src/utils/Accumulator.hpp

/*
 * Copyright (c) 2012 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifndef UTILS_ACCUMULATOR_HPP
#define UTILS_ACCUMULATOR_HPP

#include <cmath>
#include <cassert>
#include "math/Vector3.hpp"

namespace OpenMD {

  /** 
   * Basic Accumulator class for numbers. 
   */
  
  class Accumulator {    

    typedef RealType ElementType;
    typedef RealType ResultType;

  public:
    
    Accumulator() {
      this->clear();
    }

    /**
     * Accumulate another value
     */
    virtual void add(ElementType const& val) {
      Count_++;
      Avg_  += (val       - Avg_ ) / Count_;
      Avg2_ += (val * val - Avg2_) / Count_;
      Val_   = val;
      if (Count_ <= 1) {
        Max_ = val;
        Min_ = val;
      } else {
        Max_ = val > Max_ ? val : Max_;
        Min_ = val < Min_ ? val : Min_;
      }
    }
    
    /**
     * reset the Accumulator to the empty state
     */
    void clear() {
      Count_ = 0;
      Avg_   = 0;
      Avg2_  = 0;
      Val_   = 0;
    }
    
    /**
     * get the number of accumulated values
     */
    size_t count()  {
      return Count_;
    }

    /**
     * return the most recently added value
     */
    void getLastValue(ElementType &ret)  {
      ret = Val_;
      return;
    }    

    /**
     * compute the Mean
     */
    void getAverage(ResultType &ret)  {
      assert(Count_ != 0);
      ret = Avg_;
      return;
    }

    /**
     * compute the Variance
     */
    void getVariance(ResultType &ret)  {
      assert(Count_ != 0);
      ret = (Avg2_ - Avg_  * Avg_);
      return;
    }
    
    /**
     * compute error of average value
     */
    void getStdDev(ResultType &ret)  {
      assert(Count_ != 0);
      RealType var;
      this->getVariance(var);
      ret = sqrt(var);
      return;
    }

    /**
     * return the largest value
     */
    void getMax(ElementType &ret)  {
      assert(Count_ != 0);
      ret = Max_;
      return;
    }

    /**
     * return the smallest value
     */
    void getMin(ElementType &ret)  {
      assert(Count_ != 0);
      ret = Max_;
      return;
    }

  protected:
    size_t Count_;
  private:
    ElementType Val_;
    ResultType Avg_;
    ResultType Avg2_;
    ElementType Min_;
    ElementType Max_;
  };

  class VectorAccumulator : public Accumulator {
    
    typedef Vector3d ElementType;
    typedef Vector3d ResultType;
    
  public:
    VectorAccumulator() : Accumulator() {
      this->clear();
    }

    /**
     * Accumulate another value
     */
    void add(ElementType const& val) {
      Count_++;
      RealType len(0.0);
      for (unsigned int i =0; i < 3; i++) {
        Avg_[i]  += (val[i]       - Avg_[i] ) / Count_;
        Avg2_[i] += (val[i] * val[i] - Avg2_[i]) / Count_;
        Val_[i]   = val[i];
        len += val[i]*val[i];
      }
      len = sqrt(len);
      AvgLen_  += (len       - AvgLen_ ) / Count_;
      AvgLen2_ += (len * len - AvgLen2_) / Count_;

      if (Count_ <= 1) {
        Max_ = len;
        Min_ = len;
      } else {
        Max_ = len > Max_ ? len : Max_;
        Min_ = len < Min_ ? len : Min_;
      }
    }

    /**
     * reset the Accumulator to the empty state
     */
    void clear() {
      Count_ = 0;
      Avg_ = V3Zero;
      Avg2_ = V3Zero;
      Val_ = V3Zero;
      AvgLen_   = 0;
      AvgLen2_  = 0;
    }
    
    /**
     * return the most recently added value
     */
    void getLastValue(ElementType &ret) {
      ret = Val_;
      return;
    }
    
    /**
     * compute the Mean
     */
    void getAverage(ResultType &ret) {
      assert(Count_ != 0);
      ret = Avg_;
      return;
    }
    
    /**
     * compute the Variance
     */
    void getVariance(ResultType &ret) {
      assert(Count_ != 0);
      for (unsigned int i =0; i < 3; i++) {
        ret[i] = (Avg2_[i] - Avg_[i]  * Avg_[i]);
      }
      return;
    }
    
