applications/staticProps/RNEMDStats.cpp

/*
 * Copyright (c) 2005 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).
 */


#include <algorithm>
#include <fstream>
#include "applications/staticProps/RNEMDStats.hpp"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {
  
  RNEMDZ::RNEMDZ(SimInfo* info, const std::string& filename, 
                 const std::string& sele, int nzbins)
    : SlabStatistics(info, filename, sele, nzbins) {
        
    setOutputName(getPrefix(filename) + ".rnemdZ");
    
    temperature = new OutputData;
    temperature->units =  "K";
    temperature->title =  "Temperature";
    temperature->dataType = odtReal;
    temperature->dataHandling = odhAverage;
    temperature->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      temperature->accumulator.push_back( new Accumulator() );
    data_.push_back(temperature);
    
    velocity = new OutputData;
    velocity->units = "angstroms/fs";
    velocity->title =  "Velocity";  
    velocity->dataType = odtVector3;
    velocity->dataHandling = odhAverage;
    velocity->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      velocity->accumulator.push_back( new VectorAccumulator() );
    data_.push_back(velocity);
    
    density = new OutputData;
    density->units =  "g cm^-3";
    density->title =  "Density";
    density->dataType = odtReal;
    density->dataHandling = odhAverage;
    density->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      density->accumulator.push_back( new Accumulator() );
    data_.push_back(density);
  }

  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
    RealType mass = sd->getMass();
    Vector3d pos = sd->getPos();    
    Vector3d vel = sd->getVel();
    RealType KE = 0.5 * (mass * vel.lengthSquare());
    int dof = 3;

    if (sd->isDirectional()) {
      Vector3d angMom = sd->getJ();
      Mat3x3d I = sd->getI();
      if (sd->isLinear()) {
        int i = sd->linearAxis();
        int j = (i + 1) % 3;
        int k = (i + 2) % 3;
        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) + 
                     angMom[k] * angMom[k] / I(k, k));
        dof += 2;
      } else {
        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
                     angMom[1] * angMom[1] / I(1, 1) +
                     angMom[2] * angMom[2] / I(2, 2));
        dof += 3;
      }
    }
    
    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
                                PhysicalConstants::energyConvert);
    RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_;
    
    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
    dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel);
    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);

  }

  RNEMDR::RNEMDR(SimInfo* info, const std::string& filename, 
                 const std::string& sele, int nrbins)
    : ShellStatistics(info, filename, sele, nrbins) {
        

    setOutputName(getPrefix(filename) + ".rnemdR");
    
    temperature = new OutputData;
    temperature->units =  "K";
    temperature->title =  "Temperature";
    temperature->dataType = odtReal;
    temperature->dataHandling = odhAverage;
    temperature->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      temperature->accumulator.push_back( new Accumulator() );
    data_.push_back(temperature);
    
    angularVelocity = new OutputData;
    angularVelocity->units = "angstroms^2/fs";
    angularVelocity->title =  "Velocity";  
    angularVelocity->dataType = odtVector3;
    angularVelocity->dataHandling = odhAverage;
    angularVelocity->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      angularVelocity->accumulator.push_back( new VectorAccumulator() );
    data_.push_back(angularVelocity);
    
    density = new OutputData;
    density->units =  "g cm^-3";
    density->title =  "Density";
    density->dataType = odtReal;
    density->dataHandling = odhAverage;
    density->accumulator.reserve(nBins_);
    for (int i = 0; i < nBins_; i++) 
      density->accumulator.push_back( new Accumulator() );
    data_.push_back(density);
  }

  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
    RealType mass = sd->getMass();
    Vector3d vel = sd->getVel();
    Vector3d rPos = sd->getPos() - coordinateOrigin_;
    Vector3d aVel = cross(rPos, vel);

    RealType KE = 0.5 * (mass * vel.lengthSquare());
    int dof = 3;

    if (sd->isDirectional()) {
      Vector3d angMom = sd->getJ();
      Mat3x3d I = sd->getI();
      if (sd->isLinear()) {
        int i = sd->linearAxis();
        int j = (i + 1) % 3;
        int k = (i + 2) % 3;
        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) + 
                     angMom[k] * angMom[k] / I(k, k));
        dof += 2;
      } else {
        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
                     angMom[1] * angMom[1] / I(1, 1) +
                     angMom[2] * angMom[2] / I(2, 2));
        dof += 3;
      }
    }
    
    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
                                PhysicalConstants::energyConvert);

    RealType rinner = (RealType)bin * binWidth_;
    RealType router = (RealType)(bin+1) * binWidth_;
    RealType den = mass * 3.0 * PhysicalConstants::densityConvert
      / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
    
    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
    dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel);
    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);

