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, 234107 (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 {


  class BaseAccumulator {
  public:
    virtual void clear() = 0;
    /**
     * get the number of accumulated values
     */
    virtual size_t count()  {
      return Count_;
    }
  protected:
    size_t Count_;

  };   


  /** 
   * Basic Accumulator class for numbers. 
   */  
  class Accumulator : public BaseAccumulator {    

    typedef RealType ElementType;
    typedef RealType ResultType;

  public:
    
    Accumulator() : BaseAccumulator() {
      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;
    }
    

    /**
     * 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;
    }

  private:
    ElementType Val_;
    ResultType Avg_;
    ResultType Avg2_;
    ElementType Min_;
    ElementType Max_;
  };

  class VectorAccumulator : public BaseAccumulator {
    
    typedef Vector3d ElementType;
    typedef Vector3d ResultType;
    
  public:
    VectorAccumulator() : BaseAccumulator() {
      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;
    }

  private:
    ResultType Val_;
    ResultType Avg_;
    ResultType Avg2_;
    RealType AvgLen_;
    RealType AvgLen2_;
    RealType Min_;
    RealType Max_;

  };

  class MatrixAccumulator : public BaseAccumulator {
    
    typedef Mat3x3d ElementType;
    typedef Mat3x3d ResultType;
    
  public:
    MatrixAccumulator() : BaseAccumulator() {
      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;
    }
        
  private:
    ElementType Val_;
    ResultType Avg_;
    ResultType Avg2_;
  };


