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"
#include <cstdio>

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

    if( !orthoRhombic_ )
      pos = hmat_ * scaled;    
    else {

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

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

    if( !orthoRhombic_ )
      scaled = invHmat_* pos;
    else {
      // calc the scaled coordinates.
      for (int i=0; i<3; i++) 
        scaled[i] = pos[i] * 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 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:	1568
Committed:	Wed May 25 16:20:37 2011 UTC (13 years, 11 months ago) by gezelter
File size:	5704 byte(s)
Log Message:	Added neighbor list check, and migrated skinThickness into ForceDecomposition (and out of the InteractionManager). Removed a spurious inline.
#	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	jmarr	1401	#include <cstdio>
55
56	gezelter	1390	namespace OpenMD {
57	gezelter	246
58	gezelter	507	void Snapshot::setHmat(const Mat3x3d& m) {
59	gezelter	246	hmat_ = m;
60			invHmat_ = hmat_.inverse();
61
62			//prepare fortran Hmat
63	tim	963	RealType fortranHmat[9];
64			RealType fortranInvHmat[9];
65	gezelter	246	hmat_.getArray(fortranHmat);
66			invHmat_.getArray(fortranInvHmat);
67
68			//determine whether the box is orthoTolerance or not
69			int oldOrthoRhombic = orthoRhombic_;
70
71	tim	963	RealType smallDiag = fabs(hmat_(0, 0));
72	gezelter	246	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
73			if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
74	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
75	gezelter	246
76			orthoRhombic_ = 1;
77
78			for (int i = 0; i < 3; i++ ) {
79	gezelter	507	for (int j = 0 ; j < 3; j++) {
80			if (i != j) {
81			if (orthoRhombic_) {
82			if ( fabs(hmat_(i, j)) >= tol)
83			orthoRhombic_ = 0;
84			}
85			}
86			}
87	gezelter	246	}
88
89			if( oldOrthoRhombic != orthoRhombic_ ){
90
91	gezelter	507	if( orthoRhombic_ ) {
92			sprintf( painCave.errMsg,
93	gezelter	1390	"OpenMD is switching from the default Non-Orthorhombic\n"
94	gezelter	507	"\tto the faster Orthorhombic periodic boundary computations.\n"
95	gezelter	890	"\tThis is usually a good thing, but if you want the\n"
96	gezelter	507	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
97			"\tvariable ( currently set to %G ) smaller.\n",
98	gezelter	1021	orthoTolerance_);
99	gezelter	1390	painCave.severity = OPENMD_INFO;
100	gezelter	507	simError();
101			}
102			else {
103			sprintf( painCave.errMsg,
104	gezelter	1390	"OpenMD is switching from the faster Orthorhombic to the more\n"
105	gezelter	507	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
106			"\tThis is usually because the box has deformed under\n"
107	gezelter	890	"\tNPTf integration. If you want to live on the edge with\n"
108	gezelter	507	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
109			"\tvariable ( currently set to %G ) larger.\n",
110	gezelter	1021	orthoTolerance_);
111	gezelter	1390	painCave.severity = OPENMD_WARNING;
112	gezelter	507	simError();
113			}
114	gezelter	246	}
115
116			//notify fortran simulation box has changed
117	gezelter	1550	// setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
118	gezelter	507	}
119	gezelter	246
120
121	gezelter	1568	void Snapshot::wrapVector(Vector3d& pos) {
122	gezelter	1562
123			Vector3d scaled = scaleVector(pos);
124	gezelter	1568
125	gezelter	1562	for (int i = 0; i < 3; i++)
126			scaled[i] -= roundMe(scaled[i]);
127	gezelter	246
128	gezelter	1562	if( !orthoRhombic_ )
129	gezelter	507	pos = hmat_ * scaled;
130	gezelter	1562	else {
131	gezelter	246
132	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
133	gezelter	1562	for (int i=0; i<3; i++) {
134	gezelter	507	pos[i] = scaled[i] * hmat_(i, i);
135	gezelter	1540	}
136	gezelter	246	}
137	gezelter	507	}
138	gezelter	246
139	gezelter	1562	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
140
141			Vector3d scaled;
142
143			if( !orthoRhombic_ )
144			scaled = invHmat_* pos;
145			else {
146			// calc the scaled coordinates.
147			for (int i=0; i<3; i++)
148			scaled[i] = pos[i] * invHmat_(i, i);
149			}
150
151			return scaled;
152			}
153
154	gezelter	1104	Vector3d Snapshot::getCOM() {
155			if( !hasCOM_ ) {
156			sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
157	gezelter	1390	painCave.severity = OPENMD_ERROR;
158	gezelter	1104	simError();
159			}
160			return COM_;
161			}
162
163			Vector3d Snapshot::getCOMvel() {
164			if( !hasCOM_ ) {
165			sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
166	gezelter	1390	painCave.severity = OPENMD_ERROR;
167	gezelter	1104	simError();
168			}
169			return COMvel_;
170			}
171
172			Vector3d Snapshot::getCOMw() {
173			if( !hasCOM_ ) {
174			sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
175	gezelter	1390	painCave.severity = OPENMD_ERROR;
176	gezelter	1104	simError();
177			}
178			return COMw_;
179			}
180	gezelter	246	}
181