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, 9 months ago) by gezelter
File size:	9200 byte(s)
Log Message:	Forgot to add Accumulator.hpp on the last commit.
#	Content
1	/*
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