  }
}

Revision:	1865
Committed:	Wed Apr 17 18:24:08 2013 UTC (12 years ago) by gezelter
File size:	7654 byte(s)
Log Message:	Adding spatial statistics analysers.
#	User	Rev	Content
1	gezelter	1865	/*
2			* Copyright (c) 2005 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			*/
41
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/RNEMDStats.hpp"
46			#include "utils/PhysicalConstants.hpp"
47
48			namespace OpenMD {
49
50			RNEMDZ::RNEMDZ(SimInfo* info, const std::string& filename,
51			const std::string& sele, int nzbins)
52			: SlabStatistics(info, filename, sele, nzbins) {
53
54			setOutputName(getPrefix(filename) + ".rnemdZ");
55
56			temperature = new OutputData;
57			temperature->units = "K";
58			temperature->title = "Temperature";
59			temperature->dataType = odtReal;
60			temperature->dataHandling = odhAverage;
61			temperature->accumulator.reserve(nBins_);
62			for (int i = 0; i < nBins_; i++)
63			temperature->accumulator.push_back( new Accumulator() );
64			data_.push_back(temperature);
65
66			velocity = new OutputData;
67			velocity->units = "angstroms/fs";
68			velocity->title = "Velocity";
69			velocity->dataType = odtVector3;
70			velocity->dataHandling = odhAverage;
71			velocity->accumulator.reserve(nBins_);
72			for (int i = 0; i < nBins_; i++)
73			velocity->accumulator.push_back( new VectorAccumulator() );
74			data_.push_back(velocity);
75
76			density = new OutputData;
77			density->units = "g cm^-3";
78			density->title = "Density";
79			density->dataType = odtReal;
80			density->dataHandling = odhAverage;
81			density->accumulator.reserve(nBins_);
82			for (int i = 0; i < nBins_; i++)
83			density->accumulator.push_back( new Accumulator() );
84			data_.push_back(density);
85			}
86
87			void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
88			RealType mass = sd->getMass();
89			Vector3d pos = sd->getPos();
90			Vector3d vel = sd->getVel();
91			RealType KE = 0.5 * (mass * vel.lengthSquare());
92			int dof = 3;
93
94			if (sd->isDirectional()) {
95			Vector3d angMom = sd->getJ();
96			Mat3x3d I = sd->getI();
97			if (sd->isLinear()) {
98			int i = sd->linearAxis();
99			int j = (i + 1) % 3;
100			int k = (i + 2) % 3;
101			KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
102			angMom[k] * angMom[k] / I(k, k));
103			dof += 2;
104			} else {
105			KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
106			angMom[1] * angMom[1] / I(1, 1) +
107			angMom[2] * angMom[2] / I(2, 2));
108			dof += 3;
109			}
110			}
111
112			RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
113			PhysicalConstants::energyConvert);
114			RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_;
115
116			dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
117			dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel);
118			dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
119
120			}
121
122			RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
123			const std::string& sele, int nrbins)
124			: ShellStatistics(info, filename, sele, nrbins) {
125
126
127			setOutputName(getPrefix(filename) + ".rnemdR");
128
129			temperature = new OutputData;
130			temperature->units = "K";
131			temperature->title = "Temperature";
132			temperature->dataType = odtReal;
133			temperature->dataHandling = odhAverage;
134			temperature->accumulator.reserve(nBins_);
135			for (int i = 0; i < nBins_; i++)
136			temperature->accumulator.push_back( new Accumulator() );
137			data_.push_back(temperature);
138
139			angularVelocity = new OutputData;
140			angularVelocity->units = "angstroms^2/fs";
141			angularVelocity->title = "Velocity";
142			angularVelocity->dataType = odtVector3;
143			angularVelocity->dataHandling = odhAverage;
144			angularVelocity->accumulator.reserve(nBins_);
145			for (int i = 0; i < nBins_; i++)
146			angularVelocity->accumulator.push_back( new VectorAccumulator() );
147			data_.push_back(angularVelocity);
148
149			density = new OutputData;
150			density->units = "g cm^-3";
151			density->title = "Density";
152			density->dataType = odtReal;
153			density->dataHandling = odhAverage;
154			density->accumulator.reserve(nBins_);
155			for (int i = 0; i < nBins_; i++)
156			density->accumulator.push_back( new Accumulator() );
157			data_.push_back(density);
158			}
159
160			void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
161			RealType mass = sd->getMass();
162			Vector3d vel = sd->getVel();
163			Vector3d rPos = sd->getPos() - coordinateOrigin_;
164			Vector3d aVel = cross(rPos, vel);
165
166			RealType KE = 0.5 * (mass * vel.lengthSquare());
167			int dof = 3;
168
169			if (sd->isDirectional()) {
170			Vector3d angMom = sd->getJ();
171			Mat3x3d I = sd->getI();
172			if (sd->isLinear()) {
173			int i = sd->linearAxis();
174			int j = (i + 1) % 3;
175			int k = (i + 2) % 3;
176			KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
177			angMom[k] * angMom[k] / I(k, k));
178			dof += 2;
179			} else {
180			KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
181			angMom[1] * angMom[1] / I(1, 1) +
182			angMom[2] * angMom[2] / I(2, 2));
183			dof += 3;
184			}
185			}
186
187			RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
188			PhysicalConstants::energyConvert);
189
190			RealType rinner = (RealType)bin * binWidth_;
191			RealType router = (RealType)(bin+1) * binWidth_;
192			RealType den = mass * 3.0 * PhysicalConstants::densityConvert
193			/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
194
195			dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
196			dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel);
197			dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
198
199			}
200			}
201