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 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
#	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, 234107 (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	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	/**
70	* Basic Accumulator class for numbers.
71	*/
72	class Accumulator : public BaseAccumulator {
73
74	typedef RealType ElementType;
75	typedef RealType ResultType;
76
77	public:
78
79	Accumulator() : BaseAccumulator() {
80	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	class VectorAccumulator : public BaseAccumulator {
175
176	typedef Vector3d ElementType;
177	typedef Vector3d ResultType;
178
179	public:
180	VectorAccumulator() : BaseAccumulator() {
181	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
309	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	class MatrixAccumulator : public BaseAccumulator {
321
322	typedef Mat3x3d ElementType;
323	typedef Mat3x3d ResultType;
324
325	public:
326	MatrixAccumulator() : BaseAccumulator() {
327	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