1 |
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#include "Integrator.hpp" |
2 |
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#include "simError.h" |
3 |
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#include <cmath> |
4 |
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
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: T(theInfo, the_ff), fz(NULL), curZPos(NULL), |
6 |
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indexOfZConsMols(NULL), forcePolicy(NULL), curZconsTime(0) |
7 |
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{ |
8 |
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|
9 |
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//get properties from SimInfo |
10 |
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GenericData* data; |
11 |
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ZConsParaData* zConsParaData; |
12 |
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DoubleData* sampleTime; |
13 |
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DoubleData* tolerance; |
14 |
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StringData* policy; |
15 |
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StringData* filename; |
16 |
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double COM[3]; |
17 |
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|
18 |
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//by default, the direction of constraint is z |
19 |
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// 0 --> x |
20 |
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// 1 --> y |
21 |
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// 2 --> z |
22 |
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whichDirection = 2; |
23 |
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|
24 |
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//estimate the force constant of harmonical potential |
25 |
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double Kb = 1.986E-3 ; //in kcal/K |
26 |
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|
27 |
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double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
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zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
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|
30 |
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//creat force substraction policy |
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data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
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if(!data){ |
33 |
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sprintf( painCave.errMsg, |
34 |
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"ZConstraint Warning: User does not set force substraction policy, " |
35 |
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"average force substraction policy is used\n"); |
36 |
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painCave.isFatal = 0; |
37 |
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simError(); |
38 |
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|
39 |
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forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
40 |
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} |
41 |
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else{ |
42 |
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policy = dynamic_cast<StringData*>(data); |
43 |
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|
44 |
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if(!policy){ |
45 |
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sprintf( painCave.errMsg, |
46 |
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"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
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"average force substraction policy is used\n"); |
48 |
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painCave.isFatal = 0; |
49 |
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simError(); |
50 |
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|
51 |
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forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
52 |
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} |
53 |
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else{ |
54 |
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if(policy->getData() == "BYNUMBER") |
55 |
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forcePolicy = (ForceSubstractionPolicy*) new PolicyByNumber(this); |
56 |
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else if(policy->getData() == "BYMASS") |
57 |
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forcePolicy = (ForceSubstractionPolicy*) new PolicyByMass(this); |
58 |
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else{ |
59 |
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sprintf( painCave.errMsg, |
60 |
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"ZConstraint Warning: unknown force substraction policy, " |
61 |
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"average force substraction policy is used\n"); |
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painCave.isFatal = 0; |
63 |
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simError(); |
64 |
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} |
65 |
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} |
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} |
67 |
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|
68 |
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|
69 |
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|
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//retrieve sample time of z-contraint |
71 |
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data = info->getProperty(ZCONSTIME_ID); |
72 |
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|
73 |
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if(!data) { |
74 |
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|
75 |
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sprintf( painCave.errMsg, |
76 |
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"ZConstraint error: If you use an ZConstraint\n" |
77 |
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" , you must set sample time.\n"); |
78 |
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painCave.isFatal = 1; |
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simError(); |
80 |
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} |
81 |
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else{ |
82 |
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|
83 |
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sampleTime = dynamic_cast<DoubleData*>(data); |
84 |
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|
85 |
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if(!sampleTime){ |
86 |
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|
87 |
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sprintf( painCave.errMsg, |
88 |
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"ZConstraint error: Can not get property from SimInfo\n"); |
89 |
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painCave.isFatal = 1; |
90 |
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simError(); |
91 |
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|
92 |
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} |
93 |
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else{ |
94 |
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this->zconsTime = sampleTime->getData(); |
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} |
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|
97 |
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} |
98 |
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|
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//retrieve output filename of z force |
100 |
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data = info->getProperty(ZCONSFILENAME_ID); |
101 |
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if(!data) { |
102 |
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|
103 |
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|
104 |
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sprintf( painCave.errMsg, |
105 |
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"ZConstraint error: If you use an ZConstraint\n" |
106 |
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" , you must set output filename of z-force.\n"); |
107 |
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painCave.isFatal = 1; |
108 |
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simError(); |
109 |
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|
110 |
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} |
111 |
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else{ |
112 |
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|
113 |
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filename = dynamic_cast<StringData*>(data); |
114 |
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|
115 |
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if(!filename){ |
116 |
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|
117 |
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sprintf( painCave.errMsg, |
118 |
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"ZConstraint error: Can not get property from SimInfo\n"); |
119 |
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painCave.isFatal = 1; |
120 |
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simError(); |
121 |
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|
122 |
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} |
123 |
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else{ |
124 |
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this->zconsOutput = filename->getData(); |
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} |
126 |
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|
127 |
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|
128 |
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} |
129 |
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|
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//retrieve tolerance for z-constraint molecuels |
131 |
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data = info->getProperty(ZCONSTOL_ID); |
132 |
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|
133 |
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if(!data) { |
134 |
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|
135 |
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sprintf( painCave.errMsg, |
136 |
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"ZConstraint error: can not get tolerance \n"); |
137 |
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painCave.isFatal = 1; |
138 |
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simError(); |
139 |
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} |
140 |
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else{ |
141 |
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|
142 |
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tolerance = dynamic_cast<DoubleData*>(data); |
