
558 |
> |
if (checkZConsState()){ |
559 |
|
zeroOutVel(); |
560 |
|
forcePolicy->update(); |
561 |
|
} |
562 |
< |
|
562 |
> |
|
563 |
|
zsys = calcZSys(); |
564 |
|
zSysCOMVel = calcSysCOMVel(); |
565 |
|
#ifdef IS_MPI |
566 |
< |
if(worldRank == 0){ |
566 |
> |
if (worldRank == 0){ |
567 |
|
#endif |
568 |
< |
//cout << "---------------------------------------------------------------------" <<endl; |
569 |
< |
//cout << "current time: " << info->getTime() << endl; |
570 |
< |
//cout << "center of mass at z: " << zsys << endl; |
571 |
< |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
568 |
> |
//cout << "---------------------------------------------------------------------" <<endl; |
569 |
> |
//cout << "current time: " << info->getTime() << endl; |
570 |
> |
//cout << "center of mass at z: " << zsys << endl; |
571 |
> |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
572 |
|
|
573 |
|
#ifdef IS_MPI |
574 |
|
} |
575 |
|
#endif |
576 |
|
|
577 |
|
//do zconstraint force; |
578 |
< |
if (haveFixedZMols()) |
578 |
> |
if (haveFixedZMols()){ |
579 |
|
this->doZconstraintForce(); |
580 |
+ |
} |
581 |
|
|
582 |
< |
//use harmonical poteintial to move the molecules to the specified positions |
583 |
< |
if (haveMovingZMols()) |
584 |
< |
this->doHarmonic(); |
582 |
> |
//use external force to move the molecules to the specified positions |
583 |
> |
if (haveMovingZMols()){ |
584 |
> |
if (usingSMD) |
585 |
> |
this->doHarmonic(cantPos); |
586 |
> |
else |
587 |
> |
this->doHarmonic(zPos); |
588 |
> |
} |
589 |
|
|
590 |
|
//write out forces and current positions of z-constraint molecules |
591 |
< |
if(info->getTime() >= curZconsTime){ |
592 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
591 |
> |
if (info->getTime() >= curZconsTime){ |
592 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
593 |
|
zconsMols[i]->getCOM(COM); |
594 |
< |
curZPos[i] = COM[whichDirection]; |
594 |
> |
curZPos[i] = COM[whichDirection]; |
595 |
|
|
596 |
< |
//if the z-constraint molecule is still moving, just record its force |
597 |
< |
if(states[i] == zcsMoving){ |
598 |
< |
fz[i] = 0; |
599 |
< |
Atom** movingZAtoms; |
600 |
< |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
601 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
602 |
< |
movingZAtoms[j]->getFrc(force); |
603 |
< |
fz[i] += force[whichDirection]; |
596 |
> |
//if the z-constraint molecule is still moving, just record its force |
597 |
> |
if (states[i] == zcsMoving){ |
598 |
> |
fz[i] = 0; |
599 |
> |
Atom** movingZAtoms; |
600 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
601 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
602 |
> |
movingZAtoms[j]->getFrc(force); |
603 |
> |
fz[i] += force[whichDirection]; |
604 |
> |
} |
605 |
|
} |
606 |
< |
} |
607 |
< |
} |
608 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
609 |
< |
curZconsTime += zconsTime; |
606 |
> |
} |
607 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0], |
608 |
> |
&curZPos[0], &zPos[0]); |
609 |
> |
curZconsTime += zconsTime; |
610 |
|
} |
611 |
|
|
612 |
|
zSysCOMVel = calcSysCOMVel(); |
613 |
|
#ifdef IS_MPI |
614 |
< |
if(worldRank == 0){ |
614 |
> |
if (worldRank == 0){ |
615 |
|
#endif |
616 |
< |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
616 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
617 |
|
#ifdef IS_MPI |
618 |
|
} |
619 |
|
#endif |
623 |
|
/** |
624 |
|
* |
625 |
|
*/ |
626 |
< |
|
627 |
< |
template<typename T> double ZConstraint<T>::calcZSys() |
597 |
< |
{ |
626 |
> |
|
627 |
> |
template<typename T> double ZConstraint<T>::calcZSys(){ |
628 |
|
//calculate reference z coordinate for z-constraint molecules |
629 |
|
double totalMass_local; |
630 |
|
double totalMass; |
632 |
|
double totalMZ; |
633 |
|
double massOfCurMol; |
634 |
|
double COM[3]; |
635 |
< |
|
635 |
> |
|
636 |
|
totalMass_local = 0; |
637 |
|
totalMZ_local = 0; |
638 |
< |
|
639 |
< |
for(int i = 0; i < nMols; i++){ |
638 |
> |
|
639 |
> |
for (int i = 0; i < nMols; i++){ |
640 |
