/dports/biology/bcftools/bcftools-1.14/ |
H A D | HMM.c | 131 hmm->nstates = nstates; in hmm_init() 132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot() 156 snapshot->nstates = hmm->nstates; in hmm_snapshot() 201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob() 217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob() 242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local 286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi() 307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local [all …]
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | HMM.c | 131 hmm->nstates = nstates; in hmm_init() 132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot() 156 snapshot->nstates = hmm->nstates; in hmm_snapshot() 201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob() 217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob() 242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local 286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi() 307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local [all …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | HMM.c | 131 hmm->nstates = nstates; in hmm_init() 132 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 133 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 142 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot() 156 snapshot->nstates = hmm->nstates; in hmm_snapshot() 201 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob() 217 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob() 242 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local 286 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi() 307 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local [all …]
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H A D | HMM.c.pysam.c | 133 hmm->nstates = nstates; in hmm_init() 134 hmm->curr_tprob = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 135 hmm->tmp = (double*) malloc(sizeof(double)*nstates*nstates); in hmm_init() 144 if ( snapshot && snapshot->nstates!=hmm->nstates ) in hmm_snapshot() 158 snapshot->nstates = hmm->nstates; in hmm_snapshot() 203 …ltiply_matrix(hmm->nstates, hmm->tprob_arr, hmm->tprob_arr+(i-1)*hmm->nstates*hmm->nstates, hmm->t… in hmm_set_tprob() 219 …(hmm->curr_tprob, hmm->tprob_arr+n*hmm->nstates*hmm->nstates, sizeof(*hmm->curr_tprob)*hmm->nstate… in _set_tprob() 244 int i,j, nstates = hmm->nstates; in hmm_run_viterbi() local 288 assert( iptr<nstates && hmm->vpath[i*nstates + iptr]<nstates ); in hmm_run_viterbi() 309 int i,j,k, nstates = hmm->nstates; in hmm_run_fwd_bwd() local [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylotreesse.cpp | 380 double *inv_evec = &model->getInverseEigenvectors()[ptn*nstates*nstates]; in computeTipPartialLikelihood() 512 double *this_tip_partial_lh = &tip_partial_lh[(state+nstates)*nstates]; in computeTipPartialLikelihood() 535 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood() 537 this_tip_partial_lh[m*nstates + i] = inv_evec[i*nstates+state]; in computeTipPartialLikelihood() 544 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood() 560 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood() 577 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood() 600 double *this_tip_partial_lh = &tip_partial_lh[(state+nstates)*nstates*nmixtures]; in computeTipPartialLikelihood() 603 double *inv_evec = &all_inv_evec[m*nstates*nstates]; in computeTipPartialLikelihood() 1821 size_t nstatesqr = nstates*nstates; in computeAncestralLikelihood() [all …]
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H A D | phylokernelsitemodel.cpp | 24 size_t nstates = aln->num_states; in computeSitemodelPartialLikelihoodEigen() local 29 size_t block = nstates * ncat; in computeSitemodelPartialLikelihoodEigen() 178 … memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen() 219 double partial_lh_tmp[nstates]; in computeSitemodelPartialLikelihoodEigen() 327 memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen() 412 memcpy(&partial_lh[c*nstates], &tip_partial_lh[ptn*nstates], nstates*sizeof(double)); in computeSitemodelPartialLikelihoodEigen() 540 theta += nstates; in computeSitemodelLikelihoodDervEigen() 618 partial_lh_dad += nstates; in computeSitemodelLikelihoodBranchEigen() 647 partial_lh_node += nstates; in computeSitemodelLikelihoodBranchEigen() 648 partial_lh_dad += nstates; in computeSitemodelLikelihoodBranchEigen() [all …]
