| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* distribution. |
| 28 |
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* 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). |
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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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> |
frameData.hmat = m; |
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> |
frameData.invHmat = frameData.hmat.inverse(); |
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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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– |
hmat_.getArray(fortranHmat); |
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– |
invHmat_.getArray(fortranInvHmat); |
| 66 |
– |
|
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|
//determine whether the box is orthoTolerance or not |
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< |
int oldOrthoRhombic = orthoRhombic_; |
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> |
bool oldOrthoRhombic = frameData.orthoRhombic; |
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|
|
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< |
double 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 smallDiag = fabs(frameData.hmat(0, 0)); |
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> |
if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1)); |
| 68 |
> |
if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2)); |
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> |
RealType tol = smallDiag * orthoTolerance_; |
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|
|
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< |
orthoRhombic_ = 1; |
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> |
frameData.orthoRhombic = true; |
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|
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|
for (int i = 0; i < 3; i++ ) { |
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for (int j = 0 ; j < 3; j++) { |
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if (i != j) { |
| 76 |
< |
if (orthoRhombic_) { |
| 77 |
< |
if ( fabs(hmat_(i, j)) >= tol) |
| 78 |
< |
orthoRhombic_ = 0; |
| 76 |
> |
if (frameData.orthoRhombic) { |
| 77 |
> |
if ( fabs(frameData.hmat(i, j)) >= tol) |
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> |
frameData.orthoRhombic = false; |
| 79 |
|
} |
| 80 |
|
} |
| 81 |
|
} |
| 82 |
|
} |
| 83 |
|
|
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< |
if( oldOrthoRhombic != orthoRhombic_ ){ |
| 84 |
> |
if( oldOrthoRhombic != frameData.orthoRhombic){ |
| 85 |
|
|
| 86 |
< |
if( orthoRhombic_ ) { |
| 86 |
> |
if( frameData.orthoRhombic ) { |
| 87 |
|
sprintf( painCave.errMsg, |
| 88 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 88 |
> |
"OpenMD is switching from the default Non-Orthorhombic\n" |
| 89 |
|
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 90 |
< |
"\tThis is usually a good thing, but if you wan't the\n" |
| 90 |
> |
"\tThis is usually a good thing, but if you want the\n" |
| 91 |
|
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 92 |
|
"\tvariable ( currently set to %G ) smaller.\n", |
| 93 |
< |
orthoTolerance); |
| 94 |
< |
painCave.severity = OOPSE_INFO; |
| 93 |
> |
orthoTolerance_); |
| 94 |
> |
painCave.severity = OPENMD_INFO; |
| 95 |
|
simError(); |
| 96 |
|
} |
| 97 |
|
else { |
| 98 |
|
sprintf( painCave.errMsg, |
| 99 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 99 |
> |
"OpenMD is switching from the faster Orthorhombic to the more\n" |
| 100 |
|
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 101 |
|
"\tThis is usually because the box has deformed under\n" |
| 102 |
< |
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 102 |
> |
"\tNPTf integration. If you want to live on the edge with\n" |
| 103 |
|
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 104 |
|
"\tvariable ( currently set to %G ) larger.\n", |
| 105 |
< |
orthoTolerance); |
| 106 |
< |
painCave.severity = OOPSE_WARNING; |
| 105 |
> |
orthoTolerance_); |
| 106 |
> |
painCave.severity = OPENMD_WARNING; |
| 107 |
|
simError(); |
| 108 |
|
} |
| 109 |
|
} |
| 114 |
– |
|
| 115 |
– |
//notify fortran simulation box has changed |
| 116 |
– |
setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_); |
| 110 |
|
} |
| 111 |
|
|
| 112 |
|
|
| 113 |
|
void Snapshot::wrapVector(Vector3d& pos) { |
| 114 |
+ |
|
| 115 |
+ |
Vector3d scaled = scaleVector(pos); |
| 116 |
+ |
|
| 117 |
+ |
for (int i = 0; i < 3; i++) |
| 118 |
+ |
scaled[i] -= roundMe(scaled[i]); |
| 119 |
|
|
| 120 |
< |
int i; |
| 121 |
< |
Vector3d scaled; |
| 120 |
> |
if( !frameData.orthoRhombic ) |
| 121 |
> |
pos = frameData.hmat * scaled; |
| 122 |
> |
else { |
| 123 |
|
|
| 125 |
– |
if( !orthoRhombic_ ){ |
| 126 |
– |
|
| 127 |
– |
// 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 |
– |
|
| 124 |
|
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 125 |
< |
pos = hmat_ * scaled; |
| 125 |
> |
for (int i=0; i<3; i++) { |
| 126 |
> |
pos[i] = scaled[i] * frameData.hmat(i, i); |
| 127 |
> |
} |
| 128 |
> |
} |
| 129 |
> |
} |
| 130 |
|
|
| 131 |
< |
} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element |
| 131 |
> |
inline Vector3d Snapshot::scaleVector(Vector3d& pos) { |
| 132 |
|
|
| 133 |
< |
// 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 |
< |
} |
| 133 |
> |
Vector3d scaled; |
| 134 |
|
|
| 135 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 136 |
< |
for (i=0; i<3; i++) { |
| 137 |
< |
pos[i] = scaled[i] * hmat_(i, i); |
| 138 |
< |
} |
| 139 |
< |
|
| 135 |
> |
if( !frameData.orthoRhombic ) |
| 136 |
> |
scaled = frameData.invHmat * pos; |
| 137 |
> |
else { |
| 138 |
> |
// calc the scaled coordinates. |
| 139 |
> |
for (int i=0; i<3; i++) |
| 140 |
> |
scaled[i] = pos[i] * frameData.invHmat(i, i); |
| 141 |
|
} |
| 142 |
|
|
| 143 |
+ |
return scaled; |
| 144 |
|
} |
| 145 |
< |
|
| 145 |
> |
|
| 146 |
> |
Vector3d Snapshot::getCOM() { |
| 147 |
> |
if( !hasCOM_ ) { |
| 148 |
> |
sprintf( painCave.errMsg, "COM was requested before COM was computed!\n"); |
| 149 |
> |
painCave.severity = OPENMD_ERROR; |
| 150 |
> |
simError(); |
| 151 |
> |
} |
| 152 |
> |
return frameData.COM; |
| 153 |
> |
} |
| 154 |
> |
|
| 155 |
> |
Vector3d Snapshot::getCOMvel() { |
| 156 |
> |
if( !hasCOM_ ) { |
| 157 |
> |
sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n"); |
| 158 |
> |
painCave.severity = OPENMD_ERROR; |
| 159 |
> |
simError(); |
| 160 |
> |
} |
| 161 |
> |
return frameData.COMvel; |
| 162 |
> |
} |
| 163 |
> |
|
| 164 |
> |
Vector3d Snapshot::getCOMw() { |
| 165 |
> |
if( !hasCOM_ ) { |
| 166 |
> |
sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n"); |
| 167 |
> |
painCave.severity = OPENMD_ERROR; |
| 168 |
> |
simError(); |
| 169 |
> |
} |
| 170 |
> |
return frameData.COMw; |
| 171 |
> |
} |
| 172 |
|
} |
| 173 |
|
|
