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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	7654 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
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