|
massOfCurMol = molecules[i].getTotalMass(); |
641 |
|
molecules[i].getCOM(COM); |
642 |
< |
|
642 |
> |
|
643 |
|
totalMass_local += massOfCurMol; |
644 |
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
615 |
– |
|
645 |
|
} |
646 |
< |
|
647 |
< |
|
646 |
> |
|
647 |
> |
|
648 |
|
#ifdef IS_MPI |
649 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
650 |
< |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
651 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
652 |
< |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
624 |
< |
#else |
649 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, |
650 |
> |
MPI_COMM_WORLD); |
651 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
652 |
> |
#else |
653 |
|
totalMass = totalMass_local; |
654 |
|
totalMZ = totalMZ_local; |
655 |
< |
#endif |
655 |
> |
#endif |
656 |
|
|
657 |
|
double zsys; |
658 |
|
zsys = totalMZ / totalMass; |
663 |
|
/** |
664 |
|
* |
665 |
|
*/ |
666 |
< |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
639 |
< |
|
666 |
> |
template<typename T> void ZConstraint<T>::thermalize(void){ |
667 |
|
T::thermalize(); |
668 |
|
zeroOutVel(); |
669 |
|
} |
673 |
|
*/ |
674 |
|
|
675 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
649 |
– |
|
676 |
|
Atom** fixedZAtoms; |
677 |
|
double COMvel[3]; |
678 |
|
double vel[3]; |
679 |
|
double zSysCOMVel; |
680 |
|
|
681 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
656 |
– |
|
657 |
– |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
682 |
|
|
683 |
< |
if (states[i] == zcsFixed){ |
683 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
684 |
> |
if (states[i] == zcsFixed){ |
685 |
> |
zconsMols[i]->getCOMvel(COMvel); |
686 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
687 |
|
|
661 |
– |
zconsMols[i]->getCOMvel(COMvel); |
662 |
– |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 |
– |
|
688 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
689 |
< |
|
690 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
689 |
> |
|
690 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
691 |
|
fixedZAtoms[j]->getVel(vel); |
692 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
693 |
< |
fixedZAtoms[j]->setVel(vel); |
692 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
693 |
> |
fixedZAtoms[j]->setVel(vel); |
694 |
|
} |
695 |
|
|
696 |
< |
zconsMols[i]->getCOMvel(COMvel); |
697 |
< |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
696 |
> |
zconsMols[i]->getCOMvel(COMvel); |
697 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
698 |
|
} |
675 |
– |
|
699 |
|
} |
700 |
|
|
701 |
< |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
701 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
702 |
|
|
703 |
|
zSysCOMVel = calcSysCOMVel(); |
704 |
|
#ifdef IS_MPI |
705 |
< |
if(worldRank == 0){ |
705 |
> |
if (worldRank == 0){ |
706 |
|
#endif |
707 |
< |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
707 |
> |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
708 |
|
#ifdef IS_MPI |
709 |
|
} |
710 |
|
#endif |
711 |
< |
|
711 |
> |
|
712 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
713 |
|
double MVzOfMovingMols_local; |
714 |
|
double MVzOfMovingMols; |
715 |
|
double totalMassOfMovingZMols_local; |
716 |
|
double totalMassOfMovingZMols; |
717 |
< |
|
717 |
> |
|
718 |
|
MVzOfMovingMols_local = 0; |
719 |
|
totalMassOfMovingZMols_local = 0; |
720 |
|
|
721 |
< |
for(int i =0; i < (int)(unconsMols.size()); i++){ |
721 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
722 |
|
unconsMols[i]->getCOMvel(COMvel); |
723 |
< |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
723 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
724 |
|
} |
725 |
|
|
726 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
726 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
727 |
|
if (states[i] == zcsMoving){ |
728 |
|
zconsMols[i]->getCOMvel(COMvel); |
729 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
730 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