    /**
     * compute error of average value
     */
    void getStdDev(ResultType &ret) {
      assert(Count_ != 0);
      ResultType var;
      this->getVariance(var);
      ret[0] = sqrt(var[0]);
      ret[1] = sqrt(var[1]);
      ret[2] = sqrt(var[2]);
      return;
    }

    /**
     * return the largest length
     */
    void getMaxLength(RealType &ret) {
      assert(Count_ != 0);
      ret = Max_;
      return;
    }

    /**
     * return the smallest length
     */
    void getMinLength(RealType &ret) {
      assert(Count_ != 0);
      ret = Min_;
      return;
    }

    /**
     * return the largest length
     */
    void getAverageLength(RealType &ret) {
      assert(Count_ != 0);
      ret = AvgLen_;
      return;
    }

    /**
     * compute the Variance of the length
     */
    void getLengthVariance(RealType &ret) {
      assert(Count_ != 0);      
      ret= (AvgLen2_ - AvgLen_ * AvgLen_);
      return;
    }
    
    /**
     * compute error of average value
     */
    void getLengthStdDev(RealType &ret) {
      assert(Count_ != 0);
      RealType var;
      this->getLengthVariance(var);
      ret = sqrt(var);
      return;
    }
        
  protected:
    size_t Count_;
  private:
    ResultType Val_;
    ResultType Avg_;
    ResultType Avg2_;
    RealType AvgLen_;
    RealType AvgLen2_;
    RealType Min_;
    RealType Max_;

  };

  class MatrixAccumulator : public Accumulator {
    
    typedef Mat3x3d ElementType;
    typedef Mat3x3d ResultType;
    
  public:
    MatrixAccumulator() : Accumulator() {
      this->clear();
    }

    /**
     * Accumulate another value
     */
    void add(ElementType const& val) {
      Count_++;
      for (unsigned int i = 0; i < 3; i++) {
        for (unsigned int j = 0; j < 3; j++) {          
          Avg_(i,j)  += (val(i,j)       - Avg_(i,j) ) / Count_;
          Avg2_(i,j) += (val(i,j) * val(i,j) - Avg2_(i,j)) / Count_;
          Val_(i,j)   = val(i,j);
        }
      }
    }

    /**
     * reset the Accumulator to the empty state
     */
    void clear() {
      Count_ = 0;
      Avg_ *= 0.0;
      Avg2_ *= 0.0;
      Val_ *= 0.0;
    }
    
    /**
     * return the most recently added value
     */
    void getLastValue(ElementType &ret) {
      ret = Val_;
      return;
    }
    
    /**
     * compute the Mean
     */
    void getAverage(ResultType &ret) {
      assert(Count_ != 0);
      ret = Avg_;
      return;
    }

    /**
     * compute the Variance
     */
    void getVariance(ResultType &ret) {
      assert(Count_ != 0);
      for (unsigned int i = 0; i < 3; i++) {
        for (unsigned int j = 0; j < 3; j++) {          
          ret(i,j) = (Avg2_(i,j) - Avg_(i,j)  * Avg_(i,j));
        }
      }
      return;
    }
    
    /**
     * compute error of average value
     */
    void getStdDev(ResultType &ret) {
      assert(Count_ != 0);
      Mat3x3d var;
      this->getVariance(var);
      for (unsigned int i = 0; i < 3; i++) {
        for (unsigned int j = 0; j < 3; j++) {
          ret(i,j) = sqrt(var(i,j));  
        }
      }
      return;
    }
        
  protected:
    size_t Count_;
  private:
    ElementType Val_;
    ResultType Avg_;
    ResultType Avg2_;
  };


