src/brains/Snapshot.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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @file Snapshot.cpp
 * @author tlin
 * @date 11/11/2004
 * @time 10:56am
 * @version 1.0
 */

#include "brains/Snapshot.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
#include "utils/Utility.hpp"
#include <cstdio>

namespace OpenMD {

  void  Snapshot::setHmat(const Mat3x3d& m) {
    frameData.hmat = m;
    frameData.invHmat = frameData.hmat.inverse();
    
    //determine whether the box is orthoTolerance or not
    bool oldOrthoRhombic = frameData.orthoRhombic;
    
    RealType smallDiag = fabs(frameData.hmat(0, 0));
    if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
    if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));    
    RealType tol = smallDiag * orthoTolerance_;

    frameData.orthoRhombic = true;

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0 ; j < 3; j++) {
        if (i != j) {
          if (frameData.orthoRhombic) {
            if ( fabs(frameData.hmat(i, j)) >= tol)
              frameData.orthoRhombic = false;
          }        
        }
      }
    }

    if( oldOrthoRhombic != frameData.orthoRhombic){

      if( frameData.orthoRhombic ) {
        sprintf( painCave.errMsg,
                 "OpenMD is switching from the default Non-Orthorhombic\n"
                 "\tto the faster Orthorhombic periodic boundary computations.\n"
                 "\tThis is usually a good thing, but if you want the\n"
                 "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
                 "\tvariable ( currently set to %G ) smaller.\n",
                 orthoTolerance_);
        painCave.severity = OPENMD_INFO;
        simError();
      }
      else {
        sprintf( painCave.errMsg,
                 "OpenMD is switching from the faster Orthorhombic to the more\n"
                 "\tflexible Non-Orthorhombic periodic boundary computations.\n"
                 "\tThis is usually because the box has deformed under\n"
                 "\tNPTf integration. If you want to live on the edge with\n"
                 "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
                 "\tvariable ( currently set to %G ) larger.\n",
                 orthoTolerance_);
        painCave.severity = OPENMD_WARNING;
        simError();
      }
    }    
  }


  void Snapshot::wrapVector(Vector3d& pos) {
    
    Vector3d scaled = scaleVector(pos);
    
    for (int i = 0; i < 3; i++) 
      scaled[i] -= roundMe(scaled[i]);

    if( !frameData.orthoRhombic )
      pos = frameData.hmat * scaled;    
    else {

      // calc the wrapped real coordinates from the wrapped scaled coordinates
      for (int i=0; i<3; i++) {
        pos[i] = scaled[i] * frameData.hmat(i, i);
      }   
    }
  }

  inline Vector3d Snapshot::scaleVector(Vector3d& pos) {   
    
    Vector3d scaled;

    if( !frameData.orthoRhombic )
      scaled = frameData.invHmat * pos;
    else {
      // calc the scaled coordinates.
      for (int i=0; i<3; i++) 
        scaled[i] = pos[i] * frameData.invHmat(i, i);
    }

    return scaled;
  }
  
  Vector3d Snapshot::getCOM() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return frameData.COM;
  }
  
  Vector3d Snapshot::getCOMvel() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return frameData.COMvel;
  }
  
  Vector3d Snapshot::getCOMw() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return frameData.COMw;
  }
}
  
