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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
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< |
* publication of scientific results based in part on use of the |
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< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
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|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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+ |
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
| 35 |
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* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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#include "utils/NumericConstant.hpp" |
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#include "utils/simError.h" |
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#include "utils/Utility.hpp" |
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< |
namespace oopse { |
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> |
#include <cstdio> |
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|
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+ |
namespace OpenMD { |
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+ |
|
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void Snapshot::setHmat(const Mat3x3d& m) { |
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– |
const double orthoTolerance = NumericConstant::epsilon; |
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hmat_ = m; |
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invHmat_ = hmat_.inverse(); |
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|
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+ |
|
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//prepare fortran Hmat |
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< |
double fortranHmat[9]; |
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< |
double fortranInvHmat[9]; |
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> |
RealType fortranHmat[9]; |
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> |
RealType fortranInvHmat[9]; |
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hmat_.getArray(fortranHmat); |
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invHmat_.getArray(fortranInvHmat); |
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|
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//determine whether the box is orthoTolerance or not |
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int oldOrthoRhombic = orthoRhombic_; |
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|
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< |
double smallDiag = fabs(hmat_(0, 0)); |
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> |
RealType smallDiag = fabs(hmat_(0, 0)); |
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|
if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1)); |
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if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2)); |
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< |
double tol = smallDiag * orthoTolerance; |
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> |
RealType tol = smallDiag * orthoTolerance_; |
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|
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orthoRhombic_ = 1; |
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|
|
| 91 |
|
|
| 92 |
|
if( orthoRhombic_ ) { |
| 93 |
|
sprintf( painCave.errMsg, |
| 94 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
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> |
"OpenMD is switching from the default Non-Orthorhombic\n" |
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|
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 96 |
< |
"\tThis is usually a good thing, but if you wan't the\n" |
| 96 |
> |
"\tThis is usually a good thing, but if you want the\n" |
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|
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
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|
"\tvariable ( currently set to %G ) smaller.\n", |
| 99 |
< |
orthoTolerance); |
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< |
painCave.severity = OOPSE_INFO; |
| 99 |
> |
orthoTolerance_); |
| 100 |
> |
painCave.severity = OPENMD_INFO; |
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|
simError(); |
| 102 |
|
} |
| 103 |
|
else { |
| 104 |
|
sprintf( painCave.errMsg, |
| 105 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 105 |
> |
"OpenMD is switching from the faster Orthorhombic to the more\n" |
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|
"\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" |
| 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 = OOPSE_WARNING; |
| 111 |
> |
orthoTolerance_); |
| 112 |
> |
painCave.severity = OPENMD_WARNING; |
| 113 |
|
simError(); |
| 114 |
|
} |
| 115 |
|
} |
| 158 |
|
|
| 159 |
|
} |
| 160 |
|
|
| 161 |
+ |
Vector3d Snapshot::getCOM() { |
| 162 |
+ |
if( !hasCOM_ ) { |
| 163 |
+ |
sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); |
| 164 |
+ |
painCave.severity = OPENMD_ERROR; |
| 165 |
+ |
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 |
+ |
painCave.severity = OPENMD_ERROR; |
| 174 |
+ |
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 |
+ |
painCave.severity = OPENMD_ERROR; |
| 183 |
+ |
simError(); |
| 184 |
+ |
} |
| 185 |
+ |
return COMw_; |
| 186 |
+ |
} |
| 187 |
+ |
|
| 188 |
|
} |
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|