143 |
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|
144 |
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if(!tolerance){ |
145 |
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|
146 |
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sprintf( painCave.errMsg, |
147 |
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"ZConstraint error: Can not get property from SimInfo\n"); |
148 |
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painCave.isFatal = 1; |
149 |
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simError(); |
150 |
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|
151 |
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} |
152 |
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else{ |
153 |
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this->zconsTol = tolerance->getData(); |
154 |
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} |
155 |
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|
156 |
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} |
157 |
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|
158 |
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//retrieve index of z-constraint molecules |
159 |
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data = info->getProperty(ZCONSPARADATA_ID); |
160 |
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if(!data) { |
161 |
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|
162 |
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sprintf( painCave.errMsg, |
163 |
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"ZConstraint error: If you use an ZConstraint\n" |
164 |
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" , you must set index of z-constraint molecules.\n"); |
165 |
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painCave.isFatal = 1; |
166 |
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simError(); |
167 |
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} |
168 |
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else{ |
169 |
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|
170 |
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zConsParaData = dynamic_cast<ZConsParaData*>(data); |
171 |
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|
172 |
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if(!zConsParaData){ |
173 |
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|
174 |
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sprintf( painCave.errMsg, |
175 |
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"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
176 |
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painCave.isFatal = 1; |
177 |
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simError(); |
178 |
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|
179 |
< |
} |
180 |
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else{ |
181 |
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|
182 |
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parameters = zConsParaData->getData(); |
183 |
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|
184 |
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//check the range of zconsIndex |
185 |
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//and the minimum value of index is the first one (we already sorted the data) |
186 |
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//the maximum value of index is the last one |
187 |
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|
188 |
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int maxIndex; |
189 |
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int minIndex; |
190 |
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int totalNumMol; |
191 |
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|
192 |
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minIndex = (*parameters)[0].zconsIndex; |
193 |
< |
if(minIndex < 0){ |
194 |
< |
sprintf( painCave.errMsg, |
195 |
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"ZConstraint error: index is out of range\n"); |
196 |
< |
painCave.isFatal = 1; |
197 |
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simError(); |
198 |
< |
} |
199 |
< |
|
200 |
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maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
201 |
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|
202 |
< |
#ifndef IS_MPI |
203 |
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totalNumMol = nMols; |
204 |
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#else |
205 |
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totalNumMol = mpiSim->getTotNmol(); |
206 |
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#endif |
207 |
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|
208 |
< |
if(maxIndex > totalNumMol - 1){ |
209 |
< |
sprintf( painCave.errMsg, |
210 |
< |
"ZConstraint error: index is out of range\n"); |
211 |
< |
painCave.isFatal = 1; |
212 |
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simError(); |
213 |
< |
} |
214 |
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|
215 |
< |
//if user does not specify the zpos for the zconstraint molecule |
216 |
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//its initial z coordinate will be used as default |
217 |
< |
for(int i = 0; i < parameters->size(); i++){ |
218 |
< |
|
219 |
< |
if(!(*parameters)[i].havingZPos){ |
220 |
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|
221 |
< |
#ifndef IS_MPI |
222 |
< |
for(int j = 0; j < nMols; j++){ |
223 |
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if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
224 |
< |
molecules[j].getCOM(COM); |
225 |
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break; |
226 |
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} |
227 |
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} |
228 |
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#else |
229 |
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//query which processor current zconstraint molecule belongs to |
230 |
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int *MolToProcMap; |
231 |
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int whichNode; |
232 |
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double initZPos; |
233 |
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MolToProcMap = mpiSim->getMolToProcMap(); |
234 |
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whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
235 |
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|
236 |
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//broadcast the zpos of current z-contraint molecule |
237 |
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//the node which contain this |
238 |
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|
239 |
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if (worldRank == whichNode ){ |
240 |
< |
|
241 |
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for(int j = 0; j < nMols; j++) |
242 |
< |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
243 |
< |
molecules[j].getCOM(COM); |
244 |
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break; |
245 |
< |
} |
246 |
< |
|
247 |
< |
} |
248 |
< |
|
249 |
< |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD); |
250 |
< |
#endif |
251 |
< |
|
252 |
< |
(*parameters)[i].zPos = COM[whichDirection]; |
253 |
< |
|
254 |
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sprintf( painCave.errMsg, |
255 |
< |
"ZConstraint warningr: Does not specify zpos for z-constraint molecule " |
256 |
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"initial z coornidate will be used \n"); |
257 |
< |
painCave.isFatal = 0; |
258 |
< |
simError(); |
259 |
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|
260 |
< |
} |
261 |
< |
} |
262 |
< |
|
263 |
< |
}//end if (!zConsParaData) |
264 |
< |
}//end if (!data) |
265 |
< |
|
266 |
< |
// |
267 |
< |
#ifdef IS_MPI |
268 |
< |
update(); |
269 |
< |
#else |
270 |
< |
int searchResult; |
271 |
< |
|
272 |
< |
for(int i = 0; i < nMols; i++){ |
273 |
< |
|
274 |
< |
searchResult = isZConstraintMol(&molecules[i]); |
275 |
< |
|
276 |
< |
if(searchResult > -1){ |
277 |
< |
|
278 |
< |
zconsMols.push_back(&molecules[i]); |
279 |
< |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
280 |
< |
|
281 |
< |
zPos.push_back((*parameters)[searchResult].zPos); |
282 |
< |
cout << "index: "<< (*parameters)[searchResult].zconsIndex <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
283 |
< |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
284 |
< |
|
285 |
< |
molecules[i].getCOM(COM); |
286 |
< |
} |
287 |
< |
else |
288 |
< |
{ |
289 |
< |
|
290 |
< |
unconsMols.push_back(&molecules[i]); |
291 |
< |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
292 |
< |
|
293 |
< |
} |
294 |
< |
} |
295 |
< |
|
296 |
< |
fz = new double[zconsMols.size()]; |
297 |
< |
curZPos = new double[zconsMols.size()]; |
298 |
< |
indexOfZConsMols = new int [zconsMols.size()]; |
299 |
< |
|
300 |
< |
if(!fz || !curZPos || !indexOfZConsMols){ |
301 |
< |
sprintf( painCave.errMsg, |
302 |
< |
"Memory allocation failure in class Zconstraint\n"); |
303 |
< |
painCave.isFatal = 1; |
304 |
< |
simError(); |
305 |
< |
} |
306 |
< |
|
307 |
< |
//determine the states of z-constraint molecules |
308 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
309 |
< |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
310 |
< |
|
311 |
< |
zconsMols[i]->getCOM(COM); |
312 |
< |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
313 |
< |
states.push_back(zcsFixed); |
314 |
< |
else |
315 |
< |
states.push_back(zcsMoving); |
316 |
< |
} |
317 |
< |
|
318 |
< |
#endif |
319 |
< |
|
320 |
< |
//get total masss of unconstraint molecules |
321 |
< |
double totalMassOfUncons_local; |
322 |
< |
totalMassOfUncons_local = 0; |
323 |
< |
|
324 |
< |
for(int i = 0; i < unconsMols.size(); i++) |
325 |
< |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
326 |
< |
|
327 |
< |
#ifndef IS_MPI |
328 |
< |
totalMassOfUncons = totalMassOfUncons_local; |
329 |
< |
#else |
330 |
< |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
< |
#endif |
332 |
< |
|
333 |
< |
|
334 |
< |
//get total number of unconstrained atoms |
335 |
< |
int nUnconsAtoms_local; |
336 |
< |
nUnconsAtoms_local = 0; |
337 |
< |
for(int i = 0; i < unconsMols.size(); i++) |
338 |
< |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
339 |
< |
|
340 |
< |
#ifndef IS_MPI |
341 |
< |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
342 |
< |
#else |
343 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
< |
#endif |
345 |
< |
|
346 |
< |
// creat zconsWriter |
347 |
< |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
348 |
< |
|
349 |
< |
if(!fzOut){ |
350 |
< |
sprintf( painCave.errMsg, |
351 |
< |
"Memory allocation failure in class Zconstraint\n"); |
352 |
< |
painCave.isFatal = 1; |
353 |
< |
simError(); |
354 |
< |
} |
355 |
< |
|
356 |
< |
forcePolicy->update(); |
357 |
< |
} |
358 |
< |
|
359 |
< |
template<typename T> ZConstraint<T>::~ZConstraint() |
360 |
< |
{ |
361 |
< |
if(fz) |
362 |
< |
delete[] fz; |
363 |
< |
|
364 |
< |
if(curZPos) |
365 |
< |
delete[] curZPos; |
366 |
< |
|
367 |
< |
if(indexOfZConsMols) |