} 

#endif
Revision:	1765
Committed:	Tue Jul 3 20:34:33 2012 UTC (12 years, 10 months ago) by gezelter
File size:	9200 byte(s)
Log Message:	Forgot to add Accumulator.hpp on the last commit.
#	User	Rev	Content
1	gezelter	1765	/*
2			* Copyright (c) 2012 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#ifndef UTILS_ACCUMULATOR_HPP
44			#define UTILS_ACCUMULATOR_HPP
45
46			#include <cmath>
47			#include <cassert>
48			#include "math/Vector3.hpp"
49
50			namespace OpenMD {
51
52			/**
53			* Basic Accumulator class for numbers.
54			*/
55
56			class Accumulator {
57
58			typedef RealType ElementType;
59			typedef RealType ResultType;
60
61			public:
62
63			Accumulator() {
64			this->clear();
65			}
66
67			/**
68			* Accumulate another value
69			*/
70			virtual void add(ElementType const& val) {
71			Count_++;
72			Avg_ += (val - Avg_ ) / Count_;
73			Avg2_ += (val * val - Avg2_) / Count_;
74			Val_ = val;
75			if (Count_ <= 1) {
76			Max_ = val;
77			Min_ = val;
78			} else {
79			Max_ = val > Max_ ? val : Max_;
80			Min_ = val < Min_ ? val : Min_;
81			}
82			}
83
84			/**
85			* reset the Accumulator to the empty state
86			*/
87			void clear() {
88			Count_ = 0;
89			Avg_ = 0;
90			Avg2_ = 0;
91			Val_ = 0;
92			}
93
94			/**
95			* get the number of accumulated values
96			*/
97			size_t count() {
98			return Count_;
99			}
100
101			/**
102			* return the most recently added value
103			*/
104			void getLastValue(ElementType &ret) {
105			ret = Val_;
106			return;
107			}
108
109			/**
110			* compute the Mean
111			*/
112			void getAverage(ResultType &ret) {
113			assert(Count_ != 0);
114			ret = Avg_;
115			return;
116			}
117
118			/**
119			* compute the Variance
120			*/
121			void getVariance(ResultType &ret) {
122			assert(Count_ != 0);
123			ret = (Avg2_ - Avg_ * Avg_);
124			return;
125			}
126
127			/**
128			* compute error of average value
129			*/
130			void getStdDev(ResultType &ret) {
131			assert(Count_ != 0);
132			RealType var;
133			this->getVariance(var);
134			ret = sqrt(var);
135			return;
136			}
137
138			/**
139			* return the largest value
140			*/
141			void getMax(ElementType &ret) {
142			assert(Count_ != 0);
143			ret = Max_;
144			return;
145			}
146
147			/**
148			* return the smallest value
149			*/
150			void getMin(ElementType &ret) {
151			assert(Count_ != 0);
152			ret = Max_;
153			return;
154			}
155
156			protected:
157			size_t Count_;
158			private:
159			ElementType Val_;
160			ResultType Avg_;
161			ResultType Avg2_;
162			ElementType Min_;
163			ElementType Max_;
164			};
165
166			class VectorAccumulator : public Accumulator {
167
168			typedef Vector3d ElementType;
169			typedef Vector3d ResultType;
170
171			public:
172			VectorAccumulator() : Accumulator() {
173			this->clear();
174			}
175
176			/**
177			* Accumulate another value
178			*/
179			void add(ElementType const& val) {
180			Count_++;
181			RealType len(0.0);
182			for (unsigned int i =0; i < 3; i++) {
183			Avg_[i] += (val[i] - Avg_[i] ) / Count_;
184			Avg2_[i] += (val[i] * val[i] - Avg2_[i]) / Count_;
185			Val_[i] = val[i];
186			len += val[i]*val[i];
187			}
188			len = sqrt(len);
189			AvgLen_ += (len - AvgLen_ ) / Count_;
190			AvgLen2_ += (len * len - AvgLen2_) / Count_;
191
192			if (Count_ <= 1) {
193			Max_ = len;
194			Min_ = len;
195			} else {
196			Max_ = len > Max_ ? len : Max_;
197			Min_ = len < Min_ ? len : Min_;
198			}
199			}
200
201			/**
202			* reset the Accumulator to the empty state
203			*/
204			void clear() {
205			Count_ = 0;
206			Avg_ = V3Zero;
207			Avg2_ = V3Zero;
208			Val_ = V3Zero;
209			AvgLen_ = 0;
210			AvgLen2_ = 0;
211			}
212
213			/**
214			* return the most recently added value
215			*/
216			void getLastValue(ElementType &ret) {
217			ret = Val_;