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H A D | phylokernelnonrev.cpp | 30 size_t nstates = aln->num_states; in computeNonrevPartialLikelihood() local 48 size_t block = nstates * ncat; in computeNonrevPartialLikelihood() 168 …memcpy(&partial_lh_all[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(dou… in computeNonrevPartialLikelihood() 259 for (x = 0; x < nstates; x++) { in computeNonrevPartialLikelihood() 267 vleft += nstates; in computeNonrevPartialLikelihood() 275 …memcpy(&partial_lh[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(double)… in computeNonrevPartialLikelihood() 319 for (x = 0; x < nstates; x++) { in computeNonrevPartialLikelihood() 338 …memcpy(&partial_lh[c*nstates], &tip_partial_lh[aln->STATE_UNKNOWN*nstates], nstates*sizeof(double)… in computeNonrevPartialLikelihood() 394 size_t nstatesqr = nstates*nstates; in computeNonrevLikelihoodDerv() 397 size_t block = ncat * nstates; in computeNonrevLikelihoodDerv() [all …]
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H A D | phylokernelmixrate.h | 55 const size_t nstatesqr=nstates*nstates; in computeMixratePartialLikelihoodEigenSIMD() 98 VectorClass *vc_inv_evec = aligned_alloc<VectorClass>(ncat*nstates*nstates/VCSIZE); in computeMixratePartialLikelihoodEigenSIMD() 104 vc_inv_evec[(c*nstates+i)*nstates/VCSIZE+x].load_a(&inv_evec[c*nstatesqr+i*nstates+x*VCSIZE]); in computeMixratePartialLikelihoodEigenSIMD() 151 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD() 172 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD() 234 lh_left += nstates; in computeMixratePartialLikelihoodEigenSIMD() 235 lh_right += nstates; in computeMixratePartialLikelihoodEigenSIMD() 236 partial_lh += nstates; in computeMixratePartialLikelihoodEigenSIMD() 263 size_t addr = (c*nstates+x)*nstates/VCSIZE; in computeMixratePartialLikelihoodEigenSIMD() 338 lh_left += nstates; in computeMixratePartialLikelihoodEigenSIMD() [all …]
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H A D | phylokernelsafe.h | 108 ASSERT(nstates == aln->num_states && nstates >= VCSIZE && VCSIZE == VectorClass().size()); in computePartialLikelihoodEigenSIMD() 110 const size_t nstatesqr=nstates*nstates; in computePartialLikelihoodEigenSIMD() 384 lh_left += nstates; in computePartialLikelihoodEigenSIMD() 385 lh_right += nstates; in computePartialLikelihoodEigenSIMD() 386 partial_lh += nstates; in computePartialLikelihoodEigenSIMD() 474 lh_left += nstates; in computePartialLikelihoodEigenSIMD() 476 partial_lh += nstates; in computePartialLikelihoodEigenSIMD() 486 VectorClass vc_lh_left[nstates/VCSIZE], vc_lh_right[nstates/VCSIZE]; in computePartialLikelihoodEigenSIMD() 551 partial_lh += nstates; in computePartialLikelihoodEigenSIMD() 1637 switch (nstates) { in computePartialParsimonyFastSIMD() [all …]
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H A D | phylokernelnonrev.h | 47 size_t nstates = aln->num_states; local 63 size_t block = nstates * ncat_mix; 343 for (x = 0; x < nstates; x++) { 354 lh_left += nstates; 355 partial_lh += nstates; 403 for (x = 0; x < nstates; x++) { 431 vleft += nstates; 487 for (x = 0; x < nstates; x++) { 578 size_t nstates = aln->num_states; local 580 size_t nstatesqr = nstates*nstates; [all …]
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H A D | phylokernelmixture.h | 53 const size_t nstatesqr=nstates*nstates; in computeMixturePartialLikelihoodEigenSIMD() 236 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD() 244 lh_left += nstates; in computeMixturePartialLikelihoodEigenSIMD() 245 lh_right += nstates; in computeMixturePartialLikelihoodEigenSIMD() 246 partial_lh += nstates; in computeMixturePartialLikelihoodEigenSIMD() 340 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD() 351 lh_left += nstates; in computeMixturePartialLikelihoodEigenSIMD() 353 partial_lh += nstates; in computeMixturePartialLikelihoodEigenSIMD() 382 VectorClass vc_lh_left[nstates/VCSIZE], vc_lh_right[nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD() 423 res[j] = vc_partial_lh_tmp[0] * vc_inv_evec[(m*nstates+i+j)*nstates/VCSIZE]; in computeMixturePartialLikelihoodEigenSIMD() [all …]
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H A D | phylokernelnew.h | 642 if (nstates % 2 == 0) { in dotProductTriple() 816 size_t ncat_mix, size_t nstates) in scaleLikelihood() 894 size_t nstatesqr = nstates*nstates; in computePartialInfo() 964 echild += block*nstates; in computePartialInfo() 1019 echild += block*nstates; in computePartialInfo() 1024 double expchild[nstates]; in computePartialInfo() 1068 echild += block*nstates; in computePartialInfo() 1270 const size_t states_square = nstates*nstates; in computePartialLikelihoodSIMD() 2062 theta += nstates; in computeLikelihoodBufferSIMD() 3219 theta += nstates; in computeLikelihoodFromBufferSIMD() [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/qmd/ |