368 |
< |
delete[] indexOfZConsMols; |
369 |
< |
|
370 |
< |
if(fzOut) |
371 |
< |
delete fzOut; |
372 |
< |
|
373 |
< |
if(forcePolicy) |
374 |
< |
delete forcePolicy; |
375 |
< |
} |
376 |
< |
|
377 |
< |
#ifdef IS_MPI |
378 |
< |
template<typename T> void ZConstraint<T>::update() |
379 |
< |
{ |
380 |
< |
double COM[3]; |
381 |
< |
int index; |
382 |
< |
|
383 |
< |
zconsMols.clear(); |
384 |
< |
massOfZConsMols.clear(); |
385 |
< |
zPos.clear(); |
386 |
< |
kz.clear(); |
387 |
< |
|
388 |
< |
unconsMols.clear(); |
389 |
< |
massOfUnconsMols.clear(); |
390 |
< |
|
391 |
< |
|
392 |
< |
//creat zconsMol and unconsMol lists |
393 |
< |
for(int i = 0; i < nMols; i++){ |
394 |
< |
|
395 |
< |
index = isZConstraintMol(&molecules[i]); |
396 |
< |
|
397 |
< |
if(index > -1){ |
398 |
< |
|
399 |
< |
zconsMols.push_back(&molecules[i]); |
400 |
< |
zPos.push_back((*parameters)[index].zPos); |
401 |
< |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
402 |
< |
|
403 |
< |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
404 |
< |
|
405 |
< |
molecules[i].getCOM(COM); |
406 |
< |
} |
407 |
< |
else |
408 |
< |
{ |
409 |
< |
|
410 |
< |
unconsMols.push_back(&molecules[i]); |
411 |
< |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
412 |
< |
|
413 |
< |
} |
414 |
< |
} |
415 |
< |
|
416 |
< |
//determine the states of z-constraint molecules |
417 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
418 |
< |
zconsMols[i]->getCOM(COM); |
419 |
< |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
420 |
< |
states.push_back(zcsFixed); |
421 |
< |
else |
422 |
< |
states.push_back(zcsMoving); |
423 |
< |
} |
424 |
< |
|
425 |
< |
|
426 |
< |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
427 |
< |
// that we want to make the MPI communication simple |
428 |
< |
if(fz) |
429 |
< |
delete[] fz; |
430 |
< |
|
431 |
< |
if(curZPos) |
432 |
< |
delete[] curZPos; |
433 |
< |
|
434 |
< |
if(indexOfZConsMols) |
435 |
< |
delete[] indexOfZConsMols; |
436 |
< |
|
437 |
< |
if (zconsMols.size() > 0){ |
438 |
< |
fz = new double[zconsMols.size()]; |
439 |
< |
curZPos = new double[zconsMols.size()]; |
440 |
< |
indexOfZConsMols = new int[zconsMols.size()]; |
441 |
< |
|
442 |
< |
if(!fz || !curZPos || !indexOfZConsMols){ |
443 |
< |
sprintf( painCave.errMsg, |
444 |
< |
"Memory allocation failure in class Zconstraint\n"); |
445 |
< |
painCave.isFatal = 1; |
446 |
< |
simError(); |
447 |
< |
} |
448 |
< |
|
449 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
450 |
< |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
451 |
< |
} |
452 |
< |
|
453 |
< |
} |
454 |
< |
else{ |
455 |
< |
fz = NULL; |
456 |
< |
curZPos = NULL; |
457 |
< |
indexOfZConsMols = NULL; |
458 |
< |
} |
459 |
< |
|
460 |
< |
// |
461 |
< |
forcePolicy->update(); |
462 |
< |
|
463 |
< |
} |
464 |
< |
|
465 |
< |
#endif |
466 |
< |
|
467 |
< |
/** Function Name: isZConstraintMol |
468 |
< |
** Parameter |
469 |
< |
** Molecule* mol |
470 |
< |
** Return value: |
471 |
< |
** -1, if the molecule is not z-constraint molecule, |
472 |
< |
** other non-negative values, its index in indexOfAllZConsMols vector |
473 |
< |
*/ |
474 |
< |
|
475 |
< |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
476 |
< |
{ |
477 |
< |
int index; |
478 |
< |
int low; |
479 |
< |
int high; |
480 |
< |
int mid; |
481 |
< |
|
482 |
< |
index = mol->getGlobalIndex(); |
483 |
< |
|
484 |
< |
low = 0; |
485 |
< |
high = parameters->size() - 1; |
486 |
< |
|
487 |
< |
//Binary Search (we have sorted the array) |
488 |
< |
while(low <= high){ |
489 |
< |
mid = (low + high) /2; |
490 |
< |
if ((*parameters)[mid].zconsIndex == index) |
491 |
< |
return mid; |
492 |
< |
else if ((*parameters)[mid].zconsIndex > index ) |
493 |
< |
high = mid -1; |
494 |
< |
else |
495 |
< |
low = mid + 1; |
496 |
< |
} |
497 |
< |
|
498 |
< |
return -1; |
499 |
< |
} |
500 |
< |
|
501 |
< |
template<typename T> void ZConstraint<T>::integrate(){ |
502 |
< |
|
503 |
< |
//zero out the velocities of center of mass of unconstrained molecules |
504 |
< |
//and the velocities of center of mass of every single z-constrained molecueles |
505 |
< |
zeroOutVel(); |
506 |
< |
|
507 |
< |
T::integrate(); |
508 |
< |
|
509 |
< |
} |
510 |
< |
|
511 |
< |
|
512 |
< |
/** |
513 |
< |
* |
514 |
< |
* |
515 |
< |
* |
516 |
< |
* |
517 |
< |
*/ |
518 |
< |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
519 |
< |
double zsys; |
520 |
< |
double COM[3]; |
521 |
< |
double force[3]; |
522 |
< |
|
523 |
< |
T::calcForce(calcPot, calcStress); |
524 |
< |
|
525 |
< |
if (checkZConsState()){ |
526 |
< |
zeroOutVel(); |
527 |
< |
forcePolicy->update(); |
528 |
< |
} |
529 |
< |
zsys = calcZSys(); |
530 |
< |
cout << "---------------------------------------------------------------------" <<endl; |
531 |
< |
cout << "current time: " << info->getTime() << endl; |
532 |
< |
cout << "center of mass at z: " << zsys << endl; |
533 |
< |
//cout << "before calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
534 |
< |
cout << "before calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
535 |
< |
|
536 |
< |
//cout << "before doZConstraintForce, totalForce is " << calcTotalForce() << endl; |
537 |
< |
|
538 |
< |
//do zconstraint force; |
539 |
< |
if (haveFixedZMols()) |
540 |
< |
this->doZconstraintForce(); |
541 |
< |
|
542 |
< |
//use harmonical poteintial to move the molecules to the specified positions |
543 |
< |
if (haveMovingZMols()) |
544 |
< |
this->doHarmonic(); |
545 |
< |
|
546 |
< |
//cout << "after doHarmonic, totalForce is " << calcTotalForce() << endl; |
547 |
< |
|
548 |
< |
//write out forces and current positions of z-constraint molecules |
549 |
< |
if(info->getTime() >= curZconsTime){ |
550 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
551 |
< |
zconsMols[i]->getCOM(COM); |
552 |
< |
curZPos[i] = COM[whichDirection]; |
553 |
< |
|
554 |
< |
//if the z-constraint molecule is still moving, just record its force |
555 |
< |
if(states[i] == zcsMoving){ |
556 |
< |
fz[i] = 0; |
557 |
< |
Atom** movingZAtoms; |
558 |
< |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
559 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
560 |
< |
movingZAtoms[j]->getFrc(force); |
561 |
< |
fz[i] += force[whichDirection]; |
562 |
< |
} |
563 |
< |
} |
564 |
< |
} |
565 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
566 |
< |
curZconsTime += zconsTime; |
567 |
< |
} |
568 |
< |
|
569 |
< |
//cout << "after calcForce, the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
570 |
< |
cout << "after calcForce, the COMVel of system is " << calcSysCOMVel() <<endl; |
571 |
< |
} |
572 |
< |
|
573 |
< |
template<typename T> double ZConstraint<T>::calcZSys() |
574 |
< |
{ |
575 |
< |
//calculate reference z coordinate for z-constraint molecules |
576 |
< |
double totalMass_local; |
577 |
< |
double totalMass; |
578 |
< |
double totalMZ_local; |
579 |
< |
double totalMZ; |
580 |
< |
double massOfCurMol; |
581 |
< |
double COM[3]; |
582 |
< |
|
583 |
< |
totalMass_local = 0; |
584 |
< |
totalMZ_local = 0; |
585 |
< |
|
586 |
< |
for(int i = 0; i < nMols; i++){ |
587 |
< |
massOfCurMol = molecules[i].getTotalMass(); |
588 |
< |
molecules[i].getCOM(COM); |
589 |
< |
|
590 |
< |
totalMass_local += massOfCurMol; |
591 |
< |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
592 |
< |
|
593 |
< |
} |
594 |
< |
|
595 |
< |
|
596 |
< |
#ifdef IS_MPI |
597 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
598 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
599 |
< |
#else |
600 |
< |
totalMass = totalMass_local; |
601 |
< |
totalMZ = totalMZ_local; |
602 |
< |
#endif |
603 |
< |
|
604 |
< |
double zsys; |
605 |
< |
zsys = totalMZ / totalMass; |
606 |
< |
|
607 |
< |
return zsys; |
608 |
< |
} |
609 |
< |
|
610 |
< |
/** |
611 |
< |
* |
612 |
< |
*/ |
613 |
< |
template<typename T> void ZConstraint<T>::thermalize( void ){ |
614 |
< |
|
615 |
< |
T::thermalize(); |
616 |
< |
zeroOutVel(); |
617 |
< |
} |
618 |
< |
|
619 |
< |
/** |
620 |
< |
* |
621 |
< |
* |
622 |
< |
* |
623 |
< |
*/ |
624 |
< |
|
625 |
< |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
626 |
< |
|
627 |
< |
Atom** fixedZAtoms; |
628 |
< |
double COMvel[3]; |
629 |
< |
double vel[3]; |
630 |
< |
|
631 |
< |
//zero out the velocities of center of mass of fixed z-constrained molecules |
632 |
< |
|
633 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
634 |
< |
|
635 |
< |
if (states[i] == zcsFixed){ |
636 |
< |
|
637 |
< |
zconsMols[i]->getCOMvel(COMvel); |
638 |
< |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
639 |
< |
|
640 |
< |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
641 |
< |
|
642 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
643 |
< |
fixedZAtoms[j]->getVel(vel); |
644 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
645 |
< |
fixedZAtoms[j]->setVel(vel); |
646 |
< |
} |
647 |
< |
|
648 |
< |
zconsMols[i]->getCOMvel(COMvel); |
649 |
< |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
650 |
< |
} |
651 |
< |
|
652 |
< |
} |
653 |
< |
|
654 |
< |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
655 |
< |
|
656 |
< |
#ifdef IS_MPI |
657 |
< |
if (worldRank == 0){ |
658 |
< |
#endif |
659 |
< |
cout << "before resetting the COMVel of sytem is " << calcSysCOMVel() << endl; |
660 |
< |
#ifdef IS_MPI |
661 |
< |
} |
662 |
< |
#endif |
663 |
< |
|
664 |
< |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
665 |
< |
double MVzOfMovingMols_local; |
666 |
< |
double MVzOfMovingMols; |
667 |
< |
double totalMassOfMovingZMols_local; |
668 |
< |
double totalMassOfMovingZMols; |
669 |
< |
|
670 |
< |
MVzOfMovingMols_local = 0; |
671 |
< |
totalMassOfMovingZMols_local = 0; |
672 |
< |
|
673 |
< |
for(int i =0; i < unconsMols.size(); i++){ |
674 |
< |
unconsMols[i]->getCOMvel(COMvel); |
675 |
< |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
676 |
< |
} |
677 |
< |
|
678 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
679 |
< |
if (states[i] == zcsMoving){ |
680 |
< |
zconsMols[i]->getCOMvel(COMvel); |
681 |
< |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
682 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
683 |
< |
} |
684 |
< |
|
685 |
< |
} |
686 |
< |
|
687 |
< |
#ifndef IS_MPI |
688 |
< |
MVzOfMovingMols = MVzOfMovingMols_local; |
689 |
< |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
690 |
< |
#else |
691 |
< |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
692 |
< |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
693 |
< |
#endif |
694 |
< |
|
695 |
< |
double vzOfMovingMols; |
696 |
< |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
697 |
< |
|
698 |
< |
//modify the velocites of unconstrained molecules |
699 |
< |
Atom** unconsAtoms; |
700 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
701 |
< |
|
702 |
< |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
703 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
704 |
< |
unconsAtoms[j]->getVel(vel); |
705 |
< |
vel[whichDirection] -= vzOfMovingMols; |
706 |
< |
unconsAtoms[j]->setVel(vel); |
707 |
< |
} |
708 |
< |
|
709 |
< |
} |
710 |
< |
|
711 |
< |
//modify the velocities of moving z-constrained molecuels |
712 |
< |
Atom** movingZAtoms; |
713 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
714 |
< |
|
715 |
< |
if (states[i] ==zcsMoving){ |
716 |
< |
|
