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.
#	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	/**
43	* @file Snapshot.cpp
44	* @author tlin
45	* @date 11/11/2004
46	* @time 10:56am
47	* @version 1.0
48	*/
49
50	#include "brains/Snapshot.hpp"
51	#include "utils/NumericConstant.hpp"
52	#include "utils/simError.h"
53	#include "utils/Utility.hpp"
54	#include <cstdio>
55
56	namespace OpenMD {
57
58	void Snapshot::setHmat(const Mat3x3d& m) {
59	hmat_ = m;
60	invHmat_ = hmat_.inverse();
61
62	//prepare fortran Hmat
63	RealType fortranHmat[9];
64	RealType fortranInvHmat[9];
65	hmat_.getArray(fortranHmat);
66	invHmat_.getArray(fortranInvHmat);
67
68	//determine whether the box is orthoTolerance or not
69	int oldOrthoRhombic = orthoRhombic_;
70
71	RealType smallDiag = fabs(hmat_(0, 0));
72	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
73	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
74	RealType tol = smallDiag * orthoTolerance_;
75
76	orthoRhombic_ = 1;
77
78	for (int i = 0; i < 3; i++ ) {
79	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	}
88
89	if( oldOrthoRhombic != orthoRhombic_ ){
90
91	if( orthoRhombic_ ) {
92	sprintf( painCave.errMsg,
93	"OpenMD is switching from the default Non-Orthorhombic\n"
94	"\tto the faster Orthorhombic periodic boundary computations.\n"
95	"\tThis is usually a good thing, but if you want the\n"
96	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
97	"\tvariable ( currently set to %G ) smaller.\n",
98	orthoTolerance_);
99	painCave.severity = OPENMD_INFO;
100	simError();
101	}
102	else {
103	sprintf( painCave.errMsg,
104	"OpenMD is switching from the faster Orthorhombic to the more\n"
105	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
106	"\tThis is usually because the box has deformed under\n"
107	"\tNPTf integration. If you want to live on the edge with\n"
108	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
109	"\tvariable ( currently set to %G ) larger.\n",
110	orthoTolerance_);
111	painCave.severity = OPENMD_WARNING;
112	simError();
113	}
114	}
115
116	//notify fortran simulation box has changed
117	// setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
118	}
119
120
121	void Snapshot::wrapVector(Vector3d& pos) {
122
123	Vector3d scaled = scaleVector(pos);
124
125	for (int i = 0; i < 3; i++)
126	scaled[i] -= roundMe(scaled[i]);
127
128	if( !orthoRhombic_ )
129	pos = hmat_ * scaled;
130	else {
131
132	// calc the wrapped real coordinates from the wrapped scaled coordinates
133	for (int i=0; i<3; i++) {
134	pos[i] = scaled[i] * hmat_(i, i);
135	}
136	}
137	}
138
139	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	Vector3d Snapshot::getCOM() {
155	if( !hasCOM_ ) {
156	sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
157	painCave.severity = OPENMD_ERROR;
158	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	painCave.severity = OPENMD_ERROR;
167	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	painCave.severity = OPENMD_ERROR;
176	simError();
177	}
178	return COMw_;
179	}
180	}
181