Revision:	1715
Committed:	Tue May 22 21:55:31 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5716 byte(s)
Log Message:	Adding more support structure for Fluctuating Charges.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file Snapshot.cpp
45			* @author tlin
46			* @date 11/11/2004
47			* @time 10:56am
48			* @version 1.0
49			*/
50	gezelter	246
51			#include "brains/Snapshot.hpp"
52			#include "utils/NumericConstant.hpp"
53			#include "utils/simError.h"
54			#include "utils/Utility.hpp"
55	jmarr	1401	#include <cstdio>
56
57	gezelter	1390	namespace OpenMD {
58	gezelter	246
59	gezelter	507	void Snapshot::setHmat(const Mat3x3d& m) {
60	gezelter	1715	frameData.hmat = m;
61			frameData.invHmat = frameData.hmat.inverse();
62	gezelter	246
63			//determine whether the box is orthoTolerance or not
64	gezelter	1715	bool oldOrthoRhombic = frameData.orthoRhombic;
65	gezelter	246
66	gezelter	1715	RealType smallDiag = fabs(frameData.hmat(0, 0));
67			if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
68			if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
69	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
70	gezelter	246
71	gezelter	1715	frameData.orthoRhombic = true;
72	gezelter	246
73			for (int i = 0; i < 3; i++ ) {
74	gezelter	507	for (int j = 0 ; j < 3; j++) {
75			if (i != j) {
76	gezelter	1715	if (frameData.orthoRhombic) {
77			if ( fabs(frameData.hmat(i, j)) >= tol)
78			frameData.orthoRhombic = false;
79	gezelter	507	}
80			}
81			}
82	gezelter	246	}
83
84	gezelter	1715	if( oldOrthoRhombic != frameData.orthoRhombic){
85	gezelter	246
86	gezelter	1715	if( frameData.orthoRhombic ) {
87	gezelter	507	sprintf( painCave.errMsg,
88	gezelter	1390	"OpenMD is switching from the default Non-Orthorhombic\n"
89	gezelter	507	"\tto the faster Orthorhombic periodic boundary computations.\n"
90	gezelter	890	"\tThis is usually a good thing, but if you want the\n"
91	gezelter	507	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
92			"\tvariable ( currently set to %G ) smaller.\n",
93	gezelter	1021	orthoTolerance_);
94	gezelter	1390	painCave.severity = OPENMD_INFO;
95	gezelter	507	simError();
96			}
97			else {
98			sprintf( painCave.errMsg,
99	gezelter	1390	"OpenMD is switching from the faster Orthorhombic to the more\n"
100	gezelter	507	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
101			"\tThis is usually because the box has deformed under\n"
102	gezelter	890	"\tNPTf integration. If you want to live on the edge with\n"
103	gezelter	507	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
104			"\tvariable ( currently set to %G ) larger.\n",
105	gezelter	1021	orthoTolerance_);
106	gezelter	1390	painCave.severity = OPENMD_WARNING;
107	gezelter	507	simError();
108			}
109	gezelter	246	}
110	gezelter	507	}
111	gezelter	246
112
113	gezelter	1568	void Snapshot::wrapVector(Vector3d& pos) {
114	gezelter	1562
115			Vector3d scaled = scaleVector(pos);
116	gezelter	1568
117	gezelter	1562	for (int i = 0; i < 3; i++)
118			scaled[i] -= roundMe(scaled[i]);
119	gezelter	246
120	gezelter	1715	if( !frameData.orthoRhombic )
121			pos = frameData.hmat * scaled;
122	gezelter	1562	else {
123	gezelter	246
124	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
125	gezelter	1562	for (int i=0; i<3; i++) {
126	gezelter	1715	pos[i] = scaled[i] * frameData.hmat(i, i);
127	gezelter	1540	}
128	gezelter	246	}
129	gezelter	507	}
130	gezelter	246
131	gezelter	1562	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
132
133			Vector3d scaled;
134
135	gezelter	1715	if( !frameData.orthoRhombic )
136			scaled = frameData.invHmat * pos;
137	gezelter	1562	else {
138			// calc the scaled coordinates.
139			for (int i=0; i<3; i++)
140	gezelter	1715	scaled[i] = pos[i] * frameData.invHmat(i, i);
141	gezelter	1562	}
142
143			return scaled;
144			}
145
146	gezelter	1104	Vector3d Snapshot::getCOM() {
147			if( !hasCOM_ ) {
148			sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
149	gezelter	1390	painCave.severity = OPENMD_ERROR;
150	gezelter	1104	simError();
151			}
152	gezelter	1715	return frameData.COM;
153	gezelter	1104	}
154
155			Vector3d Snapshot::getCOMvel() {
156			if( !hasCOM_ ) {
157			sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
158	gezelter	1390	painCave.severity = OPENMD_ERROR;
159	gezelter	1104	simError();
160			}
161	gezelter	1715	return frameData.COMvel;
162	gezelter	1104	}
163
164			Vector3d Snapshot::getCOMw() {
165			if( !hasCOM_ ) {
166			sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
167	gezelter	1390	painCave.severity = OPENMD_ERROR;
168	gezelter	1104	simError();
169			}
170	gezelter	1715	return frameData.COMw;
171	gezelter	1104	}
172	gezelter	246	}
173