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root/OpenMD/branches/development/src/brains/Snapshot.cpp

Comparing:
trunk/src/brains/Snapshot.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file Snapshot.cpp
45	<	* @author tlin
46	<	* @date 11/11/2004
47	<	* @time 10:56am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file Snapshot.cpp
45	>	* @author tlin
46	>	* @date 11/11/2004
47	>	* @time 10:56am
48	>	* @version 1.0
49	>	*/
50
51		#include "brains/Snapshot.hpp"
52		#include "utils/NumericConstant.hpp"
53		#include "utils/simError.h"
54		#include "utils/Utility.hpp"
55	<	namespace oopse {
55	>	#include <cstdio>
56
57	<	void  Snapshot::setHmat(const Mat3x3d& m) {
58	<	const double orthoTolerance = NumericConstant::epsilon;
57	>	namespace OpenMD {
58	>
59	>	void  Snapshot::setHmat(const Mat3x3d& m) {
60		hmat_ = m;
61		invHmat_ = hmat_.inverse();
62
63		//prepare fortran Hmat
64	<	double fortranHmat[9];
65	<	double fortranInvHmat[9];
64	>	RealType fortranHmat[9];
65	>	RealType fortranInvHmat[9];
66		hmat_.getArray(fortranHmat);
67		invHmat_.getArray(fortranInvHmat);
68
69		//determine whether the box is orthoTolerance or not
70		int oldOrthoRhombic = orthoRhombic_;
71
72	<	double smallDiag = fabs(hmat_(0, 0));
72	>	RealType smallDiag = fabs(hmat_(0, 0));
73		if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
74		if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
75	<	double tol = smallDiag * orthoTolerance;
75	>	RealType tol = smallDiag * orthoTolerance_;
76
77		orthoRhombic_ = 1;
78
79		for (int i = 0; i < 3; i++ ) {
80	<	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	<	}
80	>	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		}
89
90		if( oldOrthoRhombic != orthoRhombic_ ){
91
92	<	if( orthoRhombic_ ) {
93	<	sprintf( painCave.errMsg,
94	<	"OOPSE is switching from the default Non-Orthorhombic\n"
95	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
96	<	"\tThis is usually a good thing, but if you wan't the\n"
97	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
98	<	"\tvariable ( currently set to %G ) smaller.\n",
99	<	orthoTolerance);
100	<	painCave.severity = OOPSE_INFO;
101	<	simError();
102	<	}
103	<	else {
104	<	sprintf( painCave.errMsg,
105	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
106	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
107	<	"\tThis is usually because the box has deformed under\n"
108	<	"\tNPTf integration. If you wan't to live on the edge with\n"
109	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
110	<	"\tvariable ( currently set to %G ) larger.\n",
111	<	orthoTolerance);
112	<	painCave.severity = OOPSE_WARNING;
113	<	simError();
114	<	}
92	>	if( orthoRhombic_ ) {
93	>	sprintf( painCave.errMsg,
94	>	"OpenMD is switching from the default Non-Orthorhombic\n"
95	>	"\tto the faster Orthorhombic periodic boundary computations.\n"
96	>	"\tThis is usually a good thing, but if you want the\n"
97	>	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
98	>	"\tvariable ( currently set to %G ) smaller.\n",
99	>	orthoTolerance_);
100	>	painCave.severity = OPENMD_INFO;
101	>	simError();
102	>	}
103	>	else {
104	>	sprintf( painCave.errMsg,
105	>	"OpenMD is switching from the faster Orthorhombic to the more\n"
106	>	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
107	>	"\tThis is usually because the box has deformed under\n"
108	>	"\tNPTf integration. If you want to live on the edge with\n"
109	>	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
110	>	"\tvariable ( currently set to %G ) larger.\n",
111	>	orthoTolerance_);
112	>	painCave.severity = OPENMD_WARNING;
113	>	simError();
114	>	}
115		}
116
117		//notify fortran simulation box has changed
118	<	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
119	<	}
118	>	// setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
119	>	}
120
121
122	<	void Snapshot::wrapVector(Vector3d& pos) {
122	>	void Snapshot::wrapVector(Vector3d& pos) {
123	>
124	>	Vector3d scaled = scaleVector(pos);
125	>
126	>	for (int i = 0; i < 3; i++)
127	>	scaled[i] -= roundMe(scaled[i]);
128
129	<	int i;
130	<	Vector3d scaled;
129	>	if( !orthoRhombic_ )
130	>	pos = hmat_ * scaled;
131	>	else {
132
133	<	if( !orthoRhombic_ ){
133	>	// calc the wrapped real coordinates from the wrapped scaled coordinates
134	>	for (int i=0; i<3; i++) {
135	>	pos[i] = scaled[i] * hmat_(i, i);
136	>	}
137	>	}
138	>	}
139
140	<	// calc the scaled coordinates.
128	<	scaled = invHmat_* pos;
129	<
130	<	// wrap the scaled coordinates
131	<	for (i = 0; i < 3; ++i) {
132	<	scaled[i] -= roundMe(scaled[i]);
133	<	}
134	<
135	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
136	<	pos = hmat_ * scaled;
137	<
138	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
140	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
141
142	<	// calc the scaled coordinates.
141	<	for (i=0; i<3; i++) {
142	<	scaled[i] = pos[i] * invHmat_(i, i);
143	<	}
144	<
145	<	// wrap the scaled coordinates
146	<	for (i = 0; i < 3; ++i) {
147	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
142	>	Vector3d scaled;
143
144	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
145	<	for (i=0; i<3; i++) {
146	<	pos[i] = scaled[i] * hmat_(i, i);
147	<	}
148	<
144	>	if( !orthoRhombic_ )
145	>	scaled = invHmat_* pos;
146	>	else {
147	>	// calc the scaled coordinates.
148	>	for (int i=0; i<3; i++)
149	>	scaled[i] = pos[i] * invHmat_(i, i);
150		}
151
152	+	return scaled;
153	+	}
154	+
155	+	Vector3d Snapshot::getCOM() {
156	+	if( !hasCOM_ ) {
157	+	sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
158	+	painCave.severity = OPENMD_ERROR;
159	+	simError();
160	+	}
161	+	return COM_;
162	+	}
163	+
164	+	Vector3d Snapshot::getCOMvel() {
165	+	if( !hasCOM_ ) {
166	+	sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
167	+	painCave.severity = OPENMD_ERROR;
168	+	simError();
169	+	}
170	+	return COMvel_;
171	+	}
172	+
173	+	Vector3d Snapshot::getCOMw() {
174	+	if( !hasCOM_ ) {
175	+	sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
176	+	painCave.severity = OPENMD_ERROR;
177	+	simError();
178	+	}
179	+	return COMw_;
180	+	}
181		}
158	–
159	–	}
182

Comparing:
trunk/src/brains/Snapshot.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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