730 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
731 |
|
} |
709 |
– |
|
732 |
|
} |
733 |
|
|
734 |
|
#ifndef IS_MPI |
735 |
|
MVzOfMovingMols = MVzOfMovingMols_local; |
736 |
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
737 |
|
#else |
738 |
< |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
739 |
< |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
738 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
739 |
> |
MPI_SUM, MPI_COMM_WORLD); |
740 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
741 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
742 |
|
#endif |
743 |
|
|
744 |
|
double vzOfMovingMols; |
745 |
< |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
745 |
> |
vzOfMovingMols = MVzOfMovingMols / |
746 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
747 |
|
|
748 |
|
//modify the velocites of unconstrained molecules |
749 |
|
Atom** unconsAtoms; |
750 |
< |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
726 |
< |
|
750 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
751 |
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
752 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
752 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
753 |
|
unconsAtoms[j]->getVel(vel); |
754 |
|
vel[whichDirection] -= vzOfMovingMols; |
755 |
|
unconsAtoms[j]->setVel(vel); |
756 |
|
} |
733 |
– |
|
757 |
|
} |
758 |
|
|
759 |
|
//modify the velocities of moving z-constrained molecuels |
760 |
|
Atom** movingZAtoms; |
761 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
762 |
< |
|
740 |
< |
if (states[i] ==zcsMoving){ |
741 |
< |
|
761 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
762 |
> |
if (states[i] == zcsMoving){ |
763 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
764 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
764 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
765 |
|
movingZAtoms[j]->getVel(vel); |
766 |
|
vel[whichDirection] -= vzOfMovingMols; |
767 |
< |
movingZAtoms[j]->setVel(vel); |
767 |
> |
movingZAtoms[j]->setVel(vel); |
768 |
> |
} |
769 |
|
} |
770 |
< |
|
749 |
< |
} |
770 |
> |
} |
771 |
|
|
751 |
– |
} |
772 |
|
|
753 |
– |
|
773 |
|
zSysCOMVel = calcSysCOMVel(); |
774 |
|
#ifdef IS_MPI |
775 |
< |
if(worldRank == 0){ |
775 |
> |
if (worldRank == 0){ |
776 |
|
#endif |
777 |
< |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
777 |
> |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
778 |
|
#ifdef IS_MPI |
779 |
|
} |
780 |
|
#endif |
762 |
– |
|
781 |
|
} |
782 |
|
|
783 |
|
/** |
785 |
|
*/ |
786 |
|
|
787 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
770 |
– |
|
788 |
|
Atom** zconsAtoms; |
789 |
|
double totalFZ; |
790 |
|
double totalFZ_local; |
792 |
|
double force[3]; |
793 |
|
|
794 |
|
//constrain the molecules which do not reach the specified positions |
795 |
< |
|
795 |
> |
|
796 |
|
//Zero Out the force of z-contrained molecules |
797 |
|
totalFZ_local = 0; |
798 |
|
|
799 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
800 |
< |
|
800 |
> |
|
801 |
|
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
802 |
|
// << "total force is " << calcTotalForce() << endl; |
803 |
|
|
804 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 |
< |
|
804 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
805 |
|
if (states[i] == zcsFixed){ |
790 |
– |
|
806 |
|
zconsMols[i]->getCOM(COM); |
807 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
808 |
|
|
809 |
|
fz[i] = 0; |
810 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
810 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
811 |
|
zconsAtoms[j]->getFrc(force); |
812 |
< |
fz[i] += force[whichDirection]; |
812 |
> |
fz[i] += force[whichDirection]; |
813 |
|
} |
814 |
|
totalFZ_local += fz[i]; |
815 |
|
|
816 |
|
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
817 |
|
// <<"\tcurrent zpos: " << COM[whichDirection] |
818 |
|
// << "\tcurrent fz: " <<fz[i] << endl; |
804 |
– |
|
805 |
– |
|
819 |
|
} |
807 |
– |
|