H A D | qmd_elec_prop.F | 23 double complex zden(nstates,nstates) 26 double precision coup1(nstates,nstates) 27 double precision coup2(nstates,nstates) 201 double precision coup1(nstates,nstates) 202 double precision coup2(nstates,nstates) 205 double complex zden(nstates,nstates) 206 double complex zham(nstates,nstates) 207 double complex ztden1(nstates,nstates) 208 double complex ztden2(nstates,nstates) 209 double complex zrk4s(nstates,nstates) [all …]
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H A D | qmd_namd_init.F | 7 & k_sv,state,state_p,nstates,dt_elec, 35 integer nstates ! number of states 80 if (.not.rtdb_get(rtdb,'qmd:nstates',mt_int,1,nstates)) 96 write(LuOut,120) "Number of states:", nstates 119 if (.not.ma_push_get(mt_int,nstates,'swap occ',l_so,k_so)) 121 if (.not.ma_push_get(mt_int,nstates,'swap vir',l_sv,k_sv)) 128 if (nroots.lt.(nstates-1)) 150 if (.not.ma_push_get(mt_dbl,nstates**2,'coup_p',l_coup_p, 155 if (.not.ma_push_get(mt_dbl,nstates,'energies',l_en,k_en)) 193 call qmd_set_den(nstates,state,dcpl_mb(k_zden)) [all …]
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H A D | qmd_tdks_enmo.F | 16 integer nstates local 20 integer swap_occ(nstates) 21 integer swap_vir(nstates) 24 double precision en(nstates) 82 integer nstates local 83 integer swap_occ(nstates) 84 integer swap_vir(nstates) 187 integer nstates local 188 integer swap_occ(nstates) 235 do i=1,nstates-1 [all …]
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/qmd/ |
H A D | qmd_elec_prop.F | 23 double complex zden(nstates,nstates) 26 double precision coup1(nstates,nstates) 27 double precision coup2(nstates,nstates) 201 double precision coup1(nstates,nstates) 202 double precision coup2(nstates,nstates) 205 double complex zden(nstates,nstates) 206 double complex zham(nstates,nstates) 207 double complex ztden1(nstates,nstates) 208 double complex ztden2(nstates,nstates) 209 double complex zrk4s(nstates,nstates) [all …]
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H A D | qmd_namd_init.F | 7 & k_sv,state,state_p,nstates,dt_elec, 35 integer nstates ! number of states 80 if (.not.rtdb_get(rtdb,'qmd:nstates',mt_int,1,nstates)) 96 write(LuOut,120) "Number of states:", nstates 119 if (.not.ma_push_get(mt_int,nstates,'swap occ',l_so,k_so)) 121 if (.not.ma_push_get(mt_int,nstates,'swap vir',l_sv,k_sv)) 128 if (nroots.lt.(nstates-1)) 150 if (.not.ma_push_get(mt_dbl,nstates**2,'coup_p',l_coup_p, 155 if (.not.ma_push_get(mt_dbl,nstates,'energies',l_en,k_en)) 193 call qmd_set_den(nstates,state,dcpl_mb(k_zden)) [all …]
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H A D | qmd_tdks_enmo.F | 16 integer nstates 20 integer swap_occ(nstates) 21 integer swap_vir(nstates) 24 double precision en(nstates) 82 integer nstates 83 integer swap_occ(nstates) 84 integer swap_vir(nstates) 187 integer nstates 188 integer swap_occ(nstates) 235 do i=1,nstates-1 [all …]
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/dports/science/bagel/bagel-1.2.2/src/asd/ |
H A D | asd_base.cc | 167 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_offdiagonal_1e() 231 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_inter_2e() 232 …indices<0,2,1,3,0,1,1,1>(tmp.data(), out->data(), A.nstates(), Ap.nstates(), B.nstates(), Bp.nstat… in compute_inter_2e() 239 Matrix tmp(A.nstates()*Ap.nstates(), B.nstates()*Bp.nstates()); in compute_aET() 274 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_aET() 288 Matrix tmp(A.nstates()*Ap.nstates(), B.nstates()*Bp.nstates()); in compute_bET() 324 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_bET() 349 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_abFlip() 367 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_abET() 384 auto out = make_shared<Matrix>(A.nstates()*B.nstates(), Ap.nstates()*Bp.nstates()); in compute_aaET() [all …]
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/dports/science/quantum-espresso/q-e-qe-6.7.0/GWW/head/ |
H A D | lanczos_k.f90 | 57 allocate(psi_1(npwx,nstates),psi_2(npwx,nstates),psi_3(npwx,nstates)) 58 allocate(u_0(npwx,nstates),u_1(npwx,nstates)) 59 allocate(alpha(nstates),beta(nstates),gamma(nstates),n_1(nstates),delta(nstates)) 67 psi_1(1:npw,1:nstates)=in_states(1:npw,1:nstates) 70 do is=1,nstates 77 do is=1,nstates 106 do is=1,nstates 119 do is=1,nstates 130 do is=1,nstates 135 do is=1,nstates [all …]