717 |
< |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
718 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
719 |
< |
movingZAtoms[j]->getVel(vel); |
720 |
< |
vel[whichDirection] -= vzOfMovingMols; |
721 |
< |
movingZAtoms[j]->setVel(vel); |
722 |
< |
} |
723 |
< |
|
724 |
< |
} |
725 |
< |
|
726 |
< |
} |
727 |
< |
|
728 |
< |
#ifdef IS_MPI |
729 |
< |
if (worldRank == 0){ |
730 |
< |
#endif |
731 |
< |
cout << "after resetting the COMVel of moving molecules is " << calcSysCOMVel() <<endl; |
732 |
< |
#ifdef IS_MPI |
733 |
< |
} |
734 |
< |
#endif |
735 |
< |
|
736 |
< |
} |
737 |
< |
|
738 |
< |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
739 |
< |
|
740 |
< |
Atom** zconsAtoms; |
741 |
< |
double totalFZ; |
742 |
< |
double totalFZ_local; |
743 |
< |
double COMvel[3]; |
744 |
< |
double COM[3]; |
745 |
< |
double force[3]; |
746 |
< |
|
747 |
< |
|
748 |
< |
|
749 |
< |
//constrain the molecules which do not reach the specified positions |
750 |
< |
|
751 |
< |
//Zero Out the force of z-contrained molecules |
752 |
< |
totalFZ_local = 0; |
753 |
< |
|
754 |
< |
//calculate the total z-contrained force of fixed z-contrained molecules |
755 |
< |
|
756 |
< |
#ifdef IS_MPI |
757 |
< |
if (worldRank == 0){ |
758 |
< |
#endif |
759 |
< |
cout << "Fixed Molecules" << endl; |
760 |
< |
#ifdef IS_MPI |
761 |
< |
} |
762 |
< |
#endif |
763 |
< |
|
764 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
765 |
< |
|
766 |
< |
if (states[i] == zcsFixed){ |
767 |
< |
|
768 |
< |
zconsMols[i]->getCOM(COM); |
769 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
770 |
< |
|
771 |
< |
fz[i] = 0; |
772 |
< |
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
773 |
< |
zconsAtoms[j]->getFrc(force); |
774 |
< |
fz[i] += force[whichDirection]; |
775 |
< |
} |
776 |
< |
totalFZ_local += fz[i]; |
777 |
< |
|
778 |
< |
cout << "index: " << indexOfZConsMols[i] |
779 |
< |
<<"\tcurrent zpos: " << COM[whichDirection] |
780 |
< |
<< "\tcurrent fz: " <<fz[i] << endl; |
781 |
< |
|
782 |
< |
} |
783 |
< |
|
784 |
< |
} |
785 |
< |
|
786 |
< |
//calculate total z-constraint force |
787 |
< |
#ifdef IS_MPI |
788 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
789 |
< |
#else |
790 |
< |
totalFZ = totalFZ_local; |
791 |
< |
#endif |
792 |
< |
|
793 |
< |
|
794 |
< |
// apply negative to fixed z-constrained molecues; |
795 |
< |
force[0]= 0; |
796 |
< |
force[1]= 0; |
797 |
< |
force[2]= 0; |
798 |
< |
|
799 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
800 |
< |
|
801 |
< |
if (states[i] == zcsFixed){ |
802 |
< |
|
803 |
< |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
804 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
805 |
< |
|
806 |
< |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
807 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
808 |
< |
//force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
809 |
< |
zconsAtoms[j]->addFrc(force); |
810 |
< |
} |
811 |
< |
|
812 |
< |
} |
813 |
< |
|
814 |
< |
} |
815 |
< |
|
816 |
< |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
817 |
< |
// << "total force is " << calcTotalForce() << endl; |
818 |
< |
|
819 |
< |
//calculate the number of atoms of moving z-constrained molecules |
820 |
< |
int nMovingZAtoms_local; |
821 |
< |
int nMovingZAtoms; |
822 |
< |
|
823 |
< |
nMovingZAtoms_local = 0; |
824 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
825 |
< |
if(states[i] == zcsMoving) |
826 |
< |
nMovingZAtoms_local += zconsMols[i]->getNAtoms(); |
827 |
< |
|
828 |
< |
#ifdef IS_MPI |
829 |
< |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
830 |
< |
#else |
831 |
< |
nMovingZAtoms = nMovingZAtoms_local; |
832 |
< |
#endif |
833 |
< |
|
834 |
< |
force[0]= 0; |
835 |
< |
force[1]= 0; |
836 |
< |
force[2]= 0; |
837 |
< |
|
838 |
< |
//modify the forces of unconstrained molecules |
839 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
840 |
< |
|
841 |
< |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
842 |
< |
|
843 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
844 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
845 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
846 |
< |
unconsAtoms[j]->addFrc(force); |
847 |
< |
} |
848 |
< |
|
849 |
< |
} |
850 |
< |
|
851 |
< |
//modify the forces of moving z-constrained molecules |
852 |
< |
for(int i = 0; i < zconsMols.size(); i++) { |
853 |
< |
if (states[i] == zcsMoving){ |
854 |
< |
|
855 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
856 |
< |
|
857 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
858 |
< |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
859 |
< |
//force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
860 |
< |
movingZAtoms[j]->addFrc(force); |
861 |
< |
} |
862 |
< |
} |
863 |
< |
} |
864 |
< |
|
865 |
< |
//cout << "after substracting z-constraint force from moving molecuels " |
866 |
< |
// << "total force is " << calcTotalForce() << endl; |
867 |
< |
|
868 |
< |
} |
869 |
< |
|
870 |
< |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
871 |
< |
double COM[3]; |
872 |
< |
double diff; |
873 |
< |
|
874 |
< |
int changed_local; |
875 |
< |
int changed; |
876 |
< |
|
877 |
< |
changed_local = 0; |
878 |
< |
|
879 |
< |
for(int i =0; i < zconsMols.size(); i++){ |
880 |
< |
|
881 |
< |
zconsMols[i]->getCOM(COM); |
882 |
< |
diff = fabs(COM[whichDirection] - zPos[i]); |
883 |
< |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
884 |
< |
states[i] = zcsFixed; |
885 |
< |
changed_local = 1; |
886 |
< |
} |
887 |
< |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
888 |
< |
states[i] = zcsMoving; |
889 |
< |
changed_local = 1; |
890 |
< |
} |
891 |
< |
|
892 |
< |
} |
893 |
< |
|
894 |
< |
#ifndef IS_MPI |
895 |
< |
changed =changed_local; |
896 |
< |
#else |
897 |
< |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
898 |
< |
#endif |
899 |
< |
|
900 |
< |
return changed > 0 ? true : false; |
901 |
< |
} |
902 |
< |
|
903 |
< |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
904 |
< |
|
905 |
< |
int havingFixed_local; |
906 |
< |
int havingFixed; |
907 |
< |
|
908 |
< |
havingFixed_local = 0; |
909 |
< |
|
910 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
911 |
< |
if (states[i] == zcsFixed){ |
912 |
< |
havingFixed_local = 1; |
913 |
< |
break; |
914 |
< |
} |
915 |
< |
|
916 |
< |
#ifndef IS_MPI |
917 |
< |
havingFixed = havingFixed_local; |
918 |
< |
#else |
919 |
< |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
920 |
< |
#endif |
921 |
< |
|
922 |
< |
return havingFixed > 0 ? true : false; |
923 |
< |
} |
924 |
< |
|
925 |
< |
|
926 |
< |
/** |
927 |
< |
* |
928 |
< |
*/ |
929 |
< |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
930 |
< |
|
931 |
< |
int havingMoving_local; |
932 |
< |
int havingMoving; |
933 |
< |
|
934 |
< |
havingMoving_local = 0; |
935 |
< |
|
936 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
937 |
< |
if (states[i] == zcsMoving){ |
938 |
< |
havingMoving_local = 1; |
939 |
< |
break; |
940 |
< |
} |
941 |
< |
|
942 |
< |
#ifndef IS_MPI |
943 |
< |
havingMoving = havingMoving_local; |
944 |
< |
#else |
945 |
< |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
946 |
< |
#endif |
947 |
< |
|
948 |
< |
return havingMoving > 0 ? true : false; |
949 |
< |
|
950 |
< |
} |
951 |
< |
|
952 |
< |
/** |
953 |
< |
* |
954 |
< |
* |
955 |
< |
*/ |
956 |
< |
|
957 |
< |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
958 |
< |
double force[3]; |
959 |
< |
double harmonicU; |
960 |
< |
double harmonicF; |
961 |
< |
double COM[3]; |
962 |
< |
double diff; |
963 |
< |
double totalFZ_local; |
964 |
< |
double totalFZ; |
965 |
< |
|
966 |
< |
force[0] = 0; |
967 |
< |
force[1] = 0; |
968 |
< |
force[2] = 0; |
969 |
< |
|
970 |
< |
totalFZ_local = 0; |
971 |
< |
|
972 |
< |
#ifdef IS_MPI |
973 |
< |
if (worldRank == 0){ |
974 |
< |
#endif |
975 |
< |
cout << "Moving Molecules" << endl; |
976 |
< |
#ifdef IS_MPI |
977 |
< |
} |
978 |
< |
#endif |
979 |
< |
|
980 |
< |
|
981 |
< |
for(int i = 0; i < zconsMols.size(); i++) { |
982 |
< |
|
983 |
< |
if (states[i] == zcsMoving){ |
984 |
< |
zconsMols[i]->getCOM(COM); |
985 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
986 |
< |
|
987 |
< |
diff = COM[whichDirection] -zPos[i]; |
988 |
< |
|
989 |
< |
harmonicU = 0.5 * kz[i] * diff * diff; |
990 |
< |
info->lrPot += harmonicU; |
991 |
< |
|
992 |
< |
harmonicF = - kz[i] * diff; |
993 |
< |
totalFZ_local += harmonicF; |
994 |
< |
|
995 |
< |
//adjust force |
996 |
< |
|
997 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
998 |
< |
|
999 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
1000 |
< |
force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
1001 |
< |
//force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
1002 |
< |
movingZAtoms[j]->addFrc(force); |
1003 |
< |
} |
1004 |
< |
} |
1005 |
< |
|
1006 |
< |
} |
1007 |
< |
|
1008 |
< |
#ifndef IS_MPI |
1009 |
< |
totalFZ = totalFZ_local; |
1010 |
< |
#else |
1011 |
< |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1012 |
< |
#endif |
1013 |
< |
|
1014 |
< |
force[0]= 0; |
1015 |
< |
force[1]= 0; |
1016 |
< |
force[2]= 0; |
1017 |
< |
|
1018 |
< |
//modify the forces of unconstrained molecules |
1019 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
1020 |
< |
|
1021 |
< |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
1022 |
< |
|
1023 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
1024 |
< |
force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
1025 |
< |
//force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
1026 |
< |
unconsAtoms[j]->addFrc(force); |
1027 |
< |
} |
1028 |
< |
} |
1029 |
< |
|
1030 |
< |
} |
1031 |
< |
|
1032 |
< |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1033 |
< |
{ |
1034 |
< |
double MVzOfMovingMols_local; |
1035 |
< |
double MVzOfMovingMols; |
1036 |
< |
double totalMassOfMovingZMols_local; |
1037 |
< |
double totalMassOfMovingZMols; |
1038 |
< |
double COMvel[3]; |
1039 |
< |
|
1040 |
< |
MVzOfMovingMols_local = 0; |
1041 |
< |
totalMassOfMovingZMols_local = 0; |
1042 |
< |
|
1043 |
< |
for(int i =0; i < unconsMols.size(); i++){ |
1044 |
< |
unconsMols[i]->getCOMvel(COMvel); |
1045 |
< |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1046 |
< |
} |
1047 |
< |
|
1048 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
1049 |
< |
|
1050 |
< |
if (states[i] == zcsMoving){ |
1051 |
< |
zconsMols[i]->getCOMvel(COMvel); |
1052 |
< |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1053 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1054 |
< |
} |
1055 |
< |
|
1056 |
< |
} |
1057 |
< |
|
1058 |
< |
#ifndef IS_MPI |
1059 |
< |
MVzOfMovingMols = MVzOfMovingMols_local; |
1060 |
< |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1061 |
< |
#else |
1062 |
< |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1063 |
< |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1064 |
< |
#endif |
1065 |
< |
|
1066 |
< |
double vzOfMovingMols; |
1067 |
< |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1068 |
< |
|
1069 |
< |
return vzOfMovingMols; |
1070 |
< |
} |
1071 |
< |
|
1072 |
< |
|
1073 |
< |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1074 |
< |
{ |
1075 |
< |
double COMvel[3]; |
1076 |
< |
double tempMVz_local; |
1077 |
< |
double tempMVz; |
1078 |
< |
double massOfZCons_local; |