820 |
|
} |
821 |
|
|
822 |
|
//calculate total z-constraint force |
823 |
|
#ifdef IS_MPI |
824 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
824 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
825 |
|
#else |
826 |
|
totalFZ = totalFZ_local; |
827 |
|
#endif |
828 |
|
|
829 |
< |
|
829 |
> |
|
830 |
|
// apply negative to fixed z-constrained molecues; |
831 |
< |
force[0]= 0; |
832 |
< |
force[1]= 0; |
833 |
< |
force[2]= 0; |
831 |
> |
force[0] = 0; |
832 |
> |
force[1] = 0; |
833 |
> |
force[2] = 0; |
834 |
|
|
835 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
836 |
< |
|
825 |
< |
if (states[i] == zcsFixed){ |
826 |
< |
|
835 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
836 |
> |
if (states[i] == zcsFixed){ |
837 |
|
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
838 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
839 |
< |
|
840 |
< |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
839 |
> |
|
840 |
> |
for (int j = 0; j < nAtomOfCurZConsMol; j++){ |
841 |
|
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
842 |
< |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
842 |
> |
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i], |
843 |
> |
zconsAtoms[j], |
844 |
> |
fz[i]); |
845 |
|
zconsAtoms[j]->addFrc(force); |
846 |
|
} |
835 |
– |
|
847 |
|
} |
837 |
– |
|
848 |
|
} |
849 |
|
|
850 |
|
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
851 |
|
// << "total force is " << calcTotalForce() << endl; |
842 |
– |
|
852 |
|
|
844 |
– |
force[0]= 0; |
845 |
– |
force[1]= 0; |
846 |
– |
force[2]= 0; |
853 |
|
|
854 |
+ |
force[0] = 0; |
855 |
+ |
force[1] = 0; |
856 |
+ |
force[2] = 0; |
857 |
+ |
|
858 |
|
//modify the forces of unconstrained molecules |
859 |
< |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
860 |
< |
|
861 |
< |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
862 |
< |
|
863 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
864 |
< |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
865 |
< |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
866 |
< |
unconsAtoms[j]->addFrc(force); |
867 |
< |
} |
858 |
< |
|
859 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
860 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
861 |
> |
|
862 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
863 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
864 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j], |
865 |
> |
totalFZ); |
866 |
> |
unconsAtoms[j]->addFrc(force); |
867 |
> |
} |
868 |
|
} |
869 |
|
|
870 |
< |
//modify the forces of moving z-constrained molecules |
871 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
870 |
> |
//modify the forces of moving z-constrained molecules |
871 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
872 |
|
if (states[i] == zcsMoving){ |
864 |
– |
|
873 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
874 |
|
|
875 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
875 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
876 |
|
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
877 |
< |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
877 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j], |
878 |
> |
totalFZ); |
879 |
|
movingZAtoms[j]->addFrc(force); |
880 |
|
} |
881 |
|
} |
882 |
|
} |
883 |
< |
// cout << "after substracting z-constraint force from moving molecuels " |
884 |
< |
// << "total force is " << calcTotalForce() << endl; |
876 |
< |
|
883 |
> |
// cout << "after substracting z-constraint force from moving molecuels " |
884 |
> |
// << "total force is " << calcTotalForce() << endl; |
885 |
|
} |
886 |
|
|
887 |
|
/** |
889 |
|
* |
890 |
|
*/ |
891 |
|
|
892 |
< |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
892 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){ |
893 |
|
double force[3]; |
894 |
|
double harmonicU; |
895 |
|
double harmonicF; |
897 |
|
double diff; |
898 |
|
double totalFZ_local; |
899 |
|
double totalFZ; |
900 |
< |
|
900 |
