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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/doc/Eqs/
H A Dmin_energy.tex6 E(r_1,r_2, \ldots ,r_N) & = & \sum_{i,j} E_{\it pair}(r_i,r_j) +
7 \sum_{ij} E_{\it bond}(r_i,r_j) +
8 \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\
9 && \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) +
10 \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) +
H A Dgran_model_hooke_hysteresis_1.tex6 \delta^*_{max} = \frac{\hat k_2}{\hat k_2 - k_1} \phi_f \frac{2 r_i r_j}{r_i + r_j}
H A Dpair_yukawa_colloid.tex6 E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/src/libcsg/
H A Dopenbox.cc25 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const { in BCShortestConnection()
26 return r_j - r_i; in BCShortestConnection()
H A Dorthorhombicbox.cc25 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const {
27 const Eigen::Array3d r_ij = r_j - r_i;
H A Dtriclinicbox.cc35 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const { in BCShortestConnection()
36 Eigen::Vector3d r_tp = r_j - r_i; in BCShortestConnection()
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/src/libcsg/
H A Dopenbox.cc25 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const { in BCShortestConnection()
26 return r_j - r_i; in BCShortestConnection()
H A Dorthorhombicbox.cc25 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const { in BCShortestConnection()
27 const Eigen::Array3d r_ij = r_j - r_i; in BCShortestConnection()
H A Dtriclinicbox.cc35 const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const { in BCShortestConnection()
36 Eigen::Vector3d r_tp = r_j - r_i; in BCShortestConnection()
/dports/science/py-ase/ase-3.22.0/ase/calculators/
H A Dtip4p.py158 r_j = pos[w + 1] # H1 pos
160 n = (r_j + r_k) / 2 - r_i
166 xatomspos[x + 1] = r_j
187 r_j = pos[w + 1] # H1 pos
189 r_ij = r_j - r_i
190 r_jk = r_k - r_j
/dports/math/py-libpoly/libpoly-0.1.11/examples/cad/
H A Dcad.py66 r_i, r_j = itertools.tee(roots)
67 next(r_j)
68 for r1, r2 in zip(r_i, r_j):
/dports/math/libpoly/libpoly-0.1.11/examples/cad/
H A Dcad.py66 r_i, r_j = itertools.tee(roots)
67 next(r_j)
68 for r1, r2 in zip(r_i, r_j):
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar_util.h34 long double r_j; in computeGenotypePriors() local
51 r_j = (isTransition((Dna)i, (Dna)j)? (double)(12.0/6.0):(double)(3.0/6.0)); in computeGenotypePriors()
59 methOptions.genPriors[i<<4| j<<2| k] = options.pHetSnp*r_j*(3.0/16.0); in computeGenotypePriors()
61 … methOptions.genPriors[i<<4| j<<2| k] = options.pHomoSnp*r_j*(3.0/16.0); // + pError ? in computeGenotypePriors()
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/
H A Dhyperfine.py230 r_j = np.linspace(0, r4, n)
237 d_j = delta(r_j, rT) - (d0 + d1 * r_j)
239 head_j = d_j * np.polyval(a_i, r_j)
240 head_j[1:] *= r_j[1:]**-beta
241 n0 += simps(head_j, r_j)
/dports/math/cppad/CppAD-20210000.8/include/cppad/core/chkpoint_one/
H A Dfor_sparse_jac.hpp121 const std::set<size_t>& r_j( r[j] ); in for_sparse_jac() local
122 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++) in for_sparse_jac()
H A Drev_sparse_hes.hpp192 const std::set<size_t>& r_j( r[j] ); in rev_sparse_hes() local
193 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++) in rev_sparse_hes()
/dports/math/openturns/openturns-1.18/python/src/
H A DEmpiricalBernsteinCopula_doc.i.in19 C(\vect{u}) = \dfrac{1}{N}\sum_{i=1}^N\prod_{j=1}^d I_{r_j^i,s_j^i}(u_j)
21 for :math:`\vect{u}\in[0,1]^d`, where :math:`r_j^i=\lceil binNumber U_j^i \rceil`, :math:`binNumber…
/dports/astro/nightfall/nightfall-1.92/
H A DLightDivide.c1169 double r_j=0; in DivideDisk() local
1426 r_j = (r_i_new+r_i_old)/2.0; in DivideDisk()
1430 ring_height = ( (diskAdd + diskProp * pow(r_j, diskExp)) / 2.0); in DivideDisk()
1463 t_temp = t_c * pow(r_j, -0.75); in DivideDisk()
1491 SurfPtr->lambda = (float) r_j * cos_phi; in DivideDisk()
1492 SurfPtr->mu = (float) r_j * sin_phi; in DivideDisk()
1554 if ( (hs_dist <= hs_ext) && (r_j >= (Rout - hs_depth)) ) in DivideDisk()
1816 t_temp = t_c * pow(r_j, -0.75); in DivideDisk()
1837 SurfPtr->lambda = (float) r_j * cos_phi; in DivideDisk()
1838 SurfPtr->mu = (float) r_j * sin_phi; in DivideDisk()
[all …]
/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_msaweight.md25 column $j$; and let $r_j$ be the number of different residues in
30 w_i = \frac{N}{L} \sum_{j=1}^{L} \frac{1}{r_j c_{j}(x_{ij})}
51 eventually every residue will be observed in every column ($r_j
64 \frac{1}{r_j c_{j}(a)} & \mbox{if } a \mbox{ is a residue} \\
/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_msaweight.md25 column $j$; and let $r_j$ be the number of different residues in
30 w_i = \frac{N}{L} \sum_{j=1}^{L} \frac{1}{r_j c_{j}(x_{ij})}
51 eventually every residue will be observed in every column ($r_j
64 \frac{1}{r_j c_{j}(a)} & \mbox{if } a \mbox{ is a residue} \\
/dports/math/R/R-4.1.2/m4/
H A Dclibs.m4170 for r_j in `echo $r_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do
171 _AC_LIST_MEMBER_IF($r_j, $r_cv_c_libs, ,
172 [r_arg="$r_arg $r_j"
173 r_cv_c_libs="$r_cv_c_libs $r_j"])
/dports/math/libRmath/R-4.1.1/m4/
H A Dclibs.m4170 for r_j in `echo $r_arg | sed -e 's/-YP,/-L/;s/:/ -L/g'`; do
171 _AC_LIST_MEMBER_IF($r_j, $r_cv_c_libs, ,
172 [r_arg="$r_arg $r_j"
173 r_cv_c_libs="$r_cv_c_libs $r_j"])
/dports/math/SCIP/scip-7.0.3/src/cppad/core/
H A Dcheckpoint.hpp873 const std::set<size_t>& r_j( r[j] ); in for_sparse_jac() local
874 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++) in for_sparse_jac()
1061 const std::set<size_t>& r_j( r[j] ); in rev_sparse_hes() local
1062 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++) in rev_sparse_hes()
1712 const std::set<size_t>& r_j( r[j] );
1713 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++)
1900 const std::set<size_t>& r_j( r[j] );
1901 for(itr_j = r_j.begin(); itr_j != r_j.end(); itr_j++)
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/include/votca/csg/
H A Dopenbox.h31 const Eigen::Vector3d &r_j) const final;
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/include/votca/csg/
H A Dopenbox.h31 const Eigen::Vector3d &r_j) const final;

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