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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 |
|
* 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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+ |
#include "math/Vector.hpp" |
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+ |
|
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|
#ifndef MATH_CHOLESKYDECOMPOSITION_HPP |
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|
#define MATH_CHOLESKYDECOMPOSITION_HPP |
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|
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< |
namespace oopse { |
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< |
template<class MatrixType> |
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< |
int CholeskyDecomposition(MatrixType& A, MatrixType& L) { |
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> |
using namespace std; |
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> |
namespace OpenMD { |
| 50 |
> |
|
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> |
template<class MatrixType> |
| 52 |
> |
void CholeskyDecomposition(MatrixType& A, MatrixType& L) { |
| 53 |
> |
|
| 54 |
|
int n = A.getNRow(); |
| 55 |
< |
assert(n == A.getNCol() && n == L.getNRow()&& n==L.getNCol()); |
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< |
for(int i = 0; i < n; ++i) { |
| 57 |
< |
double sum1 = 0; |
| 58 |
< |
for (int k = 0; k < i -1; ++k) { |
| 59 |
< |
sum1 +=L(i,k)*L(i,k); |
| 55 |
> |
assert(n == A.getNCol() && n == L.getNRow() && n == L.getNCol()); |
| 56 |
> |
|
| 57 |
> |
bool isspd(true); |
| 58 |
> |
RealType eps = A.diagonals().abs().max() * |
| 59 |
> |
(numeric_limits<RealType>::epsilon())/100; |
| 60 |
> |
|
| 61 |
> |
|
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> |
for(int j = 0; j < n; j++) { |
| 63 |
> |
RealType d(0.0); |
| 64 |
> |
for (int k = 0; k < j; k++) { |
| 65 |
> |
RealType s(0.0); |
| 66 |
> |
|
| 67 |
> |
for (int i = 0; i < k; i++) { |
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> |
s += L(k,i) * L(j,i); |
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|
} |
| 70 |
< |
L(i, i) = sqrt(A(i, i) - sum1); |
| 71 |
< |
for (int j = i+1; j < n; ++j) { |
| 72 |
< |
double sum2 = 0; |
| 73 |
< |
for (int k = 0; k < i-1; ++k) { |
| 74 |
< |
sum2 += L(j ,k)*L(i, k); |
| 75 |
< |
} |
| 76 |
< |
A(j, i) = (A(j, i) - sum2) /L(i,i); |
| 70 |
> |
|
| 71 |
> |
// if L(k,k) != 0 |
| 72 |
> |
if (std::abs(L(k,k)) > eps) { |
| 73 |
> |
s = (A(j,k) - s) / L(k,k); |
| 74 |
> |
} else { |
| 75 |
> |
s = (A(j,k) -s); |
| 76 |
> |
isspd = false; |
| 77 |
|
} |
| 78 |
+ |
L(j,k) = s; |
| 79 |
+ |
d = d + s*s; |
| 80 |
+ |
|
| 81 |
+ |
// this is approximately doing: isspd = isspd && ( A(k,j) == A(j,k) ) |
| 82 |
+ |
isspd = isspd && (abs(A(k,j) - A(j,k)) < eps ); |
| 83 |
+ |
} |
| 84 |
+ |
d = A(j,j) - d; |
| 85 |
+ |
isspd = isspd && (d > eps); |
| 86 |
+ |
L(j,j) = sqrt(d > 0.0 ? d : 0.0); |
| 87 |
+ |
for (int k = j+1; k < n; k++) { |
| 88 |
+ |
L(j,k) = 0.0; |
| 89 |
+ |
} |
| 90 |
|
} |
| 91 |
< |
|
| 64 |
< |
return 0; |
| 65 |
< |
|
| 91 |
> |
} |
| 92 |
|
} |
| 93 |
|
|
| 68 |
– |
|
| 69 |
– |
} |
| 70 |
– |
|
| 94 |
|
#endif |