> |
|
901 |
|
force[0] = 0; |
902 |
|
force[1] = 0; |
903 |
|
force[2] = 0; |
904 |
|
|
905 |
|
totalFZ_local = 0; |
906 |
|
|
907 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
900 |
< |
|
907 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
908 |
|
if (states[i] == zcsMoving){ |
909 |
|
zconsMols[i]->getCOM(COM); |
910 |
< |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
911 |
< |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
910 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
911 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
912 |
|
|
913 |
< |
diff = COM[whichDirection] -zPos[i]; |
914 |
< |
|
913 |
> |
diff = COM[whichDirection] - resPos[i]; |
914 |
> |
|
915 |
|
harmonicU = 0.5 * kz[i] * diff * diff; |
916 |
|
info->lrPot += harmonicU; |
917 |
|
|
918 |
< |
harmonicF = - kz[i] * diff; |
918 |
> |
harmonicF = -kz[i] * diff; |
919 |
|
totalFZ_local += harmonicF; |
920 |
|
|
921 |
< |
//adjust force |
922 |
< |
|
921 |
> |
//adjust force |
922 |
> |
|
923 |
|
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
924 |
|
|
925 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
925 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
926 |
|
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
927 |
< |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
928 |
< |
movingZAtoms[j]->addFrc(force); |
929 |
< |
} |
927 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], |
928 |
> |
movingZAtoms[j], |
929 |
> |
harmonicF); |
930 |
> |
movingZAtoms[j]->addFrc(force); |
931 |
> |
} |
932 |
|
} |
924 |
– |
|
933 |
|
} |
934 |
|
|
935 |
|
#ifndef IS_MPI |
936 |
|
totalFZ = totalFZ_local; |
937 |
|
#else |
938 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
938 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
939 |
|
#endif |
940 |
|
|
941 |
|
//cout << "before substracting harmonic force from moving molecuels " |
942 |
|
// << "total force is " << calcTotalForce() << endl; |
943 |
|
|
944 |
< |
force[0]= 0; |
945 |
< |
force[1]= 0; |
946 |
< |
force[2]= 0; |
944 |
> |
force[0] = 0; |
945 |
> |
force[1] = 0; |
946 |
> |
force[2] = 0; |
947 |
|
|
948 |
|
//modify the forces of unconstrained molecules |
949 |
< |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
950 |
< |
|
951 |
< |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
952 |
< |
|
953 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
954 |
< |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
955 |
< |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
956 |
< |
unconsAtoms[j]->addFrc(force); |
957 |
< |
} |
949 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
950 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
951 |
> |
|
952 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
953 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
954 |
> |
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j], |
955 |
> |
totalFZ); |
956 |
> |
unconsAtoms[j]->addFrc(force); |
957 |
> |
} |
958 |
|
} |
959 |
|
|
960 |
|
//cout << "after substracting harmonic force from moving molecuels " |
961 |
|
// << "total force is " << calcTotalForce() << endl; |
954 |
– |
|
962 |
|
} |
963 |
|
|
964 |
|
/** |
968 |
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
969 |
|
double COM[3]; |
970 |
|
double diff; |
971 |
< |
|
971 |
> |
|
972 |
|
int changed_local; |
973 |
|
int changed; |
974 |
< |
|
974 |
> |
|
975 |
|
changed_local = 0; |
969 |
– |
|
970 |
– |
for(int i =0; i < (int)(zconsMols.size()); i++){ |
976 |
|
|
977 |
+ |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
978 |
|
zconsMols[i]->getCOM(COM); |
979 |
|
diff = fabs(COM[whichDirection] - zPos[i]); |
980 |
< |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
980 |
> |
if (diff <= zconsTol && states[i] == zcsMoving){ |
981 |
|
states[i] = zcsFixed; |
982 |
< |
changed_local = 1; |
982 |
> |
changed_local = 1; |
983 |
> |
|
984 |
> |
if(usingSMD) |
985 |
> |
prevCantPos = cantPos; |
986 |
> |
|
987 |
> |
if (hasZConsGap) |
988 |
> |
