applications/staticProps/GofRZ.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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofRZ.hpp"
#include "utils/simError.h"

namespace OpenMD {

    GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1, 
                 const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins)
        : RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){

        setOutputName(getPrefix(filename) + ".gofrz");

        deltaR_ = len_ / (double) nRBins_;
        deltaZ_ = zLen_ / (double)nZBins_;    // for solvated_NVT.md4

        histogram_.resize(nRBins_);
        avgGofr_.resize(nRBins_);
        for (int i = 0 ; i < nRBins_; ++i) {
            histogram_[i].resize(nZBins_);
            avgGofr_[i].resize(nZBins_);
        } 
    }

    void GofRZ::preProcess() {
        for (int i = 0; i < avgGofr_.size(); ++i) {
            std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
        }
    }

    void GofRZ::initalizeHistogram() {
        npairs_ = 0;
        for (int i = 0; i < histogram_.size(); ++i){
            std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
        }
    }
  
    void GofRZ::processHistogram() {
        int nPairs = getNPairs();
        RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
        RealType pairDensity = nPairs / volume * 2.0;

        for(int i = 0 ; i < histogram_.size(); ++i){

            RealType rLower = i * deltaR_;
            RealType rUpper = rLower + deltaR_;
            RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
            RealType nIdeal = volSlice * pairDensity;

            for (int j = 0; j < histogram_[i].size(); ++j){
                avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
            }
        }

    }

    void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

        if (sd1 == sd2) {
            return;
        }
        Vector3d pos1 = sd1->getPos();
        Vector3d pos2 = sd2->getPos();
        Vector3d r12 = pos2 - pos1;
        if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(r12);

        RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));

        int whichRBin = distance / deltaR_;

        if (distance <= len_) {
     
            RealType Z = fabs(r12.z());

            if (Z <= zLen_) {
                int whichZBin = Z / deltaZ_;

                ++histogram_[whichRBin][whichZBin];        
                ++npairs_;
            }
        }
    }

    void GofRZ::writeRdf() {
        std::ofstream rdfStream(outputFilename_.c_str());
        if (rdfStream.is_open()) {
            rdfStream << "#radial distribution function\n";
            rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
            rdfStream << "selection2: (" << selectionScript2_ << ")\n";
            rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
            rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
            for (int i = 0; i < avgGofr_.size(); ++i) {
                RealType r = deltaR_ * (i + 0.5);

                for(int j = 0; j < avgGofr_[i].size(); ++j) {
                    RealType z = deltaZ_ * (j + 0.5);
                    rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
                }

                rdfStream << "\n";
            }
        
        } else {
            sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
            painCave.isFatal = 1;
            simError();  
        }

        rdfStream.close();
    }

}


Revision:	1445
Committed:	Tue Jun 8 20:26:50 2010 UTC (14 years, 11 months ago) by chuckv
File size:	5260 byte(s)
Log Message:	Changes to gofrz so you can specify the z length
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include <algorithm>
43	#include <fstream>
44	#include "applications/staticProps/GofRZ.hpp"
45	#include "utils/simError.h"
46
47	namespace OpenMD {
48
49	GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1,
50	const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins)
51	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){
52
53	setOutputName(getPrefix(filename) + ".gofrz");
54
55	deltaR_ = len_ / (double) nRBins_;
56	deltaZ_ = zLen_ / (double)nZBins_; // for solvated_NVT.md4
57
58	histogram_.resize(nRBins_);
59	avgGofr_.resize(nRBins_);
60	for (int i = 0 ; i < nRBins_; ++i) {
61	histogram_[i].resize(nZBins_);
62	avgGofr_[i].resize(nZBins_);
63	}
64	}
65
66	void GofRZ::preProcess() {
67	for (int i = 0; i < avgGofr_.size(); ++i) {
68	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
69	}
70	}
71
72	void GofRZ::initalizeHistogram() {
73	npairs_ = 0;
74	for (int i = 0; i < histogram_.size(); ++i){
75	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
76	}
77	}
78
79	void GofRZ::processHistogram() {
80	int nPairs = getNPairs();
81	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
82	RealType pairDensity = nPairs / volume * 2.0;
83
84	for(int i = 0 ; i < histogram_.size(); ++i){
85
86	RealType rLower = i * deltaR_;
87	RealType rUpper = rLower + deltaR_;
88	RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
89	RealType nIdeal = volSlice * pairDensity;
90
91	for (int j = 0; j < histogram_[i].size(); ++j){
92	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93	}
94	}
95
96	}
97
98	void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99
100	if (sd1 == sd2) {
101	return;
102	}
103	Vector3d pos1 = sd1->getPos();
104	Vector3d pos2 = sd2->getPos();
105	Vector3d r12 = pos2 - pos1;
106	if (usePeriodicBoundaryConditions_)
107	currentSnapshot_->wrapVector(r12);
108
109	RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
110
111	int whichRBin = distance / deltaR_;
112
113	if (distance <= len_) {
114
115	RealType Z = fabs(r12.z());
116
117	if (Z <= zLen_) {
118	int whichZBin = Z / deltaZ_;
119
120	++histogram_[whichRBin][whichZBin];
121	++npairs_;
122	}
123	}
124	}
125
126	void GofRZ::writeRdf() {
127	std::ofstream rdfStream(outputFilename_.c_str());
128	if (rdfStream.is_open()) {
129	rdfStream << "#radial distribution function\n";
130	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
131	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
132	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
133	rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
134	for (int i = 0; i < avgGofr_.size(); ++i) {
135	RealType r = deltaR_ * (i + 0.5);
136
137	for(int j = 0; j < avgGofr_[i].size(); ++j) {
138	RealType z = deltaZ_ * (j + 0.5);
139	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
140	}
141
142	rdfStream << "\n";
143	}
144
145	} else {
146	sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
147	painCave.isFatal = 1;
148	simError();
149	}
150
151	rdfStream.close();
152	}
153
154	}
155
156
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