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) {

    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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	5912 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	chuckv	1112
63	gezelter	246	//prepare fortran Hmat
64	tim	963	RealType fortranHmat[9];
65			RealType fortranInvHmat[9];
66	gezelter	246	hmat_.getArray(fortranHmat);
67			invHmat_.getArray(fortranInvHmat);
68
69			//determine whether the box is orthoTolerance or not
70			int oldOrthoRhombic = orthoRhombic_;
71
72	tim	963	RealType smallDiag = fabs(hmat_(0, 0));
73	gezelter	246	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
74			if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
75	gezelter	1021	RealType tol = smallDiag * orthoTolerance_;
76	gezelter	246
77			orthoRhombic_ = 1;
78
79			for (int i = 0; i < 3; i++ ) {
80	gezelter	507	for (int j = 0 ; j < 3; j++) {
81			if (i != j) {
82			if (orthoRhombic_) {
83			if ( fabs(hmat_(i, j)) >= tol)
84			orthoRhombic_ = 0;
85			}
86			}
87			}
88	gezelter	246	}
89
90			if( oldOrthoRhombic != orthoRhombic_ ){
91
92	gezelter	507	if( orthoRhombic_ ) {
93			sprintf( painCave.errMsg,
94	gezelter	1390	"OpenMD is switching from the default Non-Orthorhombic\n"
95	gezelter	507	"\tto the faster Orthorhombic periodic boundary computations.\n"
96	gezelter	890	"\tThis is usually a good thing, but if you want the\n"
97	gezelter	507	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
98			"\tvariable ( currently set to %G ) smaller.\n",
99	gezelter	1021	orthoTolerance_);
100	gezelter	1390	painCave.severity = OPENMD_INFO;
101	gezelter	507	simError();
102			}
103			else {
104			sprintf( painCave.errMsg,
105	gezelter	1390	"OpenMD is switching from the faster Orthorhombic to the more\n"
106	gezelter	507	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
107			"\tThis is usually because the box has deformed under\n"
108	gezelter	890	"\tNPTf integration. If you want to live on the edge with\n"
109	gezelter	507	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
110			"\tvariable ( currently set to %G ) larger.\n",
111	gezelter	1021	orthoTolerance_);
112	gezelter	1390	painCave.severity = OPENMD_WARNING;
113	gezelter	507	simError();
114			}
115	gezelter	246	}
116
117			//notify fortran simulation box has changed
118			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
119	gezelter	507	}
120	gezelter	246
121
122	gezelter	507	void Snapshot::wrapVector(Vector3d& pos) {
123	gezelter	246
124			int i;
125			Vector3d scaled;
126
127			if( !orthoRhombic_ ){
128
129	gezelter	507	// calc the scaled coordinates.
130			scaled = invHmat_* pos;
131	gezelter	246
132	gezelter	507	// wrap the scaled coordinates
133			for (i = 0; i < 3; ++i) {
134			scaled[i] -= roundMe(scaled[i]);
135			}
136	gezelter	246
137	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
138			pos = hmat_ * scaled;
139	gezelter	246
140			} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
141
142	gezelter	507	// calc the scaled coordinates.
143			for (i=0; i<3; i++) {
144			scaled[i] = pos[i] * invHmat_(i, i);
145			}
146	gezelter	246
147	gezelter	507	// wrap the scaled coordinates
148			for (i = 0; i < 3; ++i) {
149			scaled[i] -= roundMe(scaled[i]);
150			}
151	gezelter	246
152	gezelter	507	// calc the wrapped real coordinates from the wrapped scaled coordinates
153			for (i=0; i<3; i++) {
154			pos[i] = scaled[i] * hmat_(i, i);
155			}
156	gezelter	246
157			}
158
159	gezelter	507	}
160	gezelter	246
161	gezelter	1104	Vector3d Snapshot::getCOM() {
162			if( !hasCOM_ ) {
163			sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
164	gezelter	1390	painCave.severity = OPENMD_ERROR;
165	gezelter	1104	simError();
166			}
167			return COM_;
168			}
169
170			Vector3d Snapshot::getCOMvel() {
171			if( !hasCOM_ ) {
172			sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
173	gezelter	1390	painCave.severity = OPENMD_ERROR;
174	gezelter	1104	simError();
175			}
176			return COMvel_;
177			}
178
179			Vector3d Snapshot::getCOMw() {
180			if( !hasCOM_ ) {
181			sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
182	gezelter	1390	painCave.severity = OPENMD_ERROR;
183	gezelter	1104	simError();
184			}
185			return COMw_;
186			}
187
188	gezelter	246	}
189