endFixTime[i] = info->getTime() + zconsFixTime; |
989 |
|
} |
990 |
< |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
990 |
> |
else if (diff > zconsTol && states[i] == zcsFixed){ |
991 |
|
states[i] = zcsMoving; |
992 |
< |
changed_local = 1; |
992 |
> |
changed_local = 1; |
993 |
> |
|
994 |
> |
if(usingSMD) |
995 |
> |
cantPos = prevCantPos; |
996 |
> |
|
997 |
> |
if (hasZConsGap) |
998 |
> |
endFixTime[i] = INFINITE_TIME; |
999 |
|
} |
982 |
– |
|
1000 |
|
} |
1001 |
|
|
1002 |
|
#ifndef IS_MPI |
1003 |
< |
changed =changed_local; |
1003 |
> |
changed = changed_local; |
1004 |
|
#else |
1005 |
< |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1005 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1006 |
|
#endif |
1007 |
|
|
1008 |
|
return (changed > 0); |
992 |
– |
|
1009 |
|
} |
1010 |
|
|
1011 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
996 |
– |
|
1012 |
|
int havingFixed_local; |
1013 |
|
int havingFixed; |
1014 |
|
|
1015 |
|
havingFixed_local = 0; |
1016 |
|
|
1017 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1017 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1018 |
|
if (states[i] == zcsFixed){ |
1019 |
|
havingFixed_local = 1; |
1020 |
< |
break; |
1020 |
> |
break; |
1021 |
|
} |
1022 |
|
|
1023 |
|
#ifndef IS_MPI |
1024 |
|
havingFixed = havingFixed_local; |
1025 |
|
#else |
1026 |
< |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1026 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM, |
1027 |
> |
MPI_COMM_WORLD); |
1028 |
|
#endif |
1029 |
|
|
1030 |
|
return (havingFixed > 0); |
1035 |
|
* |
1036 |
|
*/ |
1037 |
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1022 |
– |
|
1038 |
|
int havingMoving_local; |
1039 |
|
int havingMoving; |
1040 |
|
|
1041 |
|
havingMoving_local = 0; |
1042 |
|
|
1043 |
< |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1043 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1044 |
|
if (states[i] == zcsMoving){ |
1045 |
|
havingMoving_local = 1; |
1046 |
< |
break; |
1046 |
> |
break; |
1047 |
|
} |
1048 |
|
|
1049 |
|
#ifndef IS_MPI |
1050 |
|
havingMoving = havingMoving_local; |
1051 |
|
#else |
1052 |
< |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1052 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM, |
1053 |
> |
MPI_COMM_WORLD); |
1054 |
|
#endif |
1055 |
|
|
1056 |
|
return (havingMoving > 0); |
1041 |
– |
|
1057 |
|
} |
1058 |
|
|
1059 |
|
/** |
1060 |
|
* |
1061 |
|
*/ |
1062 |
|
|
1063 |
< |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1049 |
< |
{ |
1063 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){ |
1064 |
|
double MVzOfMovingMols_local; |
1065 |
|
double MVzOfMovingMols; |
1066 |
|
double totalMassOfMovingZMols_local; |
1067 |
|
double totalMassOfMovingZMols; |
1068 |
|
double COMvel[3]; |
1069 |
< |
|
1069 |
> |
|
1070 |
|
MVzOfMovingMols_local = 0; |
1071 |
|
totalMassOfMovingZMols_local = 0; |
1072 |
|
|
1073 |
< |
for(int i =0; i < unconsMols.size(); i++){ |
1073 |
> |
for (int i = 0; i < unconsMols.size(); i++){ |
1074 |
|
unconsMols[i]->getCOMvel(COMvel); |
1075 |
< |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1075 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1076 |
|
} |
1077 |
|
|
1078 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
1065 |
< |
|
1078 |
> |
for (int i = 0; i < zconsMols.size(); i++){ |
1079 |
|
if (states[i] == zcsMoving){ |
1080 |
|
zconsMols[i]->getCOMvel(COMvel); |
1081 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1082 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1082 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1083 |
|
} |
1071 |
– |
|
1084 |
|
} |
1085 |
|
|
1086 |
|
#ifndef IS_MPI |
1087 |
|
MVzOfMovingMols = MVzOfMovingMols_local; |
1088 |
|
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1089 |
|
#else |
1090 |
< |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1091 |
< |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1090 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
1091 |
> |
MPI_SUM, MPI_COMM_WORLD); |