218			return;
219			}
220
221			/**
222			* compute the Mean
223			*/
224			void getAverage(ResultType &ret) {
225			assert(Count_ != 0);
226			ret = Avg_;
227			return;
228			}
229
230			/**
231			* compute the Variance
232			*/
233			void getVariance(ResultType &ret) {
234			assert(Count_ != 0);
235			for (unsigned int i =0; i < 3; i++) {
236			ret[i] = (Avg2_[i] - Avg_[i] * Avg_[i]);
237			}
238			return;
239			}
240
241			/**
242			* compute error of average value
243			*/
244			void getStdDev(ResultType &ret) {
245			assert(Count_ != 0);
246			ResultType var;
247			this->getVariance(var);
248			ret[0] = sqrt(var[0]);
249			ret[1] = sqrt(var[1]);
250			ret[2] = sqrt(var[2]);
251			return;
252			}
253
254			/**
255			* return the largest length
256			*/
257			void getMaxLength(RealType &ret) {
258			assert(Count_ != 0);
259			ret = Max_;
260			return;
261			}
262
263			/**
264			* return the smallest length
265			*/
266			void getMinLength(RealType &ret) {
267			assert(Count_ != 0);
268			ret = Min_;
269			return;
270			}
271
272			/**
273			* return the largest length
274			*/
275			void getAverageLength(RealType &ret) {
276			assert(Count_ != 0);
277			ret = AvgLen_;
278			return;
279			}
280
281			/**
282			* compute the Variance of the length
283			*/
284			void getLengthVariance(RealType &ret) {
285			assert(Count_ != 0);
286			ret= (AvgLen2_ - AvgLen_ * AvgLen_);
287			return;
288			}
289
290			/**
291			* compute error of average value
292			*/
293			void getLengthStdDev(RealType &ret) {
294			assert(Count_ != 0);
295			RealType var;
296			this->getLengthVariance(var);
297			ret = sqrt(var);
298			return;
299			}
300
301			protected:
302			size_t Count_;
303			private:
304			ResultType Val_;
305			ResultType Avg_;
306			ResultType Avg2_;
307			RealType AvgLen_;
308			RealType AvgLen2_;
309			RealType Min_;
310			RealType Max_;
311
312			};
313
314			class MatrixAccumulator : public Accumulator {
315
316			typedef Mat3x3d ElementType;
317			typedef Mat3x3d ResultType;
318
319			public:
320			MatrixAccumulator() : Accumulator() {
321			this->clear();
322			}
323
324			/**
325			* Accumulate another value
326			*/
327			void add(ElementType const& val) {
328			Count_++;
329			for (unsigned int i = 0; i < 3; i++) {
330			for (unsigned int j = 0; j < 3; j++) {
331			Avg_(i,j) += (val(i,j) - Avg_(i,j) ) / Count_;
332			Avg2_(i,j) += (val(i,j) * val(i,j) - Avg2_(i,j)) / Count_;
333			Val_(i,j) = val(i,j);
334			}
335			}
336			}
337
338			/**
339			* reset the Accumulator to the empty state
340			*/
341			void clear() {
342			Count_ = 0;
343			Avg_ *= 0.0;
344			Avg2_ *= 0.0;
345			Val_ *= 0.0;
346			}
347
348			/**
349			* return the most recently added value
350			*/
351			void getLastValue(ElementType &ret) {
352			ret = Val_;
353			return;
354			}
355
356			/**
357			* compute the Mean
358			*/
359			void getAverage(ResultType &ret) {
360			assert(Count_ != 0);
361			ret = Avg_;
362			return;
363			}
364
365			/**
366			* compute the Variance
367			*/
368			void getVariance(ResultType &ret) {
369			assert(Count_ != 0);
370			for (unsigned int i = 0; i < 3; i++) {
371			for (unsigned int j = 0; j < 3; j++) {
372			ret(i,j) = (Avg2_(i,j) - Avg_(i,j) * Avg_(i,j));
373			}
374			}
375			return;
376			}
377
378			/**
379			* compute error of average value
380			*/
381			void getStdDev(ResultType &ret) {
382			assert(Count_ != 0);
383			Mat3x3d var;
384			this->getVariance(var);
385			for (unsigned int i = 0; i < 3; i++) {
386			for (unsigned int j = 0; j < 3; j++) {
387			ret(i,j) = sqrt(var(i,j));
388			}
389			}
390			return;
391			}
392
393			protected:
394			size_t Count_;
395			private:
396			ElementType Val_;
397			ResultType Avg_;
398			ResultType Avg2_;
399			};
400
401
402			}
403
404			#endif