} 

#endif
Revision:	1855
Committed:	Tue Apr 2 18:31:51 2013 UTC (12 years, 1 month ago) by gezelter
File size:	9276 byte(s)
Log Message:	Fixed a bunch of bugs in CubicSpline debug sections, ForceMatrix Decomp computing costhetas for non-existent rotation matrices, Hidden accumulator counts, and SMIPD non-coupling
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1765	* [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	gezelter	1813
53			class BaseAccumulator {
54			public:
55			virtual void clear() = 0;
56			/**
57			* get the number of accumulated values
58			*/
59			virtual size_t count() {
60			return Count_;
61			}
62			protected:
63			size_t Count_;
64
65			};
66
67
68
69	gezelter	1765	/**
70			* Basic Accumulator class for numbers.
71	gezelter	1813	*/
72			class Accumulator : public BaseAccumulator {
73	gezelter	1765
74			typedef RealType ElementType;
75			typedef RealType ResultType;
76
77			public:
78
79	gezelter	1813	Accumulator() : BaseAccumulator() {
80	gezelter	1765	this->clear();
81			}
82
83			/**
84			* Accumulate another value
85			*/
86			virtual void add(ElementType const& val) {
87			Count_++;
88			Avg_ += (val - Avg_ ) / Count_;
89			Avg2_ += (val * val - Avg2_) / Count_;
90			Val_ = val;
91			if (Count_ <= 1) {
92			Max_ = val;
93			Min_ = val;
94			} else {
95			Max_ = val > Max_ ? val : Max_;
96			Min_ = val < Min_ ? val : Min_;
97			}
98			}
99
100			/**
101			* reset the Accumulator to the empty state
102			*/
103			void clear() {
104			Count_ = 0;
105			Avg_ = 0;
106			Avg2_ = 0;
107			Val_ = 0;
108			}
109
110
111			/**
112			* return the most recently added value
113			*/
114			void getLastValue(ElementType &ret) {
115			ret = Val_;
116			return;
117			}
118
119			/**
120			* compute the Mean
121			*/
122			void getAverage(ResultType &ret) {
123			assert(Count_ != 0);
124			ret = Avg_;
125			return;
126			}
127
128			/**
129			* compute the Variance
130			*/
131			void getVariance(ResultType &ret) {
132			assert(Count_ != 0);
133			ret = (Avg2_ - Avg_ * Avg_);
134			return;
135			}
136
137			/**
138			* compute error of average value
139			*/
140			void getStdDev(ResultType &ret) {
141			assert(Count_ != 0);
142			RealType var;
143			this->getVariance(var);
144			ret = sqrt(var);
145			return;
146			}
147
148			/**
149			* return the largest value
150			*/
151			void getMax(ElementType &ret) {
152			assert(Count_ != 0);
153			ret = Max_;
154			return;
155			}
156
157			/**
158			* return the smallest value
159			*/
160			void getMin(ElementType &ret) {
161			assert(Count_ != 0);
162			ret = Max_;
163			return;
164			}
165
166			private:
167			ElementType Val_;
168			ResultType Avg_;
169			ResultType Avg2_;
170			ElementType Min_;
171			ElementType Max_;
172			};
173
174	gezelter	1813	class VectorAccumulator : public BaseAccumulator {
175	gezelter	1765
176			typedef Vector3d ElementType;
177			typedef Vector3d ResultType;
178
179			public:
180	gezelter	1813	VectorAccumulator() : BaseAccumulator() {
181	gezelter	1765	this->clear();
182			}
183
184			/**
185			* Accumulate another value
186			*/
187			void add(ElementType const& val) {
188			Count_++;
189			RealType len(0.0);
190			for (unsigned int i =0; i < 3; i++) {
191			Avg_[i] += (val[i] - Avg_[i] ) / Count_;
192			Avg2_[i] += (val[i] * val[i] - Avg2_[i]) / Count_;
193			Val_[i] = val[i];
194			len += val[i]*val[i];
195			}
196			len = sqrt(len);
197			AvgLen_ += (len - AvgLen_ ) / Count_;
198			AvgLen2_ += (len * len - AvgLen2_) / Count_;
199
200			if (Count_ <= 1) {
201			Max_ = len;
202			Min_ = len;
203			} else {
204			Max_ = len > Max_ ? len : Max_;
205			Min_ = len < Min_ ? len : Min_;
206			}
207			}
208
209			/**
210			* reset the Accumulator to the empty state
211			*/
212			void clear() {
213			Count_ = 0;
214			Avg_ = V3Zero;
215			Avg2_ = V3Zero;
216			Val_ = V3Zero;
217			AvgLen_ = 0;
218			AvgLen2_ = 0;
219			}
220
221			/**
222			* return the most recently added value
223			*/
224			void getLastValue(ElementType &ret) {
225			ret = Val_;
226			return;
227			}
228
229			/**
230			* compute the Mean
231			*/
232			void getAverage(ResultType &ret) {
233			assert(Count_ != 0);
234			ret = Avg_;
235			return;
236			}
237
238			/**
239			* compute the Variance
240			*/
241			void getVariance(ResultType &ret) {
242			assert(Count_ != 0);
243			for (unsigned int i =0; i < 3; i++) {
244			ret[i] = (Avg2_[i] - Avg_[i] * Avg_[i]);
245			}
246			return;
247			}
248
249			/**
250			* compute error of average value
251			*/
252			void getStdDev(ResultType &ret) {
253			assert(Count_ != 0);
254			ResultType var;
255			this->getVariance(var);
256			ret[0] = sqrt(var[0]);
257			ret[1] = sqrt(var[1]);
258			ret[2] = sqrt(var[2]);
259			return;
260			}
261
262			/**
263			* return the largest length
264			*/
265			void getMaxLength(RealType &ret) {
266			assert(Count_ != 0);
267			ret = Max_;
268			return;
269			}
270
271			/**
272			* return the smallest length
273			*/
274			void getMinLength(RealType &ret) {
275			assert(Count_ != 0);
276			ret = Min_;
277			return;
278			}
279
280			/**
281			* return the largest length
282			*/
283			void getAverageLength(RealType &ret) {
284			assert(Count_ != 0);
285			ret = AvgLen_;
286			return;
287			}
288
289			/**
290			* compute the Variance of the length
291			*/
292			void getLengthVariance(RealType &ret) {
293			assert(Count_ != 0);
294			ret= (AvgLen2_ - AvgLen_ * AvgLen_);
295			return;
296			}
297
298			/**
299			* compute error of average value
300			*/
301			void getLengthStdDev(RealType &ret) {
302			assert(Count_ != 0);
303			RealType var;
304			this->getLengthVariance(var);
305			ret = sqrt(var);
306			return;
307			}
308	gezelter	1855
309	gezelter	1765	private:
310			ResultType Val_;
311			ResultType Avg_;
312			ResultType Avg2_;
313			RealType AvgLen_;
314			RealType AvgLen2_;
315			RealType Min_;
316			RealType Max_;
317
318			};
319
320	gezelter	1813	class MatrixAccumulator : public BaseAccumulator {
321	gezelter	1765
322			typedef Mat3x3d ElementType;
323			typedef Mat3x3d ResultType;
324
325			public:
326	gezelter	1813	MatrixAccumulator() : BaseAccumulator() {
327	gezelter	1765	this->clear();
328			}
329
330			/**
331			* Accumulate another value
332			*/
333			void add(ElementType const& val) {
334			Count_++;
335			for (unsigned int i = 0; i < 3; i++) {
336			for (unsigned int j = 0; j < 3; j++) {
337			Avg_(i,j) += (val(i,j) - Avg_(i,j) ) / Count_;
338			Avg2_(i,j) += (val(i,j) * val(i,j) - Avg2_(i,j)) / Count_;
339			Val_(i,j) = val(i,j);
340			}
341			}
342			}
343
344			/**
345			* reset the Accumulator to the empty state
346			*/
347			void clear() {
348			Count_ = 0;
349			Avg_ *= 0.0;
350			Avg2_ *= 0.0;
351			Val_ *= 0.0;
352			}
353
354			/**
355			* return the most recently added value
356			*/
357			void getLastValue(ElementType &ret) {
358			ret = Val_;
359			return;
360			}
361
362			/**
363			* compute the Mean
364			*/
365			void getAverage(ResultType &ret) {
366			assert(Count_ != 0);
367			ret = Avg_;
368			return;
369			}
370
371			/**
372			* compute the Variance
373			*/
374			void getVariance(ResultType &ret) {
375			assert(Count_ != 0);
376			for (unsigned int i = 0; i < 3; i++) {
377			for (unsigned int j = 0; j < 3; j++) {
378			ret(i,j) = (Avg2_(i,j) - Avg_(i,j) * Avg_(i,j));
379			}
380			}
381			return;
382			}
383
384			/**
385			* compute error of average value
386			*/
387			void getStdDev(ResultType &ret) {
388			assert(Count_ != 0);
389			Mat3x3d var;
390			this->getVariance(var);
391			for (unsigned int i = 0; i < 3; i++) {
392			for (unsigned int j = 0; j < 3; j++) {
393			ret(i,j) = sqrt(var(i,j));
394			}
395			}
396			return;
397			}
398
399			private:
400			ElementType Val_;
401			ResultType Avg_;
402			ResultType Avg2_;
403			};
404
405
406			}
407
408			#endif