1092 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
1093 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1094 |
|
#endif |
1095 |
|
|
1096 |
|
double vzOfMovingMols; |
1097 |
< |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1097 |
> |
vzOfMovingMols = MVzOfMovingMols / |
1098 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
1099 |
|
|
1100 |
|
return vzOfMovingMols; |
1101 |
|
} |
1104 |
|
* |
1105 |
|
*/ |
1106 |
|
|
1107 |
< |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1093 |
< |
{ |
1107 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel(){ |
1108 |
|
double COMvel[3]; |
1109 |
|
double tempMVz_local; |
1110 |
|
double tempMVz; |
1112 |
|
double massOfZCons; |
1113 |
|
|
1114 |
|
|
1115 |
< |
tempMVz_local = 0; |
1115 |
> |
tempMVz_local = 0; |
1116 |
|
|
1117 |
< |
for(int i =0 ; i < nMols; i++){ |
1117 |
> |
for (int i = 0 ; i < nMols; i++){ |
1118 |
|
molecules[i].getCOMvel(COMvel); |
1119 |
< |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1119 |
> |
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection]; |
1120 |
|
} |
1121 |
|
|
1122 |
|
massOfZCons_local = 0; |
1123 |
< |
|
1124 |
< |
for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1123 |
> |
|
1124 |
> |
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){ |
1125 |
|
massOfZCons_local += massOfZConsMols[i]; |
1126 |
|
} |
1127 |
|
#ifndef IS_MPI |
1128 |
|
massOfZCons = massOfZCons_local; |
1129 |
|
tempMVz = tempMVz_local; |
1130 |
|
#else |
1131 |
< |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1132 |
< |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1131 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM, |
1132 |
> |
MPI_COMM_WORLD); |
1133 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1134 |
|
#endif |
1135 |
|
|
1136 |
< |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1136 |
> |
return tempMVz / (totalMassOfUncons + massOfZCons); |
1137 |
|
} |
1138 |
|
|
1139 |
|
/** |
1141 |
|
*/ |
1142 |
|
|
1143 |
|
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1129 |
– |
|
1144 |
|
double force[3]; |
1145 |
|
double totalForce_local; |
1146 |
|
double totalForce; |
1147 |
|
|
1148 |
|
totalForce_local = 0; |
1149 |
|
|
1150 |
< |
for(int i = 0; i < nAtoms; i++){ |
1150 |
> |
for (int i = 0; i < nAtoms; i++){ |
1151 |
|
atoms[i]->getFrc(force); |
1152 |
|
totalForce_local += force[whichDirection]; |
1153 |
|
} |
1155 |
|
#ifndef IS_MPI |
1156 |
|
totalForce = totalForce_local; |
1157 |
|
#else |
1158 |
< |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1158 |
> |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM, |
1159 |
> |
MPI_COMM_WORLD); |
1160 |
|
#endif |
1161 |
|
|
1162 |
|
return totalForce; |
1148 |
– |
|
1163 |
|
} |
1164 |
|
|
1165 |
|
/** |
1170 |
|
//calculate the number of atoms of moving z-constrained molecules |
1171 |
|
int nMovingZAtoms_local; |
1172 |
|
int nMovingZAtoms; |
1173 |
< |
|
1173 |
> |
|
1174 |
|
nMovingZAtoms_local = 0; |
1175 |
< |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1176 |
< |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1177 |
< |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1178 |
< |
|
1175 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1176 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1177 |
> |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1178 |
> |
} |
1179 |
> |
|
1180 |
|
#ifdef IS_MPI |
1181 |
< |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1181 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, |
1182 |
> |
MPI_COMM_WORLD); |
1183 |
|
#else |
1184 |
|
nMovingZAtoms = nMovingZAtoms_local; |
1185 |
|
#endif |
1186 |
|
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1187 |
|
} |
1188 |
|
|
1189 |
< |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1189 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, |
1190 |
> |
Atom* atom, |
1191 |
> |
double totalForce){ |
1192 |
|
return totalForce / mol->getNAtoms(); |
1193 |
|
} |
1194 |
|
|