1079 |
< |
double massOfZCons; |
1080 |
< |
|
1081 |
< |
|
1082 |
< |
tempMVz_local = 0; |
1083 |
< |
|
1084 |
< |
for(int i =0 ; i < nMols; i++){ |
1085 |
< |
molecules[i].getCOMvel(COMvel); |
1086 |
< |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1087 |
< |
} |
1088 |
< |
|
1089 |
< |
massOfZCons_local = 0; |
1090 |
< |
|
1091 |
< |
for(int i = 0; i < massOfZConsMols.size(); i++){ |
1092 |
< |
massOfZCons_local += massOfZConsMols[i]; |
1093 |
< |
} |
1094 |
< |
#ifndef IS_MPI |
1095 |
< |
massOfZCons = massOfZCons_local; |
1096 |
< |
tempMVz = tempMVz_local; |
1097 |
< |
#else |
1098 |
< |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1099 |
< |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1100 |
< |
#endif |
1101 |
< |
|
1102 |
< |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1103 |
< |
} |
1104 |
< |
|
1105 |
< |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1106 |
< |
|
1107 |
< |
double force[3]; |
1108 |
< |
double totalForce_local; |
1109 |
< |
double totalForce; |
1110 |
< |
|
1111 |
< |
totalForce_local = 0; |
1112 |
< |
|
1113 |
< |
for(int i = 0; i < nAtoms; i++){ |
1114 |
< |
atoms[i]->getFrc(force); |
1115 |
< |
totalForce_local += force[whichDirection]; |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
#ifndef IS_MPI |
1119 |
< |
totalForce = totalForce_local; |
1120 |
< |
#else |
1121 |
< |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1122 |
< |
#endif |
1123 |
< |
|
1124 |
< |
return totalForce; |
1125 |
< |
|
1126 |
< |
} |
1127 |
< |
|
1128 |
< |
/** |
1129 |
< |
* |
1130 |
< |
*/ |
1131 |
< |
|
1132 |
< |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1133 |
< |
//calculate the number of atoms of moving z-constrained molecules |
1134 |
< |
int nMovingZAtoms_local; |
1135 |
< |
int nMovingZAtoms; |
1136 |
< |
|
1137 |
< |
nMovingZAtoms_local = 0; |
1138 |
< |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1139 |
< |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1140 |
< |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1141 |
< |
|
1142 |
< |
#ifdef IS_MPI |
1143 |
< |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1144 |
< |
#else |
1145 |
< |
nMovingZAtoms = nMovingZAtoms_local; |
1146 |
< |
#endif |
1147 |
< |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1148 |
< |
} |
1149 |
< |
|
1150 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1151 |
< |
return totalForce / mol->getNAtoms(); |
1152 |
< |
} |
1153 |
< |
|
1154 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1155 |
< |
return totalForce / totNumOfMovingAtoms; |
1156 |
< |
} |
1157 |
< |
|
1158 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1159 |
< |
return totalForce / mol->getNAtoms(); |
1160 |
< |
} |
1161 |
< |
|
1162 |
< |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1163 |
< |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1164 |
< |
} |
1165 |
< |
|
1166 |
< |
/** |
1167 |
< |
* |
1168 |
< |
*/ |
1169 |
< |
|
1170 |
< |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1171 |
< |
//calculate the number of atoms of moving z-constrained molecules |
1172 |
< |
double massOfMovingZAtoms_local; |
1173 |
< |
double massOfMovingZAtoms; |
1174 |
< |
|
1175 |
< |
massOfMovingZAtoms_local = 0; |
1176 |
< |
for(int i = 0; i < (zconsIntegrator->zconsMols).size(); i++) |
1177 |
< |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1178 |
< |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1179 |
< |
|
1180 |
< |
#ifdef IS_MPI |
1181 |
< |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1182 |
< |
#else |
1183 |
< |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1184 |
< |
#endif |
1185 |
< |
totMassOfMovingAtoms = massOfMovingZAtoms_local + zconsIntegrator->totalMassOfUncons; |
1186 |
< |
} |
1187 |
< |
|
1188 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1189 |
< |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1190 |
< |
} |
1191 |
< |
|
1192 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1193 |
< |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1194 |
< |
} |
1195 |
< |
|
1196 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1197 |
< |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1198 |
< |
} |
1199 |
< |
|
1200 |
< |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1201 |
< |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1202 |
< |
} |
1203 |
< |
|
1 |
> |
#include "Integrator.hpp" |
2 |
> |
#include "simError.h" |
3 |
> |
#include <math.h> |
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 |
> |
indexOfZConsMols(NULL), |
9 |
> |
fz(NULL), |
10 |
> |
curZPos(NULL), |
11 |
> |
fzOut(NULL), |
12 |
> |
curZconsTime(0), |
13 |
> |
forcePolicy(NULL), |
14 |
> |
hasZConsGap(false){ |
15 |
> |
//get properties from SimInfo |
16 |
> |
GenericData* data; |
17 |
> |
ZConsParaData* zConsParaData; |
18 |
> |
DoubleData* sampleTime; |
19 |
> |
DoubleData* tolerance; |
20 |
> |
DoubleData* gap; |
21 |
> |
DoubleData* fixtime; |
22 |
> |
StringData* policy; |
23 |
> |
StringData* filename; |
24 |
> |
double COM[3]; |
25 |
> |
|
26 |
> |
//by default, the direction of constraint is z |
27 |
> |
// 0 --> x |
28 |
> |
// 1 --> y |
29 |
> |
// 2 --> z |
30 |
> |
whichDirection = 2; |
31 |
> |
|
32 |
> |
//estimate the force constant of harmonical potential |
33 |
> |
double Kb = 1.986E-3 ; //in kcal/K |
34 |
> |
|
35 |
> |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) / |
36 |
> |
2; |
37 |
> |
zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox); |
38 |
> |
|
39 |
> |
//creat force Subtraction policy |
40 |
> |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
41 |
> |
if (!data){ |
42 |
> |
sprintf(painCave.errMsg, |
43 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
44 |
> |
"PolicyByMass is used\n"); |
45 |
> |
painCave.isFatal = 0; |
46 |
> |
simError(); |
47 |
> |
|
48 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
49 |
> |
} |
50 |
> |
else{ |
51 |
> |
policy = dynamic_cast<StringData*>(data); |
52 |
> |
|
53 |
> |
if (!policy){ |
54 |
> |
sprintf(painCave.errMsg, |
55 |
> |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
56 |
> |
"PolicyByMass is used\n"); |
57 |
> |
painCave.isFatal = 0; |
58 |
> |
simError(); |
59 |
> |
|
60 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
61 |
> |
} |
62 |
> |
else{ |
63 |
> |
if (policy->getData() == "BYNUMBER") |
64 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this); |
65 |
> |
else if (policy->getData() == "BYMASS") |
66 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
67 |
> |
else{ |
68 |
> |
sprintf(painCave.errMsg, |
69 |
> |
"ZConstraint Warning: unknown force Subtraction policy, " |
70 |
> |
"PolicyByMass is used\n"); |
71 |
> |
painCave.isFatal = 0; |
72 |
> |
simError(); |
73 |
> |
forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this); |
74 |
> |
} |
75 |
> |
} |
76 |
> |
} |
77 |
> |
|
78 |
> |
|
79 |
> |
//retrieve sample time of z-contraint |
80 |
> |
data = info->getProperty(ZCONSTIME_ID); |
81 |
> |
|
82 |
> |
if (!data){ |
83 |
> |
sprintf(painCave.errMsg, |
84 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
85 |
> |
" , you must set sample time.\n"); |
86 |
> |
painCave.isFatal = 1; |
87 |
> |
simError(); |
88 |
> |
} |
89 |
> |
else{ |
90 |
> |
sampleTime = dynamic_cast<DoubleData*>(data); |
91 |
> |
|
92 |
> |
if (!sampleTime){ |
93 |
> |
sprintf(painCave.errMsg, |
94 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
95 |
> |
painCave.isFatal = 1; |
96 |
> |
simError(); |
97 |
> |
} |
98 |
> |
else{ |
99 |
> |
this->zconsTime = sampleTime->getData(); |
100 |
> |
} |
101 |
> |
} |
102 |
> |
|
103 |
> |
//retrieve output filename of z force |
104 |
> |
data = info->getProperty(ZCONSFILENAME_ID); |
105 |
> |
if (!data){ |
106 |
> |
sprintf(painCave.errMsg, |
107 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
108 |
> |
" , you must set output filename of z-force.\n"); |
109 |
> |
painCave.isFatal = 1; |
110 |
> |
simError(); |
111 |
> |
} |
112 |
> |
else{ |
113 |
> |
filename = dynamic_cast<StringData*>(data); |
114 |
> |
|
115 |
> |
if (!filename){ |
116 |
> |
sprintf(painCave.errMsg, |
117 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
118 |
> |
painCave.isFatal = 1; |
119 |
> |
simError(); |
120 |
> |
} |
121 |
> |
else{ |
122 |
> |
this->zconsOutput = filename->getData(); |
123 |
> |
} |
124 |
> |
} |
125 |
> |
|
126 |
> |
//retrieve tolerance for z-constraint molecuels |
127 |
> |
data = info->getProperty(ZCONSTOL_ID); |
128 |
> |
|
129 |
> |
if (!data){ |
130 |
> |
sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n"); |
131 |
> |
painCave.isFatal = 1; |
132 |
> |
simError(); |
133 |
> |
} |
134 |
> |
else{ |
135 |
> |
tolerance = dynamic_cast<DoubleData*>(data); |
136 |
> |
|
137 |
> |
if (!tolerance){ |
138 |
> |
sprintf(painCave.errMsg, |
139 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
140 |
> |
painCave.isFatal = 1; |
141 |
> |
simError(); |
142 |
> |
} |
143 |
> |
else{ |
144 |
> |
this->zconsTol = tolerance->getData(); |
145 |
> |
} |
146 |
> |
} |
147 |
> |
|
148 |
> |
//quick hack here |
149 |
> |
data = info->getProperty(ZCONSGAP_ID); |
150 |
> |
|
151 |
> |
if (data){ |
152 |
> |
gap = dynamic_cast<DoubleData*>(data); |
153 |
> |
} |
154 |
> |
|
155 |
> |
if (!gap){ |
156 |
> |
sprintf(painCave.errMsg, |
157 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
158 |
> |
painCave.isFatal = 1; |
159 |
> |
simError(); |
160 |
> |
} |
161 |
> |
else{ |
162 |
> |
this->hasZConsGap = true; |
163 |
> |
this->zconsGap = gap->getData(); |
164 |
> |
} |
165 |
> |
|
166 |
> |
data = info->getProperty(ZCONSFIXTIME_ID); |
167 |
> |
|
168 |
> |
if (data){ |
169 |
> |
fixtime = dynamic_cast<DoubleData*>(data); |
170 |
> |
} |
171 |
> |
|
172 |
> |
if (!fixtime){ |
173 |
> |
sprintf(painCave.errMsg, |
174 |
> |
"ZConstraint error: Can not get property from SimInfo\n"); |
175 |
> |
painCave.isFatal = 1; |
176 |
> |
simError(); |
177 |
> |
} |
178 |
> |
else{ |
179 |
> |
this->zconsFixTime = fixtime->getData(); |
180 |
> |
} |
181 |
> |
|
182 |
> |
|
183 |
> |
|
184 |
> |
//retrieve index of z-constraint molecules |
185 |
> |
data = info->getProperty(ZCONSPARADATA_ID); |
186 |
> |
if (!data){ |
187 |
> |
sprintf(painCave.errMsg, |
188 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
189 |
> |
" , you must set index of z-constraint molecules.\n"); |
190 |
> |
painCave.isFatal = 1; |
191 |
> |
simError(); |
192 |
> |
} |
193 |
> |
else{ |
194 |
> |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
195 |
> |
|
196 |
> |
if (!zConsParaData){ |
197 |
> |
sprintf(painCave.errMsg, |
198 |
> |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
199 |
> |
painCave.isFatal = 1; |
200 |
> |
simError(); |
201 |
> |
} |
202 |
> |
else{ |
203 |
> |
parameters = zConsParaData->getData(); |
204 |
> |
|
205 |
> |
//check the range of zconsIndex |
206 |
> |
//and the minimum value of index is the first one (we already sorted the data) |
207 |
> |
//the maximum value of index is the last one |
208 |
> |
|
209 |
> |
int maxIndex; |
210 |
> |
int minIndex; |
211 |
> |
int totalNumMol; |
212 |
> |
|
213 |
> |
minIndex = (*parameters)[0].zconsIndex; |
214 |
> |
if (minIndex < 0){ |
215 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
216 |
> |
painCave.isFatal = 1; |
217 |
> |
simError(); |
218 |
> |
} |
219 |
> |
|
220 |
> |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