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/dports/net/mpich2/mpich2-1.5/src/mpe2/src/unused/src/ |
H A D | states.c | 32 int *nstates; 53 &(stateDefs[*nstates].start), &(stateDefs[*nstates].end), 57 stateDefs[*nstates].start, stateDefs[*nstates].end ); 59 (*nstates)++; 84 while (i < nstates && 86 if (i==nstates) { 181 int nstates; 190 if (!nstates) { 195 for (i=0; i<nstates; i++) { 227 int nstates; [all …]
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/dports/science/bagel/bagel-1.2.2/src/asd/dmrg/ |
H A D | dmrg_block.cc | 81 …const int nstates = accumulate(p.second.begin(), p.second.end(), 0, [] (int x, DMRG::BlockPair bp)… in DMRG_Block2() local 104 auto out = make_shared<Matrix>(binfo.nstates, binfo.nstates); in spin() 109 Matrix eye(source.right.nstates, source.right.nstates); in spin() 116 Matrix eye(source.left.nstates, source.left.nstates); in spin() 124 for (int i = 0; i < source.nstates(); ++i) in spin() 172 auto out = make_shared<Matrix>(target_info.nstates, source_info.nstates); in spin_lower() 185 Matrix eyeR(source.right.nstates, source.right.nstates); eyeR.unit(); in spin_lower() 199 Matrix eyeL(source.left.nstates, source.left.nstates); eyeL.unit(); in spin_lower() 216 auto out = make_shared<Matrix>(target_info.nstates, source_info.nstates); in spin_raise() 229 Matrix eyeR(source.right.nstates, source.right.nstates); eyeR.unit(); in spin_raise() [all …]
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/dports/science/dynare/dynare-4.6.4/contrib/ms-sbvar/switch_dw/switching/ |
H A D | dw_dirichlet_restrictions.c | 70 if ((nstates <= 0)) in CreateDirichletRestrictions() 104 restrictions->nstates=nstates; in CreateDirichletRestrictions() 188 NonZeroIndex=dw_CreateRectangularArray_int(nstates,nstates); in CreateMarkovStateVariable_Mixture() 192 MQ=InitializeMatrix(CreateMatrix(nstates,nstates),1.0); in CreateMarkovStateVariable_Mixture() 194 DirichletDim[0]=nstates; in CreateMarkovStateVariable_Mixture() 210 NonZeroIndex=dw_CreateRectangularArray_int(nstates,nstates); in CreateMarkovStateVariable_NoRestrictions() 214 InitializeMatrix(MQ=CreateMatrix(nstates,nstates),1.0); in CreateMarkovStateVariable_NoRestrictions() 216 for (i=nstates-1; i >= 0; i--) DirichletDim[i]=nstates; in CreateMarkovStateVariable_NoRestrictions() 233 MQ=InitializeMatrix(CreateMatrix(nstates,nstates),0.0); in CreateMarkovStateVariable_Exclusion() 262 InitializeMatrix(MQ=CreateMatrix(nstates,nstates),0.0); in CreateMarkovStateVariable_SimpleRestrictions() [all …]
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/dports/archivers/lzfse/lzfse-4591228/src/ |
H A D | lzfse_fse.c | 31 void fse_init_encoder_table(int nstates, int nsymbols, in fse_init_encoder_table() argument 35 int n_clz = __builtin_clz(nstates); in fse_init_encoder_table() 42 t[i].s0 = (int16_t)((f << k) - nstates); in fse_init_encoder_table() 57 int fse_init_decoder_table(int nstates, int nsymbols, in fse_init_decoder_table() argument 62 int n_clz = __builtin_clz(nstates); in fse_init_decoder_table() 71 if (sum_of_freq > nstates) { in fse_init_decoder_table() 77 int j0 = ((2 * nstates) >> k) - f; in fse_init_decoder_table() 86 e.delta = (int16_t)(((f + j) << k) - nstates); in fse_init_decoder_table() 117 int n_clz = __builtin_clz(nstates); in fse_init_value_decoder_table() 125 int j0 = ((2 * nstates) >> k) - f; in fse_init_value_decoder_table() [all …]
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/dports/devel/xelfviewer/XELFViewer-0.03/XArchive/3rdparty/lzfse/src/ |
H A D | lzfse_fse.c | 31 void fse_init_encoder_table(int nstates, int nsymbols, in fse_init_encoder_table() argument 35 int n_clz = __builtin_clz(nstates); in fse_init_encoder_table() 42 t[i].s0 = (int16_t)((f << k) - nstates); in fse_init_encoder_table() 57 int fse_init_decoder_table(int nstates, int nsymbols, in fse_init_decoder_table() argument 62 int n_clz = __builtin_clz(nstates); in fse_init_decoder_table() 71 if (sum_of_freq > nstates) { in fse_init_decoder_table() 77 int j0 = ((2 * nstates) >> k) - f; in fse_init_decoder_table() 86 e.delta = (int16_t)(((f + j) << k) - nstates); in fse_init_decoder_table() 117 int n_clz = __builtin_clz(nstates); in fse_init_value_decoder_table() 125 int j0 = ((2 * nstates) >> k) - f; in fse_init_value_decoder_table() [all …]
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