1195 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1195 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, |
1196 |
> |
double totalForce){ |
1197 |
|
return totalForce / totNumOfMovingAtoms; |
1198 |
|
} |
1199 |
|
|
1200 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1201 |
< |
return totalForce / mol->getNAtoms(); |
1200 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, |
1201 |
> |
Atom* atom, |
1202 |
> |
double totalForce){ |
1203 |
> |
return totalForce / mol->getNAtoms(); |
1204 |
|
} |
1205 |
|
|
1206 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1206 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, |
1207 |
> |
double totalForce){ |
1208 |
|
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1209 |
|
} |
1210 |
|
|
1216 |
|
//calculate the number of atoms of moving z-constrained molecules |
1217 |
|
double massOfMovingZAtoms_local; |
1218 |
|
double massOfMovingZAtoms; |
1219 |
< |
|
1219 |
> |
|
1220 |
|
massOfMovingZAtoms_local = 0; |
1221 |
< |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1222 |
< |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1223 |
< |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1224 |
< |
|
1221 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1222 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1223 |
> |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1224 |
> |
} |
1225 |
> |
|
1226 |
|
#ifdef IS_MPI |
1227 |
< |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1227 |
> |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE, |
1228 |
> |
MPI_SUM, MPI_COMM_WORLD); |
1229 |
|
#else |
1230 |
|
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1231 |
|
#endif |
1232 |
< |
totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1232 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms + |
1233 |
> |
zconsIntegrator->totalMassOfUncons; |
1234 |
|
} |
1235 |
|
|
1236 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1236 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, |
1237 |
> |
Atom* atom, |
1238 |
> |
double totalForce){ |
1239 |
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1240 |
|
} |
1241 |
|
|
1242 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1243 |
< |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1242 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom, |
1243 |
> |
double totalForce){ |
1244 |
> |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1245 |
|
} |
1246 |
|
|
1247 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1247 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, |
1248 |
> |
Atom* atom, |
1249 |
> |
double totalForce){ |
1250 |
|
return totalForce * atom->getMass() / mol->getTotalMass(); |
1251 |
|
} |
1252 |
|
|
1253 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1254 |
< |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1253 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, |
1254 |
> |
double totalForce){ |
1255 |
> |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1256 |
|
} |
1257 |
|
|
1258 |
+ |
template<typename T> void ZConstraint<T>::updateZPos(){ |
1259 |
+ |
double curTime; |
1260 |
+ |
double COM[3]; |
1261 |
+ |
|
1262 |
+ |
curTime = info->getTime(); |
1263 |
+ |
|
1264 |
+ |
for (size_t i = 0; i < zconsMols.size(); i++){ |
1265 |
+ |
|
1266 |
+ |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){ |
1267 |
+ |
zPos[i] += zconsGap; |
1268 |
+ |
|
1269 |
+ |
if (usingSMD){ |
1270 |
+ |
zconsMols[i]->getCOM(COM); |
1271 |
+ |
cantPos[i] = COM[whichDirection]; |
1272 |
+ |
} |
1273 |
+ |
|
1274 |
+ |
} |
1275 |
+ |
|
1276 |
+ |
} |
1277 |
+ |
|
1278 |
+ |
} |
1279 |
+ |
|
1280 |
+ |
template<typename T> void ZConstraint<T>::updateCantPos(){ |
1281 |
+ |
double curTime; |
1282 |
+ |
double dt; |
1283 |
+ |
|
1284 |
+ |
curTime = info->getTime(); |
1285 |
+ |
dt = info->dt; |
1286 |
+ |
|
1287 |
+ |
for (size_t i = 0; i < zconsMols.size(); i++){ |
1288 |
+ |
if (states[i] == zcsMoving){ |
1289 |
+ |
cantPos[i] += cantVel[i] * dt; |
1290 |
+ |
} |
1291 |
+ |
} |
1292 |
+ |
|
1293 |
+ |
} |