221 |
> |
|
222 |
> |
#ifndef IS_MPI |
223 |
> |
totalNumMol = nMols; |
224 |
> |
#else |
225 |
> |
totalNumMol = mpiSim->getTotNmol(); |
226 |
> |
#endif |
227 |
> |
|
228 |
> |
if (maxIndex > totalNumMol - 1){ |
229 |
> |
sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n"); |
230 |
> |
painCave.isFatal = 1; |
231 |
> |
simError(); |
232 |
> |
} |
233 |
> |
|
234 |
> |
//if user does not specify the zpos for the zconstraint molecule |
235 |
> |
//its initial z coordinate will be used as default |
236 |
> |
for (int i = 0; i < (int) (parameters->size()); i++){ |
237 |
> |
if (!(*parameters)[i].havingZPos){ |
238 |
> |
#ifndef IS_MPI |
239 |
> |
for (int j = 0; j < nMols; j++){ |
240 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 |
> |
molecules[j].getCOM(COM); |
242 |
> |
break; |
243 |
> |
} |
244 |
> |
} |
245 |
> |
#else |
246 |
> |
//query which processor current zconstraint molecule belongs to |
247 |
> |
int* MolToProcMap; |
248 |
> |
int whichNode; |
249 |
> |
|
250 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
251 |
> |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
252 |
> |
|
253 |
> |
//broadcast the zpos of current z-contraint molecule |
254 |
> |
//the node which contain this |
255 |
> |
|
256 |
> |
if (worldRank == whichNode){ |
257 |
> |
for (int j = 0; j < nMols; j++) |
258 |
> |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
259 |
> |
molecules[j].getCOM(COM); |
260 |
> |
break; |
261 |
> |
} |
262 |
> |
} |
263 |
> |
|
264 |
> |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, |
265 |
> |
MPI_COMM_WORLD); |
266 |
> |
#endif |
267 |
> |
|
268 |
> |
(*parameters)[i].zPos = COM[whichDirection]; |
269 |
> |
|
270 |
> |
sprintf(painCave.errMsg, |
271 |
> |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
272 |
> |
"initial z coornidate will be used \n"); |
273 |
> |
painCave.isFatal = 0; |
274 |
> |
simError(); |
275 |
> |
} |
276 |
> |
} |
277 |
> |
}//end if (!zConsParaData) |
278 |
> |
|
279 |
> |
}//end if (!data) |
280 |
> |
|
281 |
> |
// |
282 |
> |
#ifdef IS_MPI |
283 |
> |
update(); |
284 |
> |
#else |
285 |
> |
int searchResult; |
286 |
> |
|
287 |
> |
for (int i = 0; i < nMols; i++){ |
288 |
> |
searchResult = isZConstraintMol(&molecules[i]); |
289 |
> |
|
290 |
> |
if (searchResult > -1){ |
291 |
> |
zconsMols.push_back(&molecules[i]); |
292 |
> |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
293 |
> |
|
294 |
> |
zPos.push_back((*parameters)[searchResult].zPos); |
295 |
> |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
296 |
> |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
297 |
> |
|
298 |
> |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
299 |
> |
molecules[i].getCOM(COM); |
300 |
> |
} |
301 |
> |
else{ |
302 |
> |
unconsMols.push_back(&molecules[i]); |
303 |
> |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
304 |
> |
} |
305 |
> |
} |
306 |
> |
|
307 |
> |
fz = new double[zconsMols.size()]; |
308 |
> |
curZPos = new double[zconsMols.size()]; |
309 |
> |
indexOfZConsMols = new int [zconsMols.size()]; |
310 |
> |
|
311 |
> |
if (!fz || !curZPos || !indexOfZConsMols){ |
312 |
> |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
313 |
> |
painCave.isFatal = 1; |
314 |
> |
simError(); |
315 |
> |
} |
316 |
> |
|
317 |
> |
//determine the states of z-constraint molecules |
318 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
319 |
> |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
320 |
> |
|
321 |
> |
zconsMols[i]->getCOM(COM); |
322 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
323 |
> |
states.push_back(zcsFixed); |
324 |
> |
|
325 |
> |
if (hasZConsGap) |
326 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
327 |
> |
} |
328 |
> |
else{ |
329 |
> |
states.push_back(zcsMoving); |
330 |
> |
|
331 |
> |
if (hasZConsGap) |
332 |
> |
endFixTime.push_back(INFINITE_TIME); |
333 |
> |
} |
334 |
> |
} |
335 |
> |
|
336 |
> |
#endif |
337 |
> |
|
338 |
> |
//get total masss of unconstraint molecules |
339 |
> |
double totalMassOfUncons_local; |
340 |
> |
totalMassOfUncons_local = 0; |
341 |
> |
|
342 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++) |
343 |
> |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
344 |
> |
|
345 |
> |
#ifndef IS_MPI |
346 |
> |
totalMassOfUncons = totalMassOfUncons_local; |
347 |
> |
#else |
348 |
> |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE, |
349 |
> |
MPI_SUM, MPI_COMM_WORLD); |
350 |
> |
#endif |
351 |
> |
|
352 |
> |
//get total number of unconstrained atoms |
353 |
> |
int nUnconsAtoms_local; |
354 |
> |
nUnconsAtoms_local = 0; |
355 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++) |
356 |
> |
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
357 |
> |
|
358 |
> |
#ifndef IS_MPI |
359 |
> |
totNumOfUnconsAtoms = nUnconsAtoms_local; |
360 |
> |
#else |
361 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM, |
362 |
> |
MPI_COMM_WORLD); |
363 |
> |
#endif |
364 |
> |
|
365 |
> |
forcePolicy->update(); |
366 |
> |
} |
367 |
> |
|
368 |
> |
template<typename T> ZConstraint<T>::~ZConstraint(){ |
369 |
> |
if (fz){ |
370 |
> |
delete[] fz; |
371 |
> |
} |
372 |
> |
|
373 |
> |
if (curZPos){ |
374 |
> |
delete[] curZPos; |
375 |
> |
} |
376 |
> |
|
377 |
> |
if (indexOfZConsMols){ |
378 |
> |
delete[] indexOfZConsMols; |
379 |
> |
} |
380 |
> |
|
381 |
> |
if (fzOut){ |
382 |
> |
delete fzOut; |
383 |
> |
} |
384 |
> |
|
385 |
> |
if (forcePolicy){ |
386 |
> |
delete forcePolicy; |
387 |
> |
} |
388 |
> |
} |
389 |
> |
|
390 |
> |
|
391 |
> |
/** |
392 |
> |
* |
393 |
> |
*/ |
394 |
> |
|
395 |
> |
#ifdef IS_MPI |
396 |
> |
template<typename T> void ZConstraint<T>::update(){ |
397 |
> |
double COM[3]; |
398 |
> |
int index; |
399 |
> |
|
400 |
> |
zconsMols.clear(); |
401 |
> |
massOfZConsMols.clear(); |
402 |
> |
zPos.clear(); |
403 |
> |
kz.clear(); |
404 |
> |
|
405 |
> |
unconsMols.clear(); |
406 |
> |
massOfUnconsMols.clear(); |
407 |
> |
|
408 |
> |
|
409 |
> |
//creat zconsMol and unconsMol lists |
410 |
> |
for (int i = 0; i < nMols; i++){ |
411 |
> |
index = isZConstraintMol(&molecules[i]); |
412 |
> |
|
413 |
> |
if (index > -1){ |
414 |
> |
zconsMols.push_back(&molecules[i]); |
415 |
> |
zPos.push_back((*parameters)[index].zPos); |
416 |
> |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
417 |
> |
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
418 |
> |
|
419 |
> |
molecules[i].getCOM(COM); |
420 |
> |
} |
421 |
> |
else{ |
422 |
> |
unconsMols.push_back(&molecules[i]); |
423 |
> |
massOfUnconsMols.push_back(molecules[i].getTotalMass()); |
424 |
> |
} |
425 |
> |
} |
426 |
> |
|
427 |
> |
|
428 |
> |
//The reason to declare fz and indexOfZconsMols as pointer to array is |
429 |
> |
// that we want to make the MPI communication simple |
430 |
> |
if (fz){ |
431 |
> |
delete[] fz; |
432 |
> |
} |
433 |
> |
|
434 |
> |
if (curZPos){ |
435 |
> |
delete[] curZPos; |
436 |
> |
} |
437 |
> |
|
438 |
> |
if (indexOfZConsMols){ |
439 |
> |
delete[] indexOfZConsMols; |
440 |
> |
} |
441 |
> |
|
442 |
> |
if (zconsMols.size() > 0){ |
443 |
> |
fz = new double[zconsMols.size()]; |
444 |
> |
curZPos = new double[zconsMols.size()]; |
445 |
> |
indexOfZConsMols = new int[zconsMols.size()]; |
446 |
> |
|
447 |
> |
if (!fz || !curZPos || !indexOfZConsMols){ |
448 |
> |
sprintf(painCave.errMsg, |
449 |
> |
"Memory allocation failure in class Zconstraint\n"); |
450 |
> |
painCave.isFatal = 1; |
451 |
> |
simError(); |
452 |
> |
} |
453 |
> |
|
454 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
455 |
> |
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
456 |
> |
} |
457 |
> |
} |
458 |
> |
else{ |
459 |
> |
fz = NULL; |
460 |
> |
curZPos = NULL; |
461 |
> |
indexOfZConsMols = NULL; |
462 |
> |
} |
463 |
> |
|
464 |
> |
//determine the states of z-constraint molecules |
465 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
466 |
> |
zconsMols[i]->getCOM(COM); |
467 |
> |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){ |
468 |
> |
states.push_back(zcsFixed); |
469 |
> |
|
470 |
> |
if (hasZConsGap) |
471 |
> |
endFixTime.push_back(info->getTime() + zconsFixTime); |
472 |
> |
} |
473 |
> |
else{ |
474 |
> |
states.push_back(zcsMoving); |
475 |
> |
|
476 |
> |
if (hasZConsGap) |
477 |
> |
endFixTime.push_back(INFINITE_TIME); |
478 |
> |
} |
479 |
> |
} |
480 |
> |
// |
481 |
> |
forcePolicy->update(); |
482 |
> |
} |
483 |
> |
|
484 |
> |
#endif |
485 |
> |
|
486 |
> |
/** |
487 |
> |
* Function Name: isZConstraintMol |
488 |
> |
* Parameter |
489 |
> |
* Molecule* mol |
490 |
> |
* Return value: |
491 |
> |
* -1, if the molecule is not z-constraint molecule, |
492 |
> |
* other non-negative values, its index in indexOfAllZConsMols vector |
493 |
> |
*/ |
494 |
> |
|
495 |
> |
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){ |
496 |
> |
int index; |
497 |
> |
int low; |
498 |
> |
int high; |
499 |
> |
int mid; |
500 |
> |
|
501 |
> |
index = mol->getGlobalIndex(); |
502 |
> |
|
503 |
> |
low = 0; |
504 |
> |
high = parameters->size() - 1; |
505 |
> |
|
506 |
> |
//Binary Search (we have sorted the array) |
507 |
> |
while (low <= high){ |
508 |
> |
mid = (low + high) / 2; |
509 |
> |
if ((*parameters)[mid].zconsIndex == index) |
510 |
> |
return mid; |
511 |
> |
else if ((*parameters)[mid].zconsIndex > index) |
512 |
> |
high = mid - 1; |
513 |
> |
else |
514 |
> |
low = mid + 1; |
515 |
> |
} |
516 |
> |
|
517 |
> |
return -1; |
518 |
> |
} |
519 |
> |
|
520 |
> |
template<typename T> void ZConstraint<T>::integrate(){ |
521 |
> |
// creat zconsWriter |
522 |
> |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
523 |
> |
|
524 |
> |
if (!fzOut){ |
525 |
> |
sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n"); |
526 |
> |
painCave.isFatal = 1; |
527 |
> |
simError(); |
528 |
> |
} |
529 |
> |
|
530 |
> |
//zero out the velocities of center of mass of unconstrained molecules |
531 |
> |
//and the velocities of center of mass of every single z-constrained molecueles |
532 |
> |
zeroOutVel(); |
533 |
> |
|
534 |
> |
curZconsTime = zconsTime + info->getTime(); |
535 |
> |
|
536 |
> |
T::integrate(); |
537 |
> |
} |
538 |
> |
|
539 |
> |
|
540 |
> |
/** |
541 |
> |
* |
542 |
> |
* |
543 |
> |
* |
544 |
> |
* |
545 |
> |
*/ |
546 |
> |
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
547 |
> |
double zsys; |
548 |
> |
double COM[3]; |
549 |
> |
double force[3]; |
550 |
> |
double zSysCOMVel; |
551 |
> |
|
552 |
> |
T::calcForce(calcPot, calcStress); |
553 |
> |
|
554 |
> |
|
555 |
> |
if (hasZConsGap){ |
556 |
> |
updateZPos(); |
557 |
> |
} |
558 |
> |
|
559 |
> |
if (checkZConsState()){ |
560 |
> |
zeroOutVel(); |
561 |
> |
forcePolicy->update(); |
562 |
> |
} |
563 |
> |
|
564 |
> |
zsys = calcZSys(); |
565 |
> |
zSysCOMVel = calcSysCOMVel(); |
566 |
> |
#ifdef IS_MPI |
567 |
> |
if (worldRank == 0){ |
568 |
> |
#endif |
569 |
> |
//cout << "---------------------------------------------------------------------" <<endl; |
570 |
> |
//cout << "current time: " << info->getTime() << endl; |
571 |
> |
//cout << "center of mass at z: " << zsys << endl; |
572 |
> |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
573 |
> |
|
574 |
> |
#ifdef IS_MPI |
575 |
> |
} |
576 |
> |
#endif |
577 |
> |
|
578 |
> |
//do zconstraint force; |
579 |
> |
if (haveFixedZMols()){ |
580 |
> |
