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]  Vardeman & Gezelter, in progress (2009).                        
 */
  
/**
 * @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"
namespace OpenMD {

  void  Snapshot::setHmat(const Mat3x3d& m) {
    hmat_ = m;
    invHmat_ = hmat_.inverse();
    

    //prepare fortran Hmat 
    RealType fortranHmat[9];
    RealType fortranInvHmat[9];
    hmat_.getArray(fortranHmat);
    invHmat_.getArray(fortranInvHmat);

    //determine whether the box is orthoTolerance or not
    int oldOrthoRhombic = orthoRhombic_;
    
    RealType smallDiag = fabs(hmat_(0, 0));
    if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
    if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));    
    RealType tol = smallDiag * orthoTolerance_;

    orthoRhombic_ = 1;

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0 ; j < 3; j++) {
        if (i != j) {
          if (orthoRhombic_) {
            if ( fabs(hmat_(i, j)) >= tol)
              orthoRhombic_ = 0;
          }        
        }
      }
    }

    if( oldOrthoRhombic != orthoRhombic_ ){

      if( 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();
      }
    }    

    //notify fortran simulation box has changed
    setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
  }


  void Snapshot::wrapVector(Vector3d& pos) {

    int i;
    Vector3d scaled;

    if( !orthoRhombic_ ){

      // calc the scaled coordinates.
      scaled = invHmat_* pos;

      // wrap the scaled coordinates
      for (i = 0; i < 3; ++i) {
        scaled[i] -= roundMe(scaled[i]);
      }

      // calc the wrapped real coordinates from the wrapped scaled coordinates
      pos = hmat_ * scaled;    

    } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
    
      // calc the scaled coordinates.
      for (i=0; i<3; i++) {
        scaled[i] = pos[i] * invHmat_(i, i);
      }
        
      // wrap the scaled coordinates
      for (i = 0; i < 3; ++i) {
        scaled[i] -= roundMe(scaled[i]);
      }

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

  }

  Vector3d Snapshot::getCOM() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COM_;
  }
  
  Vector3d Snapshot::getCOMvel() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COMvel_;
  }
  
  Vector3d Snapshot::getCOMw() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COMw_;
  }
 
}
  
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	5893 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	gezelter	507	/**
43			* @file Snapshot.cpp
44			* @author tlin
45			* @date 11/11/2004
46			* @time 10:56am
47			* @version 1.0
48			*/
49	gezelter	246
50			#include "brains/Snapshot.hpp"
51			#include "utils/NumericConstant.hpp"
52			#include "utils/simError.h"
53			#include "utils/Utility.hpp"
54	gezelter	1390	namespace OpenMD {
55	gezelter	246
56	gezelter	507	void Snapshot::setHmat(const Mat3x3d& m) {
57	gezelter	246	hmat_ = m;
58			invHmat_ = hmat_.inverse();
59
60	chuckv	1112
61	gezelter	246	//prepare fortran Hmat
62	tim	963	RealType fortranHmat[9];
63			RealType fortranInvHmat[9];
64	gezelter	246	hmat_.getArray(fortranHmat);
65			invHmat_.getArray(fortranInvHmat);
66
67			//determine whether the box is orthoTolerance or not
68			int oldOrthoRhombic = orthoRhombic_;
69
70	tim	963	RealType smallDiag = fabs(hmat_(0, 0));
71	gezelter	246	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
72			if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
73	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
74	gezelter	246
75			orthoRhombic_ = 1;
76
77			for (int i = 0; i < 3; i++ ) {
78	gezelter	507	for (int j = 0 ; j < 3; j++) {
79			if (i != j) {
80			if (orthoRhombic_) {
81			if ( fabs(hmat_(i, j)) >= tol)
82			orthoRhombic_ = 0;
83			}
84			}
85			}
86	gezelter	246	}
87
88			if( oldOrthoRhombic != orthoRhombic_ ){
89
90	gezelter	507	if( orthoRhombic_ ) {
91			sprintf( painCave.errMsg,
92	gezelter	1390	"OpenMD is switching from the default Non-Orthorhombic\n"
93	gezelter	507	"\tto the faster Orthorhombic periodic boundary computations.\n"
94	gezelter	890	"\tThis is usually a good thing, but if you want the\n"
95	gezelter	507	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
96			"\tvariable ( currently set to %G ) smaller.\n",
97	gezelter	1021	orthoTolerance_);
98	gezelter	1390	painCave.severity = OPENMD_INFO;
99	gezelter	507	simError();
100			}
101			else {
102			sprintf( painCave.errMsg,
103	gezelter	1390	"OpenMD is switching from the faster Orthorhombic to the more\n"
104	gezelter	507	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
105			"\tThis is usually because the box has deformed under\n"
106	gezelter	890	"\tNPTf integration. If you want to live on the edge with\n"
107	gezelter	507	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
108			"\tvariable ( currently set to %G ) larger.\n",
109	gezelter	1021	orthoTolerance_);
110	gezelter	1390	painCave.severity = OPENMD_WARNING;
111	gezelter	507	simError();
112			}
113	gezelter	246	}
114
115			//notify fortran simulation box has changed
116			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
117	gezelter	507	}
118	gezelter	246
119
120	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
121	gezelter	246
122			int i;
123			Vector3d scaled;
124
125			if( !orthoRhombic_ ){
126
127	gezelter	507	// calc the scaled coordinates.
128			scaled = invHmat_* pos;
129	gezelter	246
130	gezelter	507	// wrap the scaled coordinates
131			for (i = 0; i < 3; ++i) {
132			scaled[i] -= roundMe(scaled[i]);
133			}
134	gezelter	246
135	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
136			pos = hmat_ * scaled;
137	gezelter	246
138			} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
139
140	gezelter	507	// calc the scaled coordinates.
141			for (i=0; i<3; i++) {
142			scaled[i] = pos[i] * invHmat_(i, i);
143			}
144	gezelter	246
145	gezelter	507	// wrap the scaled coordinates
146			for (i = 0; i < 3; ++i) {
147			scaled[i] -= roundMe(scaled[i]);
148			}
149	gezelter	246
150	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
151			for (i=0; i<3; i++) {
152			pos[i] = scaled[i] * hmat_(i, i);
153			}
154	gezelter	246
155			}
156
157	gezelter	507	}
158	gezelter	246
159	gezelter	1104	Vector3d Snapshot::getCOM() {
160			if( !hasCOM_ ) {
161			sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
162	gezelter	1390	painCave.severity = OPENMD_ERROR;
163	gezelter	1104	simError();
164			}
165			return COM_;
166			}
167
168			Vector3d Snapshot::getCOMvel() {
169			if( !hasCOM_ ) {
170			sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
171	gezelter	1390	painCave.severity = OPENMD_ERROR;
172	gezelter	1104	simError();
173			}
174			return COMvel_;
175			}
176
177			Vector3d Snapshot::getCOMw() {
178			if( !hasCOM_ ) {
179			sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
180	gezelter	1390	painCave.severity = OPENMD_ERROR;
181	gezelter	1104	simError();
182			}
183			return COMw_;
184			}
185
186	gezelter	246	}
187