this->doZconstraintForce(); |
581 |
> |
} |
582 |
> |
|
583 |
> |
//use harmonical poteintial to move the molecules to the specified positions |
584 |
> |
if (haveMovingZMols()){ |
585 |
> |
this->doHarmonic(); |
586 |
> |
} |
587 |
> |
|
588 |
> |
//write out forces and current positions of z-constraint molecules |
589 |
> |
if (info->getTime() >= curZconsTime){ |
590 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
591 |
> |
zconsMols[i]->getCOM(COM); |
592 |
> |
curZPos[i] = COM[whichDirection]; |
593 |
> |
|
594 |
> |
//if the z-constraint molecule is still moving, just record its force |
595 |
> |
if (states[i] == zcsMoving){ |
596 |
> |
fz[i] = 0; |
597 |
> |
Atom** movingZAtoms; |
598 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
599 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
600 |
> |
movingZAtoms[j]->getFrc(force); |
601 |
> |
fz[i] += force[whichDirection]; |
602 |
> |
} |
603 |
> |
} |
604 |
> |
} |
605 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, |
606 |
> |
curZPos, &zPos[0]); |
607 |
> |
curZconsTime += zconsTime; |
608 |
> |
} |
609 |
> |
|
610 |
> |
zSysCOMVel = calcSysCOMVel(); |
611 |
> |
#ifdef IS_MPI |
612 |
> |
if (worldRank == 0){ |
613 |
> |
#endif |
614 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
615 |
> |
#ifdef IS_MPI |
616 |
> |
} |
617 |
> |
#endif |
618 |
> |
} |
619 |
> |
|
620 |
> |
|
621 |
> |
/** |
622 |
> |
* |
623 |
> |
*/ |
624 |
> |
|
625 |
> |
template<typename T> double ZConstraint<T>::calcZSys(){ |
626 |
> |
//calculate reference z coordinate for z-constraint molecules |
627 |
> |
double totalMass_local; |
628 |
> |
double totalMass; |
629 |
> |
double totalMZ_local; |
630 |
> |
double totalMZ; |
631 |
> |
double massOfCurMol; |
632 |
> |
double COM[3]; |
633 |
> |
|
634 |
> |
totalMass_local = 0; |
635 |
> |
totalMZ_local = 0; |
636 |
> |
|
637 |
> |
for (int i = 0; i < nMols; i++){ |
638 |
> |
massOfCurMol = molecules[i].getTotalMass(); |
639 |
> |
molecules[i].getCOM(COM); |
640 |
> |
|
641 |
> |
totalMass_local += massOfCurMol; |
642 |
> |
totalMZ_local += massOfCurMol * COM[whichDirection]; |
643 |
> |
} |
644 |
> |
|
645 |
> |
|
646 |
> |
#ifdef IS_MPI |
647 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM, |
648 |
> |
MPI_COMM_WORLD); |
649 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
650 |
> |
#else |
651 |
> |
totalMass = totalMass_local; |
652 |
> |
totalMZ = totalMZ_local; |
653 |
> |
#endif |
654 |
> |
|
655 |
> |
double zsys; |
656 |
> |
zsys = totalMZ / totalMass; |
657 |
> |
|
658 |
> |
return zsys; |
659 |
> |
} |
660 |
> |
|
661 |
> |
/** |
662 |
> |
* |
663 |
> |
*/ |
664 |
> |
template<typename T> void ZConstraint<T>::thermalize(void){ |
665 |
> |
T::thermalize(); |
666 |
> |
zeroOutVel(); |
667 |
> |
} |
668 |
> |
|
669 |
> |
/** |
670 |
> |
* |
671 |
> |
*/ |
672 |
> |
|
673 |
> |
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
674 |
> |
Atom** fixedZAtoms; |
675 |
> |
double COMvel[3]; |
676 |
> |
double vel[3]; |
677 |
> |
double zSysCOMVel; |
678 |
> |
|
679 |
> |
//zero out the velocities of center of mass of fixed z-constrained molecules |
680 |
> |
|
681 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
682 |
> |
if (states[i] == zcsFixed){ |
683 |
> |
zconsMols[i]->getCOMvel(COMvel); |
684 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
685 |
> |
|
686 |
> |
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
687 |
> |
|
688 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
689 |
> |
fixedZAtoms[j]->getVel(vel); |
690 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
691 |
> |
fixedZAtoms[j]->setVel(vel); |
692 |
> |
} |
693 |
> |
|
694 |
> |
zconsMols[i]->getCOMvel(COMvel); |
695 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
696 |
> |
} |
697 |
> |
} |
698 |
> |
|
699 |
> |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
700 |
> |
|
701 |
> |
zSysCOMVel = calcSysCOMVel(); |
702 |
> |
#ifdef IS_MPI |
703 |
> |
if (worldRank == 0){ |
704 |
> |
#endif |
705 |
> |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
706 |
> |
#ifdef IS_MPI |
707 |
> |
} |
708 |
> |
#endif |
709 |
> |
|
710 |
> |
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
711 |
> |
double MVzOfMovingMols_local; |
712 |
> |
double MVzOfMovingMols; |
713 |
> |
double totalMassOfMovingZMols_local; |
714 |
> |
double totalMassOfMovingZMols; |
715 |
> |
|
716 |
> |
MVzOfMovingMols_local = 0; |
717 |
> |
totalMassOfMovingZMols_local = 0; |
718 |
> |
|
719 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
720 |
> |
unconsMols[i]->getCOMvel(COMvel); |
721 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
722 |
> |
} |
723 |
> |
|
724 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
725 |
> |
if (states[i] == zcsMoving){ |
726 |
> |
zconsMols[i]->getCOMvel(COMvel); |
727 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
728 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
729 |
> |
} |
730 |
> |
} |
731 |
> |
|
732 |
> |
#ifndef IS_MPI |
733 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
734 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
735 |
> |
#else |
736 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
737 |
> |
MPI_SUM, MPI_COMM_WORLD); |
738 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
739 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
740 |
> |
#endif |
741 |
> |
|
742 |
> |
double vzOfMovingMols; |
743 |
> |
vzOfMovingMols = MVzOfMovingMols / |
744 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
745 |
> |
|
746 |
> |
//modify the velocites of unconstrained molecules |
747 |
> |
Atom** unconsAtoms; |
748 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
749 |
> |
unconsAtoms = unconsMols[i]->getMyAtoms(); |
750 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
751 |
> |
unconsAtoms[j]->getVel(vel); |
752 |
> |
vel[whichDirection] -= vzOfMovingMols; |
753 |
> |
unconsAtoms[j]->setVel(vel); |
754 |
> |
} |
755 |
> |
} |
756 |
> |
|
757 |
> |
//modify the velocities of moving z-constrained molecuels |
758 |
> |
Atom** movingZAtoms; |
759 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
760 |
> |
if (states[i] == zcsMoving){ |
761 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
762 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
763 |
> |
movingZAtoms[j]->getVel(vel); |
764 |
> |
vel[whichDirection] -= vzOfMovingMols; |
765 |
> |
movingZAtoms[j]->setVel(vel); |
766 |
> |
} |
767 |
> |
} |
768 |
> |
} |
769 |
> |
|
770 |
> |
|
771 |
> |
zSysCOMVel = calcSysCOMVel(); |
772 |
> |
#ifdef IS_MPI |
773 |
> |
if (worldRank == 0){ |
774 |
> |
#endif |
775 |
> |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
776 |
> |
#ifdef IS_MPI |
777 |
> |
} |
778 |
> |
#endif |
779 |
> |
} |
780 |
> |
|
781 |
> |
/** |
782 |
> |
* |
783 |
> |
*/ |
784 |
> |
|
785 |
> |
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
786 |
> |
Atom** zconsAtoms; |
787 |
> |
double totalFZ; |
788 |
> |
double totalFZ_local; |
789 |
> |
double COM[3]; |
790 |
> |
double force[3]; |
791 |
> |
|
792 |
> |
//constrain the molecules which do not reach the specified positions |
793 |
> |
|
794 |
> |
//Zero Out the force of z-contrained molecules |
795 |
> |
totalFZ_local = 0; |
796 |
> |
|
797 |
> |
//calculate the total z-contrained force of fixed z-contrained molecules |
798 |
> |
|
799 |
> |
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
800 |
> |
// << "total force is " << calcTotalForce() << endl; |
801 |
> |
|
802 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
803 |
> |
if (states[i] == zcsFixed){ |
804 |
> |
zconsMols[i]->getCOM(COM); |
805 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
806 |
> |
|
807 |
> |
fz[i] = 0; |
808 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
809 |
> |
zconsAtoms[j]->getFrc(force); |
810 |
> |
fz[i] += force[whichDirection]; |
811 |
> |
} |
812 |
> |
totalFZ_local += fz[i]; |
813 |
> |
|
814 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
815 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
816 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
817 |
> |
} |
818 |
> |
} |
819 |
> |
|
820 |
> |
//calculate total z-constraint force |
821 |
> |
#ifdef IS_MPI |
822 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
823 |
> |
#else |
824 |
> |
totalFZ = totalFZ_local; |
825 |
> |
#endif |
826 |
> |
|
827 |
> |
|
828 |
> |
// apply negative to fixed z-constrained molecues; |
829 |
> |
force[0] = 0; |
830 |
> |
force[1] = 0; |
831 |
> |
force[2] = 0; |
832 |
> |
|
833 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
834 |
> |
if (states[i] == zcsFixed){ |
835 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
836 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
837 |
> |
|
838 |
> |
for (int j = 0; j < nAtomOfCurZConsMol; j++){ |
839 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
840 |
> |
force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i], |
841 |
> |
zconsAtoms[j], |
842 |
> |
fz[i]); |
843 |
> |
zconsAtoms[j]->addFrc(force); |
844 |
> |
} |
845 |
> |
} |
846 |
> |
} |
847 |
> |
|
848 |
> |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
849 |
> |
// << "total force is " << calcTotalForce() << endl; |
850 |
> |
|
851 |
> |
|
852 |
> |
force[0] = 0; |
853 |
> |
force[1] = 0; |
854 |
> |
force[2] = 0; |
855 |
> |
|
856 |
> |
//modify the forces of unconstrained molecules |
857 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
858 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
859 |
> |
|
860 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
861 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
862 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j], |
863 |
> |
totalFZ); |
864 |
> |
unconsAtoms[j]->addFrc(force); |
865 |
> |
} |
866 |
> |
} |
867 |
> |
|
868 |
> |
//modify the forces of moving z-constrained molecules |
869 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
870 |
> |
if (states[i] == zcsMoving){ |
871 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
872 |
> |
|
873 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
874 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
875 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j], |
876 |
> |
totalFZ); |
877 |
> |
movingZAtoms[j]->addFrc(force); |
878 |
> |
} |
879 |
> |
} |
880 |
> |
} |
881 |
> |
// cout << "after substracting z-constraint force from moving molecuels " |
882 |
> |
// << "total force is " << calcTotalForce() << endl; |
883 |
> |
} |
884 |
> |
|
885 |
> |
/** |
886 |
> |
* |
887 |
> |
* |
888 |
> |
*/ |
889 |
> |
|
890 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
891 |
> |
double force[3]; |
892 |
> |
double harmonicU; |
893 |
> |
double harmonicF; |
894 |
> |
double COM[3]; |
895 |
> |
double diff; |
896 |
> |
double totalFZ_local; |
897 |
> |
double totalFZ; |
898 |
> |
|
899 |
> |
force[0] = 0; |
900 |
> |
force[1] = 0; |
901 |
> |
force[2] = 0; |
902 |
> |
|
903 |
> |
totalFZ_local = 0; |
904 |
> |
|
905 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
906 |
> |
if (states[i] == zcsMoving){ |
907 |
> |
zconsMols[i]->getCOM(COM); |
908 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
909 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
910 |
> |
|
911 |
> |
diff = COM[whichDirection] - zPos[i]; |
912 |
> |
|
913 |
> |
harmonicU = 0.5 * kz[i] * diff * diff; |
914 |
> |
info->lrPot += harmonicU; |
915 |
> |
|
916 |
> |
harmonicF = -kz[i] * diff; |
917 |
> |
totalFZ_local += harmonicF; |
918 |
> |
|
919 |
> |
//adjust force |
920 |
> |
|
921 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
922 |
> |
|
923 |
> |
for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
924 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
925 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], |
926 |
> |
movingZAtoms[j], |
927 |
> |
harmonicF); |
928 |
> |
movingZAtoms[j]->addFrc(force); |
929 |
> |
} |
930 |
> |
} |
931 |
> |
} |
932 |
> |
|
933 |
> |
#ifndef IS_MPI |
934 |
> |
totalFZ = totalFZ_local; |
935 |
> |
#else |
936 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
937 |
> |
#endif |
938 |
> |
|
939 |
> |
//cout << "before substracting harmonic force from moving molecuels " |
940 |
> |
// << "total force is " << calcTotalForce() << endl; |
941 |
> |
|
942 |
> |
force[0] = 0; |
943 |
> |
force[1] = 0; |
944 |
> |
force[2] = 0; |
945 |
> |
|
946 |
> |
//modify the forces of unconstrained molecules |
947 |
> |
for (int i = 0; i < (int) (unconsMols.size()); i++){ |
948 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
949 |
> |
|
950 |
> |
for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
951 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
952 |
> |
force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j], |
953 |
> |
totalFZ); |
954 |
> |
unconsAtoms[j]->addFrc(force); |
955 |
> |
} |
956 |
> |
} |
957 |
> |
|
958 |
> |
//cout << "after substracting harmonic force from moving molecuels " |
959 |
> |
// << "total force is " << calcTotalForce() << endl; |
960 |
> |
} |
961 |
> |
|
962 |
> |
/** |
963 |
> |
* |
964 |
> |
*/ |
965 |
> |
|
966 |
> |
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
967 |
> |
double COM[3]; |
968 |
> |
double diff; |
969 |
> |
|
970 |
> |
int changed_local; |
971 |
> |
int changed; |
972 |
> |
|
973 |
> |
changed_local = 0; |
974 |
> |
|
975 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++){ |
976 |
> |
zconsMols[i]->getCOM(COM); |
977 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
978 |
> |
if (diff <= zconsTol && states[i] == zcsMoving){ |
979 |
> |
states[i] = zcsFixed; |
980 |
> |
changed_local = 1; |
981 |
> |
|
982 |
> |
if (hasZConsGap) |
983 |
> |
endFixTime[i] = info->getTime() + zconsFixTime; |
984 |
> |
} |
985 |
> |
else if (diff > zconsTol && states[i] == zcsFixed){ |
986 |
> |
states[i] = zcsMoving; |
987 |
> |
changed_local = 1; |
988 |
> |
|
989 |
> |
if (hasZConsGap) |
990 |
> |
endFixTime[i] = INFINITE_TIME; |
991 |
> |
} |
992 |
> |
} |
993 |
> |
|
994 |
> |
#ifndef IS_MPI |
995 |
> |
changed = changed_local; |
996 |
> |
#else |
997 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
998 |
> |
#endif |
999 |
> |
|
1000 |
> |
return (changed > 0); |
1001 |
> |
} |
1002 |
> |
|
1003 |
> |
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
1004 |
> |
int havingFixed_local; |
1005 |
> |
int havingFixed; |
1006 |
> |
|
1007 |
> |
havingFixed_local = 0; |
1008 |
> |
|
1009 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1010 |
> |
if (states[i] == zcsFixed){ |
1011 |
> |
havingFixed_local = 1; |
1012 |
> |
break; |
1013 |
> |
} |
1014 |
> |
|
1015 |
> |
#ifndef IS_MPI |
1016 |
> |
havingFixed = havingFixed_local; |
1017 |
> |
#else |
1018 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM, |
1019 |
> |
MPI_COMM_WORLD); |
1020 |
> |
#endif |
1021 |
> |
|
1022 |
> |
return (havingFixed > 0); |
1023 |
> |
} |
1024 |
> |
|
1025 |
> |
|
1026 |
> |
/** |
1027 |
> |
* |
1028 |
> |
*/ |
1029 |
> |
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
1030 |
> |
int havingMoving_local; |
1031 |
> |
int havingMoving; |
1032 |
> |
|
1033 |
> |
havingMoving_local = 0; |
1034 |
> |
|
1035 |
> |
for (int i = 0; i < (int) (zconsMols.size()); i++) |
1036 |
> |
if (states[i] == zcsMoving){ |
1037 |
> |
havingMoving_local = 1; |
1038 |
> |
break; |
1039 |
> |
} |
1040 |
> |
|
1041 |
> |
#ifndef IS_MPI |
1042 |
> |
havingMoving = havingMoving_local; |
1043 |
> |
#else |
1044 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM, |
1045 |
> |
MPI_COMM_WORLD); |
1046 |
> |
#endif |
1047 |
> |
|
1048 |
> |
return (havingMoving > 0); |
1049 |
> |
} |
1050 |
> |
|
1051 |
> |
/** |
1052 |
> |
* |
1053 |
> |
*/ |
1054 |
> |
|
1055 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){ |
1056 |
> |
double MVzOfMovingMols_local; |
1057 |
> |
double MVzOfMovingMols; |
1058 |
> |
double totalMassOfMovingZMols_local; |
1059 |
> |
double totalMassOfMovingZMols; |
1060 |
> |
double COMvel[3]; |
1061 |
> |
|
1062 |
> |
MVzOfMovingMols_local = 0; |
1063 |
> |
totalMassOfMovingZMols_local = 0; |
1064 |
> |
|
1065 |
> |
for (int i = 0; i < unconsMols.size(); i++){ |
1066 |
> |
unconsMols[i]->getCOMvel(COMvel); |
1067 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1068 |
> |
} |
1069 |
> |
|
1070 |
> |
for (int i = 0; i < zconsMols.size(); i++){ |
1071 |
> |
if (states[i] == zcsMoving){ |
1072 |
> |
zconsMols[i]->getCOMvel(COMvel); |
1073 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1074 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1075 |
> |
} |
1076 |
> |
} |
1077 |
> |
|
1078 |
> |
#ifndef IS_MPI |
1079 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
1080 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1081 |
> |
#else |
1082 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE, |
1083 |
> |
MPI_SUM, MPI_COMM_WORLD); |
1084 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, |
1085 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1086 |
> |
#endif |
1087 |
> |
|
1088 |
> |
double vzOfMovingMols; |
1089 |
> |
vzOfMovingMols = MVzOfMovingMols / |
1090 |
> |
(totalMassOfUncons + totalMassOfMovingZMols); |
1091 |
> |
|
1092 |
> |
return vzOfMovingMols; |
1093 |
> |
} |
1094 |
> |
|
1095 |
> |
/** |
1096 |
> |
* |
1097 |
> |
*/ |
1098 |
> |
|
1099 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel(){ |
1100 |
> |
double COMvel[3]; |
1101 |
> |
double tempMVz_local; |
1102 |
> |
double tempMVz; |
1103 |
> |
double massOfZCons_local; |
1104 |
> |
double massOfZCons; |
1105 |
> |
|
1106 |
> |
|
1107 |
> |
tempMVz_local = 0; |
1108 |
> |
|
1109 |
> |
for (int i = 0 ; i < nMols; i++){ |
1110 |
> |
molecules[i].getCOMvel(COMvel); |
1111 |
> |
tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection]; |
1112 |
> |
} |
1113 |
> |
|
1114 |
> |
massOfZCons_local = 0; |
1115 |
> |
|
1116 |
> |
for (int i = 0; i < (int) (massOfZConsMols.size()); i++){ |
1117 |
> |
massOfZCons_local += massOfZConsMols[i]; |
1118 |
> |
} |
1119 |
> |
#ifndef IS_MPI |
1120 |
> |
massOfZCons = massOfZCons_local; |
1121 |
> |
tempMVz = tempMVz_local; |
1122 |
> |
#else |
1123 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM, |
1124 |
> |
MPI_COMM_WORLD); |
1125 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
1126 |
> |
#endif |
1127 |
> |
|
1128 |
> |
return tempMVz / (totalMassOfUncons + massOfZCons); |
1129 |
> |
} |
1130 |
> |
|
1131 |
> |
/** |
1132 |
> |
* |
1133 |
> |
*/ |
1134 |
> |
|
1135 |
> |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1136 |
> |
double force[3]; |
1137 |
> |
double totalForce_local; |
1138 |
> |
double totalForce; |
1139 |
> |
|
1140 |
> |
totalForce_local = 0; |
1141 |
> |
|
1142 |
> |
for (int i = 0; i < nAtoms; i++){ |
1143 |
> |
atoms[i]->getFrc(force); |
1144 |
> |
totalForce_local += force[whichDirection]; |
1145 |
> |
} |
1146 |
> |
|
1147 |
> |
#ifndef IS_MPI |
1148 |
> |
totalForce = totalForce_local; |
1149 |
> |
#else |
1150 |
> |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM, |
1151 |
> |
MPI_COMM_WORLD); |
1152 |
> |
#endif |
1153 |
> |
|
1154 |
> |
return totalForce; |
1155 |
> |
} |
1156 |
> |
|
1157 |
> |
/** |
1158 |
> |
* |
1159 |
> |
*/ |
1160 |
> |
|
1161 |
> |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1162 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1163 |
> |
int nMovingZAtoms_local; |
1164 |
> |
int nMovingZAtoms; |
1165 |
> |
|
1166 |
> |
nMovingZAtoms_local = 0; |
1167 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1168 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1169 |
> |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1170 |
> |
} |
1171 |
> |
|
1172 |
> |
#ifdef IS_MPI |
1173 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, |
1174 |
> |
MPI_COMM_WORLD); |
1175 |
> |
#else |
1176 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
1177 |
> |
#endif |
1178 |
> |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1179 |
> |
} |
1180 |
> |
|
1181 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, |
1182 |
> |
Atom* atom, |
1183 |
> |
double totalForce){ |
1184 |
> |
return totalForce / mol->getNAtoms(); |
1185 |
> |
} |
1186 |
> |
|
1187 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, |
1188 |
> |
double totalForce){ |
1189 |
> |
return totalForce / totNumOfMovingAtoms; |
1190 |
> |
} |
1191 |
> |
|
1192 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, |
1193 |
> |
Atom* atom, |
1194 |
> |
double totalForce){ |
1195 |
> |
return totalForce / mol->getNAtoms(); |
1196 |
> |
} |
1197 |
> |
|
1198 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, |
1199 |
> |
double totalForce){ |
1200 |
> |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1201 |
> |
} |
1202 |
> |
|
1203 |
> |
/** |
1204 |
> |
* |
1205 |
> |
*/ |
1206 |
> |
|
1207 |
> |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1208 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1209 |
> |
double massOfMovingZAtoms_local; |
1210 |
> |
double massOfMovingZAtoms; |
1211 |
> |
|
1212 |
> |
massOfMovingZAtoms_local = 0; |
1213 |
> |
for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++) |
1214 |
> |
if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){ |
1215 |
> |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1216 |
> |
} |
1217 |
> |
|
1218 |
> |
#ifdef IS_MPI |
1219 |
> |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE, |
1220 |
> |
MPI_SUM, MPI_COMM_WORLD); |
1221 |
> |
#else |
1222 |
> |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1223 |
> |
#endif |
1224 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms + |
1225 |
> |
zconsIntegrator->totalMassOfUncons; |
1226 |
> |
} |
1227 |
> |
|
1228 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, |
1229 |
> |
Atom* atom, |
1230 |
> |
double totalForce){ |
1231 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1232 |
> |
} |
1233 |
> |
|
1234 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom, |
1235 |
> |
double totalForce){ |
1236 |
> |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1237 |
> |
} |
1238 |
> |
|
1239 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, |
1240 |
> |
Atom* atom, |
1241 |
> |
double totalForce){ |
1242 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1243 |
> |
} |
1244 |
> |
|
1245 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, |
1246 |
> |
double totalForce){ |
1247 |
> |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1248 |
> |
} |
1249 |
> |
|
1250 |
> |
template<typename T> void ZConstraint<T>::updateZPos(){ |
1251 |
> |
double curTime; |
1252 |
> |
|
1253 |
> |
curTime = info->getTime(); |
1254 |
> |
|
1255 |
> |
for (size_t i = 0; i < zconsMols.size(); i++){ |
1256 |
> |
if (states[i] == zcsFixed && curTime >= endFixTime[i]){ |
1257 |
> |
zPos[i] += zconsGap; |
1258 |
> |
} |
1259 |
> |
} |
